[Chimera-users] New user-visualizing coulombic

Minor, Armond minoav69 at suny.oneonta.edu
Fri Feb 15 18:04:31 PST 2013


Hello,
  I am just starting out using the program for a project with my
Biochemistry professor.  We are trying to develop a simple procedure to
visualize the Coulombic surface of short DNA sequences.  I have very little
experience working with Chimera and do not know if I am going about it in
correct way that will yield meaningful data.  I have tried following the
instruction but must of them seem to be for people who are more familiar
with the programs than I am.  Basically what I have tried is opening a pdb
file, running PDB2PQR, opening the pqr file then running APBS on that. I am
not sure what to do with the .dx file that comes out and how to use it to
color the surface.  If I use it to color the Electrostatic potential map I
get a range of values that seem to be not what my professor is expecting.
 If I instead use the coulombic surface tool I get values like she expects
but I am not sure if these are connected to the .dx file or just the
pdb2pqr file.  Any help would be greatly appreciated thank you.

Armond Minor
Student, Biochemistry, SUNY Oneonta
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