Xsight - XtalView Commands

Xsight

C XtalView Commands

Xcontur program

Portions of this chapter are extracted with permission from the standard XtalView documentation, written by Dr. Duncan McRee.

Xcontur is a page-based program for contouring crystallographic Fourier maps. Maps are contoured in sections of x, y, or z.

Figure 1 . Xcontur graphics window

You must supply a Fourier map from Xfft or some other external program. The output appears in a window that is the same size as an 8-1/2 X 11" page. The program produces PostScript output, which can be plotted on any Postscript compatible printer. The screen display represents the hardcopy that can be generated; however, nicer fonts are available on a laser-printer. Stereo is available and labels and bonds (lines) can be added or read from files. No interpolation is used in the contouring. If smoother sections are desired, calculate the map on a finer grid.

Clicking MB1, while the cursor is in the graphics window, returns the fractional coordinates of that point in the message window. If you are displaying more than one section simultaneously (Slab > 1), the vertical coordinate with the maximum density is returned. This allows you to locate the coordinates of a peak. The density value printed is an interpolated value, and is almost always lower than the standard peak value. If you click and hold MB1 while the cursor is in the graphics region, the mouse can then be dragged and the outline of the map will follow. Clicking the Draw button re-displays the contours in the new location.

Main menu

You can use the buttons at the top of this menu to generate supplemental menus. Map and contour characteristics are set in the main menu. Clicking the Draw button puts the main menu changes into effect.

Figure 2 . Xcontur main menu

Table 1. Xcontur main menu widgets

Widget Function

Quit Exits the program.

File Opens the File menu.

Print Opens the Print menu.

View Opens the View menu.

Labels Opens the Labels menu.

Defaults Opens the Defaults menu.

Crystal Lists the name of the current crystal file, and allows you to load a new crystal file.

Cell Displays the unit cell (used to scale the axes) from the current crystal file.

NX, NY, NZ Displays the integers (stored in the .map file) representing the number of divisions along the a, b, and c axes.

Planes Sets the sectioning direction as either x, y, or z. If you change this parameter, the Rows and Columns parameters are also changed so that they do not conflict. No attempt is made to detect left-handed configurations. If you stack up sections for a mini-map you may need to stack downwards or upwards to get the proper handedness.

Plane Sets the level along the sectioning axis. This can be established by entering the section number (type it in the numeric field or use the arrow boxes) or entering the crystallographic fractional coordinate in the second numeric field. In addition a menu button is available that allows quick selection of 0.0, 0.5 or 1.0 levels. If the number of sections is odd, the nearest section is given for 0.5.

Slab Specifies the number of sections to contour simultaneously. They are all overlaid on the screen, although when they are plotted they can be either overlaid or plotted on separate sheets. The slab always starts at the Plane section and then increases.

Rows Establishes the horizontal screen axis (overrides the Columns parameter).

Row Min Establishes the minimum value of the Row axis.

Row Max Establishes the maximum value of the Row axis.

Columns Establishes the vertical screen axis.

Col Min Sets minimum value of the Column axis.

Col Max Sets maximum value of the Column axis.

Contour Levels The Number, Interval, and Start contour parameters control the contour levels. Number sets total number of contour levels, Interval sets interval between successive contours, and Start sets the level of the first contour. The map is scaled so that an interval of 50 is equal to 1.

Draw Redraws the map, accounting for changed parameters.

Resize Resizes the map when you click the button. Click two points in the graphic to define two diagonal corners, and then click the button again.

