[Chimera-users] Consurf

Tom Goddard goddard at sonic.net
Tue Nov 9 11:16:50 PST 2010

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 


> 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
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
A non-text attachment was scrubbed...
Name: 3m8l_consurf_5fold.jpg
Type: image/jpeg
Size: 193587 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20101109/c3ce252d/attachment.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 3m8l_consurf.jpg
Type: image/jpeg
Size: 479853 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20101109/c3ce252d/attachment-0001.jpg>

More information about the Chimera-users mailing list