[Chimera-users] Renaming chain directly in Chimera

Damien Larivière damien.lariviere at fourmentinguilbert.org
Tue Mar 10 06:26:03 PDT 2009

Dear Elaine and Tom,

Thank you for these replies !

The molmap method works very well. No more need for previously editing 
the PDB.

All the best


Tom Goddard a écrit :
> Hi Damien,
>  Chimera does export the colors in VRML including per-vertex colors on 
> multiscale surfaces.  I just tested this with the Octaga Player vrml 
> viewer on Mac.
>  As Elaine says Chimera is not able to edit chain ids of PDB models.
>  Perhaps the effect you want can be achieved using the molmap Chimera 
> command instead of the multiscale tool.  This will only be useful if 
> you are not using the symmetry replication capability of multiscale.  
> You can create a surface for any set of residues at any desired 
> resolution with molmap, for example,
>    molmap #1:57-96.B 12
> makes a 12 angstrom surface using residues 57 through 96 of chain B of 
> molecule #1.  To improve the smoothness of the surface add the grid 
> spacing argument
>    molmap #1:57-96.B 12 grid 2
> Grid spacing defaults to 1/3 of resolution.  The molmap command adds 
> Gaussians for each atom to make a volume and displays a contour surface.
>    http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html
>  Tom
> Elaine Meng wrote:
>> Hi Damien,
>> For a more reliable response, please send mail to 
>> chimera-users at cgl.ucsf.edu   rather than to me directly -- sometimes 
>> the others know the answer  when I don't, and sometimes I'm away from 
>> work.
>> Chimera doesn't provide a way to just choose some set of residues 
>> and  give them any chain ID you want.  It can reassign chain IDs if 
>> you are  merging models, for example if you had two models that were 
>> both chain  A, it could combine them into another model with chains A 
>> and B.   However, I can't think of how that process could be used to 
>> do what  you want in this situation.
>> I've come across a few PDB-editing web servers, but I don't know 
>> which  of these might do what you want.  You may need to use SPDBV 
>> for pre- processing in this case.  Here are the web servers in case 
>> they are of  general interest:
>> <http://www.igs.cnrs-mrs.fr/Caspr2/magicPDB.cgi>
>> <http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/inