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Xsight



B       Insight II Commands


Xsight module

You start Xsight from within Insight II by clicking the Molecular Simulations logo with the mouse and selecting Xsight from the resulting list. The Xsight module is organized into several pulldowns that divide the different programs into functionality classes.

This module allows you to perform calculations associated with the analysis and modeling of X-ray diffraction data obtained from macromolecular crystals. From this module you can access:

The Xsight pulldowns are displayed on the lower menu bar. The pulldowns are: Utilities, Data_Control, MAD, MIR, Mol_Replacement, Modify_Density, Model_Building, Refinement, ProStat, Symmetry, and Background_Job.

Some of the commands that are available in these pulldowns are used to spawn XtalView programs. In such cases, the command parameters control the input and/or output files that will be used for the spawned programs. The Insight II software requires that you fill in all filename parameters in order to execute the command. In some cases it may not be clear which files you want to use until you are running the spawned programs. For that reason, the Pass_Files option is available. If this parameter is turned off, you can wait and select all files from within the XtalView program.

Utilities pulldown

The Utilities pulldown is used to define and set crystals and projects. These are two concepts that are used in the XtalView package and in the Xsight module in order to manage the multitude of projects and structures that a macromolecular crystallographer might be working on at one time. It is necessary to select a project before running any of the commands in the Xsight module. Until a project is selected, all other commands are unavailable.

A crystal is defined by a file that contains information that is general to all related projects. For example, a crystal file contains unit cell parameters, space group information, non-crystallographic symmetry information, etc. A project is defined by the directory that contains the data to be worked on and the name of the crystal file to associate with the project. With this system it is easy to keep track of related data sets and to work on multiple structures at the same time. The names of all crystal files are stored in a file named crystals. All projects are defined in a single file called projects.

The Utilities pulldown also contains a PostScript viewer for examining PostScript plots that are generated by many of the programs within Xsight.

Also under the Utilities pulldown is the Display_Density command for displaying electron density maps in conjunction with the various atomic model representations available within Insight II.

Utilities/Crystal

The Utilities/Crystal command is used to create a new crystal file, to edit an existing crystal file, and to change the directory that specifies where the crystal files are stored.

The Crystal_Directory contains the path of the directory that contains the database files, projects, crystals, and all of the files that are listed in the crystals file. This directory is defined by the environment variable, $CRYSTALDATA and normally does not need to be changed. Utilities/Crystal specifies the name of the currently selected crystal file.

You can edit an existing crystal file by clicking the Edit button. You can create a new crystal file by entering a new name in the Crystal parameter and clicking the Edit button. Once in Edit mode, you can modify the Title, the Unit Cell parameters (A, B, C, Alpha, Beta, Gamma) and the Space_Group. In order to change the space group, select the Space_Group parameter and a value-aid will appear that contains a list of all space groups in the current Crystal_Class. Select a different Crystal_Class in order to change the list of available space groups.

If the Crystal_Delete option is toggled on, the crystal will be deleted when you select Execute.

The Add_NCS_Information option is available for adding matrices describing non-crystallographic symmetry to the crystal file. If you toggle on the Add_NCS_Information option the name of the file containing the non-crystallographic symmetry matrices is be entered as the NCS_Transform_File. This file is usually denoted by the extension .ncs and can be entered using the NCS_Transform_Files value-aid. The .ncs file is usually generated using the Modify_Density/Non_Cryst_Symmetry command.

Utilities/Project

The Utilities/Project command is used to select the current project. Selecting a project implies two things: a particular crystal file will be accessed for all crystallographic information and the working directory will be established. In addition, a new project can be added with this command. The project must be selected before any of the other Xsight pulldowns are accessible.

An existing project is selected from the Project_List value-aid or a new project is added by entering a new Project_Name. Click the Edit button to access the Crystal and Project_Directory parameters.

If the Project_Delete option is toggled on, the project is deleted when you select Execute.

Utilities/View_PostScript

The Utilities/View_PostScript command is used to view PostScript files. You can select and existing PostScript file from the PostScript_Files value-aid or enter the filename in the PostScript_File parameter.

Utilities/Display_Density

The Utilities/Density_Density command converts a Fourier map file into an Insight II grid file which can be rendered in a solid fashion. This function requires that you calculate and save a Fourier map file using the MIR/Calc_Fourier command. The Fourier map file must be in the standard Xsight/XtalView map format, that is, a binary file that contains a 3D Fourier map for the entire unit cell. In addition, the relevant molecule must be loaded into Insight II.

Once you have entered the Utilities/Display_Density command, there are three options in the Density_Operation parameter block.

The Map_File parameter is the name of the Fourier map file. It is assumed that the extension will be .map (although any filename will be accepted) and all files with that extension will be displayed in the Map_File_List value-aid.
The Reference_Molecule parameter refers to the molecule that is to be read and can be obtained from the Object value-aid.
The Scalar_Grid_Name parameter is the name assigned to the internal grid object that is created.
The Display_Density operation is used to display the internal grid object that was generated in the Read_Density_Map operation.
The Scalar_Grid_Name parameter is the name assigned to the internal grid object.
The Contour Level parameter is the value of the isosurface to be contoured.
The Density_Color parameter specifies the color of the contoured surface and has a value-aid color palette associated with it. If you select the Density_Color parameter, a color palette appears that allows you to adjust the colors. This can be done by either adjusting the relative RGB components with the three sliders or by selecting one of the 16 predefined colors in the menu. The Density_Color parameter can also be specified by name or by three integers that specify the corresponding RGB composition. Each color integer can range from 0-256, where 0 means no contribution from that color component and 256 means a full contribution. A fourth integer can be added to the color description in order to specify transparency. A value of 0 is completely transparent and a value of 256 is totally opaque.
The electron density can be displayed using either a standard grid line representation or using a solid surface representation. All of the Fourier map grid points that fall within a box of dimensions Size_X by Size_Y by Size_Z Å and centered on the Center are contoured and displayed.
The Center parameter can be specified at either the molecule, subset, monomer, or atom level. The level determines what the density is centered about. Center is selected either by clicking in the display or by typing in the specification in the standard Insight II format (for example, to specify residue 24 of the CCP molecule, you enter CCP:24 as the Center parameter). Center is a trigger parameter, so each time another center is selected, the density is recentered. In this fashion, you can pick different centers in the display: each time the density is displayed at the selected center without selecting Execute on the Display_Display menu.
The contour level can be adjusted interactively by using one of the built-in grid functions. Select the Contour Level parameter and a slider appears. This value-aid can be used to change the contour level interactively.
By toggling on the Bounding_Box option, you can draw a box around the density that is being displayed.
When the Mask_Density option is toggled on you can access the Mask_Radius parameter. Density further than Mask_Radius from any atom is not displayed.
The Delete_Density_Map operation allows you to remove the density grid specified by the Scalar Grid Name parameter. The current grids are listed in the Grid_List value-aid.

Data_Control pulldown

The Data_Control pulldown contains commands for importing structure factor data for use with the Xsight system.

Data_Control/Import_Data

The Data_Control/Import_Data command is used to import structure factor data from a wide variety of ASCII formats and convert the data to one of the file formats used by the Xsight system. This command also allows manipulations such as sorting and re-indexing to be performed on the input data.

The Input_File_Format options correspond to various arrangements of data items that may be imported. In the format specification codes, hkl refers to reflection indices, F1 and F2 refer to observed structure factor amplitudes (perhaps Bijvoet pairs), SIG1 and SIG2 refer to the standard deviations of the observed data, FOM refers to the figure of merit for a phase angle, FC refers to calculated structure factor, PHS refers to a phase angle, I refers to intensity data and DELANOM refers to the difference between Bijvoet pairs. In particular, you should note that the format specification hkl_F1_SIG1_F2_SIG2 is the Xsight/XtalView Fin file format and the format specification hkl_F1_FOM_PHS is the Xsight/XtalView Phase file format.

These data items are read as free format items unless the Use_Format_Spec option is toggled on. If the Use_Format_Spec option is toggled on the FTN_Format_Spec parameter wil appear. This option allows the user to specify a FORTRAN style specification for the selected Input_File_Format option. By using the FORTRAN format specifer with inserted spaces (i.e., X's) it is possible to bypass characters or unwanted variables in the input data file and, therefore, cause other types of data file to conform to one of the Input_File_Format options.

The Input_File_Name is the name of the file containing the input structure factor data.

The Output_File_Format option may be set to Fin(.fin), Phase(.phs), or XPLOR(.fob) depending on the type of output data file that is required. The program will eliminate or create data items that are required for these formats. For example, if the input file does not contain any phase information, then a `fake' Phase file is created. If an CNX-formatted file is created than all the input data items are transfered with appropriate CNX keywords.

The Output_File_Name parameter is the name of the output file. The extensions .fin and .phs are used for the Xsight/XtalView Fin and Phase file formats. The extension .fob is used as default for the CNX file format.

The Separate_Free_R option is available for removing a subset of diffraction data from the data set and placing it in a separate file. This option may be useful if the user is doing crystallographic calculations with many different programs and wants to remain absolutely sure that working and test sets of data remain separate. When the Separate_Free_R option is toggled on the Percentage_Data and Free_R_Output_File parameter blocks will appear. The Percentage_Data parameter is the percentage of the input data set that will be transferred to the output file named in the Free_R_Output_File parameter block.

The Low_Res_Limit and High_Res_Limit parameters are lower and upper resolution limits for accepting structure factor data.

The F_Over_Sigma_Cut parameter is the minimum number of standard deviations required for accepting a structure factor amplitude.

The Regroup_Bijvoets option is applicable if the Fin format is used for the output file. This option provides the capability for collecting separated Bijvoet reflection pairs in the input reflection file and regrouping them on the same line of the output file.

The Reduce_Data option is used to re-index the structure factor data so that it lies in a unique reciprocal-space asymmetric unit. This option does not allow users to choose the asymmetric unit but it does re-index the data in a unique way.

The Sort_Data option is used to sort the structure factor data from low indices to high indices with l running fastest and h running most slowly.

If the Index_Permutation option is toggled on the New_H, New_K, and New_L parameters will be made available. This option might be used to re-index data so that a new data set is indexed with the same `hand' as a previously collected set of data.

If the input data file contains Bijvoet reflection pairs on the same line , as in the hkl_F1_SIG1_F2_SIG2 format or the hkl_F1_SIG1_DELANOM format, the F1_F2_Treatment options are made available. The Merge option combines the F1 and F2 measurements into a single measurement. The Leave option is used to retain F1 and F2 as distinct measurements on the same line of an output Fin format file. The Split option retains F1 and F2 as distinct Bijvoet pair measurements but places them on different lines of the output data file. The Swap option is used to interchange F1 and F2 on the same line of an output Fin format data file.

Data_Control/Display_Recip_Space

The Data_Control/Display_Recip_Space command is used to spawn the XtalView program, Xrspace, a program that is used for displaying views of reciprocal space in an undistorted format. If you decide to pass the filename containing the reflections to be displayed, you can select from four types of reflection files to pass. See Xrspace program for more information.

Data_Control/Data_Processing

The Data_Control/Data_Processing command is used to spawn the Cerius2 package, which contains the X-GEN data-processing program. You need to have Cerius2 and X-GEN installed on your system for this command to function.

MAD pulldown

The MAD pulldown contains commands that relate to multi-wavelength anomalous scattering phasing calculations.

MAD/Combine_MAD_Data

The MAD/Combine_MAD_Data command is used to combine MAD data sets into a single file and carry out preliminary scaling between the data. This command is divided into eight operations.

The Job_Control operation is used to provide name and title information for this command and sets basic information on the number of data files and number of batch groups within data files.
The Combine_Job_Name parameter is the name of the MADSYS job.
The Combine_Job_Title parameter is the title for the MADSYS job. This title default to the information in the crystal file.
The MAD_Low_Res_Limit and MAD_High_Res_Limit parameters are the lower and upper resolution limits for data that will be used in this command.
The Num_Wavelengths parameter is the number of wavelengths at which MAD data were collected. This is equal to the number of input data files that you will use.
The Import_Data_Files operation is used to specify the names of the input data files.
The File_Operation parameter is set to Edit or Done depending on whether you are entering files or have completed the process of entering files.
The File_Format parameter may be set to Scalepack, CCP4 or Use_Format_Spec depending on whether the input reflection file is in the Scalepack format, an ASCII form of the CCP4/Agrovata format or you wish to enter a FORTRAN file specification for the input data. If the Use_Format_Spec option is toggled on then the FTN_Format parameter is available for entering the format specification. Required input items are h,k,l,batch number, intensity, standard deviation.
The Wavelength_Number parameter is an automatically generated value that is used to set a file number for each data file that is entered.
The WL_File_Name parameter is connected to the WL_File_Names value-aid and is used to enter data files.
The Define_Data_Groups operation is used to specify the experimental geometry for batch groups in the data files.
The Group_Operation is set to Edit or Done depending on whether you are entering information for the batch groups or have completed entering information.
The Data_Group_Number is an automatically generated parameter that is used to identify the group for which information is being specified.
The Geometry_Type parameter may be set to Mirror, Inverse, or Random depending on the diffraction geometry of the experiment.
For any Geometry_Type, the Start_Batch_Number, End_Batch_Number. and Pairing_Tolerance parameters are used to specify the first batch number, the last batch number and the number of frames by which the experiment deviated from the expected geometry.
If the Geometry_Type is set to Mirror then the Spindle Axis parameter may be set to one or more of pos_a_star, neg_a_star, pos_b_star, neg_b_star, pos_c_star, neg_c_star, depending on the orientation of the reciprocal crystal axes to the spindle. Note that the spindle axis may be specified by a combination of these axes, for example, both pos_a_star and pos_b_star may be set to indicate a spindle axis on +a*+b*.
If the Geometry_Type is set to Inverse the Direct_Inverse_Diff parameter is used to specify the difference in batch number between reflections in the direct and inverse beam.
This operation may be used to apply parameterized local scaling of Bijvoet reflection pairs.
The F_Over_Sigma_Cutoff parameter is used to reject reflections for which the measurement is smaller than the specified number of standard deviations.
The Anom_RMS_Cutoff parameter is used to reject reflections for which the Bijvoet difference is less than the the root mean square anomalous differerence.
The Num_Bv_Selections parameter is used to enter the number of resolution-dependent groups that will be used for the scaling of Bijvoet reflection pairs.
The Bv_Scale_Selection parameter may be set to Edit_Selection or Done depending on whether you are providing information for the selection or have finished entering this information.
The Bv_Scale_Select_Num parameter is an automatically set parameter that is used to identify the resolution group for which you are specifying selection information.
The Bv_Scale_Operation parameter may be set to Bv_Scale_Limits or Bv_Scale_Groups depending on whether you are specifying the resolution range for this scaling group or whether you are specifying which batch groups to include in this scaling group.
If the Bv_Scale_Operation parameter is set to Bv_Scale_Limits the Bv_Low_Res_Limit and the Bv_High_Res_Limit parameters are available for entering the lower and upper resolution limits for this scaling group.
If the Bv_Scale_Operation is set to Bv_Scale_Groups the Group_Selection parameter may be set to one of All_Groups, Include_Group, Omit_Group or Next_Selection. When the Include_Group or Omit_Group options are used the Group_Number parameter is available to specify a batch group for inclusion or omission from the scaling selection.
The Scale_Wavelength operation is used to carry out preliminary scaling of data recorded at different wavelengths.
If the Scale_Bijvoets operation was not used the F_Over_Sigma_Cutoff and Anom_RMS_Cutoff parameters are available. The meaning of these parameters is the same as described for the Scale_Bijvoets operation.
The Absolute_rmsF parameter will normally be generated by the Calc_Absolute_Scatt command and provides the expected root mean square value for the structure factor data on an absolute scale.
If the Use_Bv_Selection option is toggled on the same choice of resolution-dependent scaling groups and batch groups that was made in the Scale_Bijvoets operation will be used. If this option is toggled off the selection parameters descibed below are made available.
The Num_WL_Selections parameter is used to enter the number of resolution-dependent groups that will be used for the scaling of equivalent reflections measured at different wavelengths.
The WL_Scale_Selection parameter may be set to Edit_Selection or Done depending on whether you are providing information for the selection or have finished entering this information.
The WL_Scale_Select_Num parameter is an automatically set parameter that is used to identify the resolution group for which you are specifying selection information.
The WL_Scale_Operation parameter may be set to WL_Scale_Limits or WL_Scale_Groups depending on whether you are specifying the resolution range for this scaling group or whether you are specifying which batch groups to include in this scaling group.
If the WL_Scale_Operation parameter is set to WL_Scale_Limits the WL_Low_Res_Limit and the WL_High_Res_Limit parameters are available for entering the lower and upper resolution limits for this scaling group.
If the WL_Scale_Operation is set to WL_Scale_Groups the Group_Selection parameter may be set to one of All_Groups, Include_Group, Omit_Group or Next_Selection. When the Include_Group or Omit_Group options are used the Group_Number parameter is available to specify a batch group for inclusion or omission from the scaling selection.
The Run operation is used to specify the names of the output and script files and control the type of run of the MADSYS program that is required.
The MAD_Output_File parameter contains the name of the output file that will contain the scaled reflection data from all of the input files.
The MAD_Run_Mode parameter may be set to Run_Now, Save_Script_Only or Run_Saved_Script depending on whether you wish the MADSYS job to execute immediately, you wish to save the script or you wish to run a previously generated script.
The MAD_Script_File parameter spscifies the name of the script file for controling the MADSYS job.
The Analyze command is used to obtain key information from the log file resulting from the MADSYS run.
The Combine_Log_File parameter is connected to the MAD_Log_Files value-aid and is used to spscify the name of the log file that resulted from the MADSYS run in the Combine_MAD_Data command.
This operation is used to leave the MAD/Combine_MAD_Data command.

