[Chimera-users] Surface-display option

Elaine Meng meng at cgl.ucsf.edu
Fri Dec 4 08:56:51 PST 2015


Dear Sujith,
This page lists possible workarounds to surface calculation failures:

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

Sounds like you already tried #1 and #2 in that page, but the “molmap” method (#3) should always work, as it uses a completely different calculation.

As to the other methods and whether they are needed, it depends on how you made the assembly.  If I use the following commands, I get a tetramer from 1Q90 and each monomer is already a separate model, so there is no reason to split.  I can show the surfaces without any problems on my machine, but perhaps it is a numerical failure on yours:

open 1q90
sym #0
focus
rainbow models
surface

If I open the model panel, I can see that the original model is #0 and the additional copies are models #1.1, 1.2, 1.3.  I don’t know which two are the dimer you want, but if the above works for you, you can just hide or close the models you don’t want.
I hope this helps,
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 3, 2015, at 6:14 PM, Puthiyaveetil, Sujith <s.puthiyaveetil at wsu.edu> wrote:

> Hi Chimera developer,
> I encounter a problem with surface calculation/display when using the biological assembly (dimer) of 1Q90. The monomer on its own, as in pdb file 1Q90, displays the surface with no problem. I have tried the “split” command without success on the biological assembly. Also tried changing parameters to no effect. Would you please help.
> Regards, 
> Sujith
>  




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