User:Speleo3
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My name is Thomas Holder and I am a bioinformatician at the MPI for Developmental Biology in Tübingen, Germany.
I was awarded the Warren L. DeLano Memorial PyMOL Open-Source Fellowship for 2011-2012.
Contact
- speleo3/users.sourceforge.net
- thomas.holder/tuebingen.mpg.de
Scripts written by me
- AAindex
- AngleBetweenHelices
- Extra fit
- PluginDirectory
- Pml2py
- Polarpairs
- Save settings
- Show bumps
- Sidechaincenters
- Spectrumany
- Spectrum states
- Supercell
Scripts Pastebin
Some random scripts with no dedicated PyMOLWiki page.
Launch interactive python terminal with PyMOL process: (see also Launching From a Script)
#!/usr/bin/python2.6 -i
import sys, os
# autocompletion
import readline
import rlcompleter
readline.parse_and_bind('tab: complete')
# pymol environment
moddir='/opt/pymol-svn/modules'
sys.path.insert(0, moddir)
os.putenv('PYMOL_PATH', os.path.join(moddir, 'pymol/pymol_path'))
# pymol launching
import pymol
pymol.pymol_argv = ['pymol','-qc'] + sys.argv[1:]
pymol.finish_launching()
cmd = pymol.cmd
Build PyMOL: (see also Linux Install)
#!/bin/bash -e
src=/tmp
prefix=/opt/pymol-git
pyinstall() {
cd $src
name=$(basename $2)
if [[ -e $name ]]; then
cd $name && $1 pull
else
$1 clone $2 && cd $name
fi
python setup.py build install \
--home=$prefix \
--install-lib=$prefix/modules \
--install-scripts=$prefix
}
pyinstall git git@github.com:speleo3/pymol
pyinstall git git@github.com:speleo3/pymol-psico
pyinstall hg https://hg.codeplex.com/csb
Build FREEMOL (see also MovieSchool 6)
#!/bin/bash -e
src=/tmp
prefix=/opt/pymol-git
export FREEMOL=$prefix/freemol
freemoltrunk=$src/freemol-trunk
if [[ ! -e $freemoltrunk ]]; then
svn co svn://bioinformatics.org/svnroot/freemol/trunk $freemoltrunk
fi
cd $freemoltrunk
for name in mpeg_encode mengine apbs pdb2pqr; do
(cd src/$name && ./configure && make && make install)
done
ln -s $FREEMOL $prefix/modules/pymol/pymol_path/freemol
Download all PyMOL scripts from Robert L. Campbell's website:
wget -r -np -nd --level=1 -A .py \
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/