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.
Contact
- speleo3/users.sourceforge.net
- thomas.holder/tuebingen.mpg.de
Scripts written by me
Scripts Pastebin
Some random scripts with no dedicated PyMOLWiki page.
def extra_fit(selection='(all)', reference=None, method=cmd.align):
'''
DESCRIPTION
Like "intra_fit", but for multiple objects instead of
multiple states.
'''
models = cmd.get_object_list(selection)
if reference is None:
reference = models[0]
models = models[1:]
elif reference in models:
models.remove(reference)
if cmd.is_string(method):
method = eval(method)
for model in models:
print model, method(model, reference)
cmd.extend('extra_fit', extra_fit)
def mse2met(selection='all', quiet=1):
'''
DESCRIPTION
Mutate selenomethionine to methionine
'''
quiet = int(quiet)
x = cmd.alter('(%s) and MSE/SE' % selection, 'name="SD";elem="S"')
cmd.alter('(%s) and MSE/' % selection, 'resn="MET";type="ATOM"')
if not quiet:
print 'Altered %d MSE residues to MET' % (x)
cmd.sort()
cmd.extend('mse2met', mse2met)
def remove_alt(selection='all', keep='A', quiet=1):
'''
DESCRIPTION
Remove alternative location atoms.
ARGUMENTS
selection = string: atom selection
keep = string: AltLoc to keep {default: A}
'''
cmd.remove('(%s) and not alt +%s' % (selection, keep), quiet=int(quiet))
cmd.alter(selection, 'alt=""')
cmd.sort()
cmd.extend('remove_alt', remove_alt)
def cbm(selection='(all)'):
'''
DESCRIPTION
Color by molecule
'''
col = 2
for model in cmd.get_object_list(selection):
cmd.color(col, '%s and (%s)' % (model, selection))
col += 1
cmd.extend('cbm', cbm)
def dev2b(selection='name CA'):
'''
DESCRIPTION
Determine the RMSD per residue for a multi-state object and assign b-factor
'''
import numpy
stored.x = dict()
stored.b = dict()
for state in range(1, cmd.count_states()+1):
cmd.iterate_state(state, selection, 'stored.x.setdefault((model,segi,chain,resi,name), []).append([x,y,z])')
for key, coord_list in stored.x.iteritems():
b_sq = numpy.array(coord_list).var(0).mean() # var over states, mean over x,y,z
stored.b[key] = numpy.sqrt(b_sq) * 10.0
cmd.alter(selection, 'b = stored.b[model,segi,chain,resi,name]')
cmd.extend('dev2b', dev2b)
def select_extendbyss(selection, name=None, quiet=0):
'''
DESCRIPTION
Extend selection by connected secondary structure elements.
ARGUMENTS
selection = string: selection-expression
name = string: create a named atom selection if not None {default: None}
'''
def in_intervals(i, intervals):
for interval in intervals:
if interval[0] <= i and i <= interval[1]:
return True
return False
quiet = int(quiet)
stored.x = set()
