[Chimera-users] command line mode

snoze pa snoze.pa at gmail.com
Tue Feb 26 12:24:50 PST 2008

Hi Eric,
 The scripts is not working.. It is giving me following error message.  Is
it possible to call the minimization step inside the script so that i can
use the bcc charges?
Thanks a lot for your help.

chimera --nogui x.mol2 script.py
Sorry: IndentationError: ('expected an indented block', ('script.py', 6, 8,
'residues = m.residues\n'))Opening x.mol2...Compiling script.py...Compiling
script.py succeededExecuting script.py...
Traceback (most recent call last):
  File "/usr/local/chimera/share/__main__.py", line 59, in ?
    value = chimeraInit.init(sys.argv)
  File "CHIMERA/share/chimeraInit.py", line 350, in init
    chimera.openModels.open(a, prefixableType=1)
  File "CHIMERA/share/chimera/__init__.py", line 1378, in open
  File "CHIMERA/share/chimera/__init__.py", line 865, in _openPython
IndentationError: expected an indented block (script.py, line 6)
Error while processing script.py:
IndentationError: expected an indented block (script.py, line 6)
(see reply log for Python traceback info)

On Mon, Feb 4, 2008 at 4:00 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Snoze, I'm going to guess, like Elaine, that your purpose is to add
> partial charges.  If your 1000 compounds are in one big mol2 file, here is a
> script that would do the job:
> from chimera import openModels, Molecule
> from AddCharge import
> addNonstandardResCharges, estimateFormalCharge, ChargeError
> mols = openModels.list(modelTypes=[Molecule])
> log = open("errlog", "w")
> for m in mols:
> residues = m.residues
> atoms = [a for r in residues for a in r.atoms]
> fc = estimateFormalCharge(atoms)
> try:
> addNonstandardResCharges(m.residues, fc)
> except ChargeError:
> print>>log, "Charge estimate (%d) or protonation wrong for %s (%s)" % (
> fc, m.name, m.oslIdent())
> from WriteMol2 import writeMol2
> writeMol2(mols, "output.mol2")
> log.close()
> If you save the above in a file named script.py and your 1000 compounds
> are in a file named input.mol2, then running:
> chimera --nogui input.mol2 script.py
> will produce a file named output.mol2 with the charges included.  Any
> problems it had charging particular compounds will be saved in a file named
> errlog.
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
> On Feb 1, 2008, at 10:36 AM, Elaine Meng wrote:
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