[Chimera-users] Chimera pdb error

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 3 08:51:40 PDT 2018

This surface area calculation is meant for “real” (or at least possible) molecules, not for weird sets of atoms that might be disconnected.

If you have disconnected atoms, just calculate the surface area of a sphere with the atom radius (your choice of what radius value to use, because what are you trying to model with this disconnected atom??) to get something like solvent-excluded area, or the area of a sphere with radius = (atom radius + 1.4) to get something like solvent-accessible area.

Google “surface area of sphere” for the formula.
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 3, 2018, at 3:51 AM, 김민재 <kjh950429 at gmail.com> wrote:
> Hi! Thanks for all of your help, but I got another problem...
> I uploaded a picture of the Chimera error. The HG hydrogen atoms are not being shown in Chimera. When I extract just the CG and HG pdb lines and input them, Chimera works fine and can even calculate the surface. But, when I run it with the pdb file that I have right now, it keeps returning that error. I thought that maybe Chimera could only calculate the surface for atoms which are connected, and that the program was looking for mandatory bond between the atoms. I was wondering if there was a settings change I could make to fix this, or if there was any other way to go about straightening things out to calculate the solvent excluded area of this pdb file.

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