Xsight

Xheavy program

Xheavy is used to calculate multiple isomorphous replacement (MIR) phases and to refine heavy atom solutions. The MIR phasing is done in an iterative manner. SIR phases for each derivative are first calculated, these are combined, new errors are estimated based on the combined SIR phases and finally new phases using the new E estimates are output. The refinement method used is a recursive correlation search. Each heavy atom is moved in turn on a finer and finer grid until no improvement in the correlation between the observed and calculated difference is found and then the relative occupancies are refined. The B-values are not currently refined. Residual maps and difference maps can be calculated to locate additional heavy atom sites.

There are two menus for Xheavy; the main one and an edit menu. Click Edit to access the edit menu.

The main menu contains the following parameters:

Figure 50 . Xheavy main menu

Table 47. Xheavy Main Menu widgets

Widget	Function
Unit Cell	Specifies the Unit Cell parameters as stored in the Crystal file.
Directory	Displays the directory to be used in searching for Derivative files and the Master Fin File. It can be changed by modifying the text field. The directory associated with the current project is loaded into this parameter by default.
Derivative File	Specifies the filename of the derivative to be loaded or saved.
Load Derivative	Performs the default action of Append Derivative if clicked with MB1; displays a menu if clicked with MB3.
Load New Derivative	Reads and loads the file specified in the Derivative File parameter field as a new derivative solution. A new entry then appears in the Derivatives scrolled list.
Append Derivative	Reads and appends the file specified in the Derivative File parameter field to the currently selected derivative solution.
Save Derivative	Performs the default action of Save All Derivatives if clicked with MB1; displays the menu if clicked with MB3.
Save All Derivatives	Saves all derivative solutions in the Derivatives list to the file specified in Derivative File.
Save Selected Derivatives	Saves all derivative solutions currently selected in the Derivatives list to the file specified in Derivative File.
Phasit2 Input File	Saves all derivatives to a PHASIT type file.
Master Fin File	Specifies the name of the .fin file to use to calculate maps. If Output is set to Only if in Master, the Master Fin File will be checked and only phases for reflections that reside in the Master Fin File will be output.
Output	Outputs phases for all reflections in the data file related to the derivative if All is selected; phases only reflections which appear in the master fin file if Only if in Master is selected.
Output Phases	Defines the name of the .phs file to save phases to.
Derivatives	Contains the names of the different derivatives being used in the MIR procedure. You must select one from the list to use the Edit or Delete commands.
New	Adds a new derivative. When you click the button, a new derivative appears in the Derivatives list with the label noname. This derivative will already be selected for editing. You should then use the Edit function to add the information about the derivative.
Edit	Activates an additional menu for controlling the parameters that describe each derivative.
Delete	Deletes a derivative that has been selected in the derivatives list.
Method	Displays a menu of MIR-related calculations that can be performed with Xheavy, when clicked with MB3.
Refine Selected Derivative Only	Refines the derivative selected in the derivatives list using the correlation refinement method.
Refine All Derivatives	Refines all derivatives currently listed in the derivatives list using the correlation refinement method.
Calculate Protein Phases	Generates a .phs file with phases combined from all derivatives. Each record of the .phs file will contain h, k, l, Fo, f.o.m, and phi.
Calculate Protein Phases w/ABCD	Generates a .phs file with phases combined from all derivatives. Each record of the .phs file will contain h, k, l, Fo, f.o.m, phi, A, B, C, and D.
Map Coefficients for Selected Derivatives	Generates a .phs file with coefficients calculated for the selected derivative. Each record of the .phs file will contain h, k, l, |Fp-Fph|, (Fph-Fp)-Fhcalc, and -protein. This type of .phs file can be used to calculate Fourier maps in order to locate new heavy atom sites. To do that, use the Xfft program with either Fo coefficients to make a heavy atom difference map or Fo-Fc to make a residual map.
Clear Phases and Reread Data	Resets the program if you want to start over, but it is probably safer to exit and start the program over again.
Apply	Starts the calculation that was selected from the Method menu.
Abort	Aborts the calculation that is in progress.

Xheavy Edit menu

The Edit menu allows you to change the atomic parameters that describe the heavy atom sites.

Table 48. Xheavy Edit pop-up menu widgets

Widget	Function
Derivative	Specifies the name of a particular derivative.
DataFile	Specifies a.fin or .df file containing the difference information. You must specify the file type in the File Type parameter.
File Type	Specifies whether the data file is .fin or .df format.
Phase Type	Allows extraction of phasing information in three different ways: isomorphous differences, isomorphous differences and anomalous differences, and native anomalous differences.You can access the Phase Type menu by clicking with MB3.
Isomorphous	Uses differences between derivative and native reflections to calculate phases.
Isomorphous + Anomalous	Uses differences between derivative and native reflections as well as anomalous differences between derivative reflections to calculate phases.
Native Anomalous	Uses anomalous differences between native reflections to calculate phases.
Weight	Adjusts the relative weights of the different derivatives by assigning a weight with the slider. Larger weight values indicate a higher confidence in the derivative.
Relative Weight of Iso to Ano	Adjusts the relative weight of one contribution to the other If you select the Isomorphous + Anomalous option.
Resolution	Selects low and high resolution limits.
Sigma Cut	Eliminates weak, poorly measured reflections from the phasing procedure. If either of the members of a pair of reflections is below this value, the pair is not considered.
Delta/Average Filter	Filters out isomorphous differences which are unreasonably large. The calculated value is based on the equation: (|F1-F2|/(F1+F2)/2)*100. If the value is greater than 100, then normally the pair is rejected. A value of 100 implies that the difference is greater than the mean.
Ano Delta/Avg Filter	Filters out anomalous differences which are unreasonably large. The calculated value is based on the equation: (|F1-F2|/(F1+F2)/2)*100. If the value is greater than 30 then the pair is normally rejected.
Sites	Tabulates the heavy atom sites for the derivative being edited. Selecting one of the sites in the list loads it into the adjoining editable fields.
Label	Identifies the selected Site. Typically, you can use the element name and a number to indicate the site, e.g., AU1, AU2, etc.
X, Y, Z	Lists the fractional coordinates of the site.
Atom	Lists the atom type for the derivative. Use the associated menu button (Click it with MB3) to see the full list of supported atoms. Select the desired atom type from this list rather than typing the atom type in by hand, as improperly entered atom types are skipped.
Occupancy	Specifies the occupancy of the site.
B	Specifies the B factor for the site. B-values are not refined, so a reasonable value should be selected.
Insert	Creates a new site and adds it to the list when you enter the relevant values into the Label, X, Y, Z, Atom, Occupancy, and B parameters and then click the Insert button. If a list already exists, clicking Insert adds the new site to the end of the list if no sites are selected, or after the current selection, if a site is selected.
Replace	Updates the selected site with the values in the Label, X, Y, Z, Atom, Occupancy, and B parameter fields.
Delete	Deletes the currently selected site from the list.
Apply	Uses the modifications you have made in the Edit menu to update the solution file.
Reset	Resets the parameters to the values present when the menu was first entered.

