[Chimera-users] minimization using python

[divya neelagiri]

Hello,

I am using python to go through all the files in a directory and minimize
them using chimera. But the problem is I get and error when I try to
minimize a file having Br. I have a lot of files in that directory. So  is
there any way by which I can skip the file that has error and go onto the
next file? Any suggestion would br greatly appreciated.

Thank you,
Divya



On Sat, Jan 7, 2012 at 2:51 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi George,
> I didn't have a problem when I tried Intersurf, so must be something
> specific.
>
> To report a problem, please use Help... Report a Bug in the Chimera menu
> and include any information (you can attach a session file or structure
> file and describe all steps you did) needed to reproduce the problem.
>
> The chimera-users email address is for meant discussion and questions, not
> bug reports.
>
> Thanks,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
> On Jan 7, 2012, at 10:15 AM, George Tzotzos wrote:
>
> > Hi Elaine,
> >
> > I've done so. It kick an error message "AttributeError: 'NoneType'
> object has no attribute 'atoms'". Please see below.
> >
> > Many thanks for your help
> >
> > George
> >
> >
> > #0, chain A: odorant binding protein
> > #0, chain B: odorant binding protein
> > <type 'exceptions.AttributeError'> Exception in Tk callback
> >   Function: <function command at 0x12e233f50> (type: <type 'function'>)
> >   Args: ()
> > Traceback (innermost last):
> >   File
> "/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
> line 1747, in __call__
> >     return apply(self.func, args)
> >   File
> "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py",
> line 438, in command
> >     getattr(s, buttonFuncName(txt))()
> >   File
> "/Applications/Chimera.app/Contents/Resources/share/Intersurf/Intersurf.py",
> line 173, in Apply
> >     bias, prune, pruneDistance)
> >   File
> "/Applications/Chimera.app/Contents/Resources/share/Intersurf/Intersurf.py",
> line 179, in doApply
> >     m1_list = SurfMaker.GetAtomList(m1, m2, pruneDistance)
> >   File
> "/Applications/Chimera.app/Contents/Resources/share/Intersurf/SurfMaker.py",
> line 69, in GetAtomList
> >     rList = _pruneResidues(rList, prune, pruneDist)
> >   File
> "/Applications/Chimera.app/Contents/Resources/share/Intersurf/SurfMaker.py",
> line 46, in _pruneResidues
> >     rCentroids = _getCentroids(rList)
> >   File
> "/Applications/Chimera.app/Contents/Resources/share/Intersurf/SurfMaker.py",
> line 33, in _getCentroids
> >     for a in r.atoms:
> > <type 'exceptions.AttributeError'>: 'NoneType' object has no attribute
> 'atoms'
> >
> > AttributeError: 'NoneType' object has no attribute 'atoms'
> >
> >   File
> "/Applications/Chimera.app/Contents/Resources/share/Intersurf/SurfMaker.py",
> line 33, in _getCentroids
> >     for a in r.atoms:
> >
> > On Jan 7, 2012, at 7:01 PM, Elaine Meng wrote:
> >
> >> Hi George,
> >> Make sure you have the pruning option turned on (check the box for
> "Residue centroid distance pruning") or else the distance setting won't
> have any effect.  That is probably the problem.
> >> Best,
> >> Elaine
> >> -----
> >> Elaine C. Meng, Ph.D.
> >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> >> Department of Pharmaceutical Chemistry
> >> University of California, San Francisco
> >>
> >>
> >>
> >> On Jan 7, 2012, at 9:48 AM, George Tzotzos wrote:
> >>
> >>> Hi everybody and happy New Year
> >>>
> >>> I'm using Intersurf to define the interface between two sub-units of a
> protein.
> >>>
> >>> Intersurf selects the atoms which appear to be far from the interface.
> Changing the prune distance from the default value of 30 to, say 10 or less
> has no effect on the atom selection. Is this right? Is there a way to
> select atoms that lie, say 5 Angstrom on either side of the interface.
> >>>
> >>> Thanks and best regards
> >>>
> >>> George
> >>>
> >>
> >
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120110/7da57729/attachment.html>