Table 1. Xcontur main menu widgets
Widget	Function
Quit	Exits the program.
File	Opens the File menu.
Print	Opens the Print menu.
View	Opens the View menu.
Labels	Opens the Labels menu.
Defaults	Opens the Defaults menu.
Crystal	Lists the name of the current crystal file, and allows you to load a new crystal file.
Cell	Displays the unit cell (used to scale the axes) from the current crystal file.
NX, NY, NZ	Displays the integers (stored in the .map file) representing the number of divisions along the a, b, and c axes.
Planes	Sets the sectioning direction as either x, y, or z. If you change this parameter, the Rows and Columns parameters are also changed so that they do not conflict. No attempt is made to detect left-handed configurations. If you stack up sections for a mini-map you may need to stack downwards or upwards to get the proper handedness.
Plane	Sets the level along the sectioning axis. This can be established by entering the section number (type it in the numeric field or use the arrow boxes) or entering the crystallographic fractional coordinate in the second numeric field. In addition a menu button is available that allows quick selection of 0.0, 0.5 or 1.0 levels. If the number of sections is odd, the nearest section is given for 0.5.
Slab	Specifies the number of sections to contour simultaneously. They are all overlaid on the screen, although when they are plotted they can be either overlaid or plotted on separate sheets. The slab always starts at the Plane section and then increases.
Rows	Establishes the horizontal screen axis (overrides the Columns parameter).
Row Min	Establishes the minimum value of the Row axis.
Row Max	Establishes the maximum value of the Row axis.
Columns	Establishes the vertical screen axis.
Col Min	Sets minimum value of the Column axis.
Col Max	Sets maximum value of the Column axis.
Contour Levels	The Number, Interval, and Start contour parameters control the contour levels. Number sets total number of contour levels, Interval sets interval between successive contours, and Start sets the level of the first contour. The map is scaled so that an interval of 50 is equal to 1.
Draw	Redraws the map, accounting for changed parameters.
Resize	Resizes the map when you click the button. Click two points in the graphic to define two diagonal corners, and then click the button again.

Supplemental menus

File menu

You can use the File menu to specify and load map files. In addition, you can load label files (atom and vector positions) and bond files.

Figure 3 . Xcontur File menu

Table 2. Xcontur File menu widgets

Widget Function

Filter Filters the files listed in the associated list box (default is *.map).

List Updates the list box (you must click this if you change the Filter parameter).

Directory Specifies the directory path for loading and saving files.

Map File Specifies which file to load. Clicking a name in the file list box will automatically load the name into the Map File parameter.

Load Map Loads the file specified b the Map File parameter.

Labels File The name of the labels file you want to work with.

Load Labels Loads and displays the specified labels file. You can either load a labels file for display or save a labels file based on the labels of the current display. A labels file contains one record for each label; each record contains the positional coordinates, x, y, and z as well as the text of the label. The Patterson prediction program, Xpatpred, creates a labels file that can be displayed within Xcontur.

Save Labels Saves the displayed labels to the specified file.

Bonds File The name of the bonds file you wish to work with. You can either load a bonds file for display or remove bonds from the current display. The bond file has the vu format: lines of x1 y1 z1 x2 y2 z2 color, where x1, y1, z1 are the starting coordinates of a line and x2, y2, z2 are the end coordinates. The color is not used by the current version of Xcontur. Xfit also displays/creates vu files and a number of utilities for producing vu files from PDB files and other sources exist (e.g., grinchbones).

Number of Bonds The number of bonds is displayed (not modifiable).

Table 2. Xcontur File menu widgets
Widget	Function
Filter	Filters the files listed in the associated list box (default is *.map).
List	Updates the list box (you must click this if you change the Filter parameter).
Directory	Specifies the directory path for loading and saving files.
Map File	Specifies which file to load. Clicking a name in the file list box will automatically load the name into the Map File parameter.
Load Map	Loads the file specified b the Map File parameter.
Labels File	The name of the labels file you want to work with.
Load Labels	Loads and displays the specified labels file. You can either load a labels file for display or save a labels file based on the labels of the current display. A labels file contains one record for each label; each record contains the positional coordinates, x, y, and z as well as the text of the label. The Patterson prediction program, Xpatpred, creates a labels file that can be displayed within Xcontur.
Save Labels	Saves the displayed labels to the specified file.
Bonds File	The name of the bonds file you wish to work with. You can either load a bonds file for display or remove bonds from the current display. The bond file has the vu format: lines of x1 y1 z1 x2 y2 z2 color, where x1, y1, z1 are the starting coordinates of a line and x2, y2, z2 are the end coordinates. The color is not used by the current version of Xcontur. Xfit also displays/creates vu files and a number of utilities for producing vu files from PDB files and other sources exist (e.g., grinchbones).
Number of Bonds	The number of bonds is displayed (not modifiable).

