[Chimera-users] OS differences in Chimera

[Elaine Meng]

Hi Marco,
Yes, it is a numerical problem, thus hard to predict and frequently platform-specific. If your reason for showing surfaces is mainly display (as opposed to surface area calculations), then #3 “alternative types of surfaces” may be the best way to go in Chimera:

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

I've put all the Chimera workarounds I know of into this page.

Another suggestion is to use ChimeraX, which uses a completely different and more robust molecular surface calculation.
<http://www.rbvi.ucsf.edu/chimerax/index.html>

However, you may still need to use Chimera depending on which other features are important for your workflow.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 11, 2019, at 9:28 AM, Marco J. Müller <marco.mueller at tu-bs.de> wrote:
> 
> Dear Chimera team,
> 
> I do have a question regarding differences between OSes. Our group
> recently encountered a problem in the surface creation of proteins,
> which might be related to the OS.
> 
> Recently, for some structures, directly obtained from the PDB (e.g.
> 6GB5, 1H97, 4YLJ) or prepared single-chain structures for docking runs,
> the surface creation of the proteins resulted in error 5 from
> mscalc.exe. This, however, seems to be an isolated problem of the
> Windows versions of ucsf chimera 1.12-1.13.1, as the same versions of
> chimera on macOS or Linux (Lubuntu) could successfully create these
> surfaces. Even more strangely, we are pretty sure that we could show
> surfaces of the very same files about half a year ago with these
> versions (1.12 and 1.13rc1). Did a recent update of Windows change the
> behavior of chimera? ChimeraX could actually show these surfaces on
> Windows, but gave us some other troubles.
> 
> We did have a look at
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2016-November/012874.html
> which did solve our problem for now, but we would like to know whether
> we can improve the reliability of chimera's functions, aside from tips
> mentioned in
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html.
> 
> An older post
> (http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-December/005805.html)
> indicates that it is a numerical problem, is this still the case and
> means that it is indeed OS-dependent?
> 
> Thank you in advance,
> Marco
> 
> -- 
> Marco J. Müller
> PhD student
> 
> Technische Universität Braunschweig
> Institute of Medicinal and Pharmaceutical Chemistry
> https://www.tu-bs.de/pharmchem
> Beethovenstr. 55 | 38106 Braunschweig | Germany
> 
> 
> 
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