MAD/Calc_Anom_Diff

The MAD/Calc_Anom_Diff command is used to derive anomalous scattering differences from the file output by the MAD/Combine_MAD_Data command and to merge the data to a unique set of structure factors. This command is divided into nine operations.

The Job_Control operation is used to provide name and title information for this command and sets basic information on the number of wavelengths for which data was obtained and number of batch groups that were specified in the initial data files. Most of these parameters will be provided automatically following use of earlier parts of the MAD pulldown.
The Anom_Job_Name parameter is the name of the MADSYS job.
The Anom_Job_Title parameter is the title for the MADSYS job. This title defaults to the information in the crystal file.
The MAD_Low_Res_Limit and MAD_High_Res_Limit parameters are the lower and upper resolution limits for data that will be used in this command.
The Num_Wavelengths parameter is the number of wavelengths at which MAD data were collected.
The Num_Data_Groups parameter is the number of batch groups that were specified in the original data files.
The Select_Data operation is used to specify the input and output files for the MAD/Calc_Anom_Diff command.
The MAD_Input_File parameter is connected to the MAD_Input_Files value-aid and is used to select the combined data file that was produced by the MAD/Combine_MAD_Data command.
The Out_Merge_Data_File parameter is the name of the output data file that will be produced by the MAD/Calc_Anom_Diff command.
If the Write_FIN_File option is toggled on the FIN_Output_File parameter is made available. This parameter is used to specify the file name for a `Fin' format file of the anomalous scattering amplitudes. This file may be used for Patterson map calculations to locate or confirm the anomalous scatterer co-ordinates.
The Overall_Params operation is used to set parameters for solving the MAD phasing equations to extract anomalous differences.
The Num_Phase_Iter parameter is the number of iterations that are used in the solution of the MAD phase equations.
The Max_Fz parameter is the maximum value of a structure factor amplitude that is permitted
The Max_FAnom parameter is the maximum value of the anomalous scattering part of the structure factor that is permitted.
The F_Sig_Cutoff parameter is the minimum number of standard deviations required for the structure factor to be included in these calculations.
The Max_Delta_Phs parameter is the maximum value of the standard deviation in the estimate of the anomalous scattering phase difference for inclusion in these calculations.
The Max_Qerror parameter is the maximum value of this MAD fitting index that is permitted for inclusion in these calculations.
The Anom_Element parameter is the code in the periodic table for the anomalous scattering element. This parameter is used to obtain values for the normal scattering factor for the element. For ions the charge is indicated by ,for example, the notation Pt2+.
This operation is used to specify the refinement of parameters for each wavelength in order to calculate the anomalous scattering signal from the sets of MAD data.
The Wave_Num_Selection parameter is set to Edit_Wave_Number or Done depending on whether you are specifying wavelength dependent parameters or have finished the specification.
The Wave_Num parameter is automatically set and is used to specify the wavelength for which refinement parameters are to be specified.
The Relative_Wave_Scale specifies the initial scale value for each set of data (i.e. data measured at a particular wavelength) relative to the first data set. If the MAD/Calc_Absolute_Scatt command has been run these values will be estimated to be different from unity because of the wavelength-dependent differences in the anomalous scattering.
The FP and FPP parameters are used to specify the initial f' and f'' values for the anomalous scatter at each wavelength.
The Refine_Scale, Refine_FP and Refine_FPP options may be toggled on to refine the relative scale, f' and f'' for each wavelength.
This operation is used to select batch groups for inclusion in the exraction of anomalous differences.
The Merge_Groups parameter may be set to All_Groups, Include_Group, Omit_Group or Done. When the Include_Group or Omit_Group options are used the Group_Number parameter is available to specify a batch group for inclusion or omission from the scaling selection.
The Merge_FA operation is used to merge the data down to a unique set and extract weighted values of the anomalous scattering differences.
The Max_Anom_Scatt and Av_Anom_Bfac parameters are used to determine a resolution dependent profile for the maximum amount of anomalous scattering that is permitted.
The Fz_Sig_Cutoff parameter is the minium number of standard deviations permitted for the final merged set of structure factor amplitudes.
The FAnom_Sig_Cutoff paramater is the minimum number of standard deviations permitted for the anomalous scattering amplitude that is obtained.
The Num_Res_Shell parameter is the number of resolution shells for statistical analysis of the merged data.
The Run operation is used to specify the names of the output and script files and control the type of run of the MADSYS program that is required.
The MAD_Run_Mode parameter may be set to Run_Now, Save_Script_Only or Run_Saved_Script depending on whether you wish the MADSYS job to execute immediately, you wish to save the script or you wish to run a previously generated script.
The MAD_Script_File parameter spscifies the name of the script file for controling the MADSYS job.
The Analyze command is used to obtain key information from the log file resulting from the MADSYS run.
The Anom_Diff_Log_File parameter is connected to the MAD_Log_Files value-aid and is used to spscify the name of the log file that resulted from the MADSYS run in the Calc_Anom_Diff command.
This operation is used to leave the MAD/Calc_Anom_Diff command.

MAD/Determine_Phases

The MAD/Determine_Phases command is used to complete the phase determination process, providing an output set phased structure factors in the `Phase' format. This command contains five operations.

The Job_Control operation is used to provide name and title information for this command and sets the resolution limits for the final phase determination.
The Phase_Job_Name parameter is the name of the MADSYS job.
The Phase_Job_Title parameter is the title for the MADSYS job. This title default to the information in the crystal file.
The MAD_Low_Res_Limit and MAD_High_Res_Limit parameters are the lower and upper resolution limits for data that will be used in this command.
The Calculate_Phases operation specifies file names and parameter information for the phase determination run.
The In_Merge_Data_File parameter is connected to the Merge_Data_Files value-aid and is used to specify the input file of merged data (i.e. the output file from the MAD/Calc_Anom_Diff command) for phase determination.
The In_XYZ_Anom_File parameter is connected to the XYZ_Anom_Files value-aid and is used to specify the input file containing the anomalous scatterer model.
The Out_Phs_File parameter is used to specify the name for the output file pf phased structure factor data. This is automatically formatted in to the `Phase' file format.
The Anom_Element parameter is the code in the periodic table for the anomalous scattering element. This parameter is used to obtain values for the normal scattering factor for the element. For ions the charge is indicated by, for example, the notation Pt2+.
The FAnom_Sig_Cutoff is the minimum number of standard deviations for the amplitude of anomalous scattering that will be used for phase determination.
The Max_FAnom and Min_FAnom are the maximum and minimum value of the anomalous scattering amplitude that will be used for phase determination.
The Max_Delta_Phs parameter is the maximum value of the standard deviation in the estimate of the anomalous scattering phase difference for inclusion in these calculations.
The Fcalc_Scale parameter is the scale factor between observed and calculated anomalous scattering. If you have used the MAD/Refine_Anom_Sites command to refine the anomalous scatterer model this value will be automatically generated.
The Run operation is used to specify the names of the output and script files and control the type of run of the MADSYS program that is required.
The MAD_Run_Mode parameter may be set to Run_Now, Save_Script_Only or Run_Saved_Script depending on whether you wish the MADSYS job to execute immediately, you wish to save the script or you wish to run a previously generated script.
The MAD_Script_File parameter spscifies the name of the script file for controling the MADSYS job.
The Analyze command is used to obtain key information from the log file resulting from the MADSYS run.
The Phase_Log_File parameter is connected to the MAD_Log_Files value-aid and is used to spscify the name of the log file that resulted from the MADSYS run in the Determine_Phases command.
This operation is used to leave the MAD/Determine_Phases command.

MAD/Calc_Absolute_Scatt

The MAD/Calc_Absolute_Scatt command is a utility that is used to estimate the amount of scattering from the crystal on an absolute scale and the contribution from the anomalous scatterers at the wavelengths used in data collection. This command contains five operations.

The Job_Control operation is used to provide name and title information for this command and sets the resolution limits for the final phase determination.
The Absolute_Job_Name parameter is the name of the MADSYS job.
The Absolute_Job_Title parameter is the title for the MADSYS job. This title default to the information in the crystal file.
The MAD_Low_Res_Limit and MAD_High_Res_Limit parameters are the lower and upper resolution limits for data that will be used in this command.
The Num_Wavelengths parameter specifies the number of different wavelengths at which you will calculate the crystal scattering.
The Overall_Params operation is used to specify the input file containing the protein amino-acid sequence and parameters relating to the number and type of atoms in the crystal.
The Input_Seq_File parameter is connected to the Input_Seq_Files value-aid and is used to specify the name for the file containing sequence data.
The Amino_Acid_Code parameter may be set to One_Letter_Code or Three_Letter_Code depending on whether the protein sequence data is to be read as one-letter or three-letter codes.
The Num_Prot_Per_Au parameter specifies the number of protein molecules per crystal asymmetric unit.
The Prot_B_Value parameter is the estimate for the overall temperature factor of the protein molecule
The Num_Anom_Scatt parameter is the number of anomalous scatterers per crystal asymmetric unit.
The Anom_B_Value parameter is the estimate for the overall temperature factor for the anomalous scatterers in the crystal.
The Anom_Element parameter is the code in the periodic table for the anomalous scattering element. This parameter is used to obtain values for the normal scattering factor for the element. For ions the charge is indicated by, for example, the notation Pt2+.
The Wavelength_Params operation is used to enter the values of f' and f'' for the anomalous scatterers at the wavelengths at which data were collected.
The Wave_Num_Selection parameter is set to either Edit_Wave_Num or Done depending on whether you are entering f' and f'' values or have completed entering this information.
The Wave_Num parameter is an automatically updated value that is used to identify the wavelength number for which data is being entered.
The FP and FPP parameters are used to specify the initial f' and f'' values for the anomalous scatter at each wavelength.
The Run operation is used to specify the names of the output and script files and control the type of run of the MADSYS program that is required.
The MAD_Run_Mode parameter may be set to Run_Now, Save_Script_Only or Run_Saved_Script depending on whether you wish the MADSYS job to execute immediately, you wish to save the script or you wish to run a previously generated script.
The MAD_Script_File parameter spscifies the name of the script file for controling the MADSYS job.
This operation is used to leave the MAD/Calc_Absolute_Scatt command.

MAD/Refine_Anom_Sites

The MAD/Refine_Anom_Sites command is a utility that used to refine the atomic model of the anomalous scatterers. This command contains six operations.

The Job_Control operation is used to provide name and title information for this command and sets the resolution limits for the refinement of parameters for the model of the anomalous scatterers..
The Anom_Site_Job_Name parameter is the name of the MADSYS job.
The Anom_Site_Job_Title parameter is the title for the MADSYS job. This title default to the information in the crystal file.
The MAD_Low_Res_Limit and MAD_High_Res_Limit parameters are the lower and upper resolution limits for data that will be used in this command.
The Refine_Files operation is used to enter the names of the input and output files that will be used in the refinement of the parameters for the model of the anomalous scatterers.
The In_Merge_Data_File parameter is connected to the Merge_Data_Files value-aid and is used to specify the file of merged diffraction data that will be used in the refinement.
The In_XYZ_Anom_File parameter is connected to the XYZ_Anom_Files value-aid and is used to specify the file containing the initial model for the anomalous scatterers.
The Out_XYZ_Anom_File parameter is used to specify the file that will contain the refined model of the anomalous scatterers.
The Refine_Params operation is used to specify parameters that will control to refinement of the model of the anomalous scatterers.
The Num_Ref_Cycles parameter specifies the number of refinement cycles that will be performed.
The FAnom_Sig_Cutoff is the minimum number of standard deviations for the amplitude of anomalous scattering that will be used for the refinement.
The Max_FAnom parameter is the maximum value of the anomalous scattering amplitude that will be used for the refinement.
The Fcalc_Scale parameter is the scale factor between observed and calculated anomalous scattering. If you have previously used the MAD/Refine_Anom_Sites command to refine the cale for anomalous scatterer model this value will be automatically updated.
The Max_Delta_Phs parameter is the maximum value of the standard deviation in the estimate of the anomalous scattering phase difference for inclusion in these calculations.
The Anom_Element parameter is the code in the periodic table for the anomalous scattering element. This parameter is used to obtain values for the normal scattering factor for the element. For ions the charge is indicated by, for example, the notation Pt2+.
The Anom_Refine_Type parameter is used to specify the type of refinement that will be performed. If set to Scale the scale factor between the observed and calculated anomalous scattering will be refined. If set to Occupancy the individual occupancy factor for the anomalous scatterers will be refined. If set to B_Factor the individual temperature factors for the anomalous scatterers will be refined. Note that with these three options the positions of the anomalous scatterers are also refined. If set to Positions_Only, only the positions of the anomalous scatterers will be refined.
The Run operation is used to specify the names of the output and script files and control the type of run of the MADSYS program that is required.
The MAD_Run_Mode parameter may be set to Run_Now, Save_Script_Only, or Run_Saved_Script, depending on whether you wish the MADSYS job to execute immediately, you wish to save the script, or you wish to run a previously generated script.
The MAD_Script_File parameter spscifies the name of the script file for controling the MADSYS job.
The Analyze command is used to obtain key information from the log file resulting from the MADSYS run.
The Refine_Log_File parameter is connected to the MAD_Log_Files value-aid and is used to spscify the name of the log file that resulted from the MADSYS run in the Refine_Anom_Sites command.
The Refine_Log_Table and Refine_Log_Graph may be toggled on to display a table and/or a graph of the R-factor for the anomalous scattering model versus refinement cycle.
This operation is used to leave the MAD/Refine_Anom_Sites command.

MIR pulldown

The MIR pulldown contains commands that relate to multiple isomorphous replacement phasing calculations.

MIR/Merge_Data

The MIR/Merge_Data command is used to spawn the XtalView program, Xmerge, a program that is used for merging and scaling two data files. If you decide to pass the file information it is necessary to enter the names of two existing .fin files for merging and scaling and the name of the output file. See Xmerge program for more information.

MIR/Calc_Fourier

The MIR/Calc_Fourier command is used to spawn the XtalView program, Xfft, a program that is used for calculating electron density or Patterson function maps by the fast Fourier transform method. This program requires a .phs file and creates a new .map file. These filenames can be passed to the program if you choose to do so. Please see Xfft program for more information.

MIR/Contour_Map_3D

The MIR/Contour_Map_3D command is used to display difference Patterson maps and cross-difference Fourier maps. This command allows the visualization of heavy stom sites in the context of these maps and contains tools for editing the heavy atom sites.

This command is divided into three operations.