Print menu

Xcontur provides you with the capability to print the current map to a PostScript printer or to save it to a PostScript file for later printing.

Figure 4 . Xcontur Print menu

Table 3. Xcontur Print menu widgets

Widget Function

Printer The name of the output printer.

Print to Sends output to either a PostScript file (enter a name in the Print File field) or to a printer (use the Printer parameter).

Print File Saves output to a PostScript file.

Print Each Plane Separately Prints each section on a separate page.

Print Prints or Saves the file.

Table 3. Xcontur Print menu widgets
Widget	Function
Printer	The name of the output printer.
Print to	Sends output to either a PostScript file (enter a name in the Print File field) or to a printer (use the Printer parameter).
Print File	Saves output to a PostScript file.
Print Each Plane Separately	Prints each section on a separate page.
Print	Prints or Saves the file.

View menu

You can select many view characteristics in this menu. You may tailor the defaults by selecting parameters here, then saving a defaults file using the Defaults button.

Figure 5 . Xcontur View menu

Table 4. Xcontur View menu widgets

Widget Function

Title Specifies the title of the plot. The title is the file name by default.

Display Type Views contoured maps (Contours) or numeric values of actual grid points (Raw Numbers). If you are using the Raw Numbers option you must set the Scale Angstroms/cm parameter to a small number in order to display the numbers.

Row Ticks Determines the number of grid lines (Draw Grid Lines turned on) or tick marks drawn perpendicular to the horizontal axis.

Column Ticks Number of grid lines (Draw Grid Lines turned on) or tick marks drawn perpendicular to the vertical axis.

Row Origin The position, in pixels, of the plot origin in the horizontal direction.

Column Origin The position, in pixels, of the plot origin in the vertical direction.

Scale Angstroms/cm Controls the plot scale. You can either enter a value in the numeric field or use the menu button (Click with MB3) to select stored values. The scale is accurate for hardcopy but can vary on the screen due to different size monitors and different resolution monitors. However, the graphics area of the menu is representative of a piece of paper, so if the graph fills the graphics region properly, it fills the paper properly.

Alternate solid and dashed contour Draws every other contour level with dashed lines.

Draw Grid of Lines Draws a grid of lines on the contour map (specified by Row ticks and Column ticks).

Auto Center Centers the plot on the page automatically.

Use Line Width for Depth Cue Produces a depth cue effect printout for section slabs on laser printers.

Draw Labels Controls label display.

Size Specifies the font size of the labels (6, 10, or 14 point).

Draw Jack at Label Position Enables/disables drawing a jack at the label position.

Size A slider which changes the size of the jack in pixel units.

Draw Bonds Specifies whether or not bonds are drawn.

Width Varies the line width of the bonds on the printed output.

Draw Side by Side Stereo Sets scale factor to half size and draws to images for side by side stereo.

Stereo Separation Determines distance between two images in a stereo plot.

Stereo Depth
Sets the relative shear angle, which modifies the apparent depth.

Apply Redraws the display based on current parameters.

Table 4. Xcontur View menu widgets
Widget	Function
Title	Specifies the title of the plot. The title is the file name by default.
Display Type	Views contoured maps (Contours) or numeric values of actual grid points (Raw Numbers). If you are using the Raw Numbers option you must set the Scale Angstroms/cm parameter to a small number in order to display the numbers.
Row Ticks	Determines the number of grid lines (Draw Grid Lines turned on) or tick marks drawn perpendicular to the horizontal axis.
Column Ticks	Number of grid lines (Draw Grid Lines turned on) or tick marks drawn perpendicular to the vertical axis.
Row Origin	The position, in pixels, of the plot origin in the horizontal direction.
Column Origin	The position, in pixels, of the plot origin in the vertical direction.
Scale Angstroms/cm	Controls the plot scale. You can either enter a value in the numeric field or use the menu button (Click with MB3) to select stored values. The scale is accurate for hardcopy but can vary on the screen due to different size monitors and different resolution monitors. However, the graphics area of the menu is representative of a piece of paper, so if the graph fills the graphics region properly, it fills the paper properly.
Alternate solid and dashed contour	Draws every other contour level with dashed lines.
Draw Grid of Lines	Draws a grid of lines on the contour map (specified by Row ticks and Column ticks).
Auto Center	Centers the plot on the page automatically.
Use Line Width for Depth Cue	Produces a depth cue effect printout for section slabs on laser printers.
Draw Labels	Controls label display.
Size	Specifies the font size of the labels (6, 10, or 14 point).
Draw Jack at Label Position	Enables/disables drawing a jack at the label position.
Size	A slider which changes the size of the jack in pixel units.
Draw Bonds	Specifies whether or not bonds are drawn.
Width	Varies the line width of the bonds on the printed output.
Draw Side by Side Stereo	Sets scale factor to half size and draws to images for side by side stereo.
Stereo Separation	Determines distance between two images in a stereo plot.
Stereo Depth	Sets the relative shear angle, which modifies the apparent depth.
Apply	Redraws the display based on current parameters.

