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@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

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