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Crystallographic software installed on dlpx1


09/6/99: molscript with JPEG, GIF and PNG support available
27/5/99: ccp4i v1.0.1 now installed


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CCP4 software

The following software is currently installed:

CCP4I (CCP4 graphical user interface) v1.0.1

Description: graphical user interface ("GUI") for the CCP4 programs.

Status: Installed and running.

Startup: The interface is started by entering the command ccp4i at the unix prompt. Typing ccp4i -h displays a help screen, and there is extensive on-line help available once the interface has started.

Known problems and fixes:

  1. There may be problems if you have already used an earlier version of the interface - ccp4i may crash on startup without any windows appearing. To fix this you need to delete all the old parameter files as follows: After doing this you will need to set up aliases for different projects all over again (this will not happen with future changes to the interface).
  2. DM interface: there was a problem with outputting maps in O format which has now been fixed. You still cannot output in Quanta format because the mbkall program is not installed on dlpx1.

Bugs etc:Please contact me ( regarding problems starting up the interface or with general problems running it (eg for printing out), these are most likely local configuration errors that I can fix. Other problems should be sent directly to Liz Potterton ( There is also a button on the interface for reporting bugs to the developers.

Useful webpages:


Description: REFMAC with anisotropic B-factor refinement.

Status: refmac_aniso is now withdrawn from /pxbin, as a later version is now the official REFMAC in v3.5.1 of CCP4.

Useful webpages:

Non-CCP4 software

Please see here for general information about the licensing arrangements.

The following software is currently installed:

The following are pending: The following are external software libraries:


Description: AMPS is a suite of programs for multiple sequence alignment. ALSCRIPT formats multiple sequence alignments into postscript.

Status: A version of alscript is available on /pxbin. amps is not currently installed.

Useful webpages:


Description: a package of programs for investigating similarities between protein structures.

Status: runs in the same way as the other Uppsala software (see above).

  1. DEJAVU - find motifs and recognise other proteins with a similar fold:

    Program Executable Function
    dejavu 6d_dejavu Fold and motif recognition
    pro1 6d_pro1 First pre-processor
    pro2 6d_pro2 second-preprocessor
    post 6d_post post-processor
    dejana 6d_dejana utility to screen O macros to only include best hits

  2. LSQMAN - superimpose and analyse multiple models and/or molecules:

    Program Executable Function
    lsqman 6d_lsqman versatile superpositioning and comparison

Useful webpages:

gd 1.3 (GIF library)

Description: a graphics library for fast GIF creation.

Status: gd 1.3 is installed in /ccpdisk/xtal/graphicslibs/gd1.3. This version is not based on the LZW compression algorithm which is currently the subject of a legal dispute, and so should be free of legal complications.

Useful webpages:

Glut library

Description:Glut implements a simple windowing programming interface for OpenGL (a 3D graphics API), and is freely distributed.

Status: Glut v3.6 is installed on dlpx1 in /ccpdisk/xtal/graphicslibs/glut_3.6/.

Useful webpages:



Status: Not installed.

Useful webpages:


Description: software to implement JPEG image compression and decompression.

JPEG is a standardized compression method for full-color and gray-scale images.

JPEG is intended for compressing "real-world" scenes; line drawings, cartoons and other non-realistic images are not its strong suit. JPEG is lossy, meaning that the output image is not exactly identical to the input image. Hence you must not use JPEG if you have to have identical output bits. However, on typical photographic images, very good compression levels can be obtained with no visible change, and remarkably high compression levels are possible if you can tolerate a low-quality image.

Status: version 6b of the JPEG software from has been installed in /ccpdisk/xtal/graphicslibs/jpeg-6b/. Note that make install was not run.

