Manpage

xtalview

a complete package for solving a macromolecular crystal structure by isomorphous replacement, including building the molecular model

Window-based Applications:

xcontur - a page-based contouring program for crystallographic maps
xdf - disk full meter
xedh - electron density histogram plotter
xfft - calculate an electron density map or a Patterson function map by the Fast Fourier Transform method
xfit - map fitting and molecular modeling program to display or manipulate models and fit to electron density
xheavy - refine heavy atom derivatives and calculate phases.
xhercules - searches for heavy atom sites.
xmerge - merge and scale two data files.
xmergephs - merge fin and phase files; phase derivatives and mutants
xpatpred - predict Patterson peaks from a list of sites.
xprepfin - prepare fin files.
xresflt - resolution filter
xrspace - reciprocal space viewer
xskel - performs skeletonization on an electron density map
xstat - analyze statistics on .fin, .df, or .phs files
xtalmgr - manage XtalView projects and applications

Nonwindow-based Applications:

colorbyB - prepare a vu file from a PDB file colored by B-value
cvtpdb - converts a pdb file between Cartesian and fractional coordinates, vice-versa, and coordinate transformations.
cvtvu - convert a vu file between Cartesian and fractional coordinates
cvtxyz - convert x,y,z between Cartesian and fractional coordinates
deh - remove hydrogens from a pdb file.
dumpphasit - reformat phasit format output files to XtalView
deriv - calculate the derivative of a difference map at each atom
grinchbones - convert a GRINCH ASCII format file to a vu file
hercules - searches for heavy atom sites. This is a brute force application of Patterson correlation methods. It is slow, but extremely robust.
matrices - dump the XtalView Cartesian/fractional conversion matrices
mkskel - performs skeletonization on an electron density map (mkskel is part of the University of North Carolina GRINCH skeletonizat ion package).
mu2fin - convert a XENGEN mulist file to an XtalView.fin file
pdbfit - align two PDB objects using rotation and translation
rescalc - calculates resolution of an index for the crystal in the CRYSTAL environment variable.
resflt - resolution filter
stfact - calculate structure factors from a PDB file.
urf2xfit - convert an XENGEN urefls file to a vu file for display in xfit
volume - calculates and displays the volume of a crystal unit cell
xplortophs - reformat XPLOR phase files

NAME
colorbyB - prepare a vu file from a PDB file colored by B- value

USAGE
colorbyB pdbfile xfit.vu -n[ormalize]

DESCRIPTION
The input pdb file is converted to colored lines using the same routines as in xfit except that the lines are colored by Bvalue. If the -normalize flag is present then the B- values are normalized before coloring. This is highly recom- mended for comparison purposes as it scales out any effect of the overall B. Unnormalized Bs are colored in intervals of 5 on B-value from cool to hot with the following color scheme: 0 - 5 cyan 5 - 10 blue 10 - 15 orchid 15 - 20 pink 20 - 25 red 25 - 30 gold 30 - 50 yellow >50 white Normalized Bs are colored based on the sigma deviation from the mean using the following color scheme: < -2.0 cyan -2.0 - -1.0 blue -1.0 - -0.5 orchid -0.5 - 0.0 pink 0.0 - 0.5 red 0.5 - 1.0 gold 1.0 - 2.0 yellow > 2.0 white The B-value coloring can be very useful for comparing muta- tions with the native structure. This same coloring can be done in xfit under View.

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1), xfit(1)
cvtpdb
cvtpdb

NAME
cvtpdb - converts a pdb file between Cartesian and frac- tional coordinates, vice-versa, and coordinate transforma- tions.

USAGE
cvtpdb crystal [-f | -c | -t | -r | -e] < file.pdb > newfile.pdb -f convert from fractional to Cartesian. -c convert from Cartesian to fractional. -t vx vy vz translate by the amount specified in vx vy vz. -r r11 r12 r13 r21 r22 r23 r31 r32 r33 rotate by matrix -e q1 q2 q3 rotate by the Eularian angles q1, q2, q3.

DISCUSSION
Note the nonstandard use of crystal on the command line instead of reading from the environment. This forces you to think carefully, since it is critical for correct operation. Converting to fractional coordinates is especially useful when applying crystallographic transformations. After transformation, convert back to Cartesian. You can pipe the output of one cvtpdb into another to chain operations together. For example to generate the second symmetry related molecule in P21 (-x, y+1/2, -z) and translate it to the unit cell at +1, 0, -1:

cvtpdb crystal -f < molecule1.pdb |\ !to fractional

cvtpdb crystal -r -1 0 0 0 1 0 0 0 -1 |\ !rotate by -x,y,-z

cvtpdb crystal -t 0 .5 0 |\ !translate by x, y+1/2, z)

cvtpdb crystal -t 1 0 1 |\ !translate by +1, 0 -1

cvtpdb crystal -c > molecule2.pdb !convert back to Cartesian
Such a complicated command is best done in a shell file and is very handy for generating packing diagrams.

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1)
cvtvu
cvtvu

NAME
cvtvu - convert a vu file between Cartesian and fractional coordinates

USAGE
cvtvu crystal -f < fractional.vu > Cartesian.vu cvtvu crystal -c < Cartesian.vu > fractional.vu

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1), xfit(1)
cvtxyz
cvtxyz

NAME
cvtxyz - convert x,y,z between Cartesian and fractional coordinates

USAGE
cvtxyz [-f|-c] [x y z]|[< file.xyz > newfile.xyz] -f convert from fractional to Cartesian -c convert from Cartesian to fractional The environmental variable CRYSTAL must be set to the correct crystal file.

DISCUSSION
If x y z are given, then these are converted and the output is reported to stdout. Otherwise stdin is converted to stdout. The file format is three floats on each line. An example use of cvtxyz is converting fractional bounds from xcontur into the Cartesian bounds expected by xfrodomap.

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1), xcontur(1)
deh
deh

NAME
deh - remove hydrogens from a pdb file.

USAGE
deh < pdb_with_hydrogens > pdb_without_hydrogens

DESCRIPTION
The output of XPLOR contains hydrogen atoms at some posi- tions and often it is desirable to get rid of them. A hydro- gen is decided on if either column 12 or 13 is 'H'. This also will remove HG+2. Does anyone know of a more reliable way to find hydrogens? (Note: xfit handles hydrogens from XPLOR and if you leave them on, you will not have to rerun generate.inp.)

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1), xfit(1)
deriv
deriv

NAME
deriv - calculate the derivative of a difference map at each atom.

USAGE
deriv file.pdb refl.phs out.vu [resmin] [resmax]

DESCRIPTION
The input is a PDB file (.pdb) and a phase file (.phs) and the output is a vu file, suitable for xfit, containing arrows showing the direction and relative magnitude of the gradient. If one resolution limit is given then it is con- sidered the minimum resolution. If two are given data between them are used, and if none are given all data is used.

PURPOSE
This function is also provided within xfit. It calculates the derivative of the difference electron density of the two amplitudes given in the phase file. If the file contains Fobs and Fcalc this is Fobs-Fcalc. Another useful construct is Fmutant-Fnative. An arrow is drawn at this position in the direction of the gradient of the difference map with the length indicating the steepness normalized for the atom type (do not take these literally, they are only relative indica- tors). This is the direction a refinement program would move the atom in the first cycle if no stereochemistry were taken into account. Also, this is not very useful at reso- lutions far from atomic resolution (say below 2.5A). This program is provided for those who want to use it with some other program (converting the vu file is their responsibility--remember it is x1 y1 z1 x2 y2 z2 color), and also because performing this calculation for an entire molecule would take quite a long time and would stop xfit while it was being done. Since xfit does not provide a mechanism for saving the vectors it calculates, if you will be using them over several sessions they should be pre- calculated with deriv.

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1), xfit(1)
dumpphasit
dumpphasit

NAME
dumpphasit - reformat phasit format output files to XtalView

USAGE
dumpphasit phasit_file > xtalview.phs

AUTHOR
PHASIT is Bill Furey's (University of Pittsburgh) phasing program from his PHASES package.

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1)
grinchbones
grinchbones

NAME
grinchbones - convert a GRINCH ASCII format file to a vu file

USAGE
grinchbones < grinch.ASCII > xfit.vu

DISCUSSION
The input is a University of North Carolina, Chapel Hill Graphics Lab GRINCH ASCII format file (made with the command ASCII save filename in interp or use the ASCII option in mkskel) and the output is an xfit vu file. The output uses the standard GRINCH color scheme for interpreted edges (i.e. main chain is green, side chain is violet, etc.) except that unknown edges are colored in bins of density from blue to red (the same as the default color scheme for the 1st map in xfit). This can be used as a background guide for building the model in xfit. Contours can be used for close-up views and detailed fitting and ridge lines can be used for larger views allowing a larger portion of map to be viewed since ridge lines require fewer lines than contours. The coloring scheme is close to that of GRINCH's except for unknown edges: M (main) green B (bridge) brown S (side) purple O (carbonyl) red F cyan G yellow R (residue) blue U (unknown) 0-14 blue, 15-28 purple, >28 orchid

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1), xfit(1)
hercules
hercules

NAME
hercules - searches for heavy atom sites. This is a brute force application of Patterson correlation methods. It is slow, but extremely robust.

USAGE
hercules control-file print-file

DESCRIPTION
control-file The control-file describes what you want done. The input data descriptions are listed below. The first five lines are string values for file names and the crystal name, and the rest of the lines in the file contain numeric data. 1. fin file with (merged native and derivative data) 2. solution file (NONE for the first round, then solution file output from xheavy or xpatpred for the second round) 3. correlations file (output) 4. correlation map file (output in xcontur/xfit for- mat) 5. crystal (crystal name) 6. grid (should be 1/4 to 1/6 resolution in Angstroms) 7. resmax, resmin (resolution limits on diffraction data) 8. xmin, xmax (in fractions of unit cell, x asym- metric unit) 9. ymin, ymax (in fractions of unit cell, y asym- metric unit) 10. zmin, zmax (in fractions of unit cell, z asym- metric unit) 11. occupancy (see description) print-file The print-file will contain some of the output from the pro- gram. Other output goes into the correlations and correla- tion map files.

