[Chimera-users] Electrostatical surface of a virus
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
> 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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