Labels menu

This menu is used to modify existing labels and to add new labels.

Figure 6 . Xcontur Labels menu

Table 5. Xcontur Labels menu widgets
Widget	Function
Labels	A list of all labels read with the Files menu or created in this menu. Click a label in the list to load it for editing.
Label	Creates a new label or loads an existing one for modification.
x	Specifies a new x-coordinate or modifies an existing one.
y	Specifies a new y-coordinate or modifies an existing one.
z	Specifies a new z-coordinate or modifies an existing one.
Insert	Includes a new label in the label list.
Delete	Deletes a label from the label list. In order to delete a label you must first select it from the list.
Replace	Replaces a label in the label list. This action requires that you first select a label and then modify the label using the Label, X, Y, and Z parameter fields.

Defaults menu

The Defaults functions allow you to set and save menu parameters so you can customize your contouring environment and easily return to it each time you use the program.The window is accessed by clicking Defaults with MB3.

Figure 7 . Xcontur Defaults menu

Table 6. Xcontur Defaults menu widgets
Widget	Function
Load xcontur.defaults	Reads an existing Xcontur parameter file. Also activated by MB1 clicking Defaults button. Only useful if an Xcontur.defaults file has been saved.
Save xcontur.defaults	Saves a template of the parameters.
Reset to startup	Resets parameters to standard defaults.

Xedh program

Xedh is used to generate electron-density histograms. When you compare these with histograms of proteins with similar solvent content at the same resolution, phase error estimates can be made.

The interface to Xedh consists of a Files menu for loading and saving files, and a plotting window, named Electron Density Histogram, for displaying the histograms.

Files menu

The Xedh Files menu handles file control.

Figure 8 . Xedh Files menu

Table 7. Xedh Files menu widgets

Widget Function

Directory Changes the directory used in searching for the Map File. Loads the directory associated with the current project by default.

Filter Limits the number and types of files that are contained in the file scroll list. If you change the filter you must click the List button to update the list. The associated arrow button contains a menu of the most common file extensions.

List Updates the list of filtered files

Map File Specifies the name of the file to import and convert.

Solvent Mask Reads a solvent mask in Wang's format and separates the solvent region from the protein region in the generation of a histogram. The Load button contains a menu of five different options for reading the mask: All Points in Map, Protein Points Only, Protein Points Full Scale, Solvent Points Only, and Solvent Points Full Scale.

Histogram Specifies a histogram file to load for analysis or specifies a file name for saving a newly created histogram.

Number Loads and displays up to 10 histograms simultaneously.

Load Reads the file specified in Histogram.

Save Histogram Saves the histogram generated from the currently loaded .map file.

Save Graph Saves the histogram generated from the currently loaded .map file as a graph.

