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My name is Thomas Holder and I | My name is Thomas Holder and I worked on PyMOL for [https://www.schrodinger.com Schrödinger] 2012-2021. | ||
I was awarded the [http://pymol.org/fellowship Warren L. DeLano Memorial PyMOL Open-Source Fellowship] for 2011-2012. | |||
== Scripts written by me == | |||
* [[AAindex]] | * [[AAindex]] | ||
* [[AngleBetweenHelices]] | * [[AngleBetweenHelices]] | ||
* [[Extra fit]] | |||
* [[PluginDirectory]] | |||
* [[Pml2py]] | * [[Pml2py]] | ||
* [[Polarpairs]] | |||
* [[Save settings]] | |||
* [[Show bumps]] | * [[Show bumps]] | ||
* [[Sidechaincenters]] | * [[Sidechaincenters]] | ||
* [[Spectrumany]] | * [[Spectrumany]] | ||
* [[Spectrum states]] | |||
* [[Supercell]] | * [[Supercell]] | ||
== Scripts Pastebin == | |||
Some random scripts with no dedicated PyMOLWiki page. | Some random scripts with no dedicated PyMOLWiki page. | ||
Launch interactive python terminal with PyMOL process: | |||
(see also [[Launching From a Script]]) | |||
<source lang="python"> | <source lang="python"> | ||
#!/usr/bin/ipython2.7 -i | |||
import threading | |||
import pymol._cmd | |||
pymol.invocation.parse_args(['pymol', '-qc']) | |||
with threading.RLock(): | |||
_COb = pymol._cmd._new(pymol, pymol.invocation.options) | |||
pymol._cmd._start(_COb, pymol.cmd) | |||
pymol.cmd._COb = _COb | |||
from pymol import cmd | |||
</source> | </source> | ||
<source lang="python"> | <source lang="python"> | ||
#!/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 | |||
</source> | |||
Build FREEMOL (see also [[MovieSchool 6]]) | |||
<source lang="bash"> | |||
#!/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 | |||
</source> | </source> | ||
Download all PyMOL scripts from Robert L. Campbell's website: | |||
<source lang="bash"> | |||
wget -r -np -nd --level=1 -A .py \ | |||
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ | |||
</source> | </source> | ||
<source lang=" | Render movie from PNG files (save as <code>png2mpeg1.sh</code>): | ||
<source lang="bash"> | |||
#!/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" | |||
</source> | </source> | ||
=== Export movie with transparent background === | |||
<source lang="python"> | <source lang="python"> | ||
# make transparent pngs | |||
set opaque_background, off | |||
set ray_trace_frames | |||
mpng foo | |||
# create movie file (use codec "qtrle" or "png") | |||
system ffmpeg -i foo%04d.png -vcodec qtrle foo.mov | |||
# clean up | |||
system rm -f foo????.png | |||
</source> | |||
=== load_mtz_cctbx: Load MTZ files with a [[CCTBX]] wrapper (3 files) === | |||
1) ~/bin/mtz2ccp4.sh | |||
<source lang="bash"> | |||
#!/bin/bash | |||
export PATH=/opt/ccp4/ccp4-6.5/bin:$PATH | |||
exec cctbx.python ~/bin/mtz2ccp4.py "$@" | |||
</source> | </source> | ||
2) ~/bin/mtz2ccp4.py | |||
<source lang="python"> | <source lang="python"> | ||
def | #!/opt/ccp4/ccp4-6.5/bin/cctbx.python | ||
import os | |||
import sys | |||
import tempfile | |||
def mtz2ccp4maps(filename, prefix='map'): | |||
''' | |||
Creates a temporary directory and dumps all maps from the given MTZ file | |||
into this directory as CCP4 maps files. Returns the path of the temporary | |||
directory. | |||