The Setup operation is used to enter the files that will be used and to select the type of map that will be displayed.
The Map_File_Type may be set to Difference_Map or Patterson_Map depending on whether the map that is to be entered is a cross-difference Fourier map or a difference Patterson map.
The Map_File parameter is connected to the Map_File_List value-aid and contains the input map.
The Contour_Sigma_Level parameter sets the base contour level for displaying the map. The contour level is given in terms of the number of standard deviations in the map density.
The Two_Level_Contour option may be toggled on to set a second contour level in the display. The High_Sigma_Level parameter is available for entering the value of the second contour level.
If the Input_Atom_Sites option is toggled the In_Solution_File parameter is available for entering a .sol file containing the heavy atom parameters.
This operation contains the Site_Edit_Operation options for manipulating the heavy atom atomic model. The options that are available depend on the type of map that was specified in the Setup operation.
For a cross-difference Fourier map the available options are Delete_Site, Add_Site, Adjust_Site, Peak_Search, Invert_Sites, Write_Solution_File and Redo_Contour.
The Delete_Site option is used to remove the heavy atom site specified by the Site_Number parameter.
The Add_Site option is used to add a new site with name given by the Site_Name parameter and at positions specified by the Fract_X, Fract_Y and Fract_Z parameters. These parameter may be set using the slide-bar. The type of heavy atom that is to be added is specified by the Scattering_Element parameter, which is connected to the Element_List value-aid. The site number for the new atom is generated in the Site_Number parameter block.
The Adjust_Site option is used to change the parameters for an existing site and uses the same parameters as the Add_Site option.
The Peak_Search option is used to place heavy atom sites on peaks in the density map at peaks greater than the value entered in the Site_Peak_Threshold parameter block. The type of heavy atom that will be added is specified by the Scattering_Element parameter, which is connected to the Element_List value-aid.
The Invert_Sites option is to change the enantiomorph of a heavy atom constellation (i.e., it changes co-ordinates x to -x, y to -y and z to -z).
The Write_Solution_File option is used to write out the modified heavy atom co-ordinates in a new file specified by the Out_Solution_File parameter.
The Redo_Contour option is used to change the density levels that are used for contouring the map. The new base contour level is specified by the New_Sigma_Level parameter. The Two_Level_Contour option may be toggled on to set a second contour level in the display. The High_Sigma_Level parameter is available for entering the value of the second contour level.
For a difference Patterson map the only available Site_Edit_Option options are Mark_Vector and Redo_Contour. The Mark_Vector option is toggled on to relate the heavy atom vectors picked from the table to the yellow cross-hairs marking the position in the difference Patterson map. The Redo_Contour option operates as descibed above for the cross-difference Fourier map.
This operation is used to leave the MIR/Contour_Map_3D command.

MIR/Find_Heavy_Atoms

This command is used to automatically locate heavy atoms sites from data sets used for MIR or MAD phasing.

The command contains two operations in the Heavy_Operation parameter block.

The Set_Parameters operation is used to specify the input parameters for the heavy atom search.
The Input_Fin_File parameter is used to enter the Fin formatted file containing the structure factor data to be used in the search. This parameter is connected to the Fin_File_List value-aid. If the Input_Data_Type is set to Isomorphous_Diff then the items in the data file will be the structure factor amplitudes for the native and the derivative data set. If Input_Data_Type is set to Bijvoet_Diff then the items in the input data file will be the Bijvoet structure factor pairs. If Input_Data_Type is set to MAD_FA_Coeffs then the F1 item in the Fin formatted file will be the MAD FA coefficient.
The Output_Sol_File parameter block is used to enter the name of the .sol file that will contain the heavy atoms sites that are located.
The Scattering_Element parameter block is used to specify the type of atom in the crystal. this parameter is connected to the Element_List value-aid.
The Low_Res_Cutoff and High_Res_Cutoff parameters are the lower and upper resolution limits for the structure factor data to be used in the heavy atom search.
The Search_Limits parameters (Start_X, Stop_X, Start_Y, Stop_Y, Start_Z, Stop_Z) are used to enter the range in fractional co-ordinates of the crystal that will be searched for heavy atom sites.
The available Search_Type options are Single_Site, Double_Site and Multi_Site and correspond to searches for one, two or many heavy atoms.
The Min_Search_Cor_On_I parameter correspond to a minimum Patterson correlation threshhold for retaining putative heavy atoms sites in the first pass of the search program (see the Theory chapter for a description of the algorithm).
The Run operation provides Run_Now, Save_Script_Only and Run_Saved_Script options. These options are used for running the heavy atom search immediately, saving the input script without running it, and running a previously created script.

MIR/Calc_Phases

The MIR/Calc_Phases command is used to spawn the XtalView program Xheavy, a program that is used for refining heavy atom derivative sites and calculating phases. You can pass the names of the input and output files from Insight II or you can turn Pass_Files off and assign files from within Xheavy. Please see Xheavy program for more information.

MIR/Merge_Phases

The MIR/Merge_Phases command is used to spawn the XtalView program, Xmergephs, a program that is used for merging phase angles with structure factor amplitudes. If you select to pass the input and output files, an existing .fin file, an existing .phs file and a new .phs file will have to be entered in the Fin_File_1, Phase_File, and Phase_Output parameters respectively. See Xmergephs program for more information.

MIR/Predict_Patterson

The MIR/Predict_Patterson command is used to spawn the XtalView program, Xpatpred, a program that is used for predicting Patterson peaks from a list of heavy atom sites. You can pass the names of the input and output files from Insight II or you can turn Pass_Files off and assign files from within Xpatpred. Please see Xpatpred program for more information.

MIR/Contour_Map

The MIR/Contour_Map command is used to spawn the XtalView program, Xcontur, a program that is used for contouring electron density maps in two dimensions. A .map file is required for running the program. You can either pass the name of the file from Insight II or you can wait until you are executing Xcontur before reading in the .map file. Please see Xcontur program for more information.

MIR/Statistics

The MIR/Statistics command is used to spawn the XtalView program Xstat, a programs that is used to create graphs of R-values and measurement errors as a function of resolution or structure factor amplitude. You can pass the name of the input file from Insight II or you can turn Pass_Files off and assign files from within Xstat. Please see Xstat Program for more information.

Mol_Replacement pulldown1

The Mol_Replacement pulldown contains commands for setting up and running the molecular replacement package REPLACE (Tong 1993; Tong & Rossmann 1990). This package includes a general (locked) rotation function program (GLRF) and a translation function program (TF). The rotation function program can carry out ordinary as well as locked self- or cross-rotation function calculations. The translation search can be based on R factors, correlation coefficients, or Patterson correlation criteria.

The Mol_Replacement pulldown is organized into five distinct commands that correspond to various steps in the determination of a structure by molecular replacement. The five commands are Search_Model, Rotation_Func, Translation_Func, Apply_Transform, and MR_Tools.

Mol_Replacement/Search_Model

The Mol_Replacement/Search_Model command is used to calculate structure factors from an atomic model for use in the Rotation function search.

The Search_Job_Name parameter is the job name that will be used to create input and print files.

The Title parameter is a text string describing the run. The text string defaults to the information in the crystal file.

The Crystal_Values option can be toggled between No Initialization, From_Crystal_File, and Triclinic Box. These options are used to load the Unit Cell parameters A, B, C, Alpha, Beta, Gamma, and Space_Group.

The Model_File_Format options can be toggled between PDB and Molecule. These options allow you to read in a Protein Data Bank file (through the PDB_File parameter block and PDB_File_List value-aid) or an Insight II molecule.

The Temp_Factor_Modify options can be toggled between No_Changes, Increment, Replace_All, and Replace_0_Values. When the Increment, Replace_All and Replace_0_Values options are toggled on, a Temp_Factor_Value appears. The value that you enter for this parameter will either be added to the current temperature factors, used to replace the existing temperature factors, or used to replace any zero temperature factors in the input model.

The Resolution Limits parameters D_Max and D_Min allow you to set the resolution limits for the structure factors that will be calculated from the model.

The Direct_Summation option is used to select between calculating the model structure factors by direct summation methods or by FFT methods.

The Run operation provides Run_Now, Save_Script_Only and Run_Saved_Script options. These options are used for running the stucture factor calculation immediately, saving the input script without running it, and running a previously created script.

Mol_Replacement/Rotation_Func

The Mol_Replacement/Rotation_Func command contains ten operations under the Rotation_Operation menu.

The name in the Rot_Job_Name parameter block is used to create input, print and map files for the rotation function calculation.
The Title parameter block contains a text string describing the run. The text string defaults to the information in the crystal file
The Rotation_Func_Type options are Self_Rotation, Cross_Rotation, Peak_Search_Only, and Contour_Only. These options allow you to select a self-rotation function, a cross-rotation function, to carry out a peak search on the results of an earlier run, or to contour the results of an earlier rotation function run.
If the Peak_Cross_Corr option is toggled on the program output will contain an analysis of the angular relationships between the number of top peaks specified by the Num_Top_Peaks parameter. This option provides a means of checking the peaks found by the cross rotation function for solutions related by non-crystallographic symmetry.
The Fast_Rotation option allows you to run the rotation function using the Crowther type of fast rotation function algorithm.
The Search_Angle parameter defines whether the search will be run in Euler or Polar angles.
The Polar_Convention parameter specifies the polar angle definition convention. Two conventions are supported: XYK and XZK. In both cases, is the angle from the Cartesian x axis. In convention XYK, as defined by Rossmann and Blow (1962), is the angle from the y axis. In convention XZK, as defined by Fitzgerald (1988), is the angle from the z axis. is the rotation around the axis defined by and .
The Euler_Convention parameter specifies the definition convention of Eulerian angles. Two conventions are currently supported, ZXZ and ZYZ, corresponding to rotation around the Cartesian z axis (3), then around the new x (and y, respectively) axis (2), and finally around the new x axis (1). ZXZ is the convention described by Rossmann and Blow (1962) and ZYZ is the conventions used by Fitzgerald (1988) in the MERLOT program.

Caution


The matrix used in this program is the transpose of the matrix as printed in Table 1 of the paper by Rossmann and Blow (1962). Therefore, if you are comparing the results from this program with other programs, be sure that the programs are using the matrices the same way. This is true whether you are using Eulerian angles or polar angles.  

Local_Symmetry operation contains parameters for specifying non-crystallographic symmetry relationships. The full parameter block is generated by toggling on the Specify_Local_Symmetry option.
The Symmetry_Type option can be set to Polar, Euler, Vector, or Directional_Cos. These options allow you to specify the non-crystallographic symmetry relationships by polar angles, Eulerian angles, a vector, or direction cosines.
When set to polar the angles describing the axis are entered in the Phi_1, Psi_1, and Kappa_1 parameter blocks.
When set to Euler the angles are entered in the Theta_A_1, Theta_B_1, and Theta_C_1 parameter blocks.
When the axis is to be described by a vector using the Cartesian coordinates of the end point of a vector from the origin the values are entered in the Vec_X_1, Vec_Y_1, and Vec_Z_1 parameter blocks.
When the axis is to be described by direction cosines the values are entered in the Cos_A_1, Cos_B_1, and Cos_C_1 parameter blocks.
For the cases when the axis is not described by polar angles you must define the order of the unique axis using the Angle_Spec parameter. The order of the unique axis can be defined by degrees (for example, 180 for a two-fold axis) or by a divisor of 360 degrees (for example, 2 for a two-fold axis) with the Degrees or Div_360_by_N options. The angular values are entered in the N_Parts_1 parameter or the Degree_1 parameter.
The Specify_Second_Symm option is used to define a second symmetry operation. When this option is toggled on you can specify a second symmetry operation using the same specification options as under Symmetry_type (above).
If the Symmetry_Expand option is toggled on, the program generates all the local symmetry operators by pairwise multiplication of all the specified operators. This allows you to only specify the unique symmetry elements. For example, for 222 symmetry, you only need to specify two orthogonal two-fold axes. For this operation to work well, the positions of the starting local symmetry axes must be specified with sufficient accuracy. If this option is toggled off, the expansion will not occur. This is useful in cases where improper rotation axes are being dealt with, for example, a local two-fold axis with a rotation of 175°.
The Symmetry_Update option allows you to modify the orientation of the local symmetry operators. You can specify the updating angles with the Symm_U_Type parameter as either Polar or Euler, and the values are entered in the Symm_U_A, Symm_U_B, and Symm_U_C parameter fields.
The Local_Orientation angles can be set in Euler or Polar angles. These angles are applied to the standard orientation of the symmetry elements to bring them to the orientation in the crystal. If set to Euler, the local orientation angles can be entered in the L_Alpha, L_Beta, and L_Gamma parameter block. If set to Polar, the angles can be entered in the L_Phi, L_Psi, and L_Kappa parameter blocks.
The Crystal_A operation allows you to enter the reflection data and the crystal parameters for the `A' crystal. For a self-rotation function the `A' crystal corresponds to your unknown crystal and there is no `B' crystal. For a cross-rotation function the set of calculated structure factors for the search model are loaded in the `A' crystal and the unknown crystal will be loaded as the `B' crystal.
The A_Crystal_Values parameter can be set to No initialization, From_Crystal_File or Triclinic_Box. These options set the Unit Cell parameters A, B, C, Alpha, Beta, Gamma, and the Space_Group parameter.
The Refl_File parameter can be chosen from the Refl_File_List value-aid. This parameter is the filename for an input set of structure factors.
The Sigma_Cutoff parameter removes structure factors less than the given number of standard deviations.
The Max_F and Min_F parameters set bounds on the magnitudes of the structure factors that will be used in the rotation function calculation. Note that setting Max_F to 0.0 disables this parameter so that no maximum value is set. The program prints out a tabulation of how many reflections are removed due to the Sigma_Cutoff, Max_F, and Min_F parameters, so reasonable inputs can be selected accordingly.
If the Remove_Origin parameter is selected, the origin of the A crystal Patterson map will be removed. In that case, an average intensity, calculated in shells of resolution, will be subtracted from each reflection.
The Crystal_B operation allows you to enter the reflection data and the crystal parameters for the `B' Crystal. For a cross-rotation function the unknown crystal is loaded as the `B' crystal.
The B_Crystal_Values parameter can be set to No_initialization, From_Crystal_file, or Triclinic_Box. These options are used to set the Unit Cell parameters A, B, C, Alpha, Beta, Gamma, and the Space_Group parameter.
The Refl_File can be chosen from the Refl_File_List value-aid. This parameter is the filename for the input set of structure factors.
The Sigma_Cutoff parameter removes structure factors less than the given number of standard deviations.
The Max_F and Min_F parameters set bounds on the magnitudes of the structure factors that will be used in the rotation function calculation. Note that setting Max_F to 0.0 disables this parameter so that no maximum value is set. The program prints out a tabulation of how many reflections are removed due to the Sigma_Cutoff, Max_F, and Min_F parameters, so reasonable inputs can be selected accordingly.
The Large_Term_Cutoff parameter is used to reduce the amount of computation time by limiting the rotation function calculation to large terms. This parameter defines the selection criterion for the strongest reflections (large terms) from the B crystal data. Reflections with I > Large_Term_Cutoff X I(average) will be saved as the large terms, where I(average) is calculated in shells of equal reciprocal volume. A Large_Term_Cutoff value of 2.0 usually results in about 10% of the data being saved as large terms, which is sufficient to obtain accurate ordinary rotation function values. For locked rotation searches, a Large_Term_Cutoff value of 5.0 usually saves about 0.5% of the reflection data. For a fast rotation function a Large_Term_Cutoff of ~0.2 is appropriate.
The Crystal_C operation enables you to enter a second unknown crystal in the cross-rotation function calculation. The parameters are the same as for the Crystal_B operation with the following exceptions.
The B_To_C_Angle option can be set to Euler or Polar. This option specifies the angle system that will be used to relate the rotation search in crystal B to crystal C.
The BTOC_Rot1, BTOC_Rot2 and BTOC_Rot3 parameters are the three angles that relate crystal B to crystal C.
The Search_Parameters operation is used to set up the angular ranges and increments for the rotation function.
The Auto_Search_Params option can be toggled on to automatically setup the unique search range if the search is carried out in Euler angles. If this option is toggled off you must enter T1_Start, T1_Stop, T2_Start, T2_Stop, T3_Start, T3_Stop, values to specify the start and stop angles for the search in the Theta1/Phi, Theta2/Psi and Theta3/Kappa angles.
The T1_inc, T2_inc, and T3_inc parameters specify the angular increment for the rotation search in each of the three angular ranges.
The Integration_Radius parameter specifies the spherical integration range for vectors in the rotation function. The value is normally set smaller than the size of the molecule.
The Refine operation provides options for improving on the solutions that are obtained in an initial rotation function search, carried out on a relatively coarse grid. The solution may be improved either by carrying out a rotation search on a finer grid around the initial solutions or by carrying out Patterson Correlation refinement on the atomic model.
If the Auto_Fine_Search option is toggled on, the Search_N_Peaks and Search_Cutoff parameters are made available. The Search_N_Peaks parameter is the number of top peaks from the initial rotation function. The Search_Cutoff parameter is the large term cutoff for conventional rotation functions. A search on a fine grid is carried out around each of the top peaks.
If the PC_Refine_Params option is toggled on, a set of parameters is made available for carrying out a Patterson correlation refinement on the atomic model. The Refine_N_Peaks parameter is the number of top peaks from the initial rotation function that will be refined. The Refinement_Cycles parameter is the number of model refinement cycles that will be carried out. The Refinement_Cutoff parameter is the large term cutoff for the PC refinement. The Temp_Factor_Modify parameter can be set to No_Changes, Increment, Replace_All, or Replace_0_Values. These choices allow you to manipulate the atomic temperature factors in the atomic coordinate file. The No_Change option specifies that the temperature factors that are currently stored in the model file will be used for calculating structure factors. The Increment option allows you to change all of the temperature factors by a constant value. The Replace_All option will change all temperature factors to the same specified value. The Replace_0_Values option will replace only temperature factors that are currently listed as 0 with a user-specified value.The PDB_Input_File is the input Protein Data Bank coordinate file. The PDB_Output_File is the output Protein Data Bank coordinate file.
If the PC_Refine_Groups option is toggled on, you can break the atomic model into a set of atomic groups which will be refined independently. When you have finished entering group specifications you can toggle the End_Groups option on to allow an exit from the Refine operation. The Clear_All_Groups option allows you to clear any existing groups that you may have entered so that you can enter a new set of groups. The Group_N and Of_Groups parameters are automatically set and give you information on the number of the group that is currently awaiting entry and the number of groups already entered. The Start Residue and Stop Residue parameters are the first and last residue numbers in a group. All residues between these parameters will be included in the group. The syntax A:1 is used, for example, if you wish to specify residue 1 from chain A.
The Run operation runs the rotation function and specifies the types of output analysis that will be performed.
The Run_Contour option provides PostScript contour plots of the rotation function. If this option is toggled on, the Contour Levels parameters L_Start, L_Stop, and L_Inc will be made available. These parameters should be set at the value for the first contour level, the last contour level, and the increment between contour levels. The contour levels can be specified as absolute values (with the maximum of the map scaled to 999) or as sigma values. In the latter case, the L_Start and L_Stop values must be specified as less than or equal to 10 and the L_Inc value must be less than or equal to 2. The Contour Sections parameters S_Start and S_Stop are also made available when the Run_Contour option is toggled on. These parameters are the numbers of the first and last section of the rotation function that are to be contoured. The default is that all sections will be contoured if there are five or fewer total sections. If there are more than five sections, the program will plot a total of five sections containing the largest peaks in the map. If no peaks are found in the map, the first five sections of the map will be contoured. The Line_Type parameter is a text string denoting the type of contour line that will be drawn. This parameter is connected to the Line_Type_List value-aid from which you can select a line type.
The Output_Map_File option is toggled on to write out a map of the rotation function. This map can be used in conjunction with the 3D visualization options in the Analyze operation. The output map filename (*.map) is based on the Rot_Job_Name that was used in the Setup operation.
The Peak_Cutoff parameter is the number of standard deviations above background a peak must be to be listed.
The Print_N_Peaks parameter is the maximum number of peaks that will be listed.
The Run_Mode parameter may be set to Run_Now, Save_Script_Only or Run_Saved_Script depending on whether you wish to run the rotation function immediately, save the rotation function function script without running it or run a previously created script. The Script_File_Name parameter contains the name of the input script file.
The Analyze operation provides a facility for viewing 3D representations of rotation functions.
The Tabulate_Peaks option is normally toggled on and provides a listing of the rotation function peaks in the table named in the Rot_Table_Name parameter.
The Rot_Print_File parameter is the name of the print file (*.prt) resulting from the rotation function and is connected to the Rot_Print_Files value-aid.
The Contour_Peaks option is normally toggled on and activates the contouring of the rotation function.
The Rot_Map_File parameter is the rotation function map filename and is connected to the Rot_Map_Files value-aid.
The Rot_Grid_Name is automatically set and specifies the Insight II grid name for the contoured map.
The Rot_Contour_Level is the contour level for the 3D representation of the rotation function.
This operation is used to leave the Mol_Replacement/Rotation_Func command.

