Computing in the Fleming Lab

Active links indicate that the programs are installed and documented. Dead links mean that we have the program, but it is not documented. Be patient - this process is on-going.

BBDEP - Backbone dependent rotamer library analysis

CHI - A program for modeling helix-helix interactions.
CNS

GIMP
Grasp - A molecular surface program - Runs on Countess only

HBPLUS - Calculates potential hydrogen bonds

Helanal - Calculates structural features of alpha helices, including bending angle, helix pitch, and residues per turn. This program is installed on the Linux manchines but is also compatible with MacOSX.

Lsqman - a program for doing structure alignment
Midas Plus - a molecular graphics program - Runs on Countess only
Moleman2 - Manipulation and analysis of PDB files

MSROLL - Molecular and accessible surface analysis

NMR Pipe

OS - Occluded surface analysis

PovRay - Generates publication quality pictures from Deep View inputs.

REDUCE - Builds hydrogens
Ribbons - a molecular graphics program - Runs on Countess only

Scwrl - Sidechain rotamer optimization
Sparky - NMR peak integration and assignment
Spock - A molecular graphics program - Turned out not to be so useful.

Uppsala Utilities

XMGR - Now called XMGRACE
Xmgrace - An XY graphing program. Type "xmgrace" to run. The command should already be in your path.
XV - A graphics viewing program.