[Chimera-users] Intersurf

[George Tzotzos]

Thanks Elaine,

I shall do so. I was not sure whether it was a bug or my "doing".

Best regards

George
On Jan 7, 2012, at 8:51 PM, Elaine Meng 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
>>>> 
>>> 
>> 
>