Chapter 6

Definition

 Prepares a vu file from a PDB file colored by B-value.
 

colorbyB pdbfile xfit.vu -n[ormalize]
 

 The input pdb file is converted to colored lines using the same routines as in xfit, except that the lines are colored by B-value. If the -normalize flag is present, then the B-values are normalized before coloring. This is highly recommended for comparison purposes, since 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 mutations with the native structure. This same coloring can be done in xfit under View.
 

SEE ALSO

Definition

 Convert a PDB file from Cartesian to fractional coordinates, vice-versa, and coordinate transformations.
 

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 Eulerian angles q1, q2, q3.
 

Note the optional use of crystal on the command line which overrides the CRYSTAL environment variable. This allows the use of multiple crystals during piped operations. Converting to fractional 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 |\ (Translate 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. (Note: the "\" characters indicate a continuation to the next line.)
 
 
 

SEE ALSO

Definition

 Convert a vu file from Cartesian to fractional coordinates and vice-versa.
 

cvtvu crystal -f < fractional.vu > cartesian.vu

cvtvu crystal -c < cartesian.vu > fractional.vu
 
 
 
 

SEE ALSO

Definition

 Converts x, y, z from Cartesian coordinates to fractional coordinates and vice-versa.
 

cvtxyz [-f|-c] [x y z]|[< file.xyz > newfile.xyz]

f = convert from fractional to Cartesian coordinates

c = convert from Cartesian to fractional coordinates
 
 

The environment variable CRYSTAL must be set to the correct crystal file.
 

If x, y, z are given, they 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 to use it to convert from fractional bounds read from xcontur into Cartesian bounds expected by FRODOMAP.
 
 
 
 

SEE ALSO

Definition

 Removes hydrogens from a pdb file.
 

deh < pdb_with_hydrogens > pdb_without_hydrogens
 

 The output of XPLOR contains hydrogen atoms at some positions and, although xfit can handle them, it is often desirable to get rid of them. However, if you leave them on you won't have to rerun generate.inp.
 

A hydrogen 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?)
 

SEE ALSO

Definition

 Reformats PHASIT format output files to XtalView.
 

dumpphasit phasit_file > xtalview.phs
 

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

SEE ALSO

Definition

 Calculates the derivative of a difference map at each atom and outputs a vu file with arrows showing the direction and relative magnitude.
 

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

 The input is a PDB file (.pdb) and a phase file (.phs). The output is a vu file suitable for xfit. If one resolution limit is given, then it is considered the minimum resolution. If two are given, data between them are used. If none are given, all data are used.
 

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 indicators.) 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 resolutions far from atomic resolution (roughly below 2.5 Å).

This program is provided for those who want to use it with some other program. Converting the vu file is your responsibility. If you do this, remember it's x1 y1 z1 x2 y2 z2 color. (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, pre-calculate them with deriv if you will be using them over several sessions.
 
 
 
 

SEE ALSO

Definition

 Converts a GRINCH ASCII format file to a vu file for displaying as a background object in xfit.
 

grinchbones < grinch.ASCII > xfit.vu

Discussion

 The input is a GRINCH ASCII format file (University of North Carolina, Chapel Hill Graphics Lab). It is made with the command ASCII save filename in interp or by using the ASCII option in mkskel). The output is an xfit vu file. The output uses the standard GRINCH color scheme for interpreted edges (i.e., a main chain is green, a 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 first map in xfit). This can be used as a background guide for building a 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
 
 

SEE ALSO

Definition

 Searches for heavy atom sites. This is a brute force application of Patterson correlation methods. It is slow, but extremely robust. (Note: hercules can only be run from the command line.)
 

hercules control-file print-file
 

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.

 fin file (with merged native and derivative data)

 solution file (NONE for the first round, then solution file output from xheavy or xpatpred for the second round)

 correlations file (output)

 correlation map file (output in xcontur/xfit format)

crystal (crystal name)

 grid (should be 1/4 to 1/6 resolution in Ångstroms)

 resmax, resmin (resolution limits on diffraction data)

 xmin, xmax (in fractions of unit cell, x asymmetric unit)

 ymin, ymax (in fractions of unit cell, y asymmetric unit)

 zmin, zmax (in fractions of unit cell, z asymmetric unit)

 occupancy (see description)

print-file

 The print-file will contain some of the output from the program. Other output goes into the correlations and correlation map files.
 