Mol_Replacement/Translation_Func

The Mol_Replacement/Translation_Func command contains seven operations in the Tran_Operation menu.

The Setup operation is available for selecting the type of translation function that you will run and specifying the angle conventions.
The Tran_Job_Name parameter is used to create input, print and map files for the rotation function calculation.
The Title parameter is a text string describing the run. The text string defaults to the information in the crystal file.
From the Search_Function menu, you can select the type of translation function that you wish to run. Available choices are Correlation_On_F, Correlation_On_I, R_Factor_On_F, R_Factor_On_I, and Patterson_Cor. The Patterson correlation function is the fastest to calculate and is recommended.
The Polar_Convention parameter specifies the polar angle definition convention. Two conventions are supported: XYK and XZK. In both cases, is the angle from the Cartesian x axis. In convention XYK, as defined by Rossmann and Blow (1962), is the angle from the y axis. In convention XZK, as defined by Fitzgerald (1988), is the angle from the z axis. is the rotation around the axis defined by and .
The Euler_Convention parameter specifies the definition convention of Eulerian angles. Two conventions are currently supported, ZXZ and ZYZ, which correspond to rotation around the Cartesian z axis (3), then around the new x (and y, respectively) axis (2), and finally around the new x axis (1). ZXZ is the convention described by Rossmann and Blow (1962) and ZYZ is the conventions used by Fitzgerald (1988) in the program MERLOT.
In the Input_Data operation you select the data that will be used for the translation function calculation.
The Refl_File parameter is used to enter your reflection file (in .fin format) and is connected to the Refl_File_List value-aid.
The Sigma_Cutoff parameter is used to eliminate data less than the given number of standard deviations from the data set used in the translation search.
The Max_F and Min_F parameters set bounds on the magnitudes of the structure factors that will be used in the rotation function calculation. Note that setting Max_F to 0.0 disables this parameter so that no maximum value is set.
In the Model operation you set up the atomic model for the translation search. This operation has the facility for entering multiple coordinate sets that could correspond to positioned molecules and molecules for which you need to solve the translation function.
When the End_Models option is toggled on, you will be able to leave the Model operation by selecting Execute.
The Clear_All_Models option enables you to eliminate any models that were previously entered.
The Model_N and Defined_N are automatically set parameters that report the number of the model on which you are currently working and the number of models that have already been entered.
The Model_File_Format option can be set to PDB or Molecule depending on whether you wish to import a Protein Data Bank file or an Insight II molecule.
If you are importing a Protein Data Bank file, the PDB_File parameter (connected to the PDB_File_List value-aid) is available for entering the coordinate filename.
The Mol_Size parameter is used to set spherical exclusion zones around the center of the search model. The translation function is not calculated in these regions since the molecules would overlap too severely.
When the Coord_Center option is toggled on, the Center_X, Center_Y, and Center_Z parameters are available. These parameters are used to set the center of the molecule at the start of the translation search and are normally set to 0.0, 0.0, 0.0.
The Coord_Rot_Type options are No_Rotation, Polar, Euler and Top_Rot_Solutions. These options are used to input the angles for rotations that will be applied to the molecule before running the translation search. (Typically, the rotations will come from a rotation search.) If you select the Euler or Polar options, the three rotation angles can be entered as the Rot_1, Rot_2, and Rot_3 parameters. If you select the Top_Rot_Solutions option the Num_Top_Solutions and Rot_Print_File parameters will be made available. The translation function calculation will then be carried out for each of the specified number of top solutions given in the output print file from the rotation function calculation.
The Coord_Tran_Type options are No_Translation, Angstroms, and Fractional. These options are used to translate the model prior to the translation search. If you select the Angstroms or Fractional options, the translations should be entered in angstroms or fractional units as the Tran_X, Tran_Y, and Tran_Z parameters.
The Coord_Position for a model can be set to Fixed or Moving. The translation search is carried out with a model that is Moving. Only one model can be Moving in a translation function.
The Temp_Factor_Modify options are No_Changes, Increment, Replace_All and Replace_0_Values. These options are used to alter the atomic temperature factors in a model. The No_Change option specifies that the temperature factors stored in the model file will be used to calculate structure factors. The Increment option allows you to add or subtract a constant value to all of the temperature factors. The Replace_All option will change all temperature factors to the same specified value. The Replace_0_Values option will replace only temperature factors that are currently 0 with a specified value.
The Search_Parameters option sets up the search range for the translation function and the resolution limits for the data that will be used in the search.
If the Auto_Search_Params option is toggled on the volume of the crystal cell which is to be searched will be defined automatically. If this option is toggled off the Deorth Fract A, Deortho Fract B and Deortho Fract C parameters will be made available for specifying the search volume.
Under Deortho Fract A are the A_Start, A_Stop, and A_Inc parameters. These parameters are the starting, stopping, and increment for the search range along the a cell edge in fractional coordinates.
Under Deortho Fract B and Deortho Fract C are the starting, stopping, and increment parameters for the translation search along the b and c cell edges.
The parameters under Resolution Limits are D_Max and D_Min. These parameters are the resolution limits for the structure factor data that will be used in the translation search.
The Run operation is used to run the rotation function and specify the types of output analysis that will be performed.
The Self_Vect_Weight parameter specifies the scaling of the self-vectors (i.e., the intra-molecular vectors for the search model) in the translation function calculation.
If the Phases_Only option is toggled on the Patterson correlation translation function calculation will only use phase information from the model rather than both phase and amplitude information.
The Large_Term_Cutoff parameter defines the selection criterion for the strongest reflections (large terms) from the crystal data. Reflections with I > Large_Term_Cutoff X I(average) will be saved as the large terms, where I(average) is calculated in shells of equal reciprocal volume. For Patterson correlation calculations, a Large_Term_Cutoff value of 1.5 usually results in about 20% of the data being saved as large terms. For correlation coefficient and R factor searches, a Large_Term_Cutoff value of 0.5 is recommended.
The Output_Map_File option allows you to write out a map of the translation function for analysis.
Only peaks with a peak height/sigma ratio above the value entered for the Peak_Cutoff parameter will be listed at the end of a translation search. The maximum number of peaks listed is fixed by the Print_N_Peak parameter.
If the Direct_Summation option is toggled on, the structure factor calculations will be calculated using the direct summation method. This option is normally toggled off and the faster FFT method is used.
You can elect to contour the result of a translation search calculation by toggling on the Run_Contour option. The contour levels can be specified as absolute values (with the maximum of the map scaled to 999) or as sigma values. In the latter case, the L_Start and L_Stop values must be specified as less than or equal to 10 and the L_Inc value must be less than or equal to 2. You can specify a range of sections to contour using the S_Start and S_Stop parameters. The default is that all sections will be contoured if there are five or fewer total sections. If there are more than five sections, the program will plot a total of five sections containing the largest peaks in the map. If no peaks are found in the map, the first five sections of the map are contoured. The Line_Type parameter is a text string denoting the type of contour line that will be drawn. This parameter is connected to the Line_Type_List value-aid, from which you can select a line type.
The Run_Mode parameter may be set to Run_Now, Save_Script_Only or Run_Saved_Script depending on whether you wish to run the translation function immediately, save the translation function script without running it or run a previously created script. The Script_File_Name parameter contains the name of the input script file.
The Analyze operation provides a facility for viewing 3D representations of translation functions.
The Top_Solution_Table option is toggled on if you wish to view a table containing the top translation function solutions without the 3D representation of the translation function. Only the Tran_Print_File and Tran_Table_Name parameters are available when this option is toggled on.
The Tabulate_Peaks option is normally toggled on and provides a listing of the translation function peaks in the table named in the Tran_Table_Name parameter block.
The Tran_Print_File parameter is the name of the print file (*.prt) resulting from the translation function run and is connected to the Tran_Print_Files value-aid.
The Contour_Peaks option is normally toggled on and activates the contouring of the translation function.
The Tran_Map_File parameter is the name of the translation function map file and is connected to the Tran_Map_Files value-aid.
The Tran_Grid_Name parameter specifies the Insight II grid name for the contoured map and is set automatically.
The Tran_Contour_Level parameter sets the contour level for the 3D representation of the translation function.
The Quit_Command operation is used to leave the Mol_Replacement/Translation_Func command.

Mol_Replacement/Apply_Transform

The Mol_Replacement/Apply_Transform command applies the solutions from the rotation and translation functions and writes out the positioned and oriented atomic model coordinates.

The Transform_Job_Name parameter is the name that will be used to generate input and print files from the Apply_Transform command.

The Title parameter is a text string describing the run. The text string defaults to the information in the crystal file.

The Polar_Convention parameter is the polar angle convention and can be set to xyk or xzk.This is the convention that will be used when polar rotation angles are applied to the model.

The Euler_Convention parameter is the Euler angle convention and can be set to zxz or zyz. This is the convention that will be used when Euler rotation angles are applied to the model.

The Unit Cell parameters (A, B, C, Alpha, Beta, and Gamma) and Space_Group are the crystal parameters for your unknown crystal. These are obtained automatically from the crystals file.

The Model_File_Format parameter is the file format in which the molecule is read. This parameter can be set to PDB, in which case a Protein Data Bank file will be read, or to Molecule to enter an Insight II Molecule.

The PDB_File parameter is the name of the Protein Data Bank input file and is connected to the PDB_File_List value-aid.

The Transformed_PDB parameter is the filename for the output coordinate file.

The Coord_Center option is used to set the coordinate center of the molecule before applying the translation. If this option is toggled on, the molecule center can be entered in fractional coordinates as the Center_X, Center_Y, and Center_Z parameters. The usual values are 0.0, 0.0, 0.0.

The Coord_Rot_Type option can be set to No_Rotation, Polar, or Euler. This option allows you to enter the rotation angles that you wish to apply. If the Polar or Euler options are used, the angles are entered as the Rot_1, Rot_2, and Rot_3 parameters.

The Coord_Tran_Type option can be set to No_Translation, Angstroms, or Fractional. This option allows you to enter the translations that you wish to apply. If the Angstroms or Fractional options are used, the required translations are entered the Tran_X, Tran_Y, and Tran_Z parameters.

The Run_Mode parameter may be set to Run_Now, Save_Script_Only or Run_Saved_Script depending on whether you wish to run the calculation immediately, save script without running it or run a previously created script. The Script_File_Name parameter contains the name of the input script file.

Mol_Replacement/MR_Tools

The Mol_Replacement/MR_Tools command contains the Rot_Matrix operation and the Show_Symmetry operation. The Rot_Matrix operation generates a rotation matrix from the solution of the rotation function. The Show_Symmetry operation identifies which peaks in the rotation function are related to each other by the crystal symmetry. Both operations make use of the same parameters except that the Show_Symmetry operation includes the Symmetry_Selection options.

The Tool_Job_Name parameter is the name that will be used to generate input and print files from the MR_Tools command.

The Title parameter is a text string describing the run. The text string defaults to the information in the crystal file.

The Polar_Convention parameter is the polar angle convention and can be set to xyk or xzk.This is the convention that will be used when polar rotation angles are applied to the model.

The Euler_Convention option selects the Euler angle convention and can be set to zxz or zyz. This is the convention that will be used when Euler rotation angles are applied to the model.

The Input_Angle parameter can be set to Polar or Euler, depending on the angle system that you are using. The three rotation angles are entered as the Angle_1, Angle_2, and Angle_3 parameters.

The Symmetry_Selection parameter can be set to Crystallographic or Local depending on the type of symmetry that you wish to investigate in the Show_Symmetry operation.

The Initialization option can be set to From_Crystal_A, From_Crystal_B, or From_Crystal_File. These options are used to load the Unit Cell parameters (A, B, C, Alpha, Beta, Gamma) and the Space_Group.

The Run_Mode parameter may be set to Run_Now, Save_Script_Only or Run_Saved_Script depending on whether you wish to run the calculation immediately, save the script without running it or run a previously created script. The Script_File_Name parameter contains the name of the input script file.