DISCUSSION
If you put "NONE" in the heavy solution file name spot (line 2), then atom data is read from the control-file. Other- wise, it is read from the file specified in that field (which may be results from a previous run). The atom data in the solution file is in the same format as that used by xheavy. For example, to use hercules to search for an initial site, enter "NONE" for the solution file (line 2), run hercules, and select the highest hit. You can put this initial site into a solution file using xpatpred. Then, to search for a second site, enter the new solution file in line 2 instead of "NONE" and run hercules again. To guess an occupancy for the second site relative to the first, examine the Patterson map. It's not very sensitive to the occupancy, so numbers like 1, .75, .5, or .25 are sufficient. Use xpatpred to display the predicted Patterson positions. To do this, enter the site and then write out a prediction file. Read this file into xcontur as a labels file. The vectors are put into the volume as 0-1, 0-1, 0-1, so they won't show up on negative sections. For multiple site solu- tions, pay particular attention to the cross-peaks. The search volume should be the asymmetric volume of the Patterson map. The input format only allows for rectangular asymmetric units. This may cause some redundant computation in high symmetry space groups. For single sites there will be extra symmetry due to the fact that both hands and all origin shifts are valid interpretations of the Patterson map. For a second site there is a two-fold ambiguity due to the hand choice. You can reduce the search volume accord- ingly. If not, note that there will be several equivalent hits (They will all give identical predictions with xpatpred). The solution can then be read directly into xheavy for refinement. If you want to use the PHASES package from Furey, then xheavy can rewrite the solution into a file that's more or less ready to use depending on the PHASES version you use. Hercules writes an fsfour style map that may be examined with xcontur. To get the coordinates in xcontur, click on the peaks. Sites are added to the solution file as they are found and the program is rerun. The peaks can be entered into xpatpred and displayed on the Patterson map to verify their correctness. Hercules only takes a .fin file, not a .df file. You can split off part of the data in a .df file to from a .fin file with awk. If you do this, you can extract the first entry in the .df file with the command: awk '{print $1,$2,$3,$4,$5,$6,$7}' < file.df > file.fin You can extract the second entry with the command: awk '{print $1,$2,$3,$8,$9,$10,$11}' < file.df > file.fin (For information about .fin and .df file formats, see Chapter 3 of the XtalView user guide.) You can view the results of a hercules run with a command such as: sort -nr +3 test.list | head -20 > top20.hits This command produces a sorted list of the top 20 hits.

EXAMPLES
Example control-file The following is an example control-file. NONE ex.list ex.map cvccp 2.5 1000.0, 6.0 0.0 0.5 0.0 0.3 0.0 0.05 1.0 On an SGI workstation, you may need to enclose each of the first five lines in double quotes to make your file look like this: "ccpniau1.fin" "NONE" "ex.list" "ex.map" "cvccp" 2.5 1000.0, 6.0 0.0 0.5 0.0 0.3 0.0 0.5 1.0

NOTES
Runs can take several hours and are proportional to the number of sites that are input.

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1), xhercules(1)
matrices
matrices

NAME
matrices - dump the XtalView Cartesian/fractional conversion matrices

USAGE
matrices crystal

DESCRIPTION
This routine returns the Cartesian to fractional and vice versa matrices used by XtalView. This is provided because there is more than one way this can be done for non- orthogonal space groups (i.e. a*bc vs. abc*) and when importing/exporting coordinates it may be useful to have these (like when you send your brand new structure off to the databank). The output is self-explanatory. The matrices are meant to be the same as the conventions used by XPLOR and FRODO but I give no guarantee.

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1)
mkskel
mkskel

NAME
mkskel- performs skeletonization on an electron density map (mkskel is part of the University of North Carolina GRINCH skeletonization package).

USAGE
mkskel mainname [-maxlen length -minden density -range low high]

DESCRIPTION
mkskel looks for mainname.mi (map information file) and mainname.map (density map file). You can create these files yourself or use the program xskel to create them for you (see xskel man pages). mkskel produces ridgeline files in ascii, binary or "edges", depending on the output file format specified. Options -maxlen takes a specific length in angstroms as an argument. This length corresponds to the longest legal bond length in the molecule. The default length is 2.0 angstroms. -minden takes a specific node density in density units as an argument. This density corresponds to the minimum density after range mapping 0-31 that will be used to make a ridge line. The default density is 10.0 density units. -range take two arguments: the highest and lowest den- sity for the map range in density units for mapping onto range 0-31 for interp. The default is 0 density units for the low and 99 density units for the high. For instructions on writing map information files see the README file in $XTALVIEWHOME/README.mkskel. mkskel ignores file lines that are blank or that start with a "#". The following elements are mandatory: 1. order - XYZ (or XZY, YXZ, ZYX, ZXY) The slowest dimension is the first, the medium dimension is second, and the fastest dimension is third. 2. dimension - slowsize middlesize fastsize slowsize is the size of the data in number of sam- pling points in the slow direction ("number of planes"). middlessize is the size in the middle direction ("number of rows"). fastsize is the size in the fast direction ("number of columns"). 3. spacing - slowspace midspace fastspace All spacings are in angstroms. 4. origin - sloworigin middleorigin fast origin The following elements are optional: 1. title - name The name of the map. 2. mapinformat - XXX Default mapinformat is character. Other possible values are: ASCII, CHAR, EBCDIC - character format FLOAT4, FLOAT - 4-byte floats FLOAT8, DOUBLE - 8-byte floats INT1, BYTE - 1-byte integer INT2 - 2-byte integer INT4 - 4-byte integer All float and integer values are signed. Sample test.mi file ################################# # test.mi mapinformat CHAR rloutformat EDGES # name of the molecule title Bovine ferricytochrome b5 fragment order XYZ dimension 27 17 17 #other stuff spacing 1.00844 0.959167 0.934687 origin -27 -15 -15 ################################# The ridgeline code mkskel was written by Tom Williams, and is supplied with Xtalview with permission from the author and the Computer Science Department, University of North Caro- lina at Chapel Hill.

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1), xskel(1) SEE ALSO
xtalview(1), xprepfin(1)
pdbfit
pdbfit

NAME
pdbfit- align two PDB objects using rotation and translation

USAGE
pdbfit [-v] <input-file

DESCRIPTION
pdbfit rotates one PDB file onto another. You can either do all the residues in both proteins or set up groups. You can also specify atom types to include and a weight. The -v option switches to verbose mode which provides descriptions of residues and matches. The input-file data descriptions are listed below. 1. name of the file to rotate (file 1) 2. name of the target file to rotate onto (file 2) 3. output coordinates 4. atom types to use and their weights 5. the number of groups The input file must also have the following information for each group in the indicated order: 1. length of group 1 2. number of the starting residue in file 1 3. number of the starting residue in file 2 4. file 1 chain identification. "*" indicates ignore 5. file 2 chain identification. "*" indicates ignore

EXAMPLES
Example input-file The following is an example input-file. 2ccy.A.pdb cvccp.A.pdb rmoncv.pdb CA 1.0 (blank line marks end of atom type list) 1 27 2 2 * *

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1)
rescalc
rescalc

NAME
rescalc - calculates resolution of an index for the crystal in the CRYSTAL environment variable.

USAGE
rescalc

DESCRIPTION
rescalc gets crystal index values from the environment cry- stal information file and calculates the resolution in angstroms.

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1)
stfact
stfact

NAME
stfact - calculate structure factors from a PDB file.

USAGE
stfact pdbfile refllist output.phs [reslimit] [reslimit]

ENVIRONMENT
The value of CRYSTAL must be set to the correct crystal for the unit cell and space group (see xtalmgr(1)). If one limit is given, it is considered the minimum resolu- tion; if two are given, then the data between them is used and if none are given all input reflections are used. The input is a PDB file (.pdb) and a list of reflections in phase file format (.phs). The value of Fobs in the input is passed to the output and Fcalc phi can have any value, including zero (but not blank). The output is a new phase file and will be on an absolute scale (i.e., Fobs is scaled to Fcalc) and is suitable for use in xfit for making maps including omit maps.

DESCRIPTION
This is a completely general structure factor calculator. This is the same structure factor calculator as used in xfit and is atom based. Since this can be quite slow compared to an FFT structure factor calculation this program is provided for doing the calculation offline (perhaps as the last step in a command file of a refinement job). If you are using XPLOR, it is faster to calculate the structure factors using XPLOR's FFT. If you use a command file, be sure to setenv CRYSTAL (e.g. setenv CRYSTAL miraclase) before running stfact.

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1), xfit(1), xtalmgr(1)
urf2xfit
urf2xfit

NAME
urf2xfit - convert an XENGEN urefls file to a vu file for display in xfit.

USAGE
urf2xfit [urefls] [xfit.vu]

DESCRIPTION
If no files are given, then the program uses stdin and stdout; if one name is given, then that file is converted to stdout.

ENVIRONMENT
CRYSTAL is the crystal file. It is used to get the unit cell for scaling the axes. The present version does not handle non-orthogonal space-groups correctly but always displays h,k and l as orthogonal axes. Still, this may be useful.

PURPOSE
By converting a urefls file to a vu file it can be displayed in three dimensions with xfit. The three axes H,K, and L are displayed as well as a jack at the position of each reflec- tion. Data that is missing becomes apparent as well as the curved nature of Ewald sphere which is often neglected in data collection strategies. Each run can be turned into a vu file and displayed in a different color (using the recolor- ing option in xfit) to see how multiple runs overlap. The output is colored in 4 bins of intensity from min to max: blue, cyan, yellow, white. The color scheme needs expanding, and coloring by phi value would be useful.

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1), xfit(1)
volume
volume

NAME
volume - calculates and displays the volume of a crystal unit cell

USAGE
volume crystal

DESCRIPTION
The argument for volume is the XtalView crystal keyword name. The unit cell dimensions for the indicated crystal are extracted from the crystal file and used to compute the volume of the unit cell.

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1)
xcontur
xcontur

NAME
xcontur - a page-based contouring program for crystallo- graphic maps

USAGE
xcontur file.map

METHOD
The map is contoured in sections of x, y, or z. 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 used on any Postscript compatible printer. The output is fairly WYSIWYG with the exception that nicer fonts are available on the laser-printer. Stereo is available by shearing 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.

