[Chimera-users] surfaces

Elaine Meng meng at cgl.ucsf.edu
Fri May 12 12:39:27 PDT 2017


Hi Arthur,
It doesn’t matter which domain(s) you specify because by default, one big surface is calculated to enclose all of them together. Specifying an individual domain only says which part of that overall surface to show, but the failure is in the calculation of the whole thing in the first place.

Here is the page with all the possible workarounds for surface failures.  (This URL is given in the error message but it is not convenient because it is not clickable.)
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>

Referring to the details in that page….
- If the domains are separate chains you could try “split” and then calculating the surface.  However, if they are all in the same chain this method won’t help.

- You could try “surfcat” to specify calculating separate surfaces for the separate domains instead of one surface enclosing them all.

- You could try the “molmap” method which always succeeds in making a surface, but then it is not so convenient to color different parts of it differently, instead of all one color.

I can’t really be specific because even if I knew what structure you were using, the calculation may work on my Mac but not on your Windows computer.
Best,
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 12, 2017, at 10:46 AM, Arthur Szabo <agszabo at outlook.com> wrote:
> 
> Working with a structure that has many domains. I would like to show the surface of three of the domains. I have hidden the ribbon residues of all but the ribbons of three domains.
>  
> I receive the following error message
>  
> <image001.png>
>  
> The domains are not contiguous in the structure, but even if I try to show the surface of  only one domain I get the same message. And going to the Selection inspector is not helpful since it is not obvious as to how that option assists the surface representation.
>  
> Over to you
>  
> Thanks
>  
> Arthur G. Szabo




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