Modify_Density pulldown

The Modify_Density pulldown contains commands for density modification by solvent flattening, histogram matching, and non-crystallographic symmetry averaging.

Modify_Density/Auto_Density_Mask

The Modify_Density/Auto_Density_Mask command is available for the automatic generation of a mask that defines the protein and solvent volumes in the crystal.

The Phase_File parameter is the name of the input file containing structure factor data with an initial set of phase angles. The Phase_File_List value-aid is available for importing this file.

The Map_File parameter is the name of a density map that will be generated from the input set of phased structure factor data.

The Density_Mask_File parameter is the name of the mask that will be generated at the end of the Modify_Density/Auto_Density_Mask command.

The Lower_Resolution and Upper_Resolution parameters are the lower and upper resolution limits of the structure factor data that will be used in the mask generation calculation.

The Solvent_Fraction parameter is the fraction of the crystal volume that is expected to consist of solvent. This value is used to set the solvent volume in the mask.

The Smoothing_Radius parameter is the range over which the density variance around each map grid point is searched to determine if the grid point belongs to the solvent or the protein. The units of this parameter are angstroms.

Modify_Density/Edit_Density_Mask

The Modify_Density/Edit_Density_Mask command is available for checking and interactively editing the mask that defines the protein and solvent regions in the crystal. This command contains six operations under the Mask_Operation menu.

The Read_Files operation enables you to enter the density map and the mask that were created with the Modify_Density/Auto_Density_Mask command.
To assist in entering these files, the Map_File parameter is connected to the Map_File_List value-aid and the Density_Mask_File parameter is connected to the Density_Mask_Files value-aid.
The Map Name parameter is an Insight II name which is set automatically.
The Set_Slab operation enables you to set the orientation, position, and size of the density slab that you will view when editing the mask.
The Map_Contour_Level parameter is the map contour level in units of the map standard deviation.
The Slab_Direction parameter can be set to XY, YZ, XZ, or Skew. This option sets the density slab so that it can be moved in any of the given directions.
The Slab_Operation parameter can be set to Specify_Skew, Specify_Size, or Specify_Center.
If the Specify_Skew option is toggled on, you can set the Direction_Type parameter for the skew plane to Polar_XYK, Polar_XZK or Vector. The two polar angle options allow you to set the skew angles using either the xyk or xzk angle convention and enter the three rotation angles as the S_Phi, S_Psi, or S_Kappa parameters. If you choose the Vector option, you are required to enter the vector as the Skew_A, Skew_B, and Skew_C parameters.
If the Specify_Size option is toggled on, then you can use the Default_Size option to set up a default slab size. Alternatively you should enter the slab size in fractional units as the Size_A, Size_B, and Size_C parameters.
If the Specify_Center option is toggled on, you can set the center of the density slab in fractional coordinates in the Center_A, Center_B, and Center_C parameters. The Step_Size gives the distance in fractional units that the density slab will move when you select the Step_Forward and Step_Back options. The Step_Direction parameter can be set to A, B, or C depending on whether you wish to step along the a, b, or c crystal axis.
The Edit_Mask operation performs interactive mask editing by allowing the user to draw polygons around unsatisfactory features in the protein/solvent mask.
By selecting the Step_Forward and Step_Back buttons, you can move the slab of density that you are viewing along the axis selected in the Set_Slab operation.
Under the Mask_Edit_Operation menu there are several options for interactively editing the protein/solvent mask.
The Filter_Mask option provides a global filtering of the mask by applying consecutive expansion and contraction operations. When the Filter_Mask option is active the Num_Filter_Steps parameter is available for specifying the number of grid steps to apply in the expansion/contraction. If the filtered mask is unsatisfactory, the Undo_Filter option is available to revert to the unfiltered mask. When the Reset_Polygon option is toggled on the polygon from the last edit is eliminated. When the Adjust_Point option is toggled on, you can use the mouse to change the position of one of the points in the polygon. When the Add_Point option is toggled on, new points can be added to a polygon by picking on the density slab with the mouse. When the Close_Polygon option is toggled on, a line is automatically drawn between the first and last polygon points, thereby closing the polygon. When the Mark_As_Protein and Mark_As_Solvent options are toggled on, you can change the contents of the mask inside the polygon to protein or solvent.
The Undo_Polygon_Edit option allows you to undo a polygon editing action from the Mask_Edit_Operation menu.
The Point_Number and Point_X, Point_Y, and Point_Z parameters are automatically set parameters that refer to the number and position of points inside a polygon.
The Save_Mask operation is used to write out a file containing the edited mask.
The Density_Mask_Output parameter is used to enter the output name of the mask file. The extension .mask is recommended for naming this file.
The Display_Options operation controls the type of rendering of the map and mask surfaces and the colors that will be used.
The Draw_Map_Contours and Draw_Mask_Contours options are used to turn on the displays of the map and mask contours.
The Map_Contour_Color and Mask_Contour_Color parameters are used to select the colors for the map and mask. When you select these parameters, a color palette with sliders appears, which you can use to change the colors.
The Map_Contour_Style and Mask_Contour_Style options can be set to Solid or Lines depending on whether you wish to display the map and mask as a solid surface or in the `cage' representation.
The Draw_Mask_Dots option can be toggled on if you wish to have automatically drawn colored dots to assist in marking out the protein and solvent parts of the mask.
This operation is used to leave the Modify_Density/Edit_Density_Mask command.

Modify_Density/Apply_Density_Mask

The Modify_Density/Apply_Density_Mask command applies the solvent flattening and histogram matching density modifications. This command is divided into five Apply_Operation operations.

In the Setup operation you enter the names of the input and output files for the density modification calculations.
The Phase_Input parameter is the name of the file containing phased reflection data. This parameter is connected to the Phase_File_List value-aid.
The Phase_Output parameter is the filename for the phased reflection file after the density modification process is completed.
The Density_Mask_File parameter is the name of the file for the protein/solvent mask. This parameter is connected to the Density_Mask_Files parameter block.
If the Extend_Phases option is toggled on the Master_Data_File parameter becomes available for entering a `Phase' formatted file containing the additional structure factor data that will be used for phase extension.
In this operation you set the parameters that will be used in the density modification.
Under the Apply_Operation option, you can select from Solvent_Flatten, Histogram_Match, and Both. These options control the density modification operation that will be carried out. The Solvent_Flatten option does solvent flattening only. The Histogram_Match option changes the histogram of the densities in the protein and solvent volumes. The Both option does both solvent flattening and histogram matching.
The Lower_Resolution and Upper_Resolution parameters are the lower and upper resolution limits for the structure factor data that will be used in the density modification process. If histogram matching is to be carried out, the Upper_Resolution parameter is also used to select the appropriate histograms from a library of histograms computed from a known structure at different resolutions.
The Number_of_Cycles parameter is the number of cycles of density modification that are to be run.
The Solvent_Flip parameter sets a scale factor for flipping density fluctuations in the solvent volume.
If the Extend_Phases option in the Setup operation was toggled on then the parameters described above are applied to a particular stage in the phase extension protocol. The phase extension protocol is set up using the options in the Modify_Schedule menu.
The New_Schedule option is used if you want to create a new schedule. If the Get_Schedule option is toggled on you may read a previously created schedule stored in the file specified by the Modify_Input_File parameter. The Add_Stage and Edit_Stage options are used to add or edit the parameters for the stage number given by the Stage_N parameter. Delete_Stage is used to eliminate a particular stage from the protocol. The Put_Schedule option activates the Modify_Output_File parameter and is used to write out a particular protocol to a file for future use. The End_Schedule parameter is used to terminate to process of setting up the density modification protocol. For the Add_Stage, Edit_Stage and Delete_Stage options the Next_Stage and Last_Stage buttons provide a means of moving forwards or backwards through the stages in the density modification protocol.
The Run operation is used to control the execution of the density modification job.
The Modify_Run_Mode parameter may be set to Run_Now, Save_Script_Only or Run_Saved_Script depending on whether you wish to run the density modification immediately, save the density modification script without running it or run a previously created script. The Modify_Script_File parameter contains the name of the input script file.
The Analyze operation is used to obtain a summary of the statistical output from the density modification program.
The Apply_Log_File parameter is used to specify the log file resulting from the density modification run. The Log_Files value-aid may be used to enter the file.
The Quit_Command operation is used to leave the Modify_Density/Apply_Density_Mask command.

Modify_Density/Set_NonCryst_Symm

The Modify_Density/Set_NonCryst_Symm command contains six operations under the NCS_Operation menu for defining crystallographic symmetry operations and creating a mask that marks out the density belonging to the unique protein sub-unit.

The Setup operation is used to enter the files that will be used by the command.
The Use_Partial_Model option should be selected if you intend to use a partial model to obtain the non-crystallographic symmetry operators. If this option is toggled on the Get_Molecule option is made available. You may use the Get_Molecule option to read in the model if you have not already read the molecule with the Insight II Molecule/Get command. When the Get_Molecule option is toggled on the PDB_File parameter is available for entered the filename for a PDB file containing the model.
The Map_File parameter is the name of the density map file that you will use when you set the non-crystallographic symmetry matrices. The Map_File_List value-aid is available for entering the map name.
The Map Name parameter is the Insight II map name, which is set automatically.
If the NCS_Mask_Input option is toggled on, the NCS_Mask_Input parameter and NCS_Mask_Files value-aid will be made available. This option will enable you to read in a file containing a non-crystallographic sub-unit mask that was created previously.
The Set_Slab operation enables you to set the orientation, position, and size of the density slab that you will view when editing the mask.
The Map_Contour_Level parameter is the map contour level in units of the map standard deviation.
The Slab_Direction option can be set to XY, YZ, XZ, or Skew. This option sets the density slab so that it can be moved in any of the given directions.
The Slab_Operation parameter can be set to Specify_Skew, Specify_Size, or Specify_Center.
If the Specify_Skew option is toggled on, then you can set the Direction_Type for the skew plane to Polar_XYK, Polar_XZK, or Vector. The two polar angle options allow you to set the skew angles with either the xyk or xzk angle convention (see the Mol_Replacement pulldown section for more details) and enter the three rotation angles as the S_Phi, S_Psi, or S_Kappa parameters. If you chose the Vector option then you are required to enter the vector as the Skew_A, Skew_B, and Skew_C parameters.
If the Specify_Size option is toggled on, then you can use the Default_Size option to set up a default slab size. Alternatively you should enter the slab size in fractional units in the Size_A, Size_B and Size_C parameters.
If the Specify_Center option is toggled on, then you can set the center of the density slab in fractional coordinates as the Center_A, Center_B, and Center_C parameters. The Step_Size parameter is the distance in fractional units the density slab will move when you select the Step_Forward and Step_Back options. The Step_Direction parameter can be set to A, B, or C depending on whether you wish to step along the a, b, or c crystal axis.
The Specify_Transforms operation contains a set of tools for deriving the non-crystallographic symmetry matrices between protein sub-units in the crystal.
By clicking the Step_Forward and Step_Back buttons you can move the slab of density that you are viewing along the pre-specified direction.
Under the Transform_Operation menu, you can select from the Add, Update, Delete, Define_N_Fold, and Remove_N_Fold options.
The Add, Update, and Delete options are coupled to the matrix specified by the Matrix_Number parameter. These three options allow you to add a new non-crystallographic symmetry matrix, change an existing matrix, or delete an existing matrix.
When using the Add option, a number of ways of specifying the non-crystallographic symmetry matrix are available through the Specification_Type options. If you select Read_NCS_File, you will be able to read previously calculated symmetry matrices from a *.ncs file. The filename is entered as the NCS_Transform_File parameter, which is connected to the NCS_Transform_Files value-aid. If you select Edit_Matrix, you will be presented with the Row and Column_1, Column_2, and Column_3 parameters. By changing these parameters you can edit the non-crystallographic symmetry matrices directly. If you select Partial_Model, you will be presented with the NCS_Unit_Fragment and Target_Fragment parameters. These allow you to enter a set of atoms for the unique protein sub-unit as the NCS_Unit_Fragment parameter and a set of atoms related by non-crystallographic symmetry as the Target_Fragment parameter. The program will calculate the non-crystallographic symmetry matrix from the superimposition of the two sets of atoms. The NCS_Unit_Marker and Target_Marker options provide an interactive way of specifying the matrices by placing 3D markers at non-crystallographically related positions in the electron density map. When you select these options, the Translation parameters are reported as Tri_X, Tri_Y, and Tri_Z, and the rotation parameters are reported as Tri_R11, Tri_R12, Tri_R13, Tri_R21, Tri_R22, Tri_R23, Tri_R31, Tri_R32, Tri_R33. When you select the Control parameter, you can set the Axis to X, Y, Z and control the rotation with the slide bar.
The Define_N_Fold option is used to obtain the rotation axis around which the sub-units can be generated. The Delete_N_Fold option is used to remove this axis. If the Define_N_Fold option is toggled on, you can set the N_Fold_Operation to Set_N_Fold or Compute_N_Fold. The Set_N_Fold option allows you to enter the N_Fold_Axis in the Axis_A, Axis_B, Axis_C, Axis_X, Axis_Y, and Axis_Z parameter blocks. More commonly, you will use the Compute_N_Fold option, which will automatically calculate the rotation axis from the symmetry matrices. The number of rotationally related copies is given by the N_Fold parameter.
This operation is used to write out a file containing the matrices that specify the non-crystallographic symmetry relations.
The NCS_Transform_File parameter is connected to the NCS_Transform_Files value-aid. This parameter allows you to specify the name of the output file. It is usual to denote these files with the extension .ncs.
The Display_Options operation controls the type of rendering of the map and mask surfaces and the colors that will be used.
The Draw_Map_Contours and Draw_Mask_Contours options are used to turn on the displays of the map and mask contours.
The Map_Contour_Color and Mask_Contour_Color parameters are used to select the colors for the map and mask. When you select these parameters, a color palette with sliders appears, which you can use to change the colors.
The Map_Contour_Style and Mask_Contour_Style options can be set to Solid or Lines depending on whether you wish to display the map and mask as a solid surface or in the `cage' representation.
The Draw_Mask_Dots option can be toggled on if you wish to have automatically drawn colored dots to assist in marking out the protein and solvent parts of the mask.
This operation is used to leave the Modify_Density/Set_NonCryst_Symm command.

Modify_Density/Set_Subunit_Mask

This command is used to set up the mask that defines the unique molecular subunit. The command is divided into eight operations.

