A Crystallographic Software Summary

The installed base has changed, notably because of the retirement of xray4 (SGI), and the archival of xray2 (SGI) and xray5 (SGI). These latter two machines now run minimal "stub" software installations and exist only as long as hardware and/or boredom permit them to remain. A new Linux box mol-xray4 now carries the load of being the NIS master, and ultimately the software master. However /home/xtal acts as an independent entity on each of our Linux boxes. Xtal1 is currently turned off and not actively updated. Xray0 is my old computational cruncher but is superceded by mol-xray9 so I don't so software updates. The list of current and past machines is xray0, xray1, xray2 (emeritus), xray4, xray5 (emeritus), xray8, mol-xray9, mol-xray4, xtal1 (resting), xtal2.

A version # indicates that the software is installed although older versions may still exist. Blank indicates that it is not installed or not verified to work. ---- means that it exceeds machine configuration or capabilities (e.g. GRASP, SETOR and RIBBONS are not available for anything except SGIs). Because of the relatively ancient nature of Xtal2's operating system, some library and operating system conflicts prevent some more recent software versions from running.

  Xray0 Mol-xray9 Boron Xtal2 Xray8 Mol-xray4 Notes
Hardware Mac/G5 Mac/Intel Mac/G5 PC/Linux PC/Linux PC/Linux  
OS 10.4 10.5 10.5 RHEL 4 Fedora 13 Fedora 13  
Application  
APBS ---- 1.3 ----- 1.3 1.3 1.3  
ARP/WARP 7.0.1 7.0.1 7.0.1 7.0.1 7.0.1 7.0.1  
CCP4 6.0.2 6.0.2 6.0.2 6.0.2 6.0.2 6.0.2  
CCP4mg 1.1 2.4.1 2.4.2 2.4.2 2.4.2 Library conflict for xtal2
Coot 0.4.1 0.6-pre 0.33 0.5.2 0.5.2 0.5.2  
CNS 1.2 1.21 1.2 1.1 1.1 1.1  
HKL ----- ----- ----- 1.97.2 1.97.2 unlicensed  
HKL2MAP 0.2 0.2 0.2 0.2 0.2 0.2  
Molscript 2.1.2 2.1.2 2.1.2 2.1.2 2.1.2 2.1.2 No new versions
O 9.0.7 9.0.7 9.0.7 9.0.7 9.0.7 9.0.7  
Phaser 2.1 2.1.1 2.1.1 2.1.1 2.1.1 2.1.1 Now part of CCP4 & Phenix
Phenix 1.4.3 1.6.4 1.6.4 1.5-2 1.6.4 1.6.4 Note: OS revision conflict for xtal2
Povray 3.6.1 3.6.1 3.6.1 3.6.1 3.6.1 3.6.1  
PyMol 1.1 1.1 1.1 1.1 1.1 1.1  
Raster3D 2.7d 2.7d 2.7d 2.7c 2.7c 2.7c  
Shake-n-Bake 2.2p2   2.2p2 2.2p1 2.2p1 2.2p1 2.3 is the most recent (2008)
Shelx 2006/1 2006/3 2006/3 2006/1 2006/1 2006/1  
Uppsala Software Factory 1/2005 2005 2005 2005 2005 2005 No new versions
XtalView 4.1 No new versions

Applications List:

Directory What Version URL
alscript.2_07a ALSCRIPT 2.07 http://www.compbio.dundee.ac.uk/Software/Alscript/alscript.html
apbs_1.3_source APBS 1.3 http://www.poissonboltzmann.org/
arp_warp_6.1.1 ARP/WARP 6.1.1 http://www.embl-hamburg.de/ARP/
bobscript Bobscript 2.5a http://www.strubi.ox.ac.uk/bobscript/
ccp4-5.0 CCP4 6.02 http://www.ccp4.ac.uk/index.php
ccp4mg CCP4 Molecular Graphics 1.1, 2.4 http://www.ysbl.york.ac.uk/~lizp/molgraphics.html
cctbx Computational Crystallography Toolbox (Mar 2004) http://cctbx.sourceforge.net/
Chooch-4.01 Chooch 4.01 http://www.ccp4.ac.uk/ccp4bin/cvsweb.cgi/chooch/chooch/
clipper Clipper libraries (July 2003) http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html
clustalw1.81 ClustalW 1.81 various
clustalw1.82 ClustalW 1.82 various
clustalx1.81.linux ClustalW 1.81 various
Cn3D Cn3D (plugin) (May 2000) http://ncbi.nih.gov/Structure/CN3D/cn3d.shtml
cns_solve_1.0 CNS/SOLVE 1.0 http://cns.csb.yale.edu/v1.0/
cns_solve_1.1 CNS/SOLVE 1.1 http://cns.csb.yale.edu/v1.1/
denzo HKL suite 1.97.2 http://www.hkl-xray.com/
dino Dino (molecular graphics) 0.8.4 http://cobra.mih.unibas.ch/dino/
dotlet Dotlet (java applet) n/d http://www.isrec.isb-sib.ch/java/dotlet/Dotlet.html
dssp DSSP CMBI/April 1,2000 http://www.cmbi.kun.nl/gv/dssp/
dssp2pdb dssp2pdb 0.03 http://keres.colorado.edu/dssp2pdb/
dvd+rw-tools-5.14.4.7.4 DVD+RW tools 5.14.4.7.4 http://fy.chalmers.se/~appro/linux/DVD+RW/
EDEN Eden (Nov 2003) http://www.edencrystallography.org/
epmr_2.5 EPMR 2.5 n/d (was Aguoron)
fasta FASTA 3.4 http://fasta.bioch.virginia.edu/
fffear FFEAR now part of CCP4 http://www.ysbl.york.ac.uk/~cowtan/fffear/fffear.html
glmaid_dist ? ? ?
glr_distr GL_RENDER (May 2001) n/d
hmmer-2.2g HMMer 2.2g http://hmmer.wustl.edu/
hmmer-2.3.2 HMMer 2.3.2 http://hmmer.wustl.edu/
hyss HySS n/d http://www.phenix-online.org/download/documentation/hyss/
hyss_build HySS n/d http://www.phenix-online.org/download/documentation/hyss/
hyss_sources HySS n/d http://www.phenix-online.org/download/documentation/hyss/
Lafire_linux Lafire (Aug 2003) http://altair.sci.hokudai.ac.jp/g6/Lafire.html
mead-2.2.0p3 MEAD 2.2.0p3 http://www.scripps.edu/mb/bashford/
mglTools MGL Tools (python) 1.5 (?) http://www.scripps.edu/~sanner/python/
mirror MIRROR 2.9 moved?
modeller MODELLER 6v1 http://salilab.org/modeller/
modeller6v1 MODELLER 6v1 http://salilab.org/modeller/
molscript-2.1.2 MOLSCRIPT 2.1.2 http://www.avatar.se/molscript/
molscript-2.1.2-opengl MOLSCRIPT 2.1.2 http://www.avatar.se/molscript/
mosflm_denzo_converter ? ? ?
msms MSMS 2.5.3 http://www.scripps.edu/~sanner/html/msms_home.html
naccess2.1.1 naccess 2.1.1 http://wolf.bms.umist.ac.uk/naccess/
NAMD NAMD 2.4b1 http://www.ks.uiuc.edu/Research/namd/
NMRPipe NMRpipe (July 2003) http://spin.niddk.nih.gov/bax/software/NMRPipe/
nmrview NMRview 5.0.4 http://onemoonscientific.com/nmrview/
O O 8.0.11 http://xray.bmc.uu.se/~alwyn/Distribution/distrib_frameset.html
O9 O 9.0.7 http://xray.bmc.uu.se/~alwyn/Distribution/distrib_frameset.html
odials n/a n/a n/a
openbabel-1.100.0 Open Babel 1.1 http://openbabel.sourceforge.net/
phaser-1.2 Phaser 1.2 http://www-structmed.cimr.cam.ac.uk/phaser/
phaser-cambridge-alpha-1.1a Phaser 1.1a http://www-structmed.cimr.cam.ac.uk/phaser/
phaser-ccp4i-1.2 Phaser 1.2 http://www-structmed.cimr.cam.ac.uk/phaser/
phaser-ccp4i-4.2-extras-1.2 Phaser 1.2 http://www-structmed.cimr.cam.ac.uk/phaser/
phaser-installer-1.2 Phaser 1.2 http://www-structmed.cimr.cam.ac.uk/phaser/