Xhercules program

Xhercules is a program that tries to determine heavy atom positions using a correlation search method. Unlike classical Patterson solution techniques, where Harker vectors are interpreted, Xhercules moves a single atom around the entire asymmetric unit on a grid, and at each position a correlation is calculated between the observed difference vectors and the calculated structure factors. The resulting atom is then placed at the position with the highest correlation. The use of a correlation function, rather than R factor, is important because the scale factor cannot be computed correctly and the correlation is independent of scale.

You then run the program a second time. A second atom is moved about the asymmetric unit and the correlation calculated with the first atom held fixed. This atom is then fixed at its highest correlation. The relative occupancies are then refined by another correlation search. A third atom can then be searched for in a similar manner. Each correlation search takes a large amount of computer time and the time goes up as more atoms are added.

Although the method can be used automatically, it is a good idea to check the results against the Patterson map. This can be done by writing out the solution, reading it into the program, Xpatpred, and displaying the output of predicted Patterson vectors on the actual map using the program Xcontur.

Figure 51 . Xhercules menu

Table 49. Xhercules menu widgets

Widget	Function
Directory	Displays the directory to search for the .fin file. Loads the directory associated with the current project by default.
Fin File	Lists the .fin file created by merging the best native data set with the derivative data set under investigation. The correlation search will be against the FH values that are estimated from the differences between F1 and F2 in the .fin file.
Solution File	Specifies the .sol file to use in looking for heavy atom sites on storing a new solution. When you are locating the first heavy atom site of a derivative, you do not want to load a .sol file. Once you have the first atom site, you can create a .sol file by using the solution editor in Xheavy. You would then read that file into Xhercules when you look for the next site.
Corr Map File	Names the file that will contain the correlation map after Xhercules is finished. You can view it with the Xcontur program.
View CorrelationMap	Spawns Xcontur with the Corr Map File automatically loaded.
Resolution Limits in Angstroms	Specifies the resolution limits for the data to be used in the correlation search. The resolution cut off should be as low as 6 for large unit cells and as high as 4 for small unit cells.
Search Grid in Angstroms	The correlation search grid needs to be at least one-fourth of the minimum resolution and preferably one-sixth.
X, Y, and Z Bounds in Fractional	An intelligent choice of the asymmetric unit will speed up the calculation. The symmetry of the correlation map is that of a Patterson map and because of that, the asymmetric unit of the correlation map will be smaller. One consequence of this is that you find both hands of a heavy atom solution and you must guess as to which one is correct. It is easy to ascertain the size of the asymmetric unit of the correlation map by viewing your first correlation map using Xcontur. The limits of the asymmetric unit should be obvious. In looking for further sites, you can adjust the fractional coordinate ranges accordingly.
Occupancy of Search Atom	The occupancy of the search atom can be guessed before running the correlation search. A menu button is available with predefined occupancy values.
Search for Top Hit	Initiates the correlation search.
Top Hit	Displays the top solution at the end of a correlation search.
Append to Solution File	Adds the Top Hit to the file specified under Solution File.

Xmerge program

The Xmerge program scales and merges two data files together. The second data file is scaled and merged to the first data file. The structure factors from the first data file are referred to as F1 and the structure factors associated with the second data set are referred to as F2.