''' | ''' | ||
from iotbx.reflection_file_reader import any_reflection_file | |||
hkl_in = any_reflection_file(file_name=filename) | |||
temp_dir = tempfile.mkdtemp() | |||
for i_map, array in enumerate(hkl_in.as_miller_arrays()): | |||
if array.is_complex_array(): | |||
fft_map = array.fft_map(resolution_factor=0.25).apply_sigma_scaling() | |||
map_filename = os.path.join(temp_dir, | |||
prefix + '_' + '_'.join(array.info().labels) + '.ccp4') | |||
fft_map.as_ccp4_map(file_name=map_filename) | |||
return temp_dir | |||
# print the name of the temporary directory to standard output | |||
print mtz2ccp4maps(*sys.argv[1:]) | |||
</source> | |||
3) ~/.pymolrc.py | |||
<source lang="python"> | |||
@cmd.extend | |||
def load_mtz_cctbx(filename, prefix=''): | |||
''' | ''' | ||
DESCRIPTION | |||
Load all maps from an MTZ file, using the mtz2ccp4.sh wrapper which | |||
uses iotbx (cctbx). | |||
''' | ''' | ||
import subprocess | |||
import glob | |||
import shutil | |||
if not prefix: | |||
prefix = os.path.basename(filename).rpartition('.')[0] | |||
outdir = subprocess.Popen([os.path.expanduser('~/bin/mtz2ccp4.sh'), | |||
filename, prefix], stdout=subprocess.PIPE).stdout.readlines()[0].strip() | |||
for mapfilename in glob.glob(os.path.join(outdir, '*.ccp4')): | |||
cmd.load(mapfilename) | |||
shutil.rmtree(outdir) | |||
</source> | </source> | ||
=== ccmutate === | |||
<source lang="python"> | <source lang="python"> | ||
def | @cmd.extend | ||
def ccmutate(code, selection='??sele|?pk1', sculpt=1): | |||
''' | ''' | ||
DESCRIPTION | |||
Mutate selected residue. | |||
ARGUMENTS | ARGUMENTS | ||
code = str: 3-letter PDBeChem chemical component identifier | |||
selection = str: single residue selection {default: pk1 or sele} | |||
sculpt = 0/1: try to adopt conformation of replaced sidechain, followed | |||
by relaxation using sculpting {default: 1} | |||
EXAMPLE | |||
fetch 1ubq, async=0 | |||
ccmutate 0HG, resi 24 | |||
SEE ALSO | SEE ALSO | ||
fetch ..., type=cc | |||
wizard mutagenesis | |||
''' | ''' | ||
code = code.upper() | |||
cmd. | tmp_sele = cmd.get_unused_name('_sele') | ||
tmp_frag = cmd.get_unused_name('_frag') | |||
tmp_Nnbr = cmd.get_unused_name('_Nnbr') | |||
tmp_back = cmd.get_unused_name('_back') | |||
tmp_tmpl = cmd.get_unused_name('_tmpl') | |||
tmp_sc_o = cmd.get_unused_name('_sc_o') | |||
tmp_sc_n = cmd.get_unused_name('_sc_n') | |||
try: | |||
cmd.select(tmp_sele, 'byres (' + selection + ')', 0) | |||
# check input selection | |||
if cmd.count_atoms('name CA & ?' + tmp_sele) != 1: | |||
raise pymol.CmdException('selection must include exactly one residue') | |||
if cmd.count_atoms('name N+CA+C & ?' + tmp_sele) != 3: | |||
raise pymol.CmdException("selected residue doesn't have N+CA+C atoms") | |||
# PDBeChem fragment | |||
cmd.fetch(code, tmp_frag, type='cc', zoom=0) | |||
# check if fragment is amino acid | |||
if cmd.count_atoms('name N+CA+C & ?' + tmp_frag) != 3: | |||
raise pymol.CmdException("residue '%s' doesn't have N+CA+C atoms" % (code)) | |||
# only keep hydrogens if target also has hydrogens | |||
if cmd.count_atoms('hydro & ?' + tmp_sele) == 0: | |||
cmd.remove('hydro & ?' + tmp_frag) | |||
# update residue name for old residue | |||
cmd.alter(tmp_sele, 'resn = ' + repr(code)) | |||
