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@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