Figure 52 . Xmerge program

Table 50. Xmerge program widgets

Widget	Function
Crystal	Lists the name of the crystal file associated with the current project. It can be changed, if necessary, by typing in the name of an existing crystal file.
Unit Cell	Displays the unit cell parameters of the current crystal file. Modification of these values has no effect on the calculations; the cell parameters are always used as they are read from the file.
Directory	Specifies the directory to use in searching for .fin files. Loads the directory associated with the current project by default.
Fin File 1	Specifies the "standard" data set. Fin File 2 is scaled to this data set. Normally this would be the best native data set.
Fin File 2	Specifies the .fin file containing the data to be scaled to Fin File 1. This is normally derivative or mutant data.
Output File	Specifies the output file for merged and scaled data. The file name should indicate what data was used to make the file. The file extension should be consistent with the output type specified in the Output Type parameter.
Output Type	Sets the format for data output (either .fin or .df). If you select .fin, the F1 and F2 values of each input .fin file are averaged before merging. This is because a .fin file contains two values of F for each record and thus each data set must be reduced in some way. The F1 and F2 values of the input .fin files are typically Bijvoet pairs, where F1 = f+ and F2 = f-. All fields are preserved in a .df file so that Bijvoet information is preserved for both input files.
Output	Controls the storage of records to an output file. Reflections in Common creates an output record for the intersection set of reflections from the input files (i.e. those reflections that are common to both files). All in 1, common in 2 creates a record for every reflection that occurs in Fin File 1 but does not create a record for reflections that occur in Fin File 2 only. All in 1 and 2 creates a record for the union of reflections from Fin File 1 and Fin File 2 (i.e., those reflections that occur in either of the files).
Sigma Cutoff	Excludes data from the scaling equations if F/(F) is less than the value specified in the Sigma Cutoff parameter.
Number of Bins	Divides the data into bins based on sin()/2, for the purposes of scaling. If you type the number in you must press <Enter> for the value to be accepted.
Scaling Type	Sets the scaling mode, scales the data in each bin isotropically. Anisotropic uses six parameters within each bin to describe the scaling. The goal of anisotropic scaling is to minimize errors due to effects such as differential absorption.
Scale	Starts the scaling procedure.

Xmergephs program

The Xmergephs program is used to combine phases from a number of different sources with a file containing structure factor amplitudes (.fin file) to produce a new phasing file (.phs file). The phases can come from either a .phs file, an CNX phase file, or a TNT hkl file. Options are available for generating phase files that can be used to look at isomorphous and Bijvoet differences.

Figure 53 . Xmergephs program

Table 51. Xmergephs program widgets

Widget	Function
Directory	Specifies the directory used to search for .fin and phase files. Loads the directory associated with the current project by default.
Fin File to Phase	Specifies the name of the .fin file.
Phase File	Specifies the phase file name. The phases can come from either a .phs file, an CNX phase file, or a TNT hkl file. The phase is normally expected to be in degrees although if you execute Xfft following the merge, radians are acceptable.
Output Phase File	Specifies the .phs file that contains structure factor amplitudes from Fin File to Phase combined with phases from Phase File.
Swap f1 and f2 (isomorphous Fourier)	Swaps f1 and f2 so that the output phase file has h, k, l, FPH, FP, and phi. This is a necessary step if f1 is the native FP in your .fin file and f2 is the derivative FPH in the Fin File to Phase parameter.This allows you to make an fo-fc Fourier map which will show the positions of the heavy atoms if protein phases are used (double difference Fourier).
Add 90 to Phase (Bijvoet Fourier)	Makes a Bijvoet difference Fourier by adding 90 to the phase and swapping f1 and f2, which is necessary if the input .fin file contains Bijvoet differences (h k l f+ sigma(f+) f- sigma(f-)) and the input phases were in degrees. Centric reflections are handled correctly if they have 0.0 in the f- position. If f+ is equal to f- then the reflections will be output, but since their difference is zero they will not contribute to the Fourier.
Merge	Begins the merging process. The program can take quite a long time if the two input files have a different sort order, as the program searches for matches in indices between the two programs. Note that if you have equivalent indices that are not numerically the same (e.g., h k l and -h -k l) the merge will fail!

Xpatpred program

Xpatpred predicts Patterson peaks from a list of sites. It allows you to enter and edit a set of sites and output these in a form that can be displayed by Xcontur. The sites can be written out in a solution file and refined using Xheavy. Different origin choices can be selected allowing a rapid way to try all possible origins and visually choose the correct one.

Figure 54 . Xpatpred program

Table 52. Xpatpred program widgets

Widget	Function
Crystal	Lists the name of the crystal file associated with the current project.
Directory	Specifies the directory used to search for the Solution File. The directory associated with the current project is loaded by default.
Solution File	Specifies the name of the solution file. The solution file (.sol extension) contains heavy atom positions obtained from the analysis of derivative data. The solution file format is similar to the .pdb file format in that each record starts with a key word. The solution files can be shared with Xheavy to refine the heavy atom sites. When a solution is written out, any origin specification that has been added to an atom site will be applied.
Load Solution	Reads in the file (.sol) specified by Solution File.
Save Solution	Writes a new solution file or updates an existing file based on the parameters currently stored in the editor.Saves the solution to the file specified in Solution FIle.
Prediction File	Specifies a file that contains a list of labels and associated coordinates which can be read into Xcontur with the Files/Load Labels command. In this way a potential heavy solution can be checked against the actual Patterson map. The labels are in fractional coordinates in u, v, w (Patterson coordinates). The coordinates relate to predicted Patterson peaks based on the heavy atom solution currently in the editor. Each label describes the vector (i.e., pt1-pt1 is a self-vector of the site pt1 and pt1-pt3 is a cross vector between pt1 and pt3). The coordinates are transformed so that they lie between 0 and 1. They are generated by looping through all symmetry operators in a pairwise fashion. It is not guaranteed that all possible symmetry related labels will be generated, therefore if a peak is not labeled, a symmetry related one should be checked.
Write Prediction	Writes the prediction file described above.
Site List Scroll Window	Lists the heavy atom sites. Clicking on a site selects it and loads its values into the associated edit fields.
Label	Identifies a specific heavy atom site. Typically you can use the element name and a number to indicate the site, e.g., AU1, AU2, etc.
X, Y, Z	Specify the fractional coordinates of the site.
Origin	Specifies the origin of the heavy atom site. Presents a menu of 8 origin choices when clicked with MB3. You must first select the site to be changed, then select the desired origin, and then click Replace. To see the effect of the origin shift on the predicted Patterson map, you must click Write Prediction and reread the vector file into Xcontur. Usually this option is used to find the relative origin of a second site while holding the first site constant. Self vectors will be unaffected by an origin choice but the cross vectors are dependent upon the relative origin choice. With 2 sites only, 4 of the origin choices will make a difference in the predicted Patterson, the others being hand choices and not detectable with a Patterson map. With three or more sites, all 8 choices may make a different pattern of cross peaks. Not all of the origin choices are valid in every space group. The possible origins are listed in the International Tables for Crystallography (1993). The origin choices given are valid for orthorhombic space groups. However, if an incorrect origin is chosen it will either make no difference (e.g., adding 0.5 to y in monoclinic makes no difference) or it will cause the self vectors not to match and so will be detectable as an incorrect origin. Other origin choices will have to be entered by hand unless they are added to a future version.
Atom	Lists the atom type for the derivative.
Occupancy	Specifies the occupancy of the site.
B	Specifies the B factor for the site. B values are not refined, so you should select a reasonable value.
Insert	Adds a new site to the list when you first enter the relevant values into the Label, X, Y, Z, Atom, Occupancy, and B parameters and click Insert. If a list already exists, and if no sites are selected, clicking Insert adds the new site to the end of the list. If a site is selected, adds the site after the current selection.
Replace	Updates the selected site using the values in the Label, X, Y, Z, Atom, Occupancy, and B parameter fields.
Delete	Deletes the currently selected site from the list.

