User:Speleo3

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My name is Thomas Holder and I work for PyMOL at Schrödinger.

I was awarded the Warren L. DeLano Memorial PyMOL Open-Source Fellowship for 2011-2012.

Contact

Scripts written by me

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
 
sed -i 's/vdwtype\[11\]/vdwtype[14]/' src/mengine/src/field.h
 
for name in mpeg_encode mengine apbs pdb2pqr; do
    (cd src/$name && ./configure && make && make install)
done
 
cp -na freemol/libpy/freemol $prefix/modules/
 
ln -sfT $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/

Render movie from PNG files (save as png2mpeg1.sh):

#!/bin/bash
 
set -e
 
usage="usage: $(basename $0) [-w width] [-f fps] [-b vbitrate] <indir> <outfile.mpeg>"
width=""
fps=25
vbitrate=16000
 
args="$(getopt w:f:b:h "$@")" || args="-h"
set -- $args
 
while [[ $# > 0 ]]; do
    case "$1" in
        --) shift; break ;;
        -w) width=$2; shift 2 ;;
        -f) fps=$2; shift 2 ;;
        -b) vbitrate=$2; shift 2 ;;
        -h) echo $usage; exit 1 ;;
        *) echo "argument error: $1"; exit 1 ;;
    esac
done
 
if [[ $# > 2 ]]; then
    echo "too many arguments: $3 ..."
    echo $usage
    exit 1
fi
 
indir="$1"
outfile="$2"
 
if [[ -z "$indir" ]]; then
    echo "error: indir missing"
    echo $usage
    exit 2
fi
 
if [[ -z "$outfile" ]]; then
    echo "error: outfile missing"
    echo $usage
    exit 3
fi
 
MENCODER="mencoder -quiet"
MPEG1ARGS="-mf type=png:fps=$fps -ovc lavc -forceidx -noskip \
    -of rawvideo -mpegopts format=mpeg1 \
    -lavcopts vcodec=mpeg1video:vbitrate=$vbitrate:vhq:trell:keyint=25"
 
if [[ -n "$width" ]]; then
    MPEG1ARGS="-zoom -xy $width -sws 9 $MPEG1ARGS"
fi
 
pattern="mf://$indir/*.png"
$MENCODER "$pattern" $MPEG1ARGS:vpass=1 -o /dev/null
$MENCODER "$pattern" $MPEG1ARGS:vpass=2 -o "$outfile"
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