The Setup operation is used to specify the files and input information that will be used in the Set_Subunit_Mask command.
If the Use_Current_Map option is toggled on then a map already loaded into InsightII will be used in this command. This option would be useful if you wanted to continue working with the map used in the Set_NonCryst_Symm command.
The Use_Partial_Model option should be selected if you intend to use a partial model to obtain the subunit mask. If this option is toggled on the Get_Molecule option is made available. You may use the Get_Molecule option to read in the model if you have not already read the molecule with the Insight II Molecule/Get command. When the Get_Molecule option is toggled on the PDB_File parameter is available for entered the filename for a PDB file containing the model.
The Map_File parameter is the name of the density map file that you will use to create the sub-unit mask. The Map_File_List value-aid ia available for entering the map name.
The Map Name parameter is the Insight II map name, which is set automatically.
If the Use_Current_Trans option is toggled on then a transform already loaded into Insight II will be used in this command. This option would be useful if you wanted to continue working with the transform just established in the Set_NonCryst_Symm command.
The Use_Crystal_NCS option may be toggled on to read the NCS information from the Xsight crystal file. Alternatively, if the Use_Current_Trans and Use_Crystal_Trans parameters are toggled off you may enter the name of the file containing the NCS transform as the NCS_Transform_File parameter.
The Read_NCS_Mask_File option may be used to enter a file containing a previously established protein mask. The NCS_Mask_Input value-aid is used to enter the name of the file containing the mask.
The Set_Slab operation enables you to set the orientation, position, and size of the density slab that you will view when editing the mask.
The Map_Contour_Level parameter is the map contour level in units of the map standard deviation.
The Slab_Direction option can be set to XY, YZ, XZ, or Skew. This option sets the density slab so that it can be moved in any of the given directions.
The Slab_Operation parameter can be set to Specify_Skew, Specify_Size, or Specify_Center.
If the Specify_Skew option is toggled on, then you can set the Direction_Type for the skew plane to Polar_XYK, Polar_XZK, or Vector. The two polar angle options allow you to set the skew angles with either the xyk or xzk angle convention (see the Mol_Replacement pulldown section for more details) and enter the three rotation angles as the S_Phi, S_Psi, or S_Kappa parameters. If you chose the Vector option then you are required to enter the vector as the Skew_A, Skew_B, and Skew_C parameters.
If the Specify_Size option is toggled on, then you can use the Default_Size option to set up a default slab size. Alternatively you should enter the slab size in fractional units in the Size_A, Size_B and Size_C parameters.
If the Specify_Center option is toggled on, then you can set the center of the density slab in fractional coordinates as the Center_A, Center_B, and Center_C parameters. The Step_Size parameter is the distance in fractional units the density slab will move when you select the Step_Forward and Step_Back options. The Step_Direction parameter can be set to A, B, or C depending on whether you wish to step along the a, b, or c crystal axis.
The Edit_NCS_Unit operation performs the interactive mask editing.
By clicking the Step_Forward and Step_Back buttons, you can move the slab of density that you are viewing along the axis selected in the Set_Slab operation.
Under NCS_Edit_Operation, there are several possible options. If the Reset_Polygon option is toggled on, the polygon that was created in your last edit will be eliminated. If the Adjust_Point option is toggled on, you can use the mouse to change the position of one of the points in the polygon. If the Add_Point option is toggled on, mouse picks on the density map will add new points to the polygon. If the Close_Polygon option is toggled on, a line between the first and last polygon points will be automatically drawn, thereby closing the polygon. If the Mark_As_NCS_Unit and Mark_As_Non_Unit options are toggled on, you can set the contents of the polygon to protein or solvent.
The Undo_Polygon_Edit option allows you to undo a polygon editing action.
The Point_Number and Point_X, Point_Y, and Point_Z parameters are set automatically and refer to the polygon point number and position.
This operation is used to generate for display subunit envelopes that are related by non-crystallographic symmetry to the unique protein envelope.
The NCS_Apply_Operation can be set to Add_NCS_Unit or Delete_NCS_Unit. The NCS_Apply_Operation is used to add or delete a non-crystallographically related envelope from the display. If the NCS_Add_Options parameter is set to Single, the envelope that is acted on by the NCS_Apply_Operation can be selected by matrix number, using the Apply_Matrix_Number parameter. If the NCS_Add_Options parameter is set to All, then all non-crystallographically related envelopes will be acted upon.
This operation is used to generate for display subunit envelopes related by crystallographic symmetry.
For the Crystal_Apply option you can choose between Add_Crystal_Symmetry and Delete_Crystal_Symmetry. These options allow you to view envelopes related by crystal symmetry or remove them.
This operation is used to write out a file containing the mask that defines the unique non-crystallographic unit.
The NCS_Mask_Output parameter is the name of the name of the output file. It is usual to denote these files with the extension .mask.
The Display_Options operation controls the type of rendering of the map and mask surfaces and the colors that will be used.
The Draw_Map_Contours and Draw_Mask_Contours options are used to turn on the displays of the map and mask contours.
The Map_Contour_Color and Mask_Contour_Color parameters are used to select the colors for the map and mask. When you select these parameters, a color palette with sliders appears, which you can use to change the colors.
The Map_Contour_Style and Mask_Contour_Style options can be set to Solid or Lines depending on whether you wish to display the map and mask as a solid surface or in the `cage' representation.
The Draw_Mask_Dots option can be toggled on if you wish to have automatically drawn colored dots to assist in marking out the protein and solvent parts of the mask.
This operation is used to leave the Modify_Density/Set_Subunit_Mask command. By using this operation files will automatically be cleaned-up.

Modify_Density/Average_NCS_Density

The Modify_Density/Average_NCS_Density command is available for averaging densities over non-crystallographic symmetry once the mask that defines the non-crystallographic sub-unit and the non-crystallographic symmetry matrices have been established. This command is divided into five operations.

The Setup operation is used to enter the names of the input and output files used in the NCS density averaging calculations.
The Phase_Input parameter is the .phs file that contains the input phased reflection data. This parameter is connected to the Phase_File_List value-aid.
The Phase_Output parameter is the name the file that will contain the phases after non-crystallographic symmetry averaging.
The NCS_Transform_File parameter is the name of the file containing the non-crystallographic symmetry matrices (usually denoted by the extension .ncs). This parameter is connected to the NCS_Transform_Files value-aid.
If the Output_NCS_Matrix option is toggled on the Refined_Transform parameter is made available for the name of the file that will contain the refined NCS matrices.
If the Extend_Phases option is toggled on the Master_Data_File parameter becomes available for entering a Phase formatted file containing the additional structure factor data that will be used for phase extension.
The Parameters operation is used to enter the parameters controling the NCS density averaging calculation.
The Phase_Combination option can be toggled on to combine the phase probability distributions from the averaged with the previous set of phases. If this option is toggled off, the phases from the averaged map will be used directly.
The Solvent_Flatten option can be toggled on to flatten electron density that is not contained in the protein sub-unit mask or any of its crystallographic or non-crystallographic equivalents. If you use this option you must have used the Apply_NCS_Symm and Apply_Cryst_Symm operations in the Modify_Density/Set_Subunit_Mask command to generate the protein sub-unit envelopes related by non-crystallographic and crystallographic symmetry.
The Lower_Resolution and Upper_Resolution parameters are the resolution limits for the data that will be used in the calculations.
The Number_Avg_Cycles parameter is the number of averaging cycles that will be performed.
The Refine_NCS_Matrix option is toggled on if you wish to refine the non-crystallographic symmetry matrices before they are used in the averaging.The Refine_Box parameter is the size, in angstroms, of the box that will be used in the search the program makes to refine the noncrystallographic symmetry matrices.
If the Extend_Phases option in the Setup operation was toggled on then the parameters described above are applied to a particular stage in the phase extension protocol. The phase extension protocol is set up using the options in the Modify_Schedule menu.
The New_Schedule option is used if you want to create a new schedule. If the Get_Schedule option is toggled on you may read a previously created schedule stored in the file specified by the Modify_Input_File parameter. The Add_Stage and Edit_Stage options are used to add or edit the parameters for the stage number given by the Stage_N parameter. Delete_Stage is used to eleminate a particular stage from the protocol. The Put_Schedule option activates the Modify_Output_File parameter and is used to write out a particular protocol to a file for future use. The End_Schedule parameter is used to terminate to process of setting up the NCS density averaging protocol. For the Add_Stage, Edit_Stage and Delete_Stage options the Next_Stage and Last_Stage buttons provide a means of moving forwards or backwards through the stages in the NCS density averaging protocol.
The Run operation is used to control the execution of the NCS density averaging job.
The Modify_Run_Mode parameter may be set to Run_Now, Save_Script_Only or Run_Saved_Script depending on whether you wish to run the NCS density averaging immediately, save the NCS density averaging script without running it or run a previously created script. The Modify_Script_File parameter contains the name of the input script file.
The Analyze operation is used to obtain a summary of the statistical output from NCS density averaging program.
The Average_Log_File parameter is used to specify the log file resulting from the NCS density averaging run. The Log_Files value-aid may be used to enter the file.
This operation is used to leave the Modify_DensityAverage_NCS_Density command.

Model_Building pulldown

The Model_Building pulldown contains commands that relate to model fitting.

Model_Building/Density_Fitting

The Model_Building/Density_Fitting command is used to spawn the XtalView program, Xfit, a program that has many functionalities, including utilities for model fitting to electron density. There are a number of files that can be passed to Xfit, including coordinate files, phase files, and precalculated map files. If you want to pass the coordinates of the molecule that currently resides within the Insight II software, leave Pass_Molecule on. In this case a file named xfit_in.pdb will be created in order to pass the current molecule. If you would prefer to pass an existing .pdb file, turn on the Pass_PDB_File parameter and select the appropriate .pdb file from the PDB_File_List value-aid.

You can pass up to two .phs files and two .map files when you invoke Xfit. You can also pass .bones, .vu, and .script files when you start Xfit from within the Insight II software. If you select the Auto_PDB_Save parameter, Xfit will automatically save your model as you modify it. Please see Xfit program for more information.

Model_Building/Molecule_Update

The Model_Building/Molecule_Update command is used to update Insight II with results from Xfit. Select the .pdb file that has been saved from Xfit. You can select either Update_Coordinates or New_Molecule for the Update_Option. If you select Update_Coordinates, only the coordinates within Insight II will be modified when the .pdb file is read. If you select New_Molecule, the .pdb file will be treated as a new file and any information about that molecule that is currently stored in Insight II will be lost.

Model_Building/Skeletonization

The Model_Building/Skeletonization command is used to spawn the XtalView program, Xskel, a program that is used for generating ridgelines to represent electron density in order to facilitate initial chain tracing. If you wish to pass the input and output files to Xskel, you will need to specify an existing .phs file and specify the filename for the .bones file that will be created. See the description of Xskel in the XtalView command summary for more information.

Model_Building/Waters

The Model_Building/Waters command is used to find and check ordered water molecules in electron density difference maps and to append these sites onto the protein coordinate file.

There are seven possible operations under the Water_Operation menu.

In the Get_Molecule operation you may enter the co-ordinate file for your structure. This option is an alternative to using the Insight II Molecule/Get command.
The PDB_File parameter is the name of the input co-ordinate file in Protein Data Bank format.
The Molecule Name parameter is the Insight II molecule name for the coordinate file and is set automatically.
In the Read_Map operation you can read the difference map that will be used to locate putative water molecules and, optionally, a second map.
The Map_File parameter is the filename for the difference map that will be used for locating waters. This parameter is connected to the Map_File_List value-aid.
If you select the Read_Second_Map option, you will obtain the Second_Map_File parameter. In this parameter you can enter a second map filename.
The Water_Grid_Name parameter is the Insight II name for the water grid and is set automatically.
In the Automatic operation you set up criteria for the automatic location of ordered water molecules.
The Water_Grid_Name parameter is the Insight II name for the water grid and is set automatically.
The Min_Dist_From_Mol parameter is the minimum allowed distance a putative water molecule is allowed to be from any atom in the current coordinate file.
The Max_Dist_From_Mol parameter is the maximum allowed distance a putative water molecule is allowed to be from any atom in the current coordinate file.
If the H_Bond_Test option is toggled on, putative water molecules must be less than the Max_H_Bond_Dist parameter from a polar atom to be selected.
The Peak_Threshold parameter is the number of standard deviations the electron density peak must be above the average density value of the difference map to be selected as putative water molecules.
In the Review operation you can check the density and atomic environments of the selected waters and decide whether or not to include them in your output coordinate file. When you enter this operation, a spread sheet appears containing the parameters for the set of putative water molecules.
The Water_Grid_Name parameter is the Insight II name for the water grid and is set automatically.
The Water_Name parameter is set automatically and contains the name of the water molecule that is currently under examination.
The options under the Review_Operation menu are Next, Accept, Delete, Adjust, Add, Accept_All, Change_to_Ion and Display_Options.
When you select Next, you will move to the next water molecule in the list for examination. When you select Accept, you make the tentative decision to accept a water molecule.When you select Delete, you make the tentative decision not to accept the molecule.When you select Adjust, you can change the position of a water molecule by selecting one of the Water_X, Water_Y, and Water_Z parameters (corresponding to movements in the x, y, and z directions) and using the slide-bar. When you select Add, the adjusted position of an existing water molecule is accepted as an additional water site. By selecting Accept_All you can accept all of the automatically selected waters without visual checking. If you select Change_to_Ion the water molecule will be converted to an ion type that may chosen from the Ion_Type parameter block and value-aid.
By selecting Display_Options you can change the default display parameters that were used for the visual check of the water sites. The contour level for the difference map is available as the Map1_Contour_Level parameter. The color of the contours in the difference map is available as the Map1_Contour_Color parameter. When you select the Map1_Contour_Color parameter, a color palette and slider are made available. The Boundary_Style option can be set to Lines or Solid. This parameter controls the style with which the density boundaries are drawn. The Size_X, Size_Y, and Size_Z parameters control the size of the box that contains the electron density around each water molecule. The size is given in angstrom units. The CPK_Water option can be toggled on to render the putative water molecules as solid spheres. If the Display_Second_Map option is toggled on, the Map2_Contour_Level and Map2_Contour_Color parameters are available. These parameters correspond to the contour level and density color of the second map and work in the same way as described for the first (difference) map.
The Add_Waters_to_Mol operation is used to append the accepted waters onto the Insight II molecule. Note that the Add_Waters_to_PDB operation is preferred, since the Insight II molecule does not contain header information or the description of discrete disorder that may have been in the original Protein Data Bank coordinate file.
The Water_Grid_Name parameter is the Insight II name for the water grid and is set automatically.
The B_Factor parameter is the temperature factor that will be used for the accepted water molecules.
The Add_Waters_to_PDB operation adds the accepted waters to a Protein Data Bank file.
The Water_Grid_Name parameter is the Insight II name for the water grid and is set automatically.
The PDB_Input_File parameter is the name of the coordinate file onto which you wish to add the accepted water molecules. This parameter is linked to the PDB_File_List value-aid.
The PDB_Output_File parameter is the name of the output coordinate file that will contain the current coordinate set with the accepted waters appended.
The B_Factor parameter is the temperature factor that will be used for the accepted water molecules.
This operation is used to leave the Model_Building/Waters command and is executed when you select Execute.
The Water_Grid_Name parameter is the Insight II name for the water grid and is set automatically.

Refinement pulldown

The Refinement pulldown contains commands related to model refinement. The first four commands (Setup_CNX, SA_Refine, Multi_Body_Refine, B_Factor_Refine) are refinement options that make use of the CNX program. The next two commands (Rigid_Body_Refine and Minimize) are used to carry out rigid-body refinement with the RotLSQ program and least-squares minimization with the ProLSQ95 program, respectively. The final option (Dictionary) is used to create stereochemical dictionaries for the CNX and ProLSQ95 refinement programs and the Xfit graphics program.

Refinement/Setup_CNX

This command is used to setup refinement problems for the CNX program prior to the actual refinement calculations.

There are three Setup_Operation operations.