Xprepfin program

Xprepfin imports and/or exports .fin files from or to other formats and, in addition, reformats existing .fin files. This program constitutes the main entry point for data into the XtalView package.

Figure 55 . Xprepfin program

Table 53. Xprepfin program

Widget	Function
Crystal	Lists the name of the crystal file associated with the current project. It can be changed, if necessary, by typing in the name of an existing crystal file.
Directory	Specifies the directory used to search for the Input File. Loads the directory associated with the current project by default.
Input File	Specifies the name of the file to be imported and converted. The type of file must be specified using Input Format.
Input Format	Specifies the format of the Input File. Possible choices include .mu files (XENGEN output), a .fin file, a .df file, an output file from the R-AXIS processing software, or an output file from the XDS processing package. In the case of the R-AXIS or XDS files, you select the option Other, and then select the file type from the Other Formats menu button.
Other Formats	Selects the appropriate format, if Input Format is set to Other. Clicking the button with MB3 presents a list of possible file types.
Use Data	Controls processing of the data from the Input File. As Is retains the input exactly, but reformats it. If the output file only contains one value of F per reflection, that is, the output file is not a .fin file, then F1 from the input file will be used. Avg F1 and F2 averages F1 and F2, if they exist in the input file. If only one F value exists, it is used as the average value. F1 then F2 uses F1 for the output file, unless it is missing, in which case F2 is used. You would use this option in a case where you had two native data sets merged into a .fin file and the first data set was considered better than the second, but you had some holes in the first data set that you wanted filled in by the second. F2 then F1 uses F2 first, if it exists in the input file, otherwise it uses F1. You would use this option in a case where you had two native data sets merged into a .fin file and the second data set was considered better than the first, but you had some holes in the second data set that you wanted filled in by the first. F1 uses F1 only, and F2 uses F2 only.
Data Are	If the input data are Bijvoet pairs, then when the indices are switched it may be necessary to reverse the Bijvoet pair. Also, when a centric reflection is output, Bijvoet pairs are averaged, placed in the first field and the second field set to zero since centric reflections do not have an anomalous scattering signal. Obviously, this should not be done to isomorphous pair data.
Switch F1 and F2	Controls whether F1 and F2 are switched. This operation is done after Use Data has been applied.
Reduce Indices	Reduces the reflection indices to produce a unique value, sorts the reflections on h, k, l, and merges any duplicates. Unfortunately, the algorithm used does not always put the data in the quadrant you desire.
Output Format	Outputs the reflection file in your choice of format: standard .fin format, ProLSQ format, CNX format, or .phs format. In generating an output file that only has one value of F per record, e.g., ProLSQ format, CNX format, or .phs format, it is best to average F1 and F2 if your input file contains Bijvoet pairs, otherwise select the F1 or F2 options. Creating a fake .phs file (fake in the sense that there are no values of Fcalc or any phase angles) is useful if you want to use a new data set to look at electron density maps. Please see Making maps and basic fitting techniques for more information.
Output File	Specifies the name of the file produced by the program.
Apply	Reads the old file and generates the new file.

Xprolsqtool program

The Xprolsqtool program is used to generate the input files and execute the programs of the ProLSQ95 refinement package.

Main menu

Figure 56 . Xprolsqtool main menu

Table 54. Xprolsqtool main menu widgets  

Widget	Function
Crystal	Lists the name of the crystal file associated with the current project. It can be changed by typing in the name of an existing crystal file. All available crystal files can be accessed by clicking the menu button with MB3.
Cell	Lists the unit cell parameters of the current crystal file.
Defaults	Specifies a defaults file, which contains a set of default parameter values. These files are created using the Save Defaults Set button. A list of available default files can be viewed by using MB3 to click and hold the Defaults menu button. Selecting a file loads it into the Defaults text box.
Load Defaults Set	Reads the file specified by the Defaults parameter and loads the values into the menu parameters.
Save Defaults Set	Saves a defaults file based on the current parameter settings. The name of the file is specified by the name that is in the Defaults text field. Files created with this command are stored in your CRYSTALDATA directory.
Directory	Specifies the directory used to search for the PDB File and Fobs File. Loads the directory associated with the current project by default.
PDB File	Specifies the name of the .pdb file to be used in creating the input to ProLSQ95 for refinement.
Fobs File	Specifies the name of the reflection file to be used in the refinement.
Run number	Uses run numbers to construct file names that allow you to distinguish between jobs.
Reflection Limits	Scans the Fobs File. Automatically sets reflection limits based on the contents of the file. Also displays a menu that lets you modify the limits determined from the file (the Reflection Data menu is only generated if you load a .fin file in the Fobs FIle parameter).
Refinement Parameters	Accesses the ten refinement parameter menus. MB1 displays the default menu, Refinement Strategy. The other menus are Geometry Restraints, Shifts Restraints, Non-Bonded Contacts, Thermal (B-values), Non-Crystallographic, Monte Carlo and Sec Str, View Protin Log File, and View Prolsq Log File.
Start Refinement	Starts the refinement procedure. Scans the PDB File first, then automatically sets up the input for Protin, and executes Protin. Then the ProLSQ95 program is executed.

