An Attempt at an Xtal Software Summary

Regrettably, the appearance in this list doesn't mean that the software is actually installed or functional. The list was constructed from the full list at MSKCC, but at Princeton only a subset of this list is installed. Eventually I hope the scope of the installation will expand. This is a heterogeneous environment, with different limitations on different machines, which tends to limit the total installed base.

Installed base at Princeton:
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).

Application Xray0
G5 Xray2
Indigo2 Xray4
Octane Xray5
Octane Helium
Linux Xtal1
G5 Xtal2
Linux Boron
G5 Xray8
Linux
ARP/WARP 6.1.1 6.1.1 6.1.1 6.1.1 6.1.1 6.1.1
ARP/WARP-ccp4i 6.1.1 6.1.1 6.1.1 6.1.1 6.1.1 6.1.1
CCP4 6.0.2 4.0 4.0 (*) 4.0 (*) 5.0.2 5.0.2 5.0.2 6.0.2 6.0.2
CCP4mg 1.1 0.12 0.12 1.1
Coot 0.4.1 ---- 0.33 0.33 0.33
CCTBX 4/2006 4/2006 4/2006
CNS 1.2 ----- 1.1 1.1 1.1 1.1 1.1 1.1 1.1
Dock ----- 4.0.1 4.0.1
Grasp ----- ----- 1.3.6 1.3.6 ----- ----- ----- ----- -----
HKL ----- ----- 1.97.2 1.97.2 1.97.2 ----- -----
HKL2MAP 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 2.1.2 2.1.2 2.1.2
O 9.0.7 9.0.7 9.0.7 9.0.7 9.0.3 9.0.7 9.0.7 9.0.7 9.0.7
Phaser 2.1 ----- 1.3.1 1.3.1 1.3.1 1.3.1
Phaser-ccp4i 2.1 ----- 1.3.1 1.3.1 1.3.1 1.3.1
Phases installed installed
Phenix installation pending

Povray 3.5 3.1 3.1 3.5 3.5 3.6
PyMol 0.97 ----- 0.97 ???
Raster3D 2.6e 2.5c 2.5c 2.5c 2.7c 2.6e 2.7c 2.6e 2.7c
Ribbons ----- ----- 3.0 3.0 ----- ----- ----- ----- -----
Setor ----- 1/2000 1/2000 ----- ----- ----- ----- -----
Shake-n-Bake 2.2p2 ----- 2.2p1 2.2p1 2.2p2 2.2p2 2.2p1
Shelx 1/2006 1/2006 1/2006 1/2006 1/2006 1/2006
Solve/Resolve 2.08 2.08 1.17 1.17 2.09
Uppsala Software Factory 1/2005 2/1999 2/1999 2/1999 7/2003 1/2005 7/2003 1/2005 7/2005
Whatcheck 4.99g 4.99g
XtalView 4.1 4.1

Application	Xray0 G5	Xray2 Indigo2	Xray4 Octane	Xray5 Octane	Helium Linux	Xtal1 G5	Xtal2 Linux	Boron G5	Xray8 Linux
ARP/WARP	6.1.1				6.1.1	6.1.1	6.1.1	6.1.1	6.1.1
ARP/WARP-ccp4i	6.1.1				6.1.1	6.1.1	6.1.1	6.1.1	6.1.1
CCP4	6.0.2	4.0	4.0 (*)	4.0 (*)	5.0.2	5.0.2	5.0.2	6.0.2	6.0.2
CCP4mg	1.1				0.12		0.12		1.1
Coot	0.4.1	----			0.33		0.33	0.33
CCTBX	4/2006					4/2006		4/2006
CNS	1.2	-----	1.1	1.1	1.1	1.1	1.1	1.1	1.1
Dock		-----	4.0.1	4.0.1
Grasp	-----	-----	1.3.6	1.3.6	-----	-----	-----	-----	-----
HKL	-----	-----	1.97.2	1.97.2	1.97.2	-----		-----
HKL2MAP	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	2.1.2	2.1.2	2.1.2
O	9.0.7	9.0.7	9.0.7	9.0.7	9.0.3	9.0.7	9.0.7	9.0.7	9.0.7
Phaser	2.1	-----				1.3.1	1.3.1	1.3.1	1.3.1
Phaser-ccp4i	2.1	-----				1.3.1	1.3.1	1.3.1	1.3.1
Phases			installed	installed
Phenix	installation pending
Povray	3.5		3.1	3.1		3.5		3.5	3.6
PyMol	0.97	-----				0.97		???
Raster3D	2.6e	2.5c	2.5c	2.5c	2.7c	2.6e	2.7c	2.6e	2.7c
Ribbons	-----	-----	3.0	3.0	-----	-----	-----	-----	-----
Setor	-----		1/2000	1/2000	-----	-----	-----	-----	-----
Shake-n-Bake	2.2p2	-----	2.2p1	2.2p1		2.2p2		2.2p2	2.2p1
Shelx	1/2006				1/2006	1/2006	1/2006	1/2006	1/2006
Solve/Resolve	2.08	2.08	1.17	1.17					2.09
Uppsala Software Factory	1/2005	2/1999	2/1999	2/1999	7/2003	1/2005	7/2003	1/2005	7/2005
Whatcheck			4.99g	4.99g
XtalView							4.1		4.1

(*): CCP4 v5.0.2 is available via /usr/people5/SGI but not enabled by default. CCP4i now works. CCP4 v5.99.5 is also installed on all three G5 Macs.

Notes:

CNS v1.1 is installed where CNS v1.2 is available but the latter is highly recommended.
The SGI xray4 was retired in 1/2008

Software Install Locations:

Xray0 : mainly /usr/local ; some in /sw via fink ; /Applications for some DMGs
Xray8 : mainly /home/xtal ; some in /usr/local
Xtal1 : mainly /usr/local ; some in /sw via fink; /Applications for some DMGs
Xtal2 : mainly /xtal ; some in /usr/local
Boron : mainly /usr/local ; some in /sw via fink; /Applications for some DMGs
Helium: mainly /linuxprogs ; Denzo in /programs2

Applications List:

Directory	What	Version	URL

alscript.2_07a	ALSCRIPT	2.07	http://www.compbio.dundee.ac.uk/Software/Alscript/alscript.html
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	5.02	http://www.ccp4.ac.uk/index.php
ccp4mg	CCP4 Molecular Graphics	n/d	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

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