The Generate_PSF_File operation is used to generate the protein structure file (PSF) and the CNX variant of the Protein Data Bank coordinate file for use with the CNX program. This operation adds hydrogen atoms to the protein and includes stereochemical parameters for any ligands that need to be included.
This operation cycles through three Generate_Step options (Job_Control, Ligands, Run).
The Job_Control option is used to control the CNX process and enter input and output file names. The Setup_Job_Name is an automatically generated name for the job. The Setup_Job_Title is an automatically generated title for the job which default to information provided in the crystal file. The PDB_Input_File parameter is the file name for the input co-ordinate set in Protein Data Bank format. The PDBX_Output_File parameter is the name that will be used for the CNX style coordinate file. A default file name will be generated for this parameter by using the input file name with the extension .pdbx. The PSF_Output_File is the name that will be provided for the output PSF file. A default file name will be generated for this parameter by using the input file name with extension .psf.
The Ligands option provides Add, Edit, Delete and No_Ligands options for entering information on any ligands that will be included in the refinement. If the Add option is toggled on the Ligand_Code parameter is used to enter the three letter amino-acid code for the ligand and the Ligand_Topol_File and Ligand_Param_File parameters are used to enter the names of the CNX topology and parameter files for the ligand. These parameters will be recorded in a table. The Edit option contains the same parameters as Add but allows you to change the values of these parameters in the table of ligand entries. The Delete option allows you to remove the ligand specified by the Ligand_Code parameter from table of ligand entries. When the End_Ligands option is toggled on the process of entering ligand entries will be terminated. If the No_Ligands option is toggled on no ligands to be included in the structure.
The Run option provides Run_Now, Save_Script_Only and Run_Saved_Script options. These are used for running the CNX job immediately, saving the input script without running it or running a previously created script. The Script_File_Name parameter records the name of the CNX input script.
The Find_Xray_Weight option is used to estimate the relative weighting between the x-ray and chemical energies for SA refinement and minimization with the CNX program.
This operation cycles through three Setup_Step options (Job_Control, Reflection_Data, Run).
The Job_Control option is used to control the job and specify input and output file names. The Weight option may be set to F or Phase depending on whether you wish to estimate the weight for refinement against a structure factor amplitude or phase. If the Repel_Potential option is toggled on, the initial minimization prior to the free dynamics run will be carried out with a soft short-range repulsive potential. The Setup_Job_Name is an automatically generated name used for the CNX run. The Setup_Job_Title is automatically generated from information in the crystal file. The PSF_Input_File is the name of the PSF file for the protein. The Data_File_Type may be set to Fin(.fin), Phase(.phs), or XPLOR(.fob), depending on the format of the file containing the reflection data. If the file format is not XPLOR(.fob), then an automatic file format conversion is carried out. The Input_Data_File is the name of the file containing the reflection data. The PDBX_Input_File is the name of the CNX coordinate file containing the atomic coordinates.
The Reflection_Data option provides the X_Low_Res_Cut_Off, X_High_Res_Cut_Off and Min_Fobs_over_Sigma parameters. These correspond to the low resolution cutoff, the high resolution cutoff and the number of standard deviations required for a reflection to be included in the CNX run.
The Run option provides Run_Now, Save_Script_Only and Run_Saved_Script options. These are used for running the CNX job immediately, saving the input script without running it or running a previously created script. The Script_File_Name parameter records the name of the CNX input script..
The Overall_B_Refine option is used to control the job and specify input and output file names.
This operation cycles through three Setup_Step options (Job_Control, Reflection_Data, Run).
The Job_Control option is used to control the job and specify input and output file names. The Setup_Job_Name is an automatically generated name used for the CNX run. The Setup_Job_Title is automatically generated from information in the crystal file. The PSF_Input_File is the name of the PSF file for the protein. The Data_File_Type may be set to Fin(.fin), Phase(.phs), or XPLOR(.fob), depending on the format of the file containing the reflection data. If the file format is not XPLOR(.fob), then an automatic file format conversion is carried out. The Input_Data_File is the name of the input file containing the reflection data. The PDBX_Input_File is the name of the input CNX coordinate file containing the atomic co-ordinates. The PDBX_Output_file is the name of the output CNX coordinate file with the refined overall temperature factor.
The Reflection_Data option provides the X_Low_Res_Cut_Off, X_High_Res_Cut_Off and Min_Fobs_over_Sigma parameters. These correspond to the low resolution cutoff, the high resolution cutoff and the number of standard deviations required for a reflection to be included in the refinement. If the Free_R_Statistic option is toggled on a free R value will be calculated using the percentage of data specified in the Percent_Free_R parameter block.
The Run option provides Run_Now, Save_Script_Only and Run_Saved_Script options. These are used for running the CNX job immediately, saving the input script without running it or running a previously created script. The Script_File_Name parameter records the name of the CNX input script.

Refinement/SA_Refine

The Refinement/SA_Refine command is used to run SA refinement and minimization of atomic co-ordinates with the CNX package. There are eight SA_Operation operations in this command.

In the Job_Control operation you specify the names of the input and output files that will be used in the refinement run.
The SA_Job_Name parameter is an automatically generated parameter that will be used for identifying the job.
The SA_Job_Title parameter is text information that can be entered about the run. This information defaults to the title in the crystals file.
The PSF_Input_File parameter is the name of the PSF file for the protein.
The Data_File_Type parameter may be set to Fin(.fin), Phase(.phs), or XPLOR(.fob), depending on the format of the file containing the reflection data. If the file format is not set to XPLOR(.fob), an automatic file format conversion is carried out.
The Input_Data_File parameter is the name of the file containing the reflection data for the refinement.
The PDBX_Input_File parameter is the name of the input CNX coordinate file containing the atomic co-ordinates and the PDBX_Output_file parameter is the name of the output CNX coordinate file containing the refined coordinates.
In the NCS_Restraints operation you may set-up noncrystallographic symmetry restraints if required.
If the Use_NCS_Restraints option is toggled on the parameters relating to setting of non-crystallographic symmetry restraints are made available.
The Atomic_Subset option may be set to All_Atoms or Backbone_Only depending on whether the ncs restraints are to be applied to all equivalent atoms or only equivalent backbone atoms.
The NCS_Weight is the value of the energy restraint that will be applied.
The NCS_Groups option is used to set up the target groups that will be equivalenced by replicate groups. This option may be set to Add, Edit, Delete, Clear_All_Groups or End_Groups. When the Add or Edit options are toggled on the Group_N parameter records the group number and the StartResidue and StopResidue parameters are used to enter the start and stop sequence numbers for this group. The Add option is used to add a new group and the Edit option is used to change the specification of the group. The Delete option is used to delete the group recorded in the Group_N parameter. The Clear_All_Groups option is used to remove all group specifications. The End_Groups option is used to finish entering group specifications.
The NCS_Replicates option is used to set up the replicate groups that will be equivalenced to the group set up with the NCS_Groups option. This option may be set to Add, Edit, Delete, Clear_All_Reps or End_Replicates. When the Add or Edit options are toggled on the Rep_N parameter records the replicate group number and the Replicate_Start and Replicate_Stop parameters are used to enter the start and stop sequence numbers for this replicate group. Add is used to add a new replicate group and Edit is used to change the specification of the replicate group. The Delete option is used to delete the replicate group recorded in the Rep_N parameter. The Clear_All_Reps option is used to remove all replicate group specifications. The End_Replicates option is used to finish entering replicate group specifications.
The Reflection_Data operation is used to specify the structure factor data that will be used in the refinement.
The X_Low_Res_Cut_Off parameter is the low resolution cutoff for the reflection data to be used in the refinement.
The X_High_Res_Cut_Off parameter is the high resolution cutoff for the reflection data to be used in the refinement.
The Min_Fobs_over_Sigma parameter is the minimum number of standard deviations for reflection to be used in the refinement.
If the Free_R_Statistic option is toggled on a free R value calculation will be carried out using the percentage of data specified in the Percent_Free_R parameter block.
The Refine_Schedule operation is used to set up a schedule for the simulated annealing and minimization runs.
The Schedule_Operation option may be set to New_Schedule, Get_Schedule, Add_Stage, Edit_Stage, Delete_Stage, Put_Schedule or End_Schedule.
The New_Schedule option is used if you want to create a new schedule.
If the Get_Schedule option is toggled on you may read a previously created schedule stored in the file specified by the In_Schedule_File parameter.
The Add_Stage option is used to build a schedule for the refinement. The Stage_N parameter records the stage number for which refinement parameters are being set. The Next_Stage and Last_Stage options allow you to step forward or back from the stage number recorded by the Stage_N parameter. The Stage_Type option may be set to Minimization, Dynamics or Torsion_Dynamics depending on whether the stage involves least-squares minimization or simulated annealing. The Weight_F and Weight_Phase parameters are the values for weighting the x-ray energies for structure factor amplitudes and phases. The Weight_F parameter will usually be generated automatically if you executed the Find_Xray_Weight option in the Setup_CNX command. If the CA_Restraints option is toggled on harmonic energy restraints with value specified by the Restraint_Energy parameter will be applied.
If the Stage_Type is set to Minimize the parameters needed for minimization are made available. If the Repel_Potential option is toggled on the conventional 6-12 non-bonded potential is replaced with a soft repulsive potential for the initial minimization cycles. The Number_of_cycles parameter is the number of minimization cycles that will be run and the Energy_Drop parameter is the energy drop that will terminate the minimization.
If the Stage_Type is set to Dynamics or Torsion_Dynamics the parameters required for the simulated annealing run are made available. The Random_Number_Seed is the random number used for initializing the dynamic trajectories. The Initial_Temp and Final_Temp parameters are the initial and final temperatures for the annealing run. The Dynamics_Time_Step is the time in pico-seconds for each dynamics step. The Number_of_Steps is the number of time steps needed to reduce the temperature by the value given by the Temp_Step parameter.
The Edit_Stage option is used to change the parameters for a particular stage in the schedule. The available parameters are the same as for the Add_Stage option.
The Delete_Stage option may be used to delete the stage number specified by the Stage_N parameter.
The Put_Schedule option is used to write out a schedule to a file specified by the Out_Schedule_File parameter.
The End_Schedule option is used to terminate the process of adding stages to a particular schedule.
The Run operation provides the Run_Now, Save_Script_Only and Run_Saved_Script options. These options are used for running the CNX job immediately, saving the input script without running it or running a previously created script. The Script_File_Name parameter records the name of the CNX input script.
The Analyze operation is used to create graphs and tables of the R-factor and free R-factor information recorded in the CNX log file.
The SA_Log parameter is the name of the CNX log file from which the statistical information will be taken.
If the Create_Log_Table option is toggled on a table of the R-factor and free R-factor information is created.
If the Create_Log_Graph option is toggled on graphs of the R-factor and free R-factor information are created.
The Convrt_to_Std_PDB operation is used to convert the CNX-style Protein Data Bank file (usually denoted with the extension .pdbx) to a conventional Protein Data Bank coordinate file.
The PDBX_Input_File parameter is the name of the CNX coordinate file.
The Remove_Hydrogens option may be toggled on to remove hydrogen atoms from this file.
The PDB_Output_File parameter is the name of the Protein Data Bank file that will be written.
The Quit_Command operation is used to leave the SA_Refine command.

Refinement/Multi_Body_Refine

The Refinement/Multi_Body_Refine command is available for setting up and running multi-domain rigid-body refinements with the CNX program. This command contains eight Multibody_Operation operations.

In the Job_Control operation you specify the names of the input and output files that will be used in the refinement run.
The Multibody_Job_Name parameter is an automatically generated parameter that will be used for identifying the job.
The Multibody_Job_Title parameter is text information that can be entered about the run. This information defaults to the title in the crystals file.
The PSF_Input_File parameter is the name of the PSF file for the protein.
The Data_File_Type parameter may be set to Fin(.fin), Phase(.phs), or XPLOR(.fob), depending on the format of the file containing the reflection data. If the file format is not set to XPLOR(.fob), an automatic file format conversion is carried out.
The Input_Data_File parameter is the name of the file containing the reflection data.
The PDBX_Input_File parameter is the name of the input CNX coordinate file containing the atomic coordinates.
The PDBX_Output_file parameter is the name of the output CNX coordinate file containing the refined coordinates.
The Define_Groups operation is used to specify the rigid groups that will be refined as independent domains.
The Multibody_Groups option may be set to Add, Edit, Delete, Clear_All_Groups or End_Groups. The Add option is used to add the specification for an atomic group. The Edit option is used to change the spacification for an atomic group. The Delete option is used to delete an atomic group. The Clear_All_Groups option is used to remove all group specifications. The End_Groups option is used to terminate the specification of atomic groups.
When the Add, Edit or Delete options are toggled on the Group_N parameter records the group number for this set of atoms.
When the Add or Edit options are toggled on the StartResidue and StopResidue parameters are used to enter the residue numbers for the first and last residue in the group.
The Reflection_Data operation is used to specify the structure factor data that will be used in the refinement.
The X_Low_Res_Cut_Off parameter is the low resolution cutoff for the reflection data to be used in the refinement.
The X_High_Res_Cut_Off parameter is the high resolution cutoff for the reflection data to be used in the refinement.
The Min_Fobs_over_Sigma parameter is the minimum number of standard deviations for reflection to be used in the refinement.
If the Free_R_Statistic option is toggled on a free R value calculation will be carried out using the percentage of data specified in the Percent_Free_R parameter block.
The Refine_Variables operation is used to specify values for refinement variables.
The Number_of_cycles parameter is the number of refinement cycles that will be run.
The Energy_Drop parameter is the energy drop that will terminate the refinement.
The Run operation provides Run_Now, Save_Script_Only and Run_Saved_Script options. These options are used for running the CNX job immediately, saving the input script without running it or running a previously created script. The Script_File_Name parameter records the name of the CNX input script.
The Analyze operation is used to create graphs and tables of the R-factor and free R-factor information recorded in the CNX log file.
The Multibody_Log parameter is the name of the CNX log file from which information will be taken.
The Create_Log_Table option is toggled on to create a table of the R-factor and free R-factor information.
The Create_Log_Graph option is toggled on to create graphs of the R-factor and free R-factor information.
The Convrt_to_Std_PDB operation is used to convert the CNX-style Protein Data Bank file (usually denoted with the extension .pdbx) to a conventional Protein Data Bank coordinate file.
The PDBX_Input_File parameter is the name of the CNX coordinate file.
The Remove_Hydrogens option may be toggled on to remove hydrogen atoms from this file.
The PDB_Output_File parameter is the name of the Protein Data Bank file that will be written.
The Quit_Command operation is used to leave the SA_Refine command.

Refinement/B_Factor_Refine

The Refinement/B_Factor_Refine command is available for setting up and running refinements of individual atomic temperature factors with the CNX program. There are seven B_Factor_Operation operations in the B_Factor_Refine command.

In the Job_Control operation you specify the names of the input and output files that will be used in the refinement run.
The B_Factor_Job_Name parameter is an automatically generated parameter that will be used for identifying the job.
The B_Factor_Job_Title parameter is text information that can be entered about the run. This information defaults to the title in the crystals file.
The PSF_Input_File parameter is the name of the PSF file for the protein.
The Data_File_Type parameter may be set to Fin(.fin), Phase(.phs), or XPLOR(.fob), depending on the format of the file containing the reflection data. If the file format is not set to XPLOR(.fob), an automatic file format conversion is carried out.
The Input_Data_File parameter is the name of the file containing the reflection data.
The PDBX_Input_File parameter is the name of the input CNX coordinate file containing the atomic coordinates and the PDBX_Output_file parameter is the name of the output CNX coordinate file containing the refined temperature factors..
The Reflection_Data operation is used to specify the structure factor data that will be used in the refinement.
The X_Low_Res_Cut_Off parameter is the low resolution cutoff for the reflection data to be used in the refinement.
The X_High_Res_Cut_Off parameter is the high resolution cutoff for the reflection data to be used in the refinement.
The Min_Fobs_over_Sigma parameter is the minimum number of standard deviations for reflection to be used in the refinement.
If the Free_R_Statistic option is toggled on a free R value calculation will be carried out using the percentage of data specified in the Percent_Free_R parameter block.
The Refine_Params operation is provide parameters that will control the temperature factor refinement.
The Number_of_cycles parameter is the number of refinement cycles that will be run.
The Energy_Drop parameter is the energy drop that will cause the refinement to terminate.
The SigmaB_Main_Bonds and the SigmaB_Side_Bonds are the target standard deveiations for temperature factors for covalently bonded main chain and side chain atoms.
The SigmaB_Main_Angles and SigmaB_Side_Angles are the target standard devaiations for temperature factors for angle related main and side chain atoms.
The Run operation provides Run_Now, Save_Script_Only and Run_Saved_Script options. These options are used for running the CNX job immediately, saving the input script without running it or running a previously created script. The Script_File_Name parameter records the name of the CNX input script.
The Analyze operation is used to create graphs and tables of the R-factor and free R-factor information recorded in the CNX log file.
The B_Factor_Log parameter is the name of the CNX log file from which information will be taken.
The Create_Log_Table option is toggled on to create a table of the R-factor and free R-factor information.
The Create_Log_Graph option is toggled on to create graphs of the R-factor and free R-factor information.
The Convrt_to_Std_PDB operation is used to convert the CNX-style Protein Data Bank file (usually denoted with the extension .pdbx) to a conventional Protein Data Bank coordinate file.
The PDBX_Input_File parameter is the name of the CNX coordinate file.
The Remove_Hydrogens option may be toggled on to remove hydrogen atoms from this file.
The PDB_Output_File parameter is the name of the Protein Data Bank file that will be written.
The Quit_Command operation is used to leave the B_Factor_Refine command.

Refinement/Rigid_Body_Refine

The Refinement/Rigid_Body_Refine command is available for setting up and running rigid-body refinements using the ROTLSQ program. Under the Refine_Operation menu there are four operations.