phaser-tutorial-1.2 Phaser 1.2 http://www-structmed.cimr.cam.ac.uk/phaser/
pov4grasp-1.31 Pov4Grasp 1.31 http://pov4grasp.free.fr/
povscript+0.9 Povscript+ 0.9 http://www.stanford.edu/~fenn/povscript/
povscript+1.5 Povscript+ 1.5 http://www.stanford.edu/~fenn/povscript/
povscript_1.65 Povscript 1.65 n/d
povscript_1.69 Povscript 1.69 n/d
ppMirror Predict Protein Mirror (Oct 2002) http://www.predictprotein.org/
predator PREDATOR ? http://www-db.embl-heidelberg.de/jss/servlet/de.embl.bk.wwwTools.GroupLeftEMBL/argos/predator/predator_info.html
ProFitV2.2 Pro Fit 2.2 http://www.bioinf.org.uk/software/
pymol PyMol ? http://pymol.sourceforge.net/
pymol_2002 PyMol ? http://pymol.sourceforge.net/
RasMol_2.7.1.1 RasMol 2.7.1.1 http://www.umass.edu/microbio/rasmol/
RasMol_2.7.2 RasMol 2.7.2 http://www.umass.edu/microbio/rasmol/
Raster3D_2.6c Raster3D 2.6c http://www.bmsc.washington.edu/raster3d/raster3d.html
Raster3D_2.7b Raster3D 2.7b http://www.bmsc.washington.edu/raster3d/raster3d.html
Raster3D_2.7c Raster3D 2.7c http://www.bmsc.washington.edu/raster3d/raster3d.html
refmac5 Refmac 5 Now part of CCP4
ribbons Ribbons ? http://sgce.cbse.uab.edu/ribbons/
ribbons3.2.2 Ribbons 3.2.2 http://sgce.cbse.uab.edu/ribbons/
sequoia Sequoia (Feb 2002) http://bruns.homeip.net/~bruns/sequoia.html
shelx SHELX (2002) http://shelx.uni-ac.gwdg.de/SHELX/
shelx-03 SHELX (2003) http://shelx.uni-ac.gwdg.de/SHELX/
shelx-04 SHELX (2004) http://shelx.uni-ac.gwdg.de/SHELX/
SnB Shake-n-Bake 2.1 http://www.hwi.buffalo.edu/SnB/
snb2.2p1 Shake-n-Bake 2.2p1 http://www.hwi.buffalo.edu/SnB/
solve-2.01 Solve/Resolve 2.01 http://www.solve.lanl.gov/
solve-2.02 Solve/Resolve 2.02 http://www.solve.lanl.gov/
solve-2.03 Solve/Resolve 2.03 http://www.solve.lanl.gov/
solve-2.05 Solve/Resolve 2.05 http://www.solve.lanl.gov/
solve-2.06 Solve/Resolve 2.06 http://www.solve.lanl.gov/
solve-2.08 Solve/Resolve 2.08 http://www.solve.lanl.gov/
SPDBV Swiss-PdbViewer 37b2 http://www.expasy.org/spdbv/
spock Spock (2002) http://mackerel.tamu.edu/spock/
stride Stride ? http://www-db.embl-heidelberg.de/jss/servlet/de.embl.bk.wwwTools.GroupLeftEMBL/argos/stride/stride_info.html
stride2pdb Stride2pdb ? http://www-db.embl-heidelberg.de/jss/servlet/de.embl.bk.wwwTools.GroupLeftEMBL/argos/stride/stride_info.html
threader3.4 Threader 3.4 http://bioinf.cs.ucl.ac.uk/threader/threader.html
Uppsala Uppsala Software Factory n/a http://alpha2.bmc.uu.se/~gerard/manuals/
validation-v2.0-linux PDB Validation Suite 2.0 http://pdb.rutgers.edu/mmcif/VAL/
vmd Visual Molecular Dynamics (VMD) ? http://www.ks.uiuc.edu/Research/vmd/
vmd-1.7.1 Visual Molecular Dynamics (VMD) 1.7.1 http://www.ks.uiuc.edu/Research/vmd/
X3DNA X3DNA (3DNA) ? http://rutchem.rutgers.edu/~xiangjun/3DNA/
xds XDS ? http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/
xplor3.851 X-PLOR 3.851 http://atb.slac.stanford.edu/xplor/
XtalView XtalView 4.0 http://www.sdsc.edu/CCMS/Packages/XTALVIEW/xtalview.html

Other things:
Item What
0_setup.com Example "setup" file for software
ARCHIVES Directory containing many install sources
COWTAN/ Kevin Cowtan's CCP4 v4 executibles
Examples/ Examples of scripts
INTEL/ CNS executibles compiled with Intel compiler
MIRROR Script to run Mirror for PDB
OSX/ Install sources for OSX 10.1 and 10.3
Papers/ One useful paper as PDF
public_html/ The website
RPMs/ A few useful RPMs for Linux
SYNCHRONIZE ~xtal synchronization script