Table 7. Xedh Files menu widgets
Widget	Function
Directory	Changes the directory used in searching for the Map File. Loads the directory associated with the current project by default.
Filter	Limits the number and types of files that are contained in the file scroll list. If you change the filter you must click the List button to update the list. The associated arrow button contains a menu of the most common file extensions.
List	Updates the list of filtered files
Map File	Specifies the name of the file to import and convert.
Solvent Mask	Reads a solvent mask in Wang's format and separates the solvent region from the protein region in the generation of a histogram. The Load button contains a menu of five different options for reading the mask: All Points in Map, Protein Points Only, Protein Points Full Scale, Solvent Points Only, and Solvent Points Full Scale.
Histogram	Specifies a histogram file to load for analysis or specifies a file name for saving a newly created histogram.
Number	Loads and displays up to 10 histograms simultaneously.
Load	Reads the file specified in Histogram.
Save Histogram	Saves the histogram generated from the currently loaded .map file.
Save Graph	Saves the histogram generated from the currently loaded .map file as a graph.

Electron Density Histogram window

This window is used to display the histograms. Once a file or files have been loaded using the Files menu, you can display the resulting plot by clicking on the Legend button.

Figure 9 . Xedh Electron Density Histogram window

Table 8. Xedh Electron Density Histogram window widgets
Widget	Function
Quit	Exits Xedh.
File	Pops the Files menu to the front of all windows.
Clear	Erases the contents of the graphics region.
Edit	Displays a list of currently open histograms and allows you to remove or replace displayed histograms.
Match	Compares displayed histograms.
Print	Generates a menu that allows you to print the display or save it as a PostScript file.
Legend	Generates a window that displays the identification of currently plotted histograms.

Xfft program

The Xfft program calculates electron density and Patterson function maps based on a variety of coefficients. The fast Fourier transform (FFT) method is employed.

Figure 10 . Xfft main menu

Table 9. Xfft main menu widgets
Widget	Function
Crystal	LIsts the name of the crystal file associated with the current project. You can change it by typing in the name of an existing crystal file.
Unit Cell	Displays the unit cell parameters of the current crystal file. If you modify these values, it will affect the calculations.
Directory	The directory used to search for the Input Phase File. You may change it by modifying this text field. Loads the directory associated with the current project by default.
Defaults	Displays a menu of three different options associated with using a default parameter file. Clicking the button with MB1 selects the default option, Load from xfft.defaults.
Direction of Planes	Lets you choose to store the three-dimensional Fourier map output to a file in sections that are divided along any three of the cell axes. This is only necessary if you plan to use the file with something other than an XtalView program; XtalView programs can read the files and display the results in any order. The options are listed as: X(yz sections) (produces sections perpendicular to a), Y(zx sections)* (produces sections perpendicular to b), and Z(xy sections)* (produces sections perpendicular to c*).
Map Type	Allows you to choose the coefficients to be used for calculating Fourier maps: *Fofom, Fo, Fc, Fo-Fc, 2Fo-Fc*, and FoFo(Patterson).
Input Phase File	Defines the name of the data file to use in the Fourier calculation. For the first four options, either a standard .phs file (h, k, l, fo, fc, and phi) or an CNX file can be used. In addition to these choices, a Patterson calculation can use a .fin or a .df file.
Phase File Type	Specifies file type for the Input Phase File, and, in the case of Patterson calculations, how to generate the coefficients. The non-Patterson choices are: h k l Fo Fc Phi(degrees) h k l Fo Fc Phi(radians) h k l Fo fom Phi(degrees) h k l Fo fom Phi(radians) h k l A B XPLOR Reflections file The Patterson choices are: finFp s(Fp) Fph s(Fph) df use (1+2) - (3+4) df use 3 - 4 df use 1 - 2 For Patterson calculations with .df formats there are three choices for defining the difference to be used in computing the Patterson coefficients. Which you use depends upon what is in each of the 4 columns in the .df file. Normally, columns 1 and 2 are native data and the associated sigma values, and columns 3 and 4 are isomorphous data (a column is a pair of f and sigma(f)). To make an isomorphous difference Patterson map, use (3+4) - (1+2), which means the average of 1 and 2 minus the average of 3 and 4, or FPH - FP. Note that when calculating the average, missing observations are not included.
Resolution Filter	Specifies minimum and maximum resolution filters. The order is unimportant.
Outlier Filter	Removes nonsensical coefficients from Patterson maps. Specifically, a reflection is rejected from the Fourier calculation if the absolute value of the difference is greater than the specified percentage of the average of the two observations. A value of 100% is a conservative value to use. On numeric fields you must press <Enter> to register the edit, if you edit the data with the keyboard.
Read Phase File	Clicking this button reads the data file. It is usually not necessary to use it, since the Calculate step determines whether the data needs to be read in. However, sometimes you may want to examine the grid before calculating the map, or you may have changed the input data file and want to force a re-reading of the input data. In any case, after reading the data, some useful information is printed in the message window for your edification. Also, if you change any of the parameters above this button after calculating a map, you must use this button to have that change take effect.
Grid Number in X, Y, Z	The number of points in x, y, and z to use in calculating the Fourier map. The FFT method requires that these be multiples of 2, 3, 5, and 7, and that the value of x be even. The program restricts you to these values if you use associated arrow boxes. Normally, you set the number of grid points using either the percentage of minimum resolution parameter or the approximate spacing in angstroms parameter. If you really want to manually set these parameters, set both percentage of minimum resolution and approximate spacing in angstroms to 0 to prevent overriding the x, y, and z fields.
percentage of minimum resolution	Sets the grid to the next largest value that will give a spacing equal to a percentage of the minimum d-spacing or resolution. For example, if the input data has a minimum d-spacing of 2.0 and 50% is selected for the percentage, the grid is then set as close to 1.0 as possible. If the cell edge is 48.3, then 48.3 is tried, but since this is not an integer it is rounded up to 49. An FFT calculation requires that the grid be at least 50% of the minimum d-spacing (actually, it is has to be twice the maximum index input, but it works out to the same thing as you can verify). The map will be smoother if you use the 33% default. A smaller percentage adds little benefit in smoothing the map and requires much more storage since the size of the map goes up as the cube of the grid size.
approximate spacing in angstroms	Sets the Grid Number parameters if both the Grid Number parameters and percentage of minimum resolution are set to 0. This parameter works by finding the x, y, z values that give the closest grid spacing and that specify a valid FFT grid. For example if you have a 77.77 cell edge and ask for a 1.0 grid, a value of 78 is first tried, but since this is not a multiple of 2,3,5, or 7, 80 is used.
Output Map File	Controls the name of the created map file. The XtalView convention uses the`.map` extension. This file is in the FSFOUR binary FORTRAN format.
Calculate	Initiates the Fourier calculation.

