[Chimera-users] Surface calculations difficulties

Sarah Piper s.piper at imb.uq.edu.au
Wed Nov 9 15:50:44 PST 2016


Hi everyone,

I’ve been struggling with getting the structure surface of my molecule shown (actions  surface - show). Even after going through a list of suggestions of how to overcome this problem (e.g. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html ), I can’t get all needed surfaces displayed.

Some other .pdb files work without a problem, but mine doesn’t or just works partially (e.g. just one chain instead of all chains), without seeing any apparent differences in the .pdb files or molecule sizes.

A while ago I did not encounter this problem (using the same molecule/file), so is this maybe a chimera version problem?
Or do the .pdb files have to be in a certain format?


I usually get the following errors:

"Surface calculation failed, mscalc returned code 2.

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”


My main use of surfaces in chimera is to display electrostatic potential files (or hydrophobicity plots) calculated in APBS and others. I’m using Chimera v1.9 on a Mac (but I had the same problems on a Linux workstation).

I'd appreciate any feedback or reply!


Many thanks for your help,


Sarah




…………………………………………………………………..
Sarah Piper, PhD student
University of Queensland, St Lucia, 4072 QLD, Australia

Phone: +61 7 3346 2325
Email: sarah.piper at uq.edu.au<mailto:sarah.piper at uq.edu.au>



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