Hi Stanislav, Elaine's suggestion to use the msc command will work, but there are a few more tricks that are needed. The first problem is that the PDB file that the ConSurf web site will give you has the header remarks stripped off. Those header remarks contain the icosahedral symmetry for the virus (REMARK 350 BIOMT records). So you should get the ConSurf PDB file which has the coloring coded in the b-factor column and use a text editor to put back the PDB header from the original PDB file for the virus. This will allow the Chimera MultiScale dialog to make the full virus capsid from the ConSurf file. The next problem is that the virus capsomere is a trimer. So you need to run ConSurf on the 3 chain separately. To combine them, I would use a text editor and copy and paste the ATOM records for the ConSurf chain A results, and the ConSurf chain B results, and the ConSurf chain C results into a single file (and paste the original PDB header back on). Load this patched together file in Chimera, and use the Chimera coloring script available on the ConSurf site to color the atoms. Then make the MultiScale model, and use the "msc" command as Elaine described. I tried this for Calicivirus, PDB 3M8L, and produced the attached images using MultiScale surface resolutions 0 to show solvent excluded surfaces. Tom
Whoops, I typed the models backwards. Should be:
msc #1 #0 5.0
to match my verbal description. Sorry about that. Elaine
On Nov 9, 2010, at 10:30 AM, Elaine Meng wrote:
Hi Stanislav, I believe if you start with one subunit with atomic coordinates and get Consurf coloring on those (or any coloring scheme, for that matter), then you can use the "msc" command to apply the same coloring to the Multiscale surface copies of that subunit. For example, if your subunit atomic coords are model 0 and the multiscale surfaces are model 1:
msc #0 #1 5.0
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/msc.html>
You may want to experiment with the cutoff distance (5.0 in the example) and the resolution of your multiscale surfaces. I hope this helps, Elaine
On Nov 9, 2010, at 7:34 AM, Sosnovtsev, Stanislav (NIH/NIAID) [E] wrote:
I wonder if there is a short way to introduce consurf output colors to multiscale models. My virus particle has 60 trimers (three chains of the same protein). Thank you in advance, Stanislav
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