MBG wiki: Search for: PyMol

View changes for these pages

Electrostatics calculations with APBS and PyMol
[[APBS]] is available on all machines *but* PyMol is only available on the newer nodes. You better sit . . . ----- Start with a clean PDB of your structure. PyMol can add missing hydrogens and side chains (?), . . . use a PDB file prepared by /psfgen/. Then : * pymol mypdb.pdb * Plugin -> APBS tools * Select . . . submenus). [[image: Electrostatics with APBS and PyMol (molecular surface)]] . . .
2K - last updated 2005-12-03 15:19 UTC by server.cluster.mbg.gr

Molecular dynamics tutorials
* Molecular dynamics tutorials (NAMD-based) : ** [[Running a molecular dynamics simulation of native . . . * [[Electrostatics calculations with APBS and PyMol]] . . .
1K - last updated 2006-09-15 14:05 UTC by server.cluster.mbg.gr

More on eigenvectors and eigenvalues
Calculation of eigenvalues and eigenvectors is the first step for performing a large number of other . . . to prepare a figure with /rasmol/ (or /vmd/, /pymol/, ...) : [[image: Motion of HrcQb due to principal . . .
6K - last updated 2006-02-22 15:12 UTC by server.cluster.mbg.gr

PyMol
See http://pymol.sourceforge.net/ . . .
1K - last updated 2005-12-03 15:07 UTC by server.cluster.mbg.gr

Software updates, known 'features', etc.
== April 11th, 2006 == * molmol v.2K-2 installed clusterwide. == March 20th, 2006 == * Haploview and . . . installed clusterwide. == Jun 15th, 2005 == * PyMol 0.98 installed on newer nodes. * OpenDX 4.3.2 . . .
2K - last updated 2006-04-11 14:20 UTC by server.cluster.mbg.gr

5 pages found.