MAIN WINDOW
Crystal The cell information is used from the crystal file. Cell The unit cell is used to scale the axes. Non- orthogonal axes are properly handled. The rows are always horizontal and the column is at alpha, beta or gamma depending upon the plane being sectioned. NX, NY, NZ This is read from the input map and cannot be changed. Planes This sets the sectioning direction in either x, y, or z. If you change this, then the rows and column direc- tions are also changed so that they do not conflict. No attempt is made to detect left-handed configura- tions. If you stack up sections for a mini-map, you may need to stack downwards or upwards to get the proper handedness. Plane There are 3 fields here. The first is a numeric field which can be used to increment/decrement the section where contouring starts. The second is the value of this plane in fractions of the unit cell. If you edit this value and enter it, the nearest plane section will found. The third is a pull down menu for choosing the three sections 0.0, 0.5 and 1.0. If the number of sec- tions is odd, the nearest section will be given for 0.5. Slab The number of sections to contour. They will all be overlaid onto each other on the screen although when they are plotted they can be either overlaid or plotted on separate sheets. The slab always starts at plane and increases. Rows Rows go horizontally across the screen. This sets whether this direction is x, y, or z. It overrides the columns when changed if it conflicts, and can be over- ridden by planes. Row min The first value is in terms of grid points in nx, ny or nz and the second is fractions of the unit cell. You must enter fractional values for them to take effect. Columns This sets the direction of the columns. It has the lowest priority and so can't actually be used to change the column direction but does indicate the direction being used. Both row and plane direction changes will override the column direction if there is a conflict. CONTOUR LEVELS Number The number of contour levels is set here from a minimum of 1 to a maximum of 20. Interval The interval between successive levels. From a minimum of 1 to the maximum value of the map. Start The level of the first contour level. May be negative. The slider ranges from the minimum of the map to the maximum. Upon loading a map both start and the inter- val are set to the root-mean-square value of the map. Draw The screen is redrawn when this button is pressed. Picking in the Canvas If you pick with the mouse button the fractional coor- dinates of that point are returned in the message win- dow. Holding down the SELECT (left) mouse button causes the outline of the section to drag so that it can be positioned on the page. When using slabs greater than 0 the vertical coordinate with the maximum density value will be printed. This allows finding the x, y, z coordinate of a peak. The density value printed is an interpolated value and as such is almost always lower than the peak value.

VIEW POP-UP
Title The title is initially set to the map file name. It is nice to edit it and put something sensible here. Display Type You can look at the contours (default) or at the raw numbers in the map file. However, for the raw numbers only a small section can be viewed before the numbers overlap each other and become unreadable. Row, Column Ticks The number of grid lines and/or tick marks to make counting from 0. Row, Column Origin The position of the upper left corner of the section. It is easier to set this by dragging with the mouse in the canvas window. Scale Angstroms/cm You can manually enter a value or pull down a menu of choices. The scale is accurate for hardcopy but is correct only if you happen to have the right size moni- tor. Remember, though, that the canvas window is the same size as a piece of paper if you haven't resized it. And so, if the graph fills the window, it will fill the paper. Alternate solid and dashed contour Check this if you wish to do this. Every other level will be dashed lines for an interesting effect that can make counting levels easier. Draw grid of lines If this is checked, a grid of lines is drawn at the frequency specified by the row, column ticks. Auto Center If this is checked the section is centered on the page automatically. Must be disabled for stereo to work properly. Use Line Width for Depth Cue While the computer screen does not have enough resolu- tion for this to be useful, it produces a nice depth cue on laser printed output and is highly recommended for multi section slabs. Best to set it just before printing. Draw Labels Enables/disables the drawing of labels. Labels can be edited using the Labels pop-up or loaded in the File pop-up. They are drawn on the section only if the x, y, z coordinate is on that section. Draw Jack at Label Position Enables/disables the drawing of a jack at the position of the label. The size of the jack can be changed with the slider: Draw Bonds Bonds can be drawn superimposed on the sections. They are drawn only if their x, y, z coordinate is on that section. The line width of the bond on the printed output can be varied from thick to thin to make it more obvious. Draw side by Side Stereo The scale is halved and two images for side by side stereo are drawn by shearing each successive section. Stereo Separation Sets the distance the two images are apart from each other. Hint: Set the contour level very high while fiddling with the stereo parameters so that drawing is quick. Once you get them right you can lower the level for the final picture. Stereo Depth This sets the shear angle and modifies the apparent depth. Apply Causes the picture to re-draw.

FILE POP-UP
Filter This sets a filter for the file list box. It defaults to *.map and all the files in the current directory that match the filter will be displayed in the file list. List Forces the file list to be updated. Use after changing the filter or the working directory. Directory The current working directory. Map File The source of the map. This field can be filled either from the command line as the first argument, by select- ing a file name in the file list, or by typing it in. Labels File The labels can be loaded from or saved to this file. It has the format of lines of x y z label, where x, y, z are the coordinates and label is a text string. Xpatpred produces a label-file that xcontur can display. Bonds File Bonds can be loaded or saved. 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 is the end coordinate. The color is not used by 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 This is for your information. It is not editable. File List To pick a file in the list, click on the file field that you want to load the input focus into (the little triangular cursor). Then select a file name using the SELECT (left) mouse button.

PRINT POP-UP
Print to You can select a file or a printer. Very large pic- tures may need to be sent to a file and then printed with the -s option because they are too large to spool directly. Printer A valid name of a printer connected to your computer. Leave blank for the default printer. File Name of the file. The directory in the files pop-up is added unless the name starts with "./" or "/". Print sections separately If this option is checked, each section is printed on a separate page. This saves you from having to print them one by one by selecting the entire slab, this option, and then printing.

LABELS POP-UP
Can be used to edit the labels list. Functions are insert/replace/delete. Use the File pop-up to load a labels file.

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1), xpatpred(1), grinchbones(1)
xdf
xdf

NAME
xdf - disk full meter

USAGE
xdf partition

DESCRIPTION
Xdf can be used to monitor disk usage. After it starts it updates the disk usage of the partition it was started with. The usage is shown on the gauge and the partition is displayed on the footer. Example: xdf /usr Shows the amount of /usr that is used. Since xdf updates every three minutes (to avoid over using computer resources), a sudden jump in disk usage will not show up immediately.

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1)
xedh
xedh

NAME
xedh - electron density histogram plotter

USAGE
xedh [file.map]

DESCRIPTION
xedh is a normalized electron-density histogram plotter. It can be used to compare histograms between phase sets and between different crystals. The histogram for a correctly phased protein with a given percent solvent and resolution range is characteristic. Any deviations are due to phase errors. By comparing your phase set with those of other well-refined proteins in the same resolution range you can guess the amount of phase error. For example, when compar- ing right and left-handed maps that include anamolous scattering information the correct hand will have the sharper histogram. If a solvent mask in B.C Wang format exists, it can be used to separate out the protein and solvent components of the histogram. The histograms can be saved and loaded in the Files window. The methods are still being developed. In the future exam- ple histograms may be available and more information on determining phase errors will be available.

POP-UP WINDOWS
xedh has several pop-up windows you can use. They are self-explanatory.

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1)
xfft
xfft

NAME
xfft - calculate an electron density map or a Patterson function map by the Fast Fourier Transform method.

USAGE
xfft phasefile mapfile

DESCRIPTION
Crystal A crystal file is needed with the cell and symm records present. Note that symm records should have centering expanded explicitly. (i.e., C2 should have 8 symm operators not 4 with the last 4 1/2+x,1/2+y,z of the first 4.) Unit Cell This is obtained from the crystal file. However, it can be overwritten by manually entering a value. But there is no way to overwrite the symmetry operators. Defaults A defaults file (hardwired as xfft.defaults) can be saved or loaded. Also, defaults can be reset to startup values. This is handy when you recalculate maps often with the same parameters. Note that you can save a defaults file and then copy it to a new name and then copy it back at a later date. In this way several standard methods can be saved. Direction of Planes The output can be in x, y, or z planes. This is only necessary for possible use of the output map by non- XtalView programs as all XtalView programs can read all 3 sort orders. Map Type There are several choices of map coefficients avail- able. Input File This file can have several different formats. For Fourier maps either the phs format (h,k,l,fo,fc,phi) or XPLOR format can be used. For Pattersons these can be used plus fin and df formats. Type Specifies the type of input file. For Pattersons with df formats there are three choices for defining the difference to be used in computing the Patterson coef- ficients. 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 its sigma's, 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 Set these values to your desired limits. Order is unimportant since computers are perfectly capable of figuring out which number is the min and which is the max (the other one). Outlier Filter This gets rid of outliers when making Patterson maps. Specifically if the absolute value of the difference is greater than x percent of the average of the two observations, the reflection is rejected. This is important when making Patterson maps so that a few bad apples don't spoil the whole bunch. A value of 100 percent is a conservative value to use. Note: On numeric fields you must enter return if you edit the data with the keyboard to register the edit. Read Phase File This button reads in the data. It is usually not necessary to use it since the calculate button (below) can figure out if the data needs to be read in. How- ever, sometimes you may want to find out the grid before calculating the map, or you may have changed the input data file and want to force a rereading of the input data. In any case, after reading the data some useful information is printed in the message window for you to edit. Also, if you change any of the data above this button after calculating a map, you must use this button to have that change take effect. Grid Number in X, Y, Z This is the number of points in x, y and z to be used in calculating the FFT. The FFT method used requires these to be multiples of 2,3,5 and 7 and nx to be even. The program restricts you to these values if you use the little arrows by the grid values to increase or decrease them. Usually you do not need to set nx, ny and nz directly as explained below. OR Percentage of minimum resolution This sets the grid to the next largest value that will give a grid spacing that is equal to the minimum d- spacing or resolution times the percentage. For exam- ple: if the input data had a minimum d-spacing of 2.0 and 50% is chosen, the grid will be set as close to 1.0 Angstroms as possible. If the cell edge was say 48.3 A, then 48.3 is tried, but since this is not an integer it is rounded up to 49. An FFT 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 the reader can verify). The map will be smoother if 33% (the default) is used. More than this usually has 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. Set this field to zero to prevent overriding the nx, ny, nz fields. OR approximate spacing in Angstroms If both nx, ny, nz and percent of minimum resolution are 0 then this field is used to set nx, ny, nz by finding the nx, ny, nz that gives the closest grid- spacing in Angstroms that is also a valid FFT grid. For example if you have a 77.77 E cell edge and ask for a 1.0 Angstrom grid then 78 is tried, but since this is not a multiple of 2,3,5, or 7, 80 is used. Output Map File The XtalView convention is to use the extension .map. This file is in FSFOUR binary FORTRAN format. Calculate This is the "Apply" button. When it is pressed the FFT is calculated and the map output. If the FFT is large then it may take several minutes to return. The pro- gram tries to ascertain if the data needs to be reread if you change various values. It usually decides to reread even when it is strictly unnecessary.

