09/6/99: molscript with JPEG, GIF and PNG support available
27/5/99: ccp4i v1.0.1 now installed
Comments, requests, complaints or compliments should be mailed to p.j.briggs@dl.ac.uk.
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:
Bugs etc:Please contact me (p.j.briggs@dl.ac.uk) 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 (lizp@yorvic.york.ac.uk There is also a button on the interface for reporting bugs to the developers.
Status: refmac_aniso is now withdrawn from /pxbin, as a later version is now the official REFMAC in v3.5.1 of CCP4.
The following software is currently installed:
Status: A version of alscript is available on /pxbin. amps is not currently installed.
Status: runs in the same way as the other Uppsala software (see above).
| 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 |
| Program | Executable | Function |
|---|---|---|
| lsqman | 6d_lsqman | versatile superpositioning and comparison |
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.
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/.
Status: Not installed.
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 ftp://ftp.uu.net/graphics/jpeg 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"):
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.
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.
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.
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 p.j.briggs@dl.ac.uk.
Status: Oplot is started using the command oplot. This is a script which runs the executable 6d_oplot_1.15.
Status:The PNG (1.0.3) and Zlib (1.1.3) libraries were obtained from ftp://ftp.uu.net/graphics/png. 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.
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 |
Status: Not installed.
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/solve.help to view this.
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:
| 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.
Status: XtalView 3.2 now installed in the directory /ccpdisk/xtal/XtalView/.
To run the programs:
Please report any problems with running the XtalView software to me at p.j.briggs@dl.ac.uk.
Thank you for your co-operation.