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

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 15 09:54:57 PST 2014


Hi Marek,
Even though the code is identical, these are numerical failures which are (a) rather unpredictable, and (b) may vary between platforms due to small rounding differences, as discussed here:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>

Sorry for the problems,
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 Dec 15, 2014, at 6:02 AM, Marek Maly <marek.maly at ujep.cz> wrote:

> 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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