ADVANCED USAGE
If you want a coefficients type that is not available, you can always precalculate them and put them in the Fo column and then make an Fo map. Example: to make a 3Fo-2Fc map using awk and xfft:

awk '{print $1,$2,$3,3*$4-2*$5,$6}' input.phs | xfft - output.map
In XtalView, a dash (-) means use stdin for input files or stdout for output files. At other times, a binary file with the phases is used. For example, to use a Furey format phasit output file (fort.31) using dumpphasit which writes its output on stdout: dumpphasit fort.31 | xfft - output.map Unfortunately, if you use stdin or stdout for I/O then the history file will know only that stdin was used but has no way of picking up the original file used and so the thread of data files will be broken at this point.

ACKNOWLEDGEMENTS
The FFT code was supplied by Lynn Ten Eyck. Andy Arvai is partly responsible for the FFT driver routine.

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1), dumpphasit(1)
xfit
xfit

NAME
xfit - display or manipulate models and fit to electron den- sity.

VERSION
xfit v3.0.

USAGE
xfit [.pdb .vu .phs .map .vp .script .bones]

DESCRIPTION
All of the files on the command line are loaded according to their extension. If you have files with different exten- sions, they can be loaded using the files option. xfit accepts PDB files, phase files, map files, and vu (vector or line) files. The -bw flag forces the program to be black and white, even on a color display. It works on the SUN only. One cannot switch to the Accelerated Canvas if one invokes it. The -std flag prevents the Accelerated Canvas from being evoked on Suns with GX graphics. It works on the SUN only. One cannot switch to the Accelerated Canvas if one invokes it. Xfit is a large and complex program with 11 windows and many possible operations. Some of xfit's more notable features include: * Model-fitting to electron density. * A built-in FFT to calculate density from structure fac- tors. * A built-in FFT to calculate structure factors for mak- ing omit maps and updating phases. * Difference-density gradient calculations. * Least-Squares Fitting of models or portions thereof. * On-the-fly omit maps. * Fast contouring of up to 20 maps. * Up to 50 models. Residues can be edited and model geometry refined. * Simultaneous refinement and fitting - the geometry anneals as the model is fit. * 100 arbitrary background objects (ridgelines, ribbons, surfaces, etc.). * X11-based interface - runs on ordinary (inexpensive) desktop workstations in 8-bit color or black and white. * Anything on the screen can be printed with color or black-and-white PostScript. * A script language for building complicated figures or saving viewpoints with multiple objects and for saving different defaults.

ENVIRONMENT VARIABLES
CRYSTAL and XTALVIEWHOME are required. Optionally, XFITDICT can be used to specify a PDB file for residue prototypes (any high-resolution file with all 20 amino acids plus any prosthetic groups, waters, etc., you need). PWD is used to override the current directory. XFITPENTDIR gives the name of the directory containing pentamer data. It is usually $XTALVIEWHOME/data/pdbvec. You can copy pdbvec to another location and change the structures used in the pentamer database by changing this environment variable. Control of the buffering method is provided through the environment variable XFIT_DBUF. Type 'setenv XFIT_DBUF colormap' to get an image with less-than- perfect depth- cueing, or 'setenv XFIT_DBUF off' to get a better-looking image that flashes badly when you manipulate the view. See the README file in the $XTALVIEWHOME/data/pdbvec direc- tory for more information.

COLORS
xfit determines the screen depth and uses color if the depth is 8 bits or greater. The color database is loaded from ./colors.dat if available, then from $XTALVIEWHOME/data/ colors.dat. Normally, the latter is used, but for special purposes the file can be overridden with ./colors.dat. How- ever, none of the built-in default colors will make sense if ./colors.dat is completely different. This option is nor- mally used to change the shades of the colors to more favor- able ones for different display devices. For example, the author uses a separate colors.dat for making slides. A lit- tle white has been added to the red, and the blue has been made closer to cyan in order to show up better on film. SUNs with GX cards use color double-buffering to make the display 3 times faster. The drawback of this is that only 8 colors are available and there is no depth-cueing. See the previous XFIT_DBUF description under "Environment Vari- ables." Note: hardware double-buffering does not work on TurboGX machines.

MOUSE
The mouse is used for rotations and translation, picking, and model manipulation. Your mouse should have 3 buttons: <Select> (left), <Adjust> (center), and <Menu> (right). (You can change the order of these buttons by editing lines in the ~/.Xdefaults file; see an XView or Open Look manual for more information.) To pick something, click the <Select> (left) button. To rotate something, hold the <Select> button down and drag the pointer. Z rotations are done by dragging left and right in the upper portion of the screen. (On certain SGIs, the upper portion of the screen has a different color. In a future release of xfit, the cursor will change to indicate whether it's controlling z or xy rotation and translation.) <Adjust> changes purpose, depending upon the mode (indicated in the lower right corner of the screen). At startup, the program is in Center mode; drag <Adjust> to center the screen. Drag near the top of the screen to adjust the z postions. To zoom the image in or out, hold down the <Select> and <Adjust> buttons simultaneously and move the pointer vertically. <Menu> brings up a menu that can be used to change the mode. The modes Translate, Rotate, and Torsion are operative if a portion of the model has been selected for fitting. Move and Translate work by dragging <Adjust> in the same way as for <Select> (described above). For torsions, you must first pick a vector around which you want to torsion (using <Select>). Hit the tail of the vec- tor first (bond), then the head, and then select Torsion in the menu. All the atoms bonded to the head and currently selected are included in the torsion group. Dragging <Adjust> left and right torsions the group about the selected vector. Stacked torsions are not supported, although once you get used to the "click-atom, click-atom, select-torsion" routine you can change torsions quickly. (Note that the pop-up menu can be pinned for easier use). Several mouse options are available in the Control window. There are three mouse event modes: Fast, Jerky, and Skip Contours. Fast assumes the picture can keep up with every mouse event and draws each one. Jerky skips ahead to the latest event, ignoring earlier ones so that the picture "jerks." Skip Contours does just that if the picture gets behind, allowing smooth rotation to the desired view and then when the event queue is empty the contours are redrawn. Determining which mode to use depends upon the computer you are using, so some experimentation is in order. You can also use the Control window to set the size of a mouse event.

KEYBOARD SHORTCUTS
If a single residue is selected for fitting, the side-chain torsions can be set up by hitting the appropiate number on the keyboard while the mouse pointer is in the Canvas win- dow. For example, hitting 1 sets up chi1 and 2 sets up chi2. This is much faster than picking atoms and selecting Torsion. Dialbox If your computer is equipped with a dialbox, you can use them instead of the mouse to change the viewpoint. The dials are set up as follows: Rotate Y Translate X Rotate X Translate Y Rotate Z Translate Z Zoom Slab Holding down the <Shift> key while rotating a dial moves the current atoms in place of the <Adjust> mouse button.

SOME DEFINITIONS
Xfit uses an atom stack for many operations. All operations use a prefix notation. First the operands are selected and put on the stack; then the command is given. Atoms are pushed onto the stack in two ways: by picking on the screen and by picking from the atom list in the Model window. Internally, xfit uses the following hierarchy to describe models: a molecule is all the atoms given in a single PDB file. A chain is all the atoms with the chain-ID column set to the same value in the PDB file. A residue is all the contiguous atoms with the same residue-ID in the PDB file and an atom is a single line in the PDB file that begins with either ATOM or HETATM. Additionally, the user can specify a group in the model window that is an arbitrary grouping of residues. Lines derived from bonds and points are drawn on the screen. Any atoms within a specified radius in the same residue are bonded. The exception is pep- tide bonds, which are made if the N-C distance is reason- able. If two adjacent residues contain only single CA atoms, they are bonded if they are less than 4.5 A apart. The leftover points (such as water) are drawn as three short orthogonal lines, or a jack. Other polymers such as DNA and carbohydrate are not connected (well, this is a protein crystallography program...). Atoms have names such as CA or CB, an occupancy, a B-value, and x,y,z coordinates. Resi- dues contain an array of atoms and have a name such as 1 or 152 and a type such as ALA, HEM, or H2O. Chains are speci- fied by a single character. Molecules are referenced by the original filename. PDB files have a record, CONECT, which can be used to specify a bond between any two atoms. These residues are read and the specified bonds put in a special list so that these bonds are always made regardless of geometry. This is useful for connecting prosthetic groups to the protein such as thio-ether linkages or metal ligand bonds. If you make a bond in xfit, use the Bond command, and then save the model, the CONECT information is written at the end of the file and will be read the next time the model is loaded.

CONTOURING METHODS
Contours are iso-values in an electron density map. Five levels are provided in xfit. The map is scaled such that one sigma is equal to 50. The startup contour levels are 1,2,3,4,5 sigma and can be adjusted later. The contouring algorithm is fast but not always pretty (for instance it makes no attempts to resolve saddle points). To make the contours prettier, use a finer map. Three times the maximum h, k, and l are usually about right. (The maximum index can be found from (cell edge)/dmin). If you have one long axis, then this one can be made twice and will still look fine. A large number of contours can slow rotations. One useful option is to select the Skip Contours option in the Control window. This causes the program to skip drawing contours if it cannot draw the contours between mouse events and then re-draw them when rotations stop. Since the model is usu- ally being used as a guide to the eye for rotations, drag- ging the map along is not always necessary. In this way, you can speed up rotations considerably. Contouring Method in the Contour Map window may be set to "Cube," "Sphere," "Different Axes," or "Blob." The first three methods define the density as bounded by a cube, sphere, or oblong box, respectively. "Blob" (the name derives from an old program of Colin Broughton's that could draw either a box-shaped or a blob-shaped map) specifies the density to be rendered as being within a specific radius of any of the current atoms. (The blob map changes whenever the current atoms change. This is useful when one wants to con- fine one's attention to density near where one is fitting; but to preserve a blob map, one should make a vu object from it.) "Cube/Sphere Radius" specifies the radius of the sphere for the Sphere method, or the half-width of the cube for the Cube method. A Axis, B Axis, and C Axis specify the dimen- sions for the Box method. "Extend blob around current atoms by" specifies the radius for the Blob method.