Reflection Limits menu

Figure 57 . Xprolsqtool Reflection Limits menu

Table 55. Xprolsqtool Reflection Limits menu widgets (Page 1 of 2)

Widget	Function
Resolution Limits	Displays the resolution limits of the Fobs File, based on reading and scanning the file. You can change this to suit your refinement strategy.
Percent Data to Reserve for free R	Selects the given percentage of data for calculating the free R value statistic.
Minimum Fobs to include	Rejects reflections with F < Fmin.
Minimum Fobs/Sigma Ratio	Rejects reflections with F/(F) less than this value from the refinement.
# of Reflections in input	Lists the number of reflections in the input Fobs file.
# of Reflections used	Lists the total number of reflections to be used, after applying the above filtering.
Reflection data weighting	Specifies the AFSIG and BFSIG terms.   Structure Factor weighting is given as 1/w2, where w = (2(F) + sigdel2)1/2 sigdel = afsig + bfsig (sin()/ - 0.1666667).
Solvent Correction	Specifies the Solvent Scale Factor and Solvent Smoothing factor for correcting the structure factor data for bulk solvent scattering.
Scan Data	Repeats the procedure of scanning the reflection file.
Reset	Resets parameter values to initial settings after scanning.
Defaults	Resets parameter values to default menu values.
Apply	Accepts parameter values for refinement.
Close	Closes the menu.

Refinement Parameters menu

Figure 58 . Xprolsqtool Refinement Parameters menu

Refinement Strategy menu

This menu defines the numbers and types of cycles of refinement. You should first select the number of steps (or cycles), then select the mode, and finally insert the new instruction in the appropriate spot. An instruction is defined as a given number of steps for a particular mode.

Figure 59 . Xprolsqtool/Refinement Parameters/Refinement Strategy menu

Table 56. Xprolsqtool/Refinement Parameters/Refinement Strategy menu widgets  

Widget	Function
Number of steps	Specifies the number of refinement cycles for one particular mode
mode	Accesses three types of refinement modes: Refine Coordinate Only, Refine Temperature Factors Only, and Refine Coordinates and Temperature Factors Simultaneously.
Insert at Top	Inserts a new instruction at the top of the file.
Insert After Selection	Inserts a new instruction after the selected instruction.
Insert at Bottom	Inserts a new instruction at the end of the list.
Replace	Replaces the selected instruction with the currently selected mode and step size.
Delete	Deletes the currently selected instruction.
Calculation Method	Selects structure factor calculations by either FFT or Summation methods.

Geometry Restraints menu

The Geometry Restraints menu is divided into four different areas: distance restraints, plane restraints, chiral centers, and torsion angle weights. For each area there is an overall weight and then individual weights for the different types of restrainable parameters. The individual weights should reflect the typical uncertainty found in derived parameters of the type restrained.

Figure 60 . Xprolsqtool/Refinement Parameters/Geometry Restraints menu

Table 57. Xprolsqtool/Refinement Parameters/Geometry Restraints menu widgets

Widget	Function
Distance Restraints
Overall Weight	Specifies the weighting scheme for distance restraints.The weighting scheme for distance restraints is given by Overall Weight / (distance)2. The (distance) parameters are established in the next set of parameters.
Bond Length(1-2)	Establishes the (distance) value in the weighting scheme given above for bonded atoms.
Angles(1-3)	Establishes the (distance) value in the weighting scheme given above for bond angles between a sequence of three bonded atoms. The restrained distance is between atoms 1 and 3 of the sequence.
Interplanar Distance(1-4)	Establishes the (distance) value in the weighting scheme given above for planar sequences of four atoms, e.g., the distance between the carbonyl carbon and the alpha carbon of adjacent residues.
H-C Bond	Establishes the (distance) value in the weighting scheme given above for bond distances involving hydrogen atoms.
H-C-X Angle	Establishes the (distance) value in the weighting scheme given above for angles between a sequence of three bonded atoms, one of which is a hydrogen atom.
Distance 6 (H bond)	Establishes the (distance) value in the weighting scheme given above for hydrogen bonds.
Distance 7 (metal)	Establishes the (distance) value in the weighting scheme given above for bonds involving metal atoms.
Plane Restraints
Overall Weight	Specifies the weighting scheme for plane restraints.The weighting scheme for plane restraints is given by (Overall Weight / (plane))2. The (plane) parameter is set in the Sigma Planes parameter.
Sigma Planes	Establishes the (plane) value in the weighting scheme given above for atoms in a planar group.
Chiral Centers
Overall Weight	Specifies the weighting scheme for chiral center restraints. The weighting scheme for plane chiral restraints is given by (Overall Weight /(chiral))2. The (chiral) parameter is set in the Sigma Chiral Centers parameter.
Sigma Chiral Centers	Establishes the (chiral) value in the weighting scheme given above for atoms in a planar group.
Torsion Angle Weights
Overall Weight	Specifies the weighting scheme for torsion angle restraints.The weighting scheme for torsion angle restraints is given by (Overall Weight /(torsion))2. The (torsion) parameters are set by the following menu parameters.
Prespecified (sec. struc.)	Establishes the (torsion) value for torsion angles that are constrained by secondary structural elements, e.g., and values of a regular secondary structure region.
Planar Angle (omega)	Establishes the (torsion) value for torsion angles that are planar, e.g., angles.
Staggered Angles (chis)	Establishes the (torsion) value for torsion angles that are staggered, e.g., 1.
Orthonormal Angle	Establishes the (torsion) value for torsion angles that are orthonormal, e.g., 2.
Reset	Resets the menu parameters to their internal default values.
Apply	Stores the current menu changes and returns to the main Xprolsqtool menu.
Defaults	Restores the menu parameters to the values stored in the defaults file, if one was loaded from the main menu.