The Job_Control operation is available for setting up input and output files.
The Refine_Job_Name parameter is the name that will be used for setting up the background job and the print files.
The Refine_Job_Title parameter is text information that can be entered about the run. This information defaults to the contents of the crystal file.
The PDB_Input_File parameter is the name of the Protein Data Bank file containing the coordinates that you wish to refine. This parameter is connected to the PDB_File_List value-aid.
The PDB_Output_File is the name of the Protein Data Bank file that will contain the refined coordinates.
The Fin_Input_File parameter is the name of the file containing the structure factor data and is connected to the Fin_File_List value-aid.
The Number_of_cycles parameter is the number of cycles that will be run of rigid-body refinement.
The Reflection_Data operation allows you to select the reflection data that you will use in the refinement.
The Low_Res_Cut_Off and High_Res_Cut_Off parameters are the lower and upper resolution limits for the structure factor data that will be used in the refinement.
The Min_Fobs_over_Sigma parameter is the maximum number of standard deviations the structure factor must be to be used in the refinement.
The Bulk Solvent Terms are the Solvent_Scale and Solvent_Smoothing parameters. These terms can be used to correct the very low resolution data for bulk solvent scattering. An explanation of the meaning of these parameters is found in Chapter 4, Methodology.
This operation is used to select the variables that will be refined.
The Scale_Factor parameter is the initial value for the scale factor between observed and calculated structure factors.
The Overall_B_Factor is the initial value for the overall temperature factor that will be used for the atomic model in the refinement.
The Theta1, Theta2 and Theta3 parameters allow you to rotate the atomic model by three Euler angles prior to refinement. These angles are given in degrees and will normally be set to 0.0, 0.0, 0.0.
The Tx, Ty, Tz parameters allow you to translate the atomic model along x, y and z directions prior to refinement. These parameters are given in angstroms and will normally be set to 0.0, 0.0, 0.0.
Each refinement variable can be toggled on or off depending on whether you wish to refine the variable or fix the variable at its initial value. The options for the refinement variables are Refine_Scale_Factor, Refine_Overall_B, Refine_Theta1, Refine_Theta2, Refine_Theta3, Refine_Tx, Refine_Ty, Refine_Tz.
The Start_Job operation is used to choose whether to run the job immediately or write out the input file for future use.
If the Run_Rigid_Now option is toggled on, the job will start when you select Execute.

Refinement/Minimize

The Refinement/Minimize command is used to spawn Xprolsqtool, a program that provides an interface and automatic setup facility to run the least squares minimization program, ProLSQ95.

When the Pass_Files option is toggled on, you can pass coordinate and data files to Xprolsqtool.

The Fin_File_1 parameter is the name of the file containing the structure factor data and is connected to the Fin_File_List value-aid.

The PDB_File parameter is the name of the file containing the atomic model that will be refined and is connected to the PDB_File_List value-aid.

The Pass_Sec_Structure option can be toggled on to pass a file that will allow atomic segments to be restrained to specific types of secondary structure. The filename is passed as the Sec_Structure_File, which is connected to the Sec_Structure_Files value-aid.

If the Standard_Dictionary option is toggled on, a standard stereochemical dictionary will be used in setting refinement restraints. The Xprolsqtool program will use a file in your working directory called ideals.dat. If this file is not present then the standard Xsight copy of ideals.dat (stored in $XTALVIEWHOME/data) will be used. If the Standard_Dictionary option is toggled off, the PROLSQ_Dictionary parameter is used to name the ProLSQ95 stereochemical dictionary that will be used. This parameter is connected to the PROLSQ_Dictionaries value-aid.

Please see Xprolsqtool program for more information Xprolsqtool.

Refinement/Dictionary

The Refinement/Dictionary command is available for setting up stereochemical dictionaries for ligands for the CNX, ProLSQ95 and Xfit programs.

The Molecule Spec parameter is the Insight II molecule name for your ligand. Under the Dict_Operation menu there are nine available operations.

This operation is available for importing a previously established dictionary file in order to create a stereochemical dictionary for the ProLSQ95 and Xfit programs. The dictionary file (usually denoted with the extension *.dct) contains a Protein Data Bank description of the atomic coordinates of the ligand and stereochemical restraint information.
The Dictionary_File parameter is the dictionary filename and is connected to the Dictionary_Files value-aid.
The Automatic_Params operation is used to automatically establish planes and chiral centers for the ligand based on the atomic structure of the ligand.
The Edit_Chiral_Centers operation is used to change the assignment of atoms as chiral centers.
The Edit_Operation option can be set to Add or Delete depending on whether you wish to add an atom as a new chiral center or remove a chiral center.
When you pick the required atom in the graphical display, the atom name will be reported as the Atom parameter.
The Edit_Planar_Groups operation is used to change the assignment of atoms in planes.
Possible operations under Plane_Operation are New_Plane, Delete_Plane, Add_Atom and Delete_Atom.
If the New_Plane option is toggled on, you can set up a new group of atoms as belonging to a plane. The Plane_Name parameter contains the new plane and the Atom 1, Atom 2, Atom 3, Atom 4 parameters report the names of the first four atoms that are used to establish the new plane.
If the Delete_Plane option is toggled on, a plane can be deleted by using the value-aid to select a plane for deletion. The name of the selected plane will appear as the Plane_Name parameter.
If the Add_Atom option is toggled on, you can add a new atom to the plane given in the Plane_Name parameter. When you pick the atom that you wish to add, the name of the atom will be reported as the Atom parameter.
If the Delete_Atom option is toggled on, you can remove an atom from the plane given in the Plane_Name parameter. When you pick the atom that you wish to delete, the name of the atom will be reported as the Atom parameter.
The Edit_Torsions operation is used to add or delete atoms contained in a torsion group to/from the restraint list.
The Edit_Operation option can be set to Add or Delete, depending on whether you are adding a torsion group or deleting a torsion group. When you pick four atoms that make up the torsion groups, their names are reported as the Atom 1, Atom 2, Atom 3, and Atom 4 parameters.
The Edit_Atom_Names operation changes the names of the atoms in your ligand. This function is sometimes necessary because unique three-letter atom names are needed for the ProLSQ95 stereochemical dictionary. If the first three letters of the atom name are not unique, this operation will be entered automatically.
The Bad_Atom_Name parameter is the name of the atom that is to be replaced. This atom name will be entered automatically if the atom name is not uniquely specified by a three-letter name.
In the New_Atom_Name parameter you should enter the new name for the atom specified by the Bad_Atom_Name parameter.
The Edit_Atom_Codes operation changes the code number used to identify the atom in the ProLSQ95 stereochemical dictionary. This code number is equal to the number of scattering electrons and used to select the correct set of scattering factors for the atom.
The Non_Standard_Atom parameter is the name of the atom for which you wish to set the atom code. This name will be entered when you pick the atom in the ligand. The standard atom defaults are set so that atoms labelled C** are considered carbon, N** nitrogen, O** oxygen, S** sulfur, P** phosphorous, and H** hydrogen. For these atom types the codes will be set automatically. Any atom code that is set will override these defaults.
The Scattering_Electron parameter is the number of scattering electrons for the atom named in the Non_Standard_Atom parameter (for instance, 2 for helium).
The Update_Dictionary operation sets up the Refinement/Dictionary restraint dictionary and adds the stereochemical restraint parameters to the ProLSQ95 and Xfit dictionaries.
The Dictionary_File parameter is the *.dct file that contains restraint information and is connected to the Dictionary_Files value-aid.
If the Update_PROLSQ option is toggled on, you will be able to add a new entry containing stereochemical restraints for your ligand to the ProLSQ95 dictionary. The PROLSQ_Old_Dict parameter is the filename for the old ProLSQ95 dictionary, to which you will add the new entry. This parameter is connected to the PROLSQ_Dictionaries value-aid. The PROLSQ_Dictionary parameter is the name that you will use for the updated dictionary, containing the new entry.
If the Update_XFit option is toggled on, you will be able to add a new entry containing stereochemical restraints for your ligand to the XFit dictionary. The XFit_Old_Dict parameter is the filename for the old XFit dictionary, to which you will add the new entry.
If the Update_XPLOR option is toggled on, you will be able to create topology and parameter files for your ligand for use with the CNX program. The Ligand_Topol_File and the Ligand_Param_File parameters are the filenames for the ligand topology and parameter files.
Quit_Command operation is used to leave the Refinement/Dictionary command. You will exit from the Refinement/Dictionary command when you select Execute.

ProStat pulldown

The ProStat pulldown contains commands related to data and model evaluation.

ProStat/Statistics

The ProStat/Statistics command is used to spawn the XtalView program Xstat, which is used for calculating and displaying various statistical comparisons of structure factors and structure-factor-derived quantities. You can pass an input file (.fin, .df, or .phs) from Insight II or you can elect to not pass a file and load the appropriate file once you begin executing Xstat. Please see Xstat program for more information.

ProStat/Struct_Check

The Struct_Check command allows you to check protein-specific bond lengths, angles, and torsions in a protein 3D structure against the corresponding values in a knowledge base derived from accurate small molecule crystallographic studies. These data can help you to highlight erroneous structural features of the 3D structure. These can then be listed to the textport or tabulated using a per-residue Spreadsheet table (this can be automatically created using the Prostat/Struct_Check command). The numerical property values in the table make use of the graphing capabilities built into the Spreadsheet window to create 2D and 3D graphs for data visualization. A spreadsheet of monomer properties can be used to create colored, variable width molecular ribbon diagrams with the Molecule/Ribbon command in Insight II.

ProStat/Residue_Dihedral

The Residue_Dihedral command enables you to tabulate peptide/protein-specific dihedral angles. These include the backbone , , and sidechain 1, 2, 3, and 4 angles. The calculation can be performed on individual molecules or on an assembly of conformers of the same molecule. In the latter case the individual dihedrals can be tabulated along with the minimum, maximum, and circular variance in the selected dihedral across the assembly. The circular variance thus provides a measure of the conformational variability across the assembly of conformers.

ProStat/SecondaryClassify

The SecondaryClassify command can compute protein secondary structure classification using either the method of Kabsch and Sanders (1983) or the existing classification derived from the PDB format file that was the source of the protein molecule. The command will either create a new residue table with a classification column, or add a classification column to an existing per-residue spreadsheet. SecondaryClassify can also create subsets for use by other Insight II commands. A residue table with a classification column can serve as input to the Molecule/SecondaryRender command.

ProStat/Access_Surf

The Access_Surf command calculates the solvent accessible surface (SAS) area for a molecule. The terminology and definitions for this procedure are taken from Lee and Richards (1971). The SAS is the area traced out by the center of a solvent molecule rolled across the surface. The algorithm is a version of the Lee and Richards (1971) method as modified by Shrake and Rupley (1973) for speed.

Symmetry pulldown

The Symmetry pulldown contains commands that allow a visualization of the relations between a protein molecule and copies related by crystallographic symmetry.

Symmetry/Packing

This command is used to generate copies of the whole protein molecule related by crystallographic symmetry to the input molecule. The command contains five Packing_Operation operations.

Ths operation is used to import the coordinate data. It may be used as an alternative to the Insight II Molecule/Get command.
The PDB_File parameter is the name of the Protein Data Bank file containg the atomic coordinates.
The Molecule Spec parameter is the Insight II name for the molecule and is set automatically.
If the Heteroatom parameter is toggled on, atoms labeled as HETATMs in the coordinate file will be read.
If the Include_Hydrogens option is toggled on hydrogen atoms in the file will be read.
The Atom_Selection option may be set to All_Atoms, Backbone or C_Alpha_Trace. The All_Atoms option will read in all atoms, the Backbone option will read in only the backbone (N, CA, C, O) atoms for each amino acid and the C_Alpha_Trace option will read only CA atoms.
The Color_Selection option may be set to By_Atom or Specified_Color. If the By_Atom option is selected the atoms will be colored according to atom element type. If the Specified_Color option is toggled on all atoms in the unique molecule will be colored according to the color given in the Molecule_Color parameter.
The Generate operation is used to generate a set of molecules related by crystallographic symmetry to the unique molecule.
The Crystal parameter reports the crystal file that will be used to generate the crystal symmetry. This will be set automatically but you can also change the crystal using the Crystal_List value-aid.
The Molecule Spec parameter is the Insight II name for the molecule and is set automatically.
When the Label_Replicates option is toggled on, the molecules in the display will be labeled.
When the Symmetry_Table option is toggled on, the crystallographic symmetry matrices will be listed in a table that can be matched up with the labels used in the Label_Replicates option.
The X_Min, X_Max, Y_Min, Y_Max, Z_Min, and Z_Max parameters are the volume limits in fractional coordinates used for generating the symmetry-related molecules. Symmetry related copies of the unique molecule which have their centers of mass within these limits will be generated.
If the Cell_Box option is toggled on the unit cell outline will be displayed.
The Symmetry_Color is the color used to display the symmetry-related molecules. When you select this option a color palette and sliders will appear for changing the color.
The Transform operation is used to apply symmetry operations to generate additional symmetry related copies of the unique molecule. This operation is also used to convert the graphical display objects that represent the replicates to Insight II molecules.
The Apply_Symmetry option may be set to Replace_Molecule, Add_Molecule or Add_Replicate.
The Replace_Molecule option is used to change the unique Insight II molecule to a graphical display object . This action takes place when you click on Execute.
The Add_Molecule option is used to convert the symmetry-related copies of the unique molecule (initially displayed as graphical objects) to Insight II molecules. The Molecule_Suffix parameter is used to report the suffix for the Insight II molecule name that will be used for naming the new molecule. If the Symmetry_Source parameter is set to the Replicate option you can use the Replicate_Name value-aid to enter the replicate that you wish to convert to an Insight II molecule. If the Symmetry_Source parameter is set to the Specified_Operator option you can enter a symmetry operator from the symmetry table as the Symmetry_Operator parameter. The unit cell translations Tran_a, Tran_b, and Tran_c will be entered automatically from the table but may also be altered.
The Add_Replicate option is used to add additional replicates to the packing diagram. The Replicate_Suffix parameter reports the suffix that will be used for naming the new replicate. The Symmetry_Color parameter is connected to a color palette with sliders and can be used to change the color of the new replicate. The Symmetry_Operator parameter is used to enter the symmetry operator that will generate the new replicate. The Tran_a, Tran_b, and Tran_c parameters are the unit cell tranlations for the replicate to be added.
The Quit_Command operation is used to leave the Symmetry pulldown.

Symmetry/Contacts

The Symmetry/Contacts command is used to analyze contacts between the unique molecule and neighbors related by crystallographic symmetry. There are four Contact_Operation operations.

Ths operation is used to import the coordinate data. It may be used as an alternative to the Insight II Molecule/Get command.
The PDB_File parameter is the name of the Protein Data Bank file containing the atomic coordinates.
The Molecule Spec parameter is the Insight II name for the molecule and is set automatically.
If the Heteroatom parameter is toggled on atoms labeled as HETATMs in the co-ordinate file will be read.
The Color_Selection option may be set to By_Atom or Specified_Color. If the By_Atom option is selected the atoms will be colored according to atom element type. If the Specified_Color option is toggled on all atoms in the unique molecule will be colored according to the color given by the Molecule_Color parameter.
The Generate operation is used to generate the set of amino acid fragments related by crystallographic symmetry to the unique molecule that are within a specified contact distance.
The Crystal parameter reports the crystal file that will be used to generate the crystal symmetry. This will be set automatically but you can also change the crystal using the Crystal_List value-aid.
The Molecule Spec parameter is the Insight II name for the molecule and is set automatically.
If the Label_Fragments option is toggled on the molecular fragments in the display will be labeled.
If the Symmetry_Table option is toggled on, the crystallographic symmetry matrices will be listed in a table. Thes matrices can be matched up with the labels applied by the Label_Fragments option.
If any atom in a neighboring molecule is less than the distance given by the Contact_Distance parameter, the residue in which this atom is contained will be drawn.
If the Show_Close_Contacts option is toggled on, atomic contacts which are closer than the distance specified by the Close_Contact_Dist parameter will be highlighted.
The Symmetry_Color is the color used to display the symmetry-related molecules. When you select this option a color palette and sliders will appear for changing the color.
The Delete operation is used to remove symmetry related fragments from the display.
The Delete_Fragments parameter may be set to All_Fragments or Fragment.
If the All_Fragments option is toggled on all of the symmetry related fragments will be deleted when you click on Execute.
If the Fragment option is toggled on you may select a fragment to delete using the Symmetry_Fragment parameter. This parameter is connected to the Objects value-aid.
The Quit_Command operation is used to leave the Symmetry pulldown.

Symmetry/Merge_Molecule

The Symmetry/Merge_Molecule command allows you to merge two molecules into a single file.

The Molecule Name parameter is the Insight II molecule name for your molecule.

The Molecule To Merge parameter is the name of the molecule that you wish to combine with the existing molecule. The Molecule To Merge parameter is connected to the Objects value-aid to enable you to select a molecule.


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Text is taken in part, with permission, from the REPLACE program notes authored by Dr. Liang Tong.

Last updated February 2000. Copyright © 2000, Molecular Simulations Inc. All rights reserved.