[Chimera-users] Chimera - Surface calculation

Braker, Jay Jay.Braker at ARS.USDA.GOV
Wed Jun 9 08:04:33 PDT 2010

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.



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