Hi Xiaobin, In theory you could compute the electrostatic potential for the entire virus capsid and then display it in Chimera. But that is a big calculation. I tried calculating the electrostatic potential for just the asymmetric unit of 1ny7 using a program called APBS (equivalent to Delphi). The 1.5 Gbytes of memory on my machine was not enough (grid spacing ~0.7A). For the full capsid with 60 copies the volume I think it would be about 4 times larger in each dimension requiring 64 (4x4x4) times more memory. So you would probably need a machine with about 128 Gbytes of physical memory. Maybe other software can break down the calculation and use less memory. So the straight-forward approach seems quite difficult. Here is a simple approach you could use in Chimera on a normal computer. You can simply color the residues by charge (positive blue, negative red) then map those colors onto the virus surface. Of course that is not as accurate as an electrostatics calculation. Here is how you would do this simple display in Chimera. Open 1ny7. The PDB version of 1ny7 only has the symmetry matrices to produce a pentamer. So I suggest using the version from the Virus Particle Explorer (VIPERdb) web site: http://viperdb.scripps.edu/cgi-bin/viper_coord.cgi?VDB=1ny7 Note that the VIPERdb 1ny7 has 3 chains (A,B,C) while the PDB 1ny7 has only 2 chains (1,2). I think the VIPERdb version is more useful in general. The structure 1ny7 comes from Jack Johnson's lab which created the VIPERdb web site. So open 1ny7.vdb. With the ".vdb" suffix Chimera will recognize this as a VIPERdb file and use the Chimera Multiscale tool to show the whole virus capsid. Now color the charged residues. First show the atomic model by pressing the select "with loaded atoms" button on the Multiscale dialog, then choose the Style Show... / Wire option in the Multiscale dialog. To do the coloring use Chimera menu entry Select / Residue / amino acid category / positive then menu entry Actions / Color / blue then Select / Residue / amino acid category / negative and Actions / Color / red Now to use the atom coloring to color the multiscale surfaces you need the Multiscale Coloring command tool that is not distributed with Chimera. Get it from the Chimera experimental features page http://www.cgl.ucsf.edu/chimera/experimental/experimental.html and install it according to the instructions given there. You have to restart Chimera after installing it so you should do this before the steps I described above. Now to color the capsid surface using the atom colors use the Chimera command msc #1 #0 5 which says to color Chimera model #1 (the multiscale surfaces) using atoms from model #0 (1ny7.vdb) within a range of 5 angstroms. To display the Chimera command-line where you type this command use Chimera menu entry Favorites / Command line Now you probably want a higher resolution virus surface. To get that press the Select All button on the multiscale dialog. Then change the resolution value in the middle of that dialog from 8 angstroms to 3 and press the Enter key or the Resurface button. You'll then have to rerun the "msc" command to get the red/blue coloring by charge. Here's an image I made for 1ny7.vdb showing what this looks like: http://www.cgl.ucsf.edu/home/goddard/temp/1ny7-charges.png I used some more tricks to make this image. I decided the red/blue coloring over the whole capsid was too confusing to look at all at once, so I selected one copy of chains B and C with the mouse, then pressed the Select Copies button in the multiscale dialog, then changed their resolution to 8 angstroms which erased their red/blue coloring for those chains. Also I used resolution equal to 0 for chain A. That makes a solvent excluded molecular surface which is higher quality and resolution than the multiscale surfaces made with resolution > 0. I did run into a problem that 1ny7 vdb failed to create solvent excluded surfaces for chain C because two atoms (number 1481 and 1485 in the file) have identical coordinates. I deleted atom 1481 from the file when I was experimenting with this model to circumvent that error in the data. This is kind of a complex process. Here's some more info on the multiscale tool, the msc command, and electrostatic coloring. http://www.cgl.ucsf.edu/chimera/tutorials/virus-howto/showvirus.html http://www.cgl.ucsf.edu/chimera/experimental/multiscale_color/msc.html http://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/07-VolumeData/tuto... http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemul... Tom