[Chimera-users] Electrostatical surface of a virus

Eduardo Sanz-Garcia esanzgar at terra.es
Wed May 23 22:54:32 PDT 2007

Thank you Tom.

Tom Goddard wrote:
> Hi Eduardo,
>  Coloring a virus by electrostatic potential was discussed on the 
> Chimera mailing list
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-November/001090.html
> 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.
>    Tom

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