# superpose fragment on backbone | |||
( | cmd.align( | ||
'name N+CA+C & ?' + tmp_frag, | |||
'name N+CA+C & ?' + tmp_sele) | |||
# extra N bonds, like in PRO | |||
cmd.select(tmp_Nnbr, 'neighbor (name N & ?' + tmp_frag + ')', 0) | |||
# backbone selection | |||
cmd.select(tmp_back, 'name CA+C+O+N+OXT', 0) | |||
cmd.select(tmp_back, 'hydro & neighbor ?' + tmp_back, 0, merge=1) | |||
# | # remove complementary atoms | ||
cmd.remove( '?' + tmp_frag + ' & ' + tmp_back) | |||
cmd.extract(tmp_tmpl, '?' + tmp_sele + ' & !' + tmp_back, zoom=0) | |||
if cmd.count_atoms(tmp_frag): | |||
# attach new sidechain | |||
cmd.fuse('name CB & ?' + tmp_frag, 'name CA & ?' + tmp_sele, mode=1, move=0) | |||
cmd.unpick() | |||
# | # new atom selections | ||
cmd.select(tmp_sc_n, '(byres ?' + tmp_sele + ') & !?' + tmp_sele, 0) | |||
cmd.select(tmp_sc_o, '?' + tmp_sc_n + ' like ?' + tmp_tmpl, 0) | |||
# extra N bonds, like in PRO | |||
( | if cmd.count_atoms(tmp_Nnbr): | ||
cmd.bond('?' + tmp_sc_n + ' like ?' + tmp_Nnbr, 'name N & ?' + tmp_sele) | |||
# adopt old conformation, if possible | |||
# | if int(sculpt): | ||
model = cmd.get_object_list('?' + tmp_sele)[0] | |||
cmd.protect(model) | |||
cmd.deprotect('?' + tmp_sc_n + ' & !?' + tmp_sc_o) | |||
cmd.sculpt_activate(model) | |||
if cmd.count_atoms(tmp_sc_o): | |||
cmd.update(tmp_sc_o, tmp_tmpl) | |||
cmd.set('sculpt_field_mask', 63) # local geom + vdw | |||
cmd.sculpt_iterate(model, cycles=100) | |||
cmd.deprotect(tmp_sc_o) | |||
cmd.set('sculpt_field_mask', 0xff) # all | |||
cmd.sculpt_iterate(model, cycles=200) | |||
cmd.set('sculpt_field_mask', 31) # local geom | |||
cmd.sculpt_iterate(model, cycles=200) | |||
finally: | |||
cmd.delete(tmp_sele) | |||
cmd.delete(tmp_frag) | |||
cmd.delete(tmp_Nnbr) | |||
cmd.delete(tmp_back) | |||
cmd.delete(tmp_tmpl) | |||
cmd.delete(tmp_sc_o) | |||
cmd.delete(tmp_sc_n) | |||
</source> | |||
=== CTRL-L ligand zoom === | |||
<source lang="python"> | |||
@cmd.set_key('CTRL-L') | |||
def ligand_zoom(): | |||
global _current_ligand | |||
s = {'ligand_set': set()} | |||
if cmd.iterate('organic', 'ligand_set.add((model,segi,chain,resi))', | |||
space=s) < 1: | |||
return | |||
ligands = sorted(s["ligand_set"]) | |||
try: | |||
i = ligands.index(_current_ligand) | |||
except (ValueError, NameError): | |||
i = -1 | |||
i = (i + 1) % len(ligands) | |||
_current_ligand = ligands[i] | |||
# use "do" for feedback | |||
cmd.do('zoom /%s/%s/%s & resi %s, animate=1, buffer=2' % ligands[i]) | |||
</source> | </source> | ||
=== Compile on FreeBSD === | |||
pkg upgrade | |||
pkg install subversion py27-Pmw glew freeglut png freetype2 libxml2 msgpack | |||
python2 setup.py install --prefix=$HOME/opt/pymol-svn |
Latest revision as of 17:55, 23 November 2021
My name is Thomas Holder and I worked on PyMOL for Schrödinger 2012-2021.
I was awarded the Warren L. DeLano Memorial PyMOL Open-Source Fellowship for 2011-2012.
Scripts written by me
- AAindex
- AngleBetweenHelices
- Extra fit
- PluginDirectory
- Pml2py
- Polarpairs
- Save settings
- Show bumps
- Sidechaincenters
- Spectrumany
- Spectrum states
- Supercell
Scripts Pastebin
Some random scripts with no dedicated PyMOLWiki page.
