This page contains descriptions of software that has been loaded onto the SAF SGI machines. There are also links to the online manuals.

List of Programs

AutoDock molecular docking
chain interactive model and display
CCP4 data refinement
Delpi electrostatics calculations
Grasp interactive model and electrostatics
Insight (Biosym) interactive model and display
denzo/scalepack/xdisp analysis of diffraction data
MidasPlus interactive display
MolMol interactive model and display
Molscript script based display
O interactive model and display
Phases data refinement
RasMol interactive display
Raster3D can render Molscript into RGB pictures
Setor interactive display
Tom interative model
VMD interactive display
XtalView interactive model, data refinement
CHAIN is an interactive modeling and display program along the lines of O, Tom, or XtalView.
Before running it, do:
    setup chain
CHAIN is unsupported at this time, but some people find it easier to learn/use than other such programs. The current version of chain is 7.1, but we cannot use that as distributed on our machines, so we have version 5 installed. A manual and a sample session are available.

O is a general purpose modeling and display program.
Before running it, do:
    setup O
Manual, Bi/Ch 170 O tutorial. More information from the O Web Page, especially the O FAQ

Insight is commercial software and is licensed only to run on rko.
Before running it, do:
    setup biosym
Insight contains many modules, most of which have online help that is not accessible from outside of the program. However, documentation for the latest version of Insight II and the modules which we have licensed may be read here.

denzo/scalepack/xdisp are parts of the commercial "HKL" software package.
Before running it, create the needed configuration files.
Manual for denzo,scalepack and xdisp (PDF format, 1.2 Mb download)

MidasPlus is probably the most capable of the visualization programs. It is especially strong at showing surfaces.
Before running it, do:
    setup midas
(postscript) Manual. There is also a MidasPlus home page and a MidasPlus tutorial.

TOM is simlar to, and related to, O.
Before running it, do:
    setup tom
Manual, Primer,

XtalView is large and comprehensive set of programs for building structures from Xray data. The program xfit may be used to visualize and modify structures as in O.
Before running it, do:
    setup XtalView
Here are some more setup instructions and the man pages for the programs that comprise XtalView. The pieces of the XtalView 3.0 User Guide (Postscript) are: Title page , Table of Contents , Preface , Introduction , Getting Started , Using XtalView , Programming XtalView , Window-based applications , Nonwindow-based applications

Setor is a very powerful, albeit somewhat buggy, visualization program for molecular structures.
Before running it, do:
    setup setor
Manual (Postscript)

RasMol is a visualization program for molecular structures. It is especially good for quick looks at proteins. Manual

Raster3D is a rendering package for converting instructions into RGB pictures. In particular, it can be used to render the output from Molscript 1.4, which would otherwise be simple postscript. Instructions

VMD is similar in purpose to Setor, but has a different interface. Start the program by giving the command "vmd". Note that as in all such programs it can take a very long time to render solids, so position your molecule(s) first as wire models, then format them. User's guide

MOLMOL is similar in purpose to Setor, but has a different interface. Start the program by giving the command "molmol". Note that as in all such programs it can take a very long time to render solids, so position your molecule(s) first as wire models, then format them. Both command line and GUI interfaces exist. Go through the Tutorial first, and refer to the manual and list of interactive commands for further ideas.

molscript is the "standard" visualization program for molecular structures. It is not interactive; one writes a simple "script" describing how a given structure is to be viewed, and molscript converts that to a postscript file which can then be printed or viewed with xpsview. Manual

DelPhi is an electrostatics program which can be used to generate maps of electrostaic potentials on PDB files. One option maps this information to the "B" temperature factor in PDB files, where it can be used by other visualization programs to color displays appropriately. Delphi can also be used to do certain types of pKa calculations for residues in proteins.
Before running it, do:
    setup delphi
Manual

GRASP is an electrostatics program related to DELPHI which can be used to generate images of electrostaic potentials from PDB files. GRASP calculates a less exact electrostatic potential than does DELPHI, but it can be induced to use DELPHI so that a more exact representation results.
Before running it, do:
    setup grasp
The Manual is monolithic - there are no hyperlinks, so use FIND or SEARCH in your browser to move around in it. There are also some thumbnail size example pictures from the Grasp distribution.

PHASES is a big package of programs for working out the Phases from X-Ray data.
Before running it, do:
    setup phases
Here is the manual.

CCP4 is a big package of programs for working out structures from X-Ray data.
Before running it, do:
    setup ccp4
Here are the (many) manuals.

AutoDock is a set of programs for docking molecules. It can also do a few other nice things, like protonate a PDB file. It isn't interactive, rather the old "set up parameter files and watch it crunch" approach.
Before running it, do:
    setup autodock
Here are is the manual in PDF and Postscript formats