RIDGELINES
If you have access to GRINCH, use the mkskel program to pro- duce an ASCII ridgeline file or use the ASCII 'save filename' option in interp. This file can then be converted to a form usable by xfit with grinchbones (see the grin- chbones man page), and is read in as a vu file. Xskel is an interface to mkskel and produces output that can be read directly inthe File window. For xskel to work, you must have a copy of mkskel, whose location is included in your PATH variable. You can also interactively change the contour level and box size. To pick an edge, set the Pick mode to edges. To color an edge, select the type you want to color the edge, select the Color Edges Pick mode and then pick the edge you want to color. An entire side chain can be colored at once by setting the pick mode to edges, then pick an edge to place it on the stack and then push Color Side Chain. The last color side chain can be undone with the Undo Color but- ton. The regular model building features of xfit can be used to build models over the ridgelines.

BACKGROUND OBJECTS
To build complex background objects, layer individual vu objects in the View window. Each vu object can be turned on and off using the Show window. For example, you can make a vu object with side chains and another with mainchain. The sidechains can then be blinked on and off by clicking on the appropriate line in the vu list. Individual residues of interest can be colored individually. Multi-colored objects are composed by building up from individual pieces. Objects with a higher number overdraw lower-numbered objects. Models overdraw vu objects, so turn off the model to see coincident vu objects. Hint: Use several individual objects instead of a few com- plicated objects.

COLORING
1. Pop up the Color window. 2. Select a color by clicking on it. 3. Select the correct object (if necessary). 4. Apply the color by clicking on the appropriate button. (This sets the object to the current color.) There are two places where the option color C* only is given. This means that only the carbon atoms are colored and the others are colored by atom type in the usual way (i.e. N is blue, O is red, H is white, Fe is brown, S is yellow). In addition, in the view window the option color-by-B-value is given. In this case the coloring is according to B-value in the same way as described for normalized B-values in the section on colorbyB. In the color window you will see 4 shades of each color. This lets you see the effect of deth-cueing on the color. On 8-bit machines these are the depth-cueing colors. A line is drawn in 4 different intensities depending upon its average z-value. On 24-bit machines the line is depth-cued by interpolating from the front to back. Colors.dat con- tains 4 intensities for each color. For instance, for red there are four entries: red, red1, red2, red3. To change the depth-cueing you change the four colors where red is the foreground and red4 is the color of the farthest point. This is probably best done by a computer program from a file containing just one entry for each color. Each color display works best with a different amount of depth-cueing. Postscript coloring is always done in terms of RGB triples, and the color for the foreground is taken from colors.dat. Depth-cueing is done by multiplying the rgb values by a scale factor from 0.25 to 1. The value 0.25 can be changed in the control window. The author has found that different color PostScript devices work best with a different value for the minimum. For instance, the dicomed slide maker needs a value of about 0.1 and the QMS-100 color printer works better with about 0.3.

LEAST-SQUARES FITTING
This can be used to superimpose two models or portions of the models, as a comparison tool, or to speed up fitting. It "roughs in" the model using edited residues with only CA or CA and CB residues (put these in the dictionary with a type such as CBA). Then standard protein pieces such as alpha- helices, beta-sheets, tight-turns, etc., are read in as extra models (up to 49 of these, plus your working model) and then least-squares-fit to the markers. Overlaps are deleted and then read out and concatenated to form the whole molecule. The initial geometry will be better, giving a faster refinement. More complicated fittings that use unconnected segments can be done with the program pdbfit instead, and then loaded into xfit.

FFT
xfit includes a reworked FFT routine from Lynn Ten Eyck that provides a fast way to calculate electron density and struc- ture factors. The electron density calculation is done with the FFT pop-up and structure factors are calculated on the sfcalc pop-up. The FFT pop-up can be used to calculate electron density directly from structure factors using coef- ficients such as Fo, Fc, Fo-Fc, 2Fo-Fc. It is usually fas- ter than reading a precalculated map file and lets you rede- fine the grid and the resolution range at any time. The same phase file can be used to make both an Fo-Fc and a 2Fo-Fc map. It also saves a lot of disk space. Say good- bye to map files! The whole unit cell is available, so there is no need to worry about map boundaries. Note: Make sure the correct crystal is specified beforehand! Structure factors can also be calculated by FFT. In this case the only information needed to make maps are the Fo's and the coordinates of the model. Make up a phase file with h k l Fo 0.0 0.0 and read this in. Make sure the correct crystal is selected before reading. Then use the sfcalc window and select "calculate all and scale". You can now make omit maps and update phases. There are two ways to calculate structure factors: FFT and summation. FFT is fast and introduces an error typically about 1%. In general this is the way to go. The only time the summation is faster is if you are doing a single atom. The FFT is done in two parts: first, a model of the elec- tron density is built from the atom coordinates and their structure factors; then this map is inverted by FFT. The FFT is very fast, and for the entire model the rho building step takes the longest. However, for a single residue the rho building is very quick and the entire FFT time is less than the corresponding summation time. The only instances in which summation is needed are when extreme accuracy is needed (given the error in our coordi- nates, we can't see when this would be needed) and if there isn't enough memory to build the entire unit cell's rho. Note: In centered space groups it is common to not calcu- late the centered symmetry operations to save computer time. If this is done, Fc will be lower than absolute scale. For instance, in C2 the Fc will be half of its correct value. Use the full symmetry operators as is the case if you use the crystal editor with xtalmgr.

OMIT MAPS ON THE FLY
To make an omit map, select the atoms to be omitted (see "How to Select") and then select the omit current atoms option in the structure Factor (sfcalc) window. Structure factors are calculated for the currently selected atoms and subtracted from the model structure factors. Then use FFT to make either an Fo map or a 2Fo-Fc map. This assumes that you have read in some phases and that Fc has been previously calculated on an absolute scale (Fo is scaled to Fc). This can be done using Calculate All and Scale. Note: Partial models (such as missing residues or waters) cannot be used to make omit maps with Fo-Fc or 2Fo-Fc maps because the relative scale of Fo to Fc is incorrect. Instead, use Fo maps. This is also true of models that still have a large amount of error where Fc is still inaccu- rate (i.e., R-factors above about 0.25).

UPDATING PHASES ON THE FLY
As you move the model, its phases change because they are calculated from the atom positions. You can either re- calculate the phases from all of the model using sfcalc.calculate_all_and_scale, or you can update just the portion being fit (which is much faster). In this case, after you move the currently selected atoms you can select sfcalc.update_current and then re-FFT the map. Update All subtracts the old position from the phases and then adds the new position. As the residue is moved you can calculate the corresponding map and compare it. For example, if there are two likely positions for a side chain you can move it to both positions and see which matches its corresponding map best. When you are finished fitting, select update current just before applying the fit to match the map.

DIFFERENCE MAP GRADIENT
At the bottom of the SFCalc pop-up is a section used for calculating the gradient of the difference density at an atom. This is represented as an arrow in the direction of the gradient scaled to its steepness or magnitude. It shows the direction an atom will move in the first cycle of a crystallographic refinement. The command implements the equations in Stout and Jensen, 2nd ed. pg. 349. It is useful for such things as analyzing mutants to look for the direction of movements and to look for concerted movements of groups of atoms. It uses a slow summation method if res < 3 and uses FFT if res > 3, so can take quite a long time for large numbers of atoms. You must first load some phases. The command works on the map currently selected at the top of the window. Set the Deriv vu number to a free vu object. The Sign of Delta is usually Fo-Fc, but to reverse the direction of the arrows select Fc-Fo. The Scale Arrows x 100 slider sets an arbitrary scale for the length of the arrows. To start the calcula- tion, select the Derivatives of Current Atoms button.

SELECTING A MODEL
A model is selected for fitting or structure factor calcula- tion by first putting the appropriate atom(s) on the stack and then selecting one of the fit options. To put an atom on the stack, pick it on the screen or select it in the Model window (see below). If you push Atom, the atom on the top of the stack is selected. If you push Atoms, all the atoms on the stack are selected. Residue selects the entire residue that contains the atom on the top of the stack. Residues selects all resi- dues that contain an atom on the entire stack. Group selects all the residues in the same group as the residue containing the atom on the top of the stack. Groups are set in the Model window. Molecule selects the entire model. The selected atoms are referred to as the current group. Bond- ing is irrelevant. Use the Clear Stack button before setting up atoms or resi- dues. If you are dissatisfied with your selection, hit Can- cel. Reset puts you back to your starting positions, and Apply commits your fit. You can undo the last 20 fits by pressing Swap. When Model is selected for fitting, its old positions are saved in one of 20 slots. Select the slot containing the model to be undone and then Swap will toggle between the saved and fit model. Judicious users will still save their model to disk often with the Save button.

SHOW WINDOW
Objects can be hidden by selecting them on the list in the Show window. Useful information about each object is also given to identify it. A difficult-to-identify object can often be found by toggling it on and off. Hide all objects that are not needed to increase the rotation speed. Object blinking is set up here (see Blinking, below). Also, con- tacts can be cleared in this window.

