[Chimera-users] Chimera - Surface calculation
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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