[Chimera-users] Electrostatical surface of a virus

Tom Goddard goddard at cgl.ucsf.edu
Wed May 23 20:09:11 PDT 2007

Hi Eduardo,

  Coloring a virus by electrostatic potential was discussed on the 
Chimera mailing list


where a simple approach was described to color the surface based on 
charge of nearby atoms.  This is admittedly a rough approximation.  
Another approach would be to compute the electrostatics for an 
asymmetric unit with APBS or Delphi as you suggest, then color the 
multiscale virus surface using that, then copy the coloring of the 
multiscale surfaces for the one asymmetric unit to all other asymmetric 
units in the capsid.  The last step of doing the copying to other 
asymmetric units is not available in Chimera but I could give you a 
Python script to do that.  This method is also a rather poor 
approximation where asymmetric units meet because the electrostatics is 
calculated for just one asym unit and they should be added for all asym 
units.  That too would be a rather poor approximation because the 
electrostatic calculation assumed solvent screening around the one asym 
unit and  that is not correct if another asym unit is packed adjacent.  
The only method without these problems involves calculating the 
potential for the full capsid which would require lots of memory 
(estimated at 128 Gbytes in the previous mailing list discussion) and 
CPU time (many days?).

  If you would like the script to copy the coloring of one multiscale 
asym unit to the others let me know.


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