CANVAS WINDOW
Objects are draw in the Canvas window. On SGIs and SUNs with XGL, the Canvas menu in the main window has two options: Accelerated Canvas and PostScript Preview Canvas. Accelerated Canvas is the default. The two canvases differ in the following ways: * The Accelerated Canvas has faster graphics. * On SGIs that support z-buffering, the Accelerated Can- vas is z-buffered. In the PostScript Preview Canvas (and in actual PostScript output), models are always drawn in front of density maps. In the Accelerted Can- vas, the model and the map are interlaced. * The z-clipping of the picture is different. In the Accelerated Canvas, if a vector crosses a z-clipping plane, the part of the vector lying inside the clipping box is shown. In the PostScript Preview Canvas (and in actual PostScript output), such a vector appears either in its entirety or not at all, depending on whether its midpoint is within the clipping box. In both canvases, part of a vector will appear if the vector crosses an x- or y- clipping plane. * Line thickness depends both on the canvas and on the platform. The line thickness of an object is 1, -- in the PostScript Preview Canvas on both the SUN and the SGI, multiplied by 2 if it's the active model; -- in the SGI Accelerated Canvas, multiplied by 2 if it's the fragment of current atoms; -- in either SGI canvas, multiplied by the Line Width set for that object in the Files->Plot menu. * In actual PostScript output, line thickness is the same as in the SGI PostScript Preview Canvas. In the SUN Accelerated Canvas, the thickness of everything is always 1. * Depth-cueing in the Accelerated Canvas is controlled with the Depth Cue slider in the Control menu. Depth- cueing in the PostScript Preview Canvas (and in actual PostScript output) is controlled with the Depth Cue slider in the Files->Plot menu. A ruler is drawn at the bottom of the screen with the scale in Angstroms. Objects can be dragged over to the ruler for measurement. In the upper is a gnomon that shows the laboratory axes. In the lower right, a small advertisement appears. The <Menu> button pulls up a menu that can be pinned and left up permanently if desired. By using the pull-up menu, you can avoid con- stantly moving back and forth between the screen and a side menu. The menu items are: Center at pick Centers at the last atom or edge picked. Center mode Puts mouse in center mode where ADJUST (middle mouse button) moves the center of screen. Translate mode Current atoms can be translated with ADJUST. Note the difference between this and center - they are easily confused. A common mistake is to forget to go back to center mode to move the screen center. Rotate mode Current atoms can be rotated with ADJUST (middle mouse button). Torsion mode Two ends of a current bond are first picked. The atoms attached to the second end will become a group that can be torsioned around the selected bond. The atoms must all be in the current group. Contour Contours at the center of the screen using the values in the contour window. Atom Selects the last-picked atom. Atoms Selects all of the atoms in the stack. Residue Selects the residue to which the top atom belongs. Group Selects the group to which the top atom belongs. (Groups are set up in the model window.) Molecule Selects the entire molecule of which the top of the stack is a member. Rotate X clockwise 90 degrees Rotate X counter-clockwise 90 degrees Rotate Y clockwise 90 degrees Rotate Y counter-clockwise 90 degrees The two rotate Y commands are especially useful for centering an object in density. First center in one view then rotate Y 90 to fix the third direction and then rotate Y -90 back to the starting view. Rotate Z clockwise 90 degrees Rotate Z counter-clockwise 90 degrees Toggle stereo Toggles stereo mode.

MOUSE FUNCTIONS IN THE CANVAS WINDOW
Use the <Select> (left) mouse button to: Click Pick atom Drag Rotate view x-y Drag top of screen Rotate z Drag + <Shift> Zoom Drag + <Ctrl> Rotate Z The function of the <Adjust> (middle) mouse button depends upon its mode, which is set with the <Menu> (right) mouse button. The default translates the view. The <Menu> (right) mouse button brings up the fitting menu to rotate, translate, and change torsion. It also allows you to change the mode of the middle mouse button to allow fit- ting of the currently seleced model. Center restores the Translate View mode. To scale or zoom the view, press the left and middle mouse buttons simultaneously.

KEYBOARD SHORTCUTS
You can use the pointer in the Canvas window for the follow- ing keyboard shortcuts. i Zoom in O Zoom out H/L Rotate y U/N Rotate x J/K Rotate z R Rocking ON r Rocking OFF x Look down x axis y Look down y axis z Look down z axis S Turn side-by-side stereo ON s Turn stereo OFF <ESC> Toggle hardware stereo If a single residue is being fit, use the following keyboard shortcuts. 1 Set up torsion CHI1 2 Set up torsion CHI2 3 Set up torsion CHI3 4 Set up torsion CHI4 5 Set up torsion CHI5 To center on an atom, pick the atom and then choose Center @ with the <Menu> mouse button. To go to a specific x,y,z, open the View window, edit the center, and click on Set View.

LABELS WINDOW
Labels can be controlled and edited in the Labels window. (The Control window contains the control for labeling picked atoms or not.) For an arbitrary label, pick an atom near where you want the label to go and then pick the atom. The new label will show up at the bottom of the list in the Label window. Select the label in the label list. You can then edit the fields for the label string and its offsets in x and y; then select Replace. The offsets in x and y are pixels from the x,y,z coordinates of the label that are independent of the rotation matrix and the scale. To delete a label, select it on the list and click on Delete. To remove all labels, select the appropiate command in the main window. To edit a label, select it on the list, edit the field you wish to change, and then select Replace. New labels can be entered here. The current center can be popped and used for an arbitrary label. You can also set the label style and select the point size of the labels when plotted. All labels will have the same size. The pixel offset on x and y is useful for moving labels into clear space so they don't overlap other objects. When labels are plotted, a drop shadow is plotted around them to make them stand out if they do overlap other objects. A "contact distance" label changes to reflect the current distance as the model moves. It is not editable. See "Con- trols Window" for more information.

CONTROLS WINDOW
Several miscellaneous controls are located in this window. Mouse Damping controls how far the model rotates with a mouse movement. The drawing mode Fast draws every mouse event. If the computer is taking too long to draw each event, then the model may keep moving after the mouse has stopped. The Jerky mode will prevent this by skipping ahead to the end of the event queue. (This mode does not work well on some SGI machines.) The Skip Contours mode will skip drawing the contours if the event queue gets too long. This allows the model to be rotated into position and then the contours will re-draw when the event queue empties. The Pick mode defaults to only picking the active model. This allows picking of superimposed models by locking the others out. In the Pick All mode, the closest atom is picked. If two atoms are in the same position, then the last one in the display list is chosen. The Pick mode is also controlled by a toggle in the Ridgelines window, which switches the Pick mode from Model to Ridgelines. To pick symmetry related edges, the mode must be All. The Symmetry Radius controls the size of the box searched for symmetry- related atoms. Making this very large will slow things considerably, since the volume increases as a power of three. The Rocking Range and Rocking Rate are controlled in this window. Xfit uses a timer that is supposed to be machine- independent, but it actually isn't; therefore, the Rocking Rate is different on different machines. The Depth-Cueing slider controls how thin the back lines are relative to the front lines when plotting in the depth-cued mode. It also controls the percent saturation of the back color to the front color when plotting in the Color mode. Contacts are also controlled in this pop-up. A contact is a dashed line drawn between two atoms with the distance at the mid-point shown in Angstroms. You can turn on/off drawing contacts whenever the distance function is used. You can also enable contacts to be drawn for picked atoms. A max- imum radius for this search can be set. The mode can be Off, all atoms within the specified radius (All), or only between atoms in a different residue (Inter-Residue). As the model is fit, these distances will update.

BLINKING
The Show window contains controls that allow you to set up two blink groups and then alternately blink them on and off. First, highlight all the groups you want in one set and make sure the others are unhighlighted. Then select Set Group 1. Now, unhighlight group 1, highlight group 2, and select Set Group 2. Objects not included in either group will not appear. Objects in both groups will stay on all the time. You can turn on and off blinking and you will not need to reset the groups unless you want to change them. The speed of the blinking is set on the Control window.

REFINE WINDOW
The Refine window is split into two parts. The upper part is for real-space refinement and the lower part is geometry refinement (early versions of xfit lacked geometry refine- ment). In real-space refinement, you select the map to refine the active model against. You can select Transla- tional, Rotational, or Torsion search. The torsion must be already selected or nothing will happen. In good cases, the model will be moved in the mode specified until the sum or electron density at each atom is maximized. This works well for torsion searches with only one axis (i.e., Phe works well but Arg does not) to search. Translate and Rotate often try to move into density that is connected but already belongs to another atom (i.e., the neighboring residue). Geometry refinement (minimization) can be done in two ways. The entire model can be refined by simply selecting Refine Active Model. Be sure to save the model first, since this cannot be undone. The ideal bond distance and angles are taken from the resi- dues in the dictionary file (see below) by using them as guides. This is done to allow different ideal lengths for different refinement packages. Also, this allows one to have all hydrogens, no hydrogens, or partial hydrogens. The resi- dues in the dictionary should be refined by the refinement program you are using. This will then maximize the agree- ment between xfit and the refinement program as to correct geometry. Planes are specified in the geometry file with the PDB extension record PLANE. This specifies the residue type and the atom types in the plane. For example: PLANE ASP 4 CB CG OD1 OD2 Since planes are supposed to be flat, it is not necessary to specify the ideal value. Connectivity is assessed by a variety of criteria. First, if in the original PDB file a TER record was found, this marks a C-terminus and no attmpt will be made to form a pep- tide bond. Second, if the 'chain id' letter changed while scanning the file, this also marks a C-terminus. Third, if the residues have recognizable names such as an amino acid (e.g., ALA, Ala, ala, or A), then a search will be made for the proper atom types for a peptide bond and plane (CA, C, O, +CA, +N, [+H]) and if the N and C atom are within 5.0 A, a peptide bond, angles and plane are formed. The algorithm for drawing lines representing bonds is dif- ferent and less stringent in order to speed up rebuilding of lines for display purposes. If incorrect bonds are drawn on the screen, they will NOT show up in the refinement. The second refinement method is to refine a portion of the model. Click on (or select) an atom in the model window and put two residues on the stack. Now use each of the pop but- tons to get these two residues in the Start At and End At fields (you cannot type these values in). Then select Set Up Refinement Residues and the selected residues will be highlighted on the screen. When you press Refine, a round of refinement will be done. If you select the Refine While Fitting option, then the selected portion will be refined in the background while you fit. You can then select a residue for fitting within the segment being refined, and as you move it around, the rest of the segment will follow along and the geometry will anneal as you fit.