 

If you put NONE in the heavy solution file name spot (line 2), then atom data is read from the control-file. Otherwise, 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 solutions, 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 limits on 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 accordingly. 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 form 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.
 

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 0.05

1.0
 
 

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

SEE ALSO

Definition

 Gets the XtalView Cartesian/fractional conversion matrices for use in other programs.
 

matrices crystal
 

 This routine returns the Cartesian to fractional and vice-versa matrices used by XtalView. This is provided because there is more than one way to do this 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 we give no guarantee.
 

SEE ALSO

Definition

 Performs skeletonization on an electron density map (mkskel is part of the University of North Carolina, Chapel Hill GRINCH skeletonization package).
 

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

Discussion

 mkskel looks for mainname.mi (map information file) and mainname.map (density map file) . You can create these files yourself or use xskel to create them for you (see xskel User Guide pages). For instruction on writing map information files see the README file in $XTALVIEWHOME/README.mkskel.

mkskel produces ridgeline files in ASCII, binary or "edges", depending on the output file format specified. The output can be read in the ridgeline menu of xfit.

Command options

 The -maxlen option takes a specific length in Ångstroms as an argument. This length corresponds to the longest legal bond length in the molecule. The default length is 2.0 Ångstroms.

 The -minden option 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.

 The -range option take two arguments: the highest and lowest density 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.
 
 

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 Carolina at Chapel Hill.
 

SEE ALSO

Definition

 Converts an XENGEN mulist file to an XtalView .fin file
 

mu2fin < mulist > file.fin
 

 mu2fin reads the Bijovet pair data from the mu file and ignores the averaged F that also appears in the mulist.
 

Make the mulist with makemu -f. The -f flag is a must.

This program is actually not needed, since xprepfin does all this and prepares a history file; therefore, xprepfin is recommended over mu2fin.
 
 

SEE ALSO

Definition

 Aligns two PDB objects using rotation and translation.
 

pdbfit [-v] < input-file
 

 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

 

 
 
 

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

*

*
 
 

 xtalview(1)
 
 

SEE ALSO

Definition

 Calculates resolution of crystal indices.
 

rescalc

 Environment

 The environment variable CRYSTAL must be set to the correct crystal file.
 
 

 rescalc gets the crystal index values from the environment crystal information file and calculates and displays the resolution in Ångstroms.
 

SEE ALSO

Definition

 Resolution filter.
 

resflt limit1 [limit2] < file > filtered_file
 

 Limit1 and limit2 are in Ångstroms. This program can filter any ASCII file with h k l as the first three fields (.fin, .phs, .mu, etc.) based on d-spacing. If one limit is given, this is taken as the minimum and the other limit is set to 1000 Å. If both limits are given, then d-spacings between them are output. The line is copied to the output exactly as input. The only requirement is that h k and l appear first and are separated by a space or tab.
 
 
 

SEE ALSO

Definition

 Calculates structure factors from a PDB file.
 

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

Environment

 The CRYSTAL value must be set to the correct crystal for the unit cell and space group (see xtalmgr).

 If one limit is given, it is considered the minimum resolution. If two are given, the data between them is used. 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 that 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).
 
 

 This is a completely general structure factor calculator. It 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 off-line (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 set the CRYSTAL environment variable (e.g., setenv CRYSTAL miraclase) before running stfact.
 
 
 

SEE ALSO

Definition

 Converts an XENGEN urefls file to a vu file for display in xfit.
 

urf2xfit [urefls] [xfit.vu]
 

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

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.
 

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 reflection. Data that is missing becomes apparent as well as the curved nature of an 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 recoloring option in xfit) to see how multiple runs overlap. The output is colored in four bins of intensity from min to max: blue, cyan, yellow, and white.
 

The color scheme needs expanding, and coloring by phi value would be useful.
 
 
 

SEE ALSO

Definition

 Calculates and displays the volume of a crystal unit cell.
 

volume crystal
 

 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.
 

Description

 Reformats XPLOR phase files.
 

xplortophs [xplor.fcalc.file] [xtalview.phs]
 

 This program scans an XPLOR phase file and reformats it for XtalView. The XPLOR file is generally produced with the XPLOR script fcalc.inp.
 
 
 

SEE ALSO

XtalView User Guide