Launch interactive python terminal with PyMOL process: (see also Launching From a Script)
#!/usr/bin/ipython2.7 -i
import threading
import pymol._cmd
pymol.invocation.parse_args(['pymol', '-qc'])
with threading.RLock():
_COb = pymol._cmd._new(pymol, pymol.invocation.options)
pymol._cmd._start(_COb, pymol.cmd)
pymol.cmd._COb = _COb
from pymol import cmd
#!/usr/bin/python2.6 -i
import sys, os
# autocompletion
import readline
import rlcompleter
readline.parse_and_bind('tab: complete')
# pymol environment
moddir='/opt/pymol-svn/modules'
sys.path.insert(0, moddir)
os.putenv('PYMOL_PATH', os.path.join(moddir, 'pymol/pymol_path'))
# pymol launching
import pymol
pymol.pymol_argv = ['pymol','-qc'] + sys.argv[1:]
pymol.finish_launching()
cmd = pymol.cmd
Build FREEMOL (see also MovieSchool 6)
#!/bin/bash -e
src=/tmp
prefix=/opt/pymol-git
export FREEMOL=$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"
Export movie with transparent background
# make transparent pngs
set opaque_background, off
set ray_trace_frames
mpng foo
# create movie file (use codec "qtrle" or "png")
system ffmpeg -i foo%04d.png -vcodec qtrle foo.mov
# clean up
system rm -f foo????.png
load_mtz_cctbx: Load MTZ files with a CCTBX wrapper (3 files)
1) ~/bin/mtz2ccp4.sh
#!/bin/bash
export PATH=/opt/ccp4/ccp4-6.5/bin:$PATH
exec cctbx.python ~/bin/mtz2ccp4.py "$@"
2) ~/bin/mtz2ccp4.py
#!/opt/ccp4/ccp4-6.5/bin/cctbx.python
import os
import sys
import tempfile
def mtz2ccp4maps(filename, prefix='map'):
'''
Creates a temporary directory and dumps all maps from the given MTZ file
into this directory as CCP4 maps files. Returns the path of the temporary
directory.
'''
from iotbx.reflection_file_reader import any_reflection_file
hkl_in = any_reflection_file(file_name=filename)
temp_dir = tempfile.mkdtemp()
for i_map, array in enumerate(hkl_in.as_miller_arrays()):
if array.is_complex_array():
fft_map = array.fft_map(resolution_factor=0.25).apply_sigma_scaling()
map_filename = os.path.join(temp_dir,
prefix + '_' + '_'.join(array.info().labels) + '.ccp4')
fft_map.as_ccp4_map(file_name=map_filename)
return temp_dir
# print the name of the temporary directory to standard output
print mtz2ccp4maps(*sys.argv[1:])
3) ~/.pymolrc.py
@cmd.extend
def load_mtz_cctbx(filename, prefix=''):
'''
DESCRIPTION
Load all maps from an MTZ file, using the mtz2ccp4.sh wrapper which
uses iotbx (cctbx).
'''
import subprocess
import glob
import shutil
if not prefix:
prefix = os.path.basename(filename).rpartition('.')[0]
outdir = subprocess.Popen([os.path.expanduser('~/bin/mtz2ccp4.sh'),
filename, prefix], stdout=subprocess.PIPE).stdout.readlines()[0].strip()
for mapfilename in glob.glob(os.path.join(outdir, '*.ccp4')):
cmd.load(mapfilename)
shutil.rmtree(outdir)
ccmutate
@cmd.extend
def ccmutate(code, selection='??sele|?pk1', sculpt=1):
'''
DESCRIPTION
Mutate selected residue.