There are several programs (now in /pxbin):

Program Function Usage
cjpeg compress an image file into JPEG format cjpeg [switches] [imagefile] >jpegfile
djpeg decompress an image file from JPEG format back into a conventional image format djpeg [switches] [jpegfile] >imagefile
jpegtran perform various useful transformations of JPEG files without fully decoding the image (i.e. lossless transformations) jpegtran [switches] [inputfile] >outputfile
rdjpgcom utility: prints out comments in JPEG file rdjpgcom [-verbose] [inputfilename]
wrjpgcom utility: adds comments to a JPEG file wrjpgcom [switches] [inputfilename] >outputfile

For more information, look at the following files in /ccpdisk/xtal/graphicslibs/jpeg-6b/ (particulary "usage.doc"):

The IJG JPEG library is in /ccpdisk/xtal/graphicslibs/jpeg-6b/libjpeg.a (see libjpeg.doc)
Nb: libjpeg.a has been compiled as -o32.


Description: molecular graphics program for studying the packing of protein molecules in the crystallographic unit cell.

Status: installed in /pxbin on dlpx1 by Martyn Winn (20/01/99).

Should run on the graphics machines (see the list under the entry for O) and is reported to work on pxelan. The program displays pdb files and is run using the command molpack.

Useful webpages:


Description: program for displaying molecular 3D structures in both schematic and detailed representations.

Status: Molscript 2.1.2 installed 2/3/99 in /ccpdisk/xtal/molscript-2.1.2/ ... Molscript 1.4 is still available on /pxbin/old.
Note that there may be problems if you use the older version of molscript in conjunction with version 2.4h of Raster3d.

Programs: There are two programs: molscript and molauto (which prepares input for molscript). See documentation for more information.

6/7/99: The versions of molauto and molscript on /pxbin include all the available formats (i.e. postscript, Raster3d, VRML 2.0, interactive OpenGL, Glut, SGI/RGB, EPS, JPEG, PNG and GIF).
These are the same as the old molscript_all and molauto_all.

Useful webpages:

Check the Academic License (local document only available on dlpx1) for conditions of use.

See the extra section on the Glut libraries which are now installed on dlpx1.


Description: General model building/manipulation/display graphics program.

Status: Existing version installed by ACR and started using command ono. Latest version 6.2.2 is installed separately in /ccpdisk/xtal/o98/ and should be run using the script ono98.

Access.o files are available for the following machines, and O (either version) should work on any of them:

Please report any problems encountered with running ono98 to

Useful webpages:

Local manual pages are only accessible from dlpx1 (and the machines listed above):


Description: 3 dimensional object plotting program.

Status: Oplot is started using the command oplot. This is a script which runs the executable 6d_oplot_1.15.

Useful webpages:


Description: PNG = Portable Network Graphics library. Zlib is an associated library which is needed by PNG

Status:The PNG (1.0.3) and Zlib (1.1.3) libraries were obtained from The libraries are in /ccpdisk/xtal/graphicslibs/libpng-1.0.3/ and /ccpdisk/xtal/graphicslibs/zlib-1.1.3/ respectively, and were compiled with -o32.


Description: tools for generating high quality raster images of proteins (or other molecules) including rendering pictures composed in molscript.

Status: the following Raster3d version 2.4h programs are installed on /pxbin:
avs2ps, balls, normal3d, render, ribbon, and rods.

Program Function
avs2ps converts AVS image input to monochtom Postscript output
balls preprocessor for preparing description of space-filling model for Raster3d
normal3d applies coordinate manipulations to Raster3d file
rastep reads PDB file and generates input for render
render image rendering program
ribbon preprocessor which prepares simple ribbon representation of protein backbone for Raster3d
rods preprocessor for ball-and-stick figures
stereo3d shell script whiich renders a single Raster3D file as side-by-side stereo pair

Useful webpages:


Description: statistical heavy atom refinement and phasing program.

Status: Not installed.

Useful webpages:


Description: Automated crystallographic structure solution for MIR and MAD.

Status: Installed and licenced (non-commercial licence) until 15th December 2096.

6/4/99: The current version is 1.15, which replaces 1.04 since the author reported the following problems:

SOLVE versions 1.10 - 1.14 contain a serious bug that affects its ability to find solutions in space groups where the asymmetric unit of the reciprocal lattice defined by SOLVE is different than the one used by CCP4. The phasing once a solution is found is unaffected, but the difference Fouriers used to find sites are affected. This bug affects trigonal and hexagonal space groups as well as some others.
If you are using one of these versions of SOLVE, would you please upgrade right away to version 1.15 (which differs from 1.14 only in 4 lines of code) where this bug is fixed.

