[Chimera-users] Molecular Representations

Jian Guan jug25 at psu.edu
Thu Aug 28 07:42:34 PDT 2014

Dear all,

I have one question about the Molecular Representations.

In chimera, molecule can be represented by ball and sphere. Sphere is with
the VDW radius for atoms and stick bonds. What about the ball? What is the
ball size? 

I tried to measure the distance between two molecules. I used command line
of "measure distance #1 #2". It shows closest distance between two sets of
atoms. When I made surface map for the same two molecules, I used the same
command, it showed different number. I understand it is the distance of VDW.
But what is the distance between atoms if I used PDB file instead of surface
map? Which one is more reliable?




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