ARGUMENTS
code = str: 3-letter PDBeChem chemical component identifier
selection = str: single residue selection {default: pk1 or sele}
sculpt = 0/1: try to adopt conformation of replaced sidechain, followed
by relaxation using sculpting {default: 1}
EXAMPLE
fetch 1ubq, async=0
ccmutate 0HG, resi 24
SEE ALSO
fetch ..., type=cc
wizard mutagenesis
'''
code = code.upper()
tmp_sele = cmd.get_unused_name('_sele')
tmp_frag = cmd.get_unused_name('_frag')
tmp_Nnbr = cmd.get_unused_name('_Nnbr')
tmp_back = cmd.get_unused_name('_back')
tmp_tmpl = cmd.get_unused_name('_tmpl')
tmp_sc_o = cmd.get_unused_name('_sc_o')
tmp_sc_n = cmd.get_unused_name('_sc_n')
try:
cmd.select(tmp_sele, 'byres (' + selection + ')', 0)
# check input selection
if cmd.count_atoms('name CA & ?' + tmp_sele) != 1:
raise pymol.CmdException('selection must include exactly one residue')
if cmd.count_atoms('name N+CA+C & ?' + tmp_sele) != 3:
raise pymol.CmdException("selected residue doesn't have N+CA+C atoms")
# PDBeChem fragment
cmd.fetch(code, tmp_frag, type='cc', zoom=0)
# check if fragment is amino acid
if cmd.count_atoms('name N+CA+C & ?' + tmp_frag) != 3:
raise pymol.CmdException("residue '%s' doesn't have N+CA+C atoms" % (code))
# only keep hydrogens if target also has hydrogens
if cmd.count_atoms('hydro & ?' + tmp_sele) == 0:
cmd.remove('hydro & ?' + tmp_frag)
# update residue name for old residue
cmd.alter(tmp_sele, 'resn = ' + repr(code))
# superpose fragment on backbone
cmd.align(
'name N+CA+C & ?' + tmp_frag,
'name N+CA+C & ?' + tmp_sele)
# extra N bonds, like in PRO
cmd.select(tmp_Nnbr, 'neighbor (name N & ?' + tmp_frag + ')', 0)
# backbone selection
cmd.select(tmp_back, 'name CA+C+O+N+OXT', 0)
cmd.select(tmp_back, 'hydro & neighbor ?' + tmp_back, 0, merge=1)
# remove complementary atoms
cmd.remove( '?' + tmp_frag + ' & ' + tmp_back)
cmd.extract(tmp_tmpl, '?' + tmp_sele + ' & !' + tmp_back, zoom=0)
if cmd.count_atoms(tmp_frag):
# attach new sidechain
cmd.fuse('name CB & ?' + tmp_frag, 'name CA & ?' + tmp_sele, mode=1, move=0)
cmd.unpick()
# new atom selections
cmd.select(tmp_sc_n, '(byres ?' + tmp_sele + ') & !?' + tmp_sele, 0)
cmd.select(tmp_sc_o, '?' + tmp_sc_n + ' like ?' + tmp_tmpl, 0)
# extra N bonds, like in PRO
if cmd.count_atoms(tmp_Nnbr):
cmd.bond('?' + tmp_sc_n + ' like ?' + tmp_Nnbr, 'name N & ?' + tmp_sele)
# adopt old conformation, if possible
if int(sculpt):
model = cmd.get_object_list('?' + tmp_sele)[0]
cmd.protect(model)
cmd.deprotect('?' + tmp_sc_n + ' & !?' + tmp_sc_o)
cmd.sculpt_activate(model)
if cmd.count_atoms(tmp_sc_o):
cmd.update(tmp_sc_o, tmp_tmpl)
cmd.set('sculpt_field_mask', 63) # local geom + vdw
cmd.sculpt_iterate(model, cycles=100)
cmd.deprotect(tmp_sc_o)
cmd.set('sculpt_field_mask', 0xff) # all
cmd.sculpt_iterate(model, cycles=200)
cmd.set('sculpt_field_mask', 31) # local geom
cmd.sculpt_iterate(model, cycles=200)
finally:
cmd.delete(tmp_sele)
cmd.delete(tmp_frag)
cmd.delete(tmp_Nnbr)
cmd.delete(tmp_back)
cmd.delete(tmp_tmpl)
cmd.delete(tmp_sc_o)
cmd.delete(tmp_sc_n)
CTRL-L ligand zoom
@cmd.set_key('CTRL-L')
def ligand_zoom():
global _current_ligand
s = {'ligand_set': set()}
if cmd.iterate('organic', 'ligand_set.add((model,segi,chain,resi))',
space=s) < 1:
return
ligands = sorted(s["ligand_set"])
try:
i = ligands.index(_current_ligand)
except (ValueError, NameError):
i = -1
i = (i + 1) % len(ligands)
_current_ligand = ligands[i]
# use "do" for feedback
cmd.do('zoom /%s/%s/%s & resi %s, animate=1, buffer=2' % ligands[i])
Compile on FreeBSD
pkg upgrade pkg install subversion py27-Pmw glew freeglut png freetype2 libxml2 msgpack python2 setup.py install --prefix=$HOME/opt/pymol-svn