Version 1.15 is installed in /ccpdisk/xtal/solve-1.15/; the previous version is still available in /ccpdisk/xtal/solve/.

Startup:Start using the command solve, type help for a list of commands. Html manual pages are available locally or from lanl (see below), and as a (massive) text file on dlpx1 - type more $SOLVEDIR/ to view this.

Useful webpages:

Uppsala software

Description: Gerard Kleywegt's programs - includes useful utilities, manipulations et cetera et cetera ...

Status: These programs were installed by Adam Ralph. The versions may be out-of-date however. Below is the complete list of available programs along with a brief description of the program function.

Manual pages for all of the various Uppsala programs (not just those below) are available here.

To execute a particular program you can either:

  1. Type the executable name (listed below), e.g. type 6d_mapman, or
  2. Use the run command, e.g. type run mapman.
Typing run and then list will return the complete list of available Uppsala programs.

Program Executable Function
ave 6d_ave single-crystal averaging
avepdb 6d_avepdb average models
cello 6d_cello cell manipulations
comap 6d_comap combine maps during multi-crystal averaging
comdem 6d_comdem combine multiple domain maps
crave 6d_crave auto-generates C-shell script for multiple multi-crystal averaging
ct2het 6d_ct2het find hetero compounds in pdb
dataman 6d_dataman manipulate reflection datasets
dcup 6d_dcup quick calculations during data collection
essens 6d_essens real-space searches for fragments or molecules
imp 6d_imp improve ncs operators
mama 6d_imp manipulate masks
mapfix 6d_mapfix add spacegroup and symmetry operators to a CCP4 map
mapman 6d_mapman manipulate maps
mappage 6d_mappage use mapman instead
mave 6d_mave multiple crystal averaging
moleman 6d_moleman use moleman2 instead...
moleman2 6d_moleman2 pdb file manipulations
ncs6d 6d_ncs6d find ncs operators
o2d 6d_o2d make 2d plots
odbm 6d_odbm analyse O datablocks
odbman 6d_odbman analyse O datablocks
odledit 6d_odeldit ????
oops 6d_oops scrutinise models and generate rebuilding macros for O
pacman 6d_pacman check packing after Molecular Replacement
pdb2ct 6d_pdb2ct ????
rmspdb 6d_rmspdb analyse multiple models (should use lsqman)
seaman 6d_seaman generate search models for Molecular Replacement
sod 6d_sod generate O datablocks from (aligned) sequences
solex 6d_solex extract best solutions from essens runs
xpand 6d_xpand expand molecules under ncs and/or spacegroup symmetry
xplo2d 6d_xplo2d manipulate X-PLOR input or output files

This is not the complete set of Uppsala software, nor does it necessarily contain the most recent versions of the programs. Please let me know if your favourite program is missing.

Useful webpages:

XtalView 3.2

Description: package for solving macromolecular crystal structure by isomorphous replacement, including building the molecular model.

Status: XtalView 3.2 now installed in the directory /ccpdisk/xtal/XtalView/.

To run the programs:

  1. First need to execute the command
    source /ccpdisk/xtal/XtalView/XtalView.env
    to set up the required environment variables etc.
  2. Then: since there are a number of programs within the XtalView package, the easiest way to access any of them is by running the command xtalmgr. This provides an interface to the different programs along with fields for selecting required input and output files.

Please report any problems with running the XtalView software to me at

Useful webpages:

This is the one you really need: Other links:

Licensing of non-CCP4 software

Please note:
  1. These various non-CCP4 programs have been installed under academic/non-profit licences, and
  2. that it is a breach of many of these licences (eg. Uppsala software) to copy the software to different (unlicensed) sites.
If you have any questions about the licensing arrangements then please contact me. I might not know the answer straightaway but I will do my best to find out!

Thank you for your co-operation.

Web-based Software

This software is not installed or maintained by me. The applications should be runnable over the web, and these are simply links to the relevant sites:
This page maintained by

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