DICTIONARY
The dictionary file is simply a PDB file with an example of each residue. If the environment variable XFITDICT is set then this file is loaded upon start-up as the dictionary. The dictionary can also be loaded and appended to in the File window. This is not used as a geometry file. New residues are found by finding the first residue in the dic- tionary that has the same name. When a residue is replaced a residue of the same new type is found in the dictionary and least-squares-fit to the old one. The standard dic- tionary is in $XTALVIEWHOME/data/dict.pdb. The dictionary can be appended to upon loading, or replaced. The append mode allows you to add a prosthetic group without having to mess up the the standard dictionary. The first residue in the dictionary is used if there are multiple copies. All of the unique residues in the dictionary appear in the the model window from a pull-down menu button to the right of the residue type field. Selecting one of these names puts this value in the residue type field and can then be accessed with the insert commands.

SCRIPT COMMANDS
xfit can accept commands from a script file. The script commands can substitute for many of the interactive opera- tions, and some operations can only be done from the script. One use of the script is to return to a given view. The Save View command writes a script file that when run returns xfit to a given viewpoint. Load View is just another method of running this script. Another common use is to build complex figures with many parts. The script also gives more control over line-widths, allowing different widths to be set for each object. There are also some animation commands such as 'roty' that rotate the view around y. The script window can be accessed from view.edit_script. Scripts can be run and edited by loading them into the Script window. The script can be altered and then re-run to see the effect of the edits. Every time the script is run, it is first saved and the old script moved to file.script% (the filename with a % added). Scripts can also be loaded from the command line if they have the extension '.script' or '.vp' (for viewpoint), at which time they are run. For example, the command 'xfit my.pdb save.vp my.map' will load the PDB file, switch to the new viewpoint in save.vp, and load and contour the map. The size and location of the canvas can also be saved. A line starting with '#' is interpreted as a comment. GENERAL COMMANDS crystal value loadpdb modelnumber file loadpdbcenter modelnumber file loadmap mapnumber file load fsfour format maps loadmapphases mapnumber file load map phases (follow with fftapply) plottofilecolor file plottofileb&w file plottofileb&wdepthcued file plottoprintercolor printer plottoprinterb&w printer plottoprinterb&wdepthcued printer OBJECT BUILDING COMMANDS color value This sets the current color. The value is either the xfit number or a name; i.e., yellow is 56 or "yellow." Buildvu uses the current color to paint its lines, so set the color first. colormodel modelnumber model modelnumber is recolored to current color colormodelatom modelnumber as above except that atoms are colored by atom type except C* atoms which are set to current color vulinewidth value sets the line width in plotted output for all subse- quent buildvu commands buildvu key modelnumber vunumber first_res last_res chainid atomfilter use * to indicate any. atomfilter should be separated by commas (i.e. "CA,CB,C,N,O") key is one of: side = protein sidechains main = protein mainchain other = non-protein all = side, main, and other link = link CAs peptide = peptide planes hbond = H-bonds Object Building Example: build the backbone of model 1 and show 2 key residues: color red Buildvu link 1 1 * * * * # links CA's of model 1 color green buildvu side 1 2 18 18 * * # side chain of residue 18 in green buildvu side 1 3 218 218 * * # side chain of residue 218 in green VIEWPOINT TRANSFORM COMMANDS zoom value frontclip value backclip value translate x y z rotation vxx vxy vxz vyx vyy vyz vzx vzy vzz the way to get this is view.save to a file and then read in the file to the script editor transform the viewpoint commands don't take affect until transform is given so that all transformations are applied at once rotx value roty value rotz value These take effect immediately - they are used to make "movies." stereo on stereo off canvasrect left top width height This sets the position and size of the canvas window. The first two set the position of the upper left corner of the window and the next two set the width and height. The units are pixels. SHOW AND HIDE OBJECTS showmap mapnumber hidemap mapnumber showmodel modelnumber hidemodel modelnumber showvu vunumber hidevu vunumber bond modelnumber1 resid1 atomid1 chainid1 modelnumber2 resid2 atomid2 chainid2 draws a line between two atoms. chainid can be * ATOM LABELING COMMANDS labelpoints value sets the point size of label in plotted output labelstyle value sets the label style according to: 0 = GLU 100 CA 1 = GLU 100 2 = GLU 3 = 100 GLU CA 4 = 100 GLU 5 = 100 6 = CA 7 = none atomlabel modelnumber resid atomid chainid forms a label of the type set by labelstyle (default 0) MAP CONTOURING COMMANDS maptocontour mapnumber sets the map to contour for all subsequent commands a map load will overwrite contourlevels value levels are turned on and off by adding numbers as fol- lows: 1= level 1 2= level 2 4= level 3 8= level 4 16=level 5 thus to turn on levels 1 and 3 only is 1 + 4 = 5. contour1level value contour2level value contour3level value contour4level value contour5level value contour level _x_ at value contourradius value contourcolor value set level value of the current map to the current color contourmap contours current map at current center FFT COMMANDS resmin value resmax value coefficents value Note misspelling. Value is one of the following: Fo Fc 2FoFc Fo-Fc Fo*Fo Fo*fom 3Fo-2Fc fftnumber mapnumber fftnx value fftny value fftnz value fftapply COMMAND SCRIPT EXAMPLE 1:

# This script was used to make two electron density

# maps with and without figure of merit weighting to

# illustrate the difference

crystal cvccp

# make the model thicker than the map to aid in

# distinguishing

maplinewidth 0.7

modellinewidth 3.0

loadpdb 1 cvccp.topdb.pdb

#the viewpoint lines are from the save viewpoint option

translation 24.965 34.205 68.649

rotation 0.6916 -0.3000 0.6570 0.6543 0.6455 -0.3941 -0.3059 0.7024 0.6427

zoom 31.10

frontclip 4.60

backclip -3.30

stereo on

transform

#load the map phase and transform

loadmapphases 1 cvccp.mir.phs

resmin 3.0

coefficents Fo

fftapply

# set the contour options and contour the map

contourlevels 1

contour1level 50

contourradius 10

contourmap

plottofileb&w mir.fo.ps

# change the coefficients of the FFT and compute a second map

coefficents Fo*fom

resmin 3.0

fftapply

contourlevels 1

contour1level 50

contourradius 10

contourmap 1

plottofileb&w mir.fofom.ps
COMMAND SCRIPT EXAMPLE 2:

# this example builds up vu objects. A backbone of

# the A chain is built and then particular side chains

# are displayed and labeled. If a mistake is made it

# is much easier to edit the script than to start over

# in interactive mode. Also the script can be saved

# to re-make the figure at a later time.

stereo on

loadpdb 1 cvccp.pdb

labelstyle 1

hidemodel 1

color 56

vulinewidth 2.0

buildvu side 1 1 * * A *

buildvu main 1 2 * * A *

buildvu other 1 3 * * A *

vulinewidth 0.9

buildvu side 1 4 * * B *

buildvu main 1 5 * * B *

buildvu other 1 6 * * B *

atomlabel 1 16 CG A

atomlabel 1 16 CG B

atomlabel 1 18 CB A

atomlabel 1 18 CG B

atomlabel 1 132 C1A A

atomlabel 1 132 C1C B

atomlabel 1 21 CD1 B

atomlabel 1 21 CZ3 A

translation 30.810 34.796 60.196

rotation 0.8504 -0.5256 -0.0256 0.5256 0.8507 -0.0075 0.0257 -0.0071 0.9996

zoom 19.8

frontclip 2.60

backclip -8.10

transform

MODEL WINDOW
The currently active model is listed in the Model window. When a residue is selected, the atoms in that residue show up in the atom list. When an atom is picked in this window, it is put onto the atom stack. It can then be used for stack-based operations such as 'center' or 'distance.' This is the quickest way to center on a particular residue. When a residue is selected, it is highlighted and becomes the focus residue. Its information is listed in the bottom of the window in the Type and Name fields. Several residues can be highlighted, but only the last one is the focus resi- due: the one that is in the lower fields. Highlighted resi- dues can be grouped together in a single group. An entire group can be moved as a unit after being selected (see above). A group number above 0 must be chosen, since 0 means ungroup. Before selecting a group, it may be wise to clear all selec- tions to prevent residues that have scrolled off the list from being accidentally added. Residues may be deleted with the Delete button. They can be undeleted at any time by hitting Delete again. The only way to clear the list of deleted residues is to write the model out and read it back in again. The Insert button has a pull-down menu with a number of features. You can insert a new residue before and after the focus residue: First select the insertion point; then edit the name and type of the residue. All of the types in the dictionary will be listed in the pull-down menu at the end of the Type field. Then select Insert.Before or Insert.After. The new residue will appear in the center of the screen. Insert.Replace is similar, except the new resi- due is least-squares fit to the focus residue and the old residue is deleted. Thus, a replace can be undone by undeleting the old residue and deleting the new residue. At the end of the Insert menu is a Pentamer pull-right menu. If it is grayed out, the pentamer information and programs have not been installed (see above). The pentamer option allows least-squares fitting a pentamer with one that has the closest geometry from a list of well-refined structures. The middle three residues can then be replaced with the pentamer residues. The only atoms that need to be in the target pentamer are CA atoms. The quickest way to build a protein model is to place single CA atoms (type 'MRK' in dict.pdb) in the density. Keep the CAs in order as much as possible, since their order matters for the pentamer fitting. Pick the first residue of 5 con- tiguous residues in the residue list and then select Insert.Pentamer.Best_fit_pentamer. A pentamer should appear as a separate model least-squares fit to the target resi- dues. If possible, select Insert.Pentamer.Replace_middle_three to replace the new residues in your model. The side chains of the new residues will be whatever was in the structure data- base. You then replace these side-chains by picking the residue to be changed in the residue list, selecting the correct type with the little pull-down button by the Type field, and selecting Insert.Replace. The side-chain is then torsioned into its density.

