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(my scripts) |
(Scripts Pastebin) |
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* [[Spectrumany]] | * [[Spectrumany]] | ||
* [[Supercell]] | * [[Supercell]] | ||
| + | |||
| + | === Scripts Pastebin === | ||
| + | |||
| + | Some random scripts with no dedicated PyMOLWiki page. | ||
| + | |||
| + | <source lang="python"> | ||
| + | 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) | ||
| + | </source> | ||
| + | |||
| + | <source lang="python"> | ||
| + | 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) | ||
| + | </source> | ||
Revision as of 22:48, 7 January 2011
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)