Defaults menu

The Xfft Defaults menu saves and/or loads a file of menu defaults. This is very useful if you have a standard set of parameter values that you like to use which are different from the standard parameters.

Figure 11 . Xfft Defaults menu

Table 10. Xfft Defaults menu
Menu Item	Function
Load from xfft.defaults	Loads an existing xfft.defaults file and resets the default parameter settings accordingly.
Save to xfft.defaults	If you prefer a different set of starting parameters from the default ones, this option will save a set of parameters to a file named xfft.defaults. You can then read this file into the menu with the Load from xfft.defaults command.
Reset to Startup values	Loads the default parameter settings.

Xcontur program

Figure 1 . Xcontur graphics window

Main menu

Figure 2 . Xcontur main menu

Table 1. Xcontur main menu widgets

Supplemental menus

File menu

Figure 3 . Xcontur File menu

Table 2. Xcontur File menu widgets

Print menu

Figure 4 . Xcontur Print menu

Table 3. Xcontur Print menu widgets

View menu

Figure 5 . Xcontur View menu

Table 4. Xcontur View menu widgets

Labels menu

Figure 6 . Xcontur Labels menu

Table 5. Xcontur Labels menu widgets

Defaults menu

Figure 7 . Xcontur Defaults menu

Table 6. Xcontur Defaults menu widgets

Xedh program

Files menu

Figure 8 . Xedh Files menu

Table 7. Xedh Files menu widgets

Electron Density Histogram window

Figure 9 . Xedh Electron Density Histogram window

Table 8. Xedh Electron Density Histogram window widgets

Xfft program

Figure 10 . Xfft main menu

Table 9. Xfft main menu widgets

Defaults menu

Figure 11 . Xfft Defaults menu

Table 10. Xfft Defaults menu