[Chimera-users] Chimera - Surface calculation

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 9 10:45:18 PDT 2010

Hi Jay,
Thanks for the tip!  One thing to note, however, is that it will then calculate a surface to separately enclose each subunit.  That is, it does not fix the inability to calculate the single surface that goes around all the subunits (but perhaps that isn't what you wanted anyway!).  

Putting in the END records has the same effect as using the "split" command, which makes the different chains into different models.  There are a bunch of earlier posts on possible alternative workarounds, but it sounds like you may have seen these already:


Finally, we are still working on our own code to possibly replace the existing surface calculations.

We appreciate your comments and kind words about Chimera!
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 9, 2010, at 8:04 AM, Braker, Jay wrote:

> I wanted to contact you about the surface representation of a protein.  I used to be able to show the surface of our protein and lately I can’t show the surface on most multiple subunit proteins because the calculation fails.  However, I noticed that on some previously edited structures (the same one as before, except I deleted some of the subunits/ligands) that the surface calculation would work.  So, I started deleting lines in the PDB file to see if I could get the surface to start working.  Sure enough, when I got to only 1 subunit left, it worked.  So after more investigation, I found that if I insert “End” between each of the subunits/ligands in the PDB file then the surface calculation works for the whole structure.  I have seen in the release notes of Chimera that some protein surface calculations fail, so having found a way to get mine to work, I thought I would pass it on in case it could shed some light on this surface calculation issue.  Or if you have another idea how to “fix” this issue I am having, I would be glad to hear about it.  Finally, I wanted to let you know that I thoroughly enjoy using Chimera, it is a great tool.  Thanks.
> Jay

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