Shifts Restraints menu

This menu controls the maximum size of shifts that will be generated in order to control excessive shifts.

Figure 61 . Xprolsqtool/Refinement Parameters/Shifts Restraints menu

Table 58. Xprolsqtool/Refinement Parameters/Shifts Restraints menu widgets

Widget	Function
Positional Shift Limit	Specifies the maximum shift, in angstroms, that will be accepted for the coordinate of any atom.
B-Value Shift Limit	Specifies the maximum for B factor shift for individual atoms.
Occupancy Shift Limits	Specifies the maximum occupancy factor shift for occupancies that are being refined.
Reset	Resets the menu values to the internal default values.
Defaults	Restores the menu parameters to the values stored in the defaults file, if you loaded one from the main menu.
Apply	Stores the current menu changes and returns to the main Xprolsqtool menu.

Non-bonded Contacts menu

This menu controls the weights assigned to nonbond distance restraints.

Figure 62 . Xprolsqtool/Refinement Parameters/Non-Bonded Contacts menu

Table 59. Xprolsqtool/Refinement Parameters/Non-Bonded Contacts menu widgets

Widget	Function
Overall Weight	Specifies the weighting scheme for van der Waals contact restraints.The weighting scheme for van der Waals contact restraints is given by (Overall Weight / (vdw))2. The (vdw) parameter is set in the Sigma VDW parameter below.
Sigma VDW	Establishes the (vdw) value in the weighting scheme given above for atoms that have nonbonded van der Waals contact.
Single Torsion Adjustment	Modifies the minimum "theoretical" van der Waals contact distance for atoms whose relative position is determined by only one torsion angle.
Multiple Torsion Adjustment	Modifies the minimum "theoretical" van der Waals contact distance for atoms whose relative position is determined by only one torsion angle.
Possible X...Y H-Bond	Modifies the minimum "theoretical" van der Waals contact distance for atoms which have possible hydrogen bonds. Specifically this parameter relates to contacts between oxygen and nitrogen atoms which are not main-chain.
Possible X-H..Y H-Bond	Modifies the minimum "theoretical" van der Waals contact distance for atoms which have possible hydrogen bonds. Specifically this parameter relates to contacts between oxygen and nitrogen atoms which are not main-chain. This parameter is the same as above except that hydrogen atoms are explicitly in the model.
Reset	Resets the menu values to the internal default values.
Defaults	Restores the menu parameters to the values stored in the defaults file, if one was loaded from the main menu.
Apply	Stores the current menu changes and returns to the main Xprolsqtool menu.

Thermal (B-Values) menu

This menu controls the weights assigned to thermal parameter restraints and whether or not individual atomic temperature factors are refined.

Figure 63 . Xprolsqtool/Refinement Parameters/Thermal (B-Values) menu

Table 60. Xprolsqtool/Refinement Parameters/Thermal (B-Values) Menu Widgets  

Widget	Function
B-Value Refinement	Sets B-Value refinement mode. You can choose between an Overall temperature factor or Individual atomic temperature factors.
Overall Weight	Specifies the weighting scheme for thermal restraints. The weighting scheme for thermal restraints is given by (Overall Weight / (B))2. The (B) parameter is specified by the parameters below based on variances in bonding distances due to dynamic fluctuations.
Main-chain bond	Establishes the (B) value in the weighting scheme given above for atoms that are in the main chain.
Main-chain Angle	Establishes the (B) value in the weighting scheme given above for terminal atoms of a three-atom sequence that are in the main chain.
Side-chain Bond	Establishes the (B) value in the weighting scheme given above for bonded atoms that are in a side chain.
Side-chain Angle	Establishes the (B) value in the weighting scheme given above for terminal atoms of a three-atom sequence that are in a side chain.
X-H Bond	Establishes the (B) value in the weighting scheme given above for bonded atoms, if one is a hydrogen atom.
X-H Angle	Establishes the (B) value in the weighting scheme given above for terminal atoms of a three-atom sequence when one of the terminal atoms is a hydrogen atom.
Other	Establishes the (B) value in the weighting scheme given above for all bonds not covered by the previous parameters.
Reset	Resets the menu values to the internal default values.
Defaults	Restores the menu parameters to the values stored in the defaults file, if one was loaded from the main menu.
Apply	Stores the current menu changes and returns to the main Xprolsqtool menu.

Non-Crystallographic menu

This menu controls the weights assigned to noncrystallographic restraints.

