I need to visualize the electrostatic surface of a virus. I don't know how to do it. I was thinking in the following sequence of instructions: 1. Use the DelPhiController to generate the potential map (*.phi) for the asymmetric unit. 2. Use Multiscale Models tool to generate the 60-related units. Is this a logic sequence ? Any hint would be appreciated. Thank you.
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
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
participants (2)
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Eduardo Sanz-Garcia -
Tom Goddard