[Chimera-users] different behavior of the Win and OS-X version seen in case of surface calculations

Marek Maly marek.maly at ujep.cz
Mon Dec 15 06:02:55 PST 2014


Hello,

I found already several times the differences between

OS-X and Win version of Chimera (1.10.).

Problem is regarding the ability to calculate molecular surface.

There are some cases when Win version of Chimera 1.10 is not able to
calculate molecular surface of some more complicated molecular structure
(e.g. protein) but on the other hand the OS-X version of Chimera (again  
1.10)
is able to do it (although writes warning that there was some partial  
problems).

Moreover when I create PY session of such molecule with surface  
calculated/visualized under OS-X
and then I want to open this session under Win version it is opened but  
without the surface
and writes many errors into the log - see below.

In both versions I am using default settings (no special changes in  
parameters important
for the surface calc.).

How is this different behavior of the same program under Win and OS-X  
possible ? Do you have any recommendation how to eliminate this problem ?

   Thank you in advance,

          Best wishes,

                 Marek

Here is the err list after the attempt to load into Win Chimera 1.10  
session containing "problematic" molecule with surface calculated under  
OS-X version of the Chimera 1.10

*****

C:\Program Files\Chimera 1.10\bin\mscalc.exe 1.400000 2.000000 0
MSMSLIB 1.3 started on Local PC
Copyright M.F. Sanner (March 2000)
Compilation flags
Surface calculation failed, mscalc returned code 5.

Surface calculation frequently fails for large, multi-chain structures.  
The calculation may be successful if the chains are treated individually,  
by using the "split" command before generating a surface.  If splitting is  
not desired or the structure is already a single chain, changing molecular  
surface parameters in the Selection Inspector or (before surface creation)  
the New Surfaces category of Preferences may allow the calculation to  
succeed. More details are given at

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html

Traceback (most recent call last):
   File "gB_2G_S16_A.py", line 2669, in <module>
     restoreCoreModels()
   File "gB_2G_S16_A.py", line 2654, in restoreCoreModels
     restoreSurfaces(surfInfo)
   File "C:\Program Files\Chimera  
1.10\share\SimpleSession\versions\v40.py", line 55, in restoreSurfaces
     elif len(customColors) != len(s.triangleData()[0]):
TypeError: 'NoneType' object has no attribute '__getitem__'
Error restoring core models:
TypeError: 'NoneType' object has no attribute '__getitem__'

   File "C:\Program Files\Chimera  
1.10\share\SimpleSession\versions\v40.py", line 55, in restoreSurfaces
     elif len(customColors) != len(s.triangleData()[0]):

See reply log for Python traceback.


Traceback (most recent call last):
   File "gB_2G_S16_A.py", line 3025, in <module>
     restoreRemainder()
   File "gB_2G_S16_A.py", line 3020, in restoreRemainder
     restoreSilhouettes(silhouettes)
   File "C:\Program Files\Chimera  
1.10\share\SimpleSession\versions\v62.py", line 265, in restoreSilhouettes
     model = idLookup(modelID)
   File "C:\Program Files\Chimera  
1.10\share\SimpleSession\versions\v23.py", line 162, in idLookup
     return globals.sessionMap[sesID]
KeyError: 27136
Error restoring post-model state:
KeyError: 27136

   File "C:\Program Files\Chimera  
1.10\share\SimpleSession\versions\v23.py", line 162, in idLookup
     return globals.sessionMap[sesID]

See reply log for Python traceback.


Warning: Could not restore surface color on surface model
with id 0.0 because that surface was not restored.
C:\Program Files\Chimera  
1.10\bin\lib\site-packages\matplotlib\axes.py:2369: UserWarning:  
Attempting to set identical left==right results
in singular transformations; automatically expanding.
left=1, right=1
   + 'left=%s, right=%s') % (left, right))



-- 
Tato zpráva byla vytvořena převratným poštovním klientem Opery:  
http://www.opera.com/mail/


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