[Chimera-users] Surfaces

hsosa at aecom.yu.edu hsosa at aecom.yu.edu
Fri Aug 15 09:18:51 PDT 2008

Hi Elaine,

The problem does not happen all the time. Sometimes I can display 
surfaces from the pdbs that cause problems. However, after displaying 
surfaces from these files, running chimera (trying to rotate or move the 
molecules) becomes very slow.

This is the error message I get when failing to display surfaces:

C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 1
Calculation of some surface components failed (code 5).
Falling back to single-component calculation.
C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0
Surface calculation failed, mscalc returned code 5

Two pdb files that I've been having problems with are 1JFF and 2P4N.



Elaine Meng wrote:
> Hi Hernando,
> Well, lots of things related to surfaces have changed, but in general 
> significantly reducing the failure rate from before -
> see "Surfaces" and "Major Bugs Fixed" in the release notes:
> http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2540.html
> There are also more messages than before, so perhaps the same errors 
> occurred before but you didn't know about them. Sometimes the error is 
> just in one component such as an interior bubble that you don't really 
> care about. Is the surface that was displayed before not displayed 
> now? Also, it is difficult to know what you mean without an example 
> (you could just give a PDB ID) and your telling us exactly what error 
> message you got.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> http://www.cgl.ucsf.edu/home/meng/index.html
> On Aug 14, 2008, at 11:56 AM, hsosa at aecom.yu.edu wrote:
>> Have something related to displaying surfaces changed in the last
>> production release version of chimera ?.
>> I now get error messages when trying to display surfaces from some pdb
>> files that used to work in the previous version.

Hernando Sosa
Dept. of Physiology and Biophysics
Albert Einstein College of Medicine
1300 Morris Park Av.
Bronx NY 10461
phone	(718) 430-3456
FAX	(718) 430-8819
email	hsosa at aecom.yu.edu

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