VIEW WINDOW
This window is used for controlling the viewpoint and for building alternate representations of the model. At the top of the window are the viewpoint matrices at the time when the View button in the main window was selected. It does not update as the model is turned, as this would seriously impede performance. Instead, you must select the View but- ton again to get the current matrices. The views can be saved and loaded from a file. The viewpoint is saved as script commands, which can be copied into a script. Also, the Load command actually just runs the script command on the file so that you can add other script commands to the viewpoint file if you wish. You can move to a specific x,y,z by entering these into the Translaton field and selecting Transform. It is less likely that the rotation matrices can be successfully entered and produce a useful result, as errors will distort things severely. Note that the script commands for the rotation are the same as those used by the program MOLSCRIPT, by P. Kraulis. The translations are of the opposite sign. Plane View splits the view into the standard viewpoint in the bottom half and the top view in the top half. This is useful for docking operations because you can see and con- trol all three axes and translations at once. (This option is not available for all display devices/modes.) Stereo turns Split Stereo on and off. The stereo can be made either cross-eyed or wall-eyed with the angle slider. The separation can also be controlled. The separation can be changed better by scaling the Canvas window width. You can also select left- and right-eye-only views. These are used for making stereo slides for photography purposes. If hardware stereo is supported, then there will be a fourth selection available: Hardware. On SGIs this is done using Crystal Eyes or StereoVision glasses. As they do not work well with windows, xfit rearranges the windows to work best with these glasses. When the <ESC> key is hit the windows return to their origi- nal positions. You can then edit the model, load files, and return to stereo viewing again. The canvas menu is avail- able in stereo, and a number of functions are available from it so that going in and out of stereo can be minimized. Picking is less reliable in hardware stereo due to percep- tion problems; therefore, it is best done in less crowded views. Make Script and Edit Script are used for script commands (see above). Make Script generates a script that returns you to where you are. It will load models and maps and restore the viewpoint. Unfortunately, becuase the original order in which these operations are done makes a difference, the resulting script file may need to be edited in order to get back what you have. It provides a great starting point, though, for complicated figures. The biggest problem is that loading a model changes the screen center. All model loads should be done before viewpoint commands. The Edit Script window allows you to edit the script and rerun it. To save the script, use the <Menu> mouse button while in the Editing window and select File.Save_New. Below this are the controls for build vu. This is a very versatile and useful command. Select which model you want to build the vu object from and between which residues. use. The default is to use all of the model. Then select one or more options. The syntax for setting an atom filter is a list of names separated by spaces, such as "CN CA O," which is the same as the Mainchain option (actaully, Mainchain also requires a peptide). An asterisk can be used as a wild card, meaning that the rest of the name does not matter; that is, C* matches C, CA, CB, CG1,..., CG* matches CG1, CG2,..., etc. In xfit, the model is never changed for viewing purposes. Instead, a vu object is built and the original model is hid- den if desired. If you want to have seven side chains, all different colors, then seven vu objects are built. Up to 200 vu objects can be built. Long lists of vu objects can be saved in a single file and read in as a single vu object later. By this means, you can overcome the 200-object limit. The script command "buildvu" corresponds to these controls. However, if use a script, you can edit your mistakes without starting over. You can edit the file, run it with "xfit file.script" to find any errors, fix them in the Edit Script window, and rerun the script. To save this, press the <Menu> mouse button in the Scipt Editing window and select the Textpane menu. The other advantage of using script commands for building vu objects is that you can change the line width between objects. Although you can't see this on the screen, the different widths show up when you plot it. This is very useful for making black-and-white publication figures in which two objects must be clearly distinguished.

PLOTTING
The current canvas can be plotted to a Postscript file or printer using the Plot command in the Files window. Enter the name of the printer or file and then select one of the two options in the pull-down menu (selected using the <Menu> mouse button on the Plot button). A number of printing options can be set in the Properties window, including Portrait and Landscape. Additional infor- mation can be plotted as a second page using the Stats On/Off option. This will add a second page with the viewpoint, the names of the objects used, and the map lev- els. You can select to plot in color mode, black and white, and black and white with depth cueing. In the depth-cueing mode, the width of the line indicates the distance from front to back (objects in back are thinner). Color is very useful for making slides that can be sent to a commercial slide service. The advantage is that the expo- sure is always right and the resolution is usuaully much higher than on the screen. The disadvantage is that the screen colors and the slide colors may differ substantially. Blue shows up especially dark on slides, so use cyan instead. The PostScript file can be edited if desired: it is a list of PostScript commands set up for easy editing. Each object is bracketed by a "BEGIN type # name" and "END." You search for each object by looking for the string "BEGIN." The most commonly edited field is the linewidth. You can also edit the "setgray level," in which 0 is black, 1 is white, and 0.5 is 50% gray. The labels are at the end of the file. It is common to want to move labels around a bit to prevent them from overwriting other objects. Objects in the file are drawn starting from the beginning of the file and going to the end. Thus, a later object overwrites an earlier one. You can change the order in the file if you wish. Labels have a shadow drawn around them so they will be readable even if they fall on an object of the same color.

MEMORY
xfit uses dynamic memory allocation for virtually every- thing. The only limits are the size of memory available in your machine (including swap space) and the largest number representable by an integer on your machine. If you get "out of memory" or "cannot allocate errors," close all unused windows. Every open window takes up memory. Next, re-read over objects that are not being used instead of creating new ones and hiding the old ones. Re-FFTing a map with a coarser grid can free up a lot of memory. If performance becomes sluggish, suggesting swapping (often you can hear your swap disk chuckling merrily away), then more RAM may be the answer. The cheapest way to speed up your workstation may be to invest in more memory. The author gets good performance with 32 Mb. Less than 16 Mb is not recommended. If you are calculating structure factors by FFT, then at least 32 Mb is needed. Most workstations are set up with small swap spaces, which becomes a liability later. If you have a choice set up at least a 100 Mb swap space.

MORE ON COLOR
It is advisable to modify only the color shades in ./colors.dat. For instance, red may be modified to add some white. It is possible to customize the colors completely if you have a minimal knowledge of the C language, rewrite colors.h and ./colors.dat, and then recompile. The colors occur in groups of 4, which are used for depth-cueing on 8- bit color systems. To change to degree of depth cueing from front to back, it is possible to change ./colors.dat to give more or less saturation.

IMPORTING OTHER FILE FORMATS
Vu files Any arbitrary line information can be loaded with a vu file. The format is lines of: x1 y1 y2 x2 y2 z2 color where x1,y1,z1 and x2,y2,z2 are the end points of a line and color is either an integer to a corresponding entry in colors.dat (see the footer message in the Color window) or an ASCII name such as "red," "yellow green," or "white." Hint: break long lines into short segments so that they will not be completely clipped when the viewport is small. A "#" as the first character in a line is interpreted as a comment. MS surface file (.surf) Surf files can be converted to .vu files with awk: awk '{ print $5,$6,$7,$5,$6,$7," white"}' file.srf > file.vu This command prints the 5th, 6th, and 7th fields of the surface file twice and adds a color. Since the begin- ning and end of the vector in the vu file are the same, a dot the size of a single pixel will be drawn at the position of the surface point making a "dot surface". Other 3D Arrays Arbitrary 3D arrays can be loaded into xfit by refor- matting them into a map file. These can then be con- toured as if they were electron- density maps. A corresponding crystal entry will be needed. To write this array, you will need to use the information in Chapter 4 of the XtalView User's Guide, "Programming XtalView." One limitation is that the map is assumed to start at 0,0,0 and extend for one cell edge in each direction. This may mean making an array bigger than is needed and padding it with 0s.

PDB FORMAT EXTENSIONS
The extensions to the PDB format use a new keyword as fol- lows. Plane PLANE res_type number_in_plane atom_name1 atom_name2 ... For example: PLANE GLU 4 CD CG OE1 OE2 This specifies a group of atoms to be restrained in a plane. The maximum number of atoms in a single plane is 20. If you need more, then use multiple overlapping planes. For convenience, the PLANE entry is usually put next to the corresponding residue and a leading minus sign references the previous residue. Thus, a peptide plane is specified as: PLANE PEP 6 CA C O +N +H +CA Synonym SYNONYM res_type atom1 atom2 For example: SYNONYM ILE CD CD1 This equivalences two residue names so that you can use either one in the PDB file. The most common example is "ILE," where "CD" is often called "CD1." In this way, you can use either name and not have a conflict with the xfit dictionary. Torsion TORSION res_type angle_id atom1 atom2 atom3 atom4 For example: TORSION ARG PHI C- N CA C TORSION ARG PSI N CA C N+ This specifies a 4-atom torsion. These are not res- trained, but are used for identifying torsions in resi- dues for fitting purposes. Note the use of a trailing plus or minus sign to indicate the next and previous residue, respectively. Future versions may have pre- ferred rotomers added to the card. All bond and angle information is derived from the coordinates of the residue in standard PDB format. If you have a new cofactor, you would generate an ideal example (in a program such as Builder) and then write this out in PDB format and append it to the dictionary as described above. Then add any PLANEs. Xfit recog- nizes CHI1-CHI5 as special and assigns these to the keys 1-5. They don't have to be real CHIs, so you can specify torsions in the cofactor to be CHI1-5 as you wish and take advantage of the shortcut key. Or you can do torsions by picking two atoms as described elsewhere in the fitting section.

ACKNOWLEDGMENTS
Xfit 3.0 was designed by Duncan McRee. Alex Shaw is respon- sible for several of the xfit modules, including the GX modules, the PHIGS modules, the AVS interface, and convert- ing the UNC GRINCH code to work with xfit. The FFT library was supplied by Lynn Ten Eyck, as were the hierarchical molecule data structures, which are responsible for much of xfit's utility. The matrix routines for rotating the screen and the dialbox code were borrowed from FLEX, written by Mike Pique. A number of users have braved many segmentation faults in debugging this code, and the author thanks them for their patience.

KNOWN BUGS
On SGIs, when going into or out of hardware stereo mode, it is necessary to pick an atom before the correct view is displayed. On SUNs with TurboGX+ graphics, hardware double buffering does not work. To make xfit usable on such machines, control of the buffering method is provided through the environment variable XFIT_DBUF, desicribed under "Environment Vari- ables."

VERSION
Release 3.0 of XtalView

SEE ALSO
xtalview(1)
xheavy
xheavy

NAME
xheavy - refine heavy atom derivatives and calculate phases.

USAGE
xheavy [file.sol file.phs]

DESCRIPTION
xheavy is used to calculate Multiple Isomorphous Replacement phases and to refine heavy atom solutions. The MIR phasing is done in an iterative manner where 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 are output using the new E estimates. 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 more heavy atom sites.