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

List of Programs

AutoDock molecular docking
CCP4 data refinement
DelPhi electrostatics calculations
MolMol interactive model and display
Molscript script based display
O interactive model and display
Phases data refinement
Raster3D can render Molscript into RGB pictures
VMD interactive display
XtalView interactive model, data refinement
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
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
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
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. Programs are noninteractive and run from the command line after parameter files are first set up. Version 3.05.
Before running it, do:
    csetup autodock
Here are is the manual in Postscript and HTML formats
last updated May 8, 2006