Figure 64 . Xprolsqtool/Refinement Parameters/Non-Crystallographic menu

Table 61. Xprolsqtool/Refinement Parameters/Non-Crystallographic menu widgets

Widget	Function
Overall Weight	Specifies the weighting scheme for non-crystallographic restraints. The weighting scheme for non-crystallographic restraints is given by (Overall Weight/(ncs))2. The (ncs) parameters are described below.
Tight Positional Restraint	Establishes the (ncs) value in the weighting scheme given above for positional restraints between atoms that are related by non-crystallographic symmetry. Defines a "tight" restraint condition.
Medium Positional Restraint	Establishes the (ncs) value in the weighting scheme given above for positional restraints between atoms that are related by noncrystallographic symmetry. Defines a "medium" restraint condition.
Loose Positional Restraints	Establishes the (ncs) value in the weighting scheme given above for positional restraints between atoms that are related by noncrystallographic symmetry. Defines a "loose" restraint condition.
Tight Thermal Restraint	Establishes the (ncs) value in the weighting scheme given above for thermal restraints between atoms that are related by non-crystallographic symmetry. Defines a "tight" restraint condition.
Medium Thermal Restraint	Establishes the (ncs) value in the weighting scheme given above for thermal restraints between atoms that are related by non-crystallographic symmetry. Defines a "medium" restraint condition.
Loose Thermal Restraint	Establishes the (ncs) value in the weighting scheme given above for thermal restraints between atoms that are related by non-crystallographic symmetry. Defines a "loose" restraint condition.
Reset	Resets the menu values to the internal default values.
Defaults	Restores the menu parameters to the values stored in the defaults file, if one was loaded from the main menu.
Apply	Stores the current menu changes and returns to the main Xprolsqtool menu.

Monte Carlo and Sec Str menu

This menu allows you to set up secondary structure restraints, based on a secondary structure table file saved from the Insight  II program. In addition, the menu allows you to select regions (e.g., loops) of the protein for the application of Monte Carlo conformational searches.

Figure 65 . Xprolsqtool/Refinement Parameters/Monte Carlo and Sec Str menu

Table 62. Xprolsqtool/Refinement Parameters/Monte Carlo and Sec Str menu widgets

Widget	Function
Secondary Structure File (*.sec)	Specifies the Secondary Structure file, which is generated by the Insight  II software using the SecondaryStructure Table command. The table must be saved as a file with the extension .sec.
Load File	Loads the file specified by the above parameter. A list of loop, alpha helix, and CA beta sheet regions are listed.
Secondary Structure List	Displays a list of the secondary structure fragments. If you select a fragment, it is loaded into the Monte Carlo input fields.
MC Refine	Performs a Monte Carlo conformational search on a specified residue sequence.
First Residue	Specifies the first residue in the sequence for a conformational search.
Chain ID	Specifies the chain ID.
Second Residue	Specifies the last residue in the sequence for a conformational search.
Random # Seed	Specifies the random number seed for the Monte Carlo search.

View Protin Log File menu

You can use this option to examine the log file from protin.

Figure 66 . Xprolsqtool/Refinement Parameters/View Protin Log File menu

Table 63. Xprolsqtool/Refinement Parameters/View Protin Log File menu widgets

Widget	Function
Next Error	Locates and displays the next error in the log file.
First Error	Locates and displays the first error in the log file.
Last Error	Locates and displays the last error in the log file.

View Prolsq Log File menu

This menu allows you to search the log file from ProLSQ95 for errors.

Figure 67 . Xprolsqtool/Refinement Parameters/View Prolsq Log File menu

Table 64. Xprolsqtool/Refinement Parameters/View Prolsq Log File menu widgets

Widget	Function
Next Error	Locates and displays the next error in the log file.
First Error	Locates and displays the first error in the log file.
Last Error	Locates and displays the last error in the log file.

Xrspace program

Xrspace is a reciprocal space viewer that can be used for examining completeness of data, differences between data sets, and intensity patterns. Use this program to check for symmetry in the diffraction pattern, for looking at heavy atom differences, and planning data collection strategies.

The application presents a window that is divided into three main areas: the control panel, a message window, and a graphics canvas where the data is displayed as specified by the control panel settings. Messages are printed in the textpane at the bottom. Note that the textpane has the ability to save output by means of its pop-up menu. Reflections are displayed with a heat scale color scheme to represent intensity variations--as the data increases in intensity it goes from black to red to yellow to white. The width of a spot is proportional to F and its area is proportional to I.

Clicking on a reflection will cause its indices and intensities to be displayed in the message window. These are the unreduced indices.

Figure 68 . Xrspace program

Table 65. Xrspace program widgets

Widget	Function
Crystal	Lists the name of the crystal file associated with the current project. It can be changed by typing in the name of an existing crystal file. The symmetry operators are read from this file and converted to the Patterson symmetry by the addition of an inversion center.
Unit Cell	Lists the unit cell parameters of the current crystal file.
Directory	Specifies the directory used in searching for the Input File. Loads the directory associated with the current project by default.
File	Specifies the name of the file to be read and displayed.
Read	Reads the file.
Type	Specifies the file type for the File parameter. Choices are .fin, .mu (a XENGEN mulist file from the makemu command), .df, or .urf (a urefls XENGEN file from integrate) format.
Display Data	Displays data from a file. Selecting Column 1 displays F1 values, Column 2 displays F2 values, and Delta 1 and 2 displays |F1 - F2| values. This last option is useful for looking at merged heavy atom datasets or for anomalous differences.
Planes of	Controls the direction of the sections to be displayed. You can select the three principal axial directions or the major diagonals.
Level	Sets the plane level (i.e., if the plane direction is h and the level is 0, then the 0kl plane is displayed).
Slab	Sets the number of planes to be displayed simultaneously. Normally the planes are drawn on top of each other but see Offset of Vertical Axis parameter below for an alternate type of display.
Spot size	Scales the size of the spots. Select the value so that spots do not overlap.
Resolution	Controls a circle that is drawn on the display at the specified resolution. It does not control the maximum resolution of the screen, which is set by the limits of the input data.
Symm	Controls whether the symmetry operators stored in the crystal file are used to generate symmetry related reflections or only the unique data is displayed.
Offset of Vertical Axis	Offsets planes from each other so that they are not drawn on top of each other. Try X=2 and Y=3 and make the Spot size smaller for an orthographic display of several planes (Slab > 1).
Draw	Draws the screen. Note that most of the buttons and sliders cause the screen to redraw automatically.
Print	Generates the Xrspace Print menu. Select the Destination (either Printer or File) and type the name of the printer or the file in the Printer text field, then click Print.

