[Chimera-users] electrostatic surface coloring

Tom Goddard goddard at cgl.ucsf.edu
Fri Aug 22 11:01:57 PDT 2008

Hi James,

  It looks like the PCE potential calculated with MEAD using the web 
server you mention will not return the potential as a 3-dimensional 
array.  That is what Chimera needs to display it on a surface.  The PQR 
file is just the atom coordinates with charges and is not sufficient.  
To get the potential file you could install APBS and run it yourself.  
You can use the PDB2PQR web service which will create an APBS input file.

  There is only a dialog interface to do the surface coloring, not a 
command.  The command will be added in the future.  Here is how to use 
the dialog:



James Fethiere wrote:
> Hi,
>    1. is there a way to use the electrostatic surface coloring from
>       the tools/surface menu, in a command file? It seems that it is
>       only available through the menu?
>    2. I have a pqr electrostatic potential file calculated from the
>       PCE server http://bioserv.rpbs.jussieu.fr/Help/PCE.html using
>       MEAD. How do I get it into chimera?
> Thanks

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