# only iterate over CAs since for example PyMOL's dss command just
# assignes ss to CAs.
cmd.iterate('bycalpha (%s)' % (selection),
'stored.x.add((model,segi,chain,resv,ss))')
elements = dict()
for model,segi,chain,resv,ss in stored.x:
key = (model,segi,chain,ss)
elements.setdefault(key, [])
if in_intervals(resv, elements[key]):
continue
stored.b = set()
cmd.iterate('/%s/%s/%s//CA and ss "%s"' % key, 'stored.b.add(resv)')
resv_min = resv
resv_max = resv
while (resv_min - 1) in stored.b:
resv_min -= 1
while (resv_max + 1) in stored.b:
resv_max += 1
elements[key].append((resv_min, resv_max))
sele_list = []
ss_names = {'S': 'Strand', 'H': 'Helix', '': 'Loop'}
for key in elements:
model,segi,chain,ss = key
for resv_min,resv_max in elements[key]:
sele = '/%s/%s/%s/%d-%d' % (model, segi, chain, resv_min, resv_max)
sele_list.append(sele)
if not quiet:
print ss_names.get(ss, ss), sele
sele = ' or '.join(sele_list)
if name is not None:
cmd.select(name, sele)
if not quiet:
print 'Selection:', sele
return sele
cmd.extend('select_extendbyss', select_extendbyss)
def diff(sele1, sele2, byres=1, name=None, operator='in', quiet=0):
'''
DESCRIPTION
Difference between two molecules
ARGUMENTS
sele1 = string: atom selection
sele2 = string: atom selection
byres = 0/1: report residues, not atoms (does not affect selection)
{default: 1}
operator = in/like/align: operator to match atoms {default: in}
SEE ALSO
symdiff
'''
byres, quiet = int(byres), int(quiet)
if name is None:
name = cmd.get_unused_name('diff')
if operator == 'align':
alnobj = cmd.get_unused_name('__aln')
cmd.align(sele1, sele2, cycles=0, transform=0, object=alnobj)
sele = '(%s) and not %s' % (sele1, alnobj)
cmd.select(name, sele)
cmd.delete(alnobj)
else:
sele = '(%s) and not ((%s) %s (%s))' % (sele1, sele1, operator, sele2)
cmd.select(name, sele)
if not quiet:
if byres:
seleiter = 'byca ' + name
expr = 'print "/%s/%s/%s/%s`%s" % (model,segi,chain,resn,resi)'
else:
seleiter = name
expr = 'print "/%s/%s/%s/%s`%s/%s" % (model,segi,chain,resn,resi,name)'
cmd.iterate(seleiter, expr)
return name
def symdiff(sele1, sele2, byres=1, name=None, operator='in', quiet=0):
'''
DESCRIPTION
Symmetric difference between two molecules
SEE ALSO
diff
'''
byres, quiet = int(byres), int(quiet)
if name is None:
name = cmd.get_unused_name('symdiff')
tmpname = cmd.get_unused_name('__tmp')
diff(sele1, sele2, byres, name, operator, quiet)
diff(sele2, sele1, byres, tmpname, operator, quiet)
cmd.select(name, tmpname, merge=1)
cmd.delete(tmpname)
return name
cmd.extend('symdiff', symdiff)
cmd.extend('diff', diff)
def polarpairs(sel1, sel2, cutoff=4.0, angle=63.0, name='', quiet=1):
'''
ARGUMENTS
sel1, sel2 = string: atom selections
cutoff = float: distance cutoff
angle = float: h-bond angle cutoff in degrees. If angle="default", take
"h_bond_max_angle" setting. If angle=0, do not detect h-bonding.
SEE ALSO
cmd.find_pairs, cmd.distance
'''
cutoff = float(cutoff)
quiet = int(quiet)
if angle == 'default':
angle = cmd.get('h_bond_max_angle', cmd.get_object_list(sel1)[0])
angle = float(angle)
mode = 1 if angle > 0 else 0
x = cmd.find_pairs('(%s) and donors' % sel1, '(%s) and acceptors' % sel2,
cutoff=cutoff, mode=mode, angle=angle) + \
cmd.find_pairs('(%s) and acceptors' % sel1, '(%s) and donors' % sel2,
cutoff=cutoff, mode=mode, angle=angle)
x = sorted(set(x))
if not quiet:
print 'Settings: cutoff=%.1fangstrom angle=%.1fdegree' % (cutoff, angle)
print 'Found %d polar contacts' % (len(x))
if len(name) > 0:
for p in x:
cmd.distance(name, '(%s`%s)' % p[0], '(%s`%s)' % p[1])
return x
cmd.extend('polarpairs', polarpairs)
Launch interactive python terminal with PyMOL process:
#!/bin/bash
moddir=/opt/pymol-svn/lib/python2.6/site-packages
export PYTHONPATH="$moddir:$PYTHONPATH"
export PYMOL_PATH="$moddir/pymol/pymol_path"
export PYMOL_DATA="$PYMOL_PATH/data"
exec python2.6 -i -c "
import readline
import rlcompleter
readline.parse_and_bind('tab: complete')
import pymol
pymol.pymol_argv = ['pymol','-qc']
pymol.finish_launching()
cmd = pymol.cmd
"