Xresflt program

Any file with records beginning with the Miller indices h k l can be filtered on resolution. The output file that is created has all reflections removed that fall outside the upper and lower limits.

Figure 69 . Xresflt program menu

Table 66. Xresflt program widgets

Widget	Function
Crystal	Lists the name of the crystal file associated with the current project.
Unit Cell	Lists the unit cell parameters of the current crystal file.
Resolution Limits	Defines the resolution range using two parameters, Limit 1 and Limit 2, which are both in units of angstroms.
Limit 1	Defines the cutoff for low resolution data.
Limit 2	Defines the cutoff for high resolution data.
Directory	Specifies the directory used to search for the Input File. Loads the directory associated with the current project by default.
Input File	Specifies the name of the file to be read and filtered.
Output File	Specifies the name of the file to be created after resolution filtering.
Filter	Reads and filters the data in the Input File, and writes it to the Output File.

Xskel program

The program Xskel provides a convenient way to generate a ridgeline or skeleton representation of an electron density map. The ridgelines are drawn along the 3D ridges in the electron density map and provide an alternative to viewing electron density contours. The advantage of viewing maps with ridgelines is that you can view a larger portion of the map at one time and it is thus easier to recognize portions of the secondary structure.

The skeletonization algorithm is based on the program GRINCH (Williams 1982), a program developed to aid in the initial chain-tracing of a map.

Figure 70 . Xskel program menu

Table 67. Xskel program widgets

Widget	Function
Crystal	Lists the name of the crystal file associated with the current project.
Unit Cell	Displays the unit cell parameters of the current crystal file. Modification of these values affects the calculations.
Directory	Specifies the directory used to search for the Input Phase File. Loads the directory associated with the current project by default.
Input Phase File	Specifies the name of the .phs file to be used to calculate the electron density map from which the ridgelines will be calculated.
Ridge Lines File	Specifies the name of the file that will contain the ridgelines. The standard file extension is .bones.
Defaults	MB1 reads the default parameter file if one exists. MB3 displays the options list. Save Defaults saves the current parameter settings so you can load them the next time you run the program.
Map Type	Specifies the Fourier coefficient to be used to calculate the map. The seven available coefficients are: Fo, Fc, 2Fo-Fc, Fo-Fc, Fo*Fm, 3Fo-2Fc, and 5Fo-3Fc.
Map bounds in fraction of unit cell x 100	Defines the region of real space that you wish to skeletonize. You can select a region of real space to skeletonize by setting the values of X-min, X-max, Y-min, Y-max, Z-min, and Z-max. The allowed values are from -1.0 to +2.0 along each axis.
Resolution	Specifies the minimum and maximum resolution to be used in calculating the electron density map that will be skeletonized.
Minimum Density (rms=50)	Specifies the minimum density to use in creating ridgelines. The maps are scaled such that a value of 50 is 1.
Maximum Density	Specifies the maximum density to use in creating ridgelines. Density values above this level will be set to this level.
Make Ridgelines	Initiates the Fourier calculation, followed by skeletonization of the map.

Xstat program

The Xstat program reads reflection files of various types and performs a number of statistical calculations. The results of the calculations are presented in a graphical format.

Figure 71 . Xstat program menu

Table 68. Xstat program widgets

Widget	Function
Crystal	Specifies the current Crystal file.
Directory	Lists the path specified in the current Project.
Input File	Specifies the name of the file to calculate statistics for.
File Type	Specifies the file type and what portions of each file record will be used. This parameter is controlled by a set of buttons, each of which specifies the type of file that was indicated by the file extension of the Input File. For the df type file you can specify which portion of the file you wish to use; in some cases, a combination of information within the file (e.g., averaging Friedel mates) is allowed before calculating statistics. The choices are: fin--This choice reads a standard .fin file. Statistics are calculated between F1 and F2 values for each stored reflection. These can be Friedel mates of the same reflection or related Fp and Fph values. df(1+2, 3+4)--The averaged values of the pair F1 and F2 and the averaged values of the pair F3 and F4 are used in the calculation of statistics. Normally F1 and F2 are the Fp+ and Fp- values and F3 and F4 are the Fph+ and Fph- values. In such cases, statistics are calculated between merged native and derivative data sets with anomalous dispersion averaged out. df(1,2)--Statistics are calculated between values of F1 and F2, which are normally Fp+and Fp- values. This option should be selected when calculating anomalous dispersion statistics for the first data set of a "double fin" file. df(3,4)--Statistics are calculated between values of F3 and F4, which are normally Fph+and Fph- values. This option should be selected when calculating anomalous dispersion statistics for the second data set of a "double fin" file. phase--Statistics are calculated between values of Fo and Fc that are stored in a .phs file.
Number of bins	Defines the number of divisions in the plot for either resolution or amplitude. The program automatically determines the range for resolution and/or amplitude, and then reflections are divided amongst the desired number of bins.
what to graph	Specifies the type of graph to be generated. Up to six different statistical graphs can be generated at once, and more than one option can be selected at the same time. Each option generates a separate plot that can be printed or saved to a PostScript file.
Graph It	Initiates the calculation and generates the plots.