[Chimera-users] surface calculation error

Elaine Meng meng at cgl.ucsf.edu
Tue May 10 09:10:38 PDT 2016


Hi Arthur,
It would just be command:

split

…to split each model into separate models for each chain.  (So if you had #0 with chains A and B, it would become model #0.1 with only chain A and model #0.2 with only chain B.)  Then when you calculate the surface it is more likely to work, since each chain will get its own surface rather then Chimera trying to make one surface go around both chains.

However, “split" is only one of a few different possible approaches to handling this common error in surface calculation.  Which way is the best depends on what you are planning to do, for example, whether it is OK for each monomer to have its separate surface, or whether you needed one surface going around the whole homodimer.  

The different ways of working around surface errors are explained here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>

If you needed a single surface around the whole dimer, for example, you could use the “molmap” method, #3 in that page, but as also described in the page, how to color that surface is a little different than how to color a regular molecular surface.

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 May 9, 2016, at 9:33 PM, A G Szabo <agszabo at bell.net> wrote:
> 
> I am trying to represent a large homodimer with 840 residues per subunit, as a surface. On a smaller protein, 350 residues I was able to get a surface representation and color different domains.
> When I try to produce the surface representation of the larger molecule, I receive an error message saying that I have to split it because it is too large a molecule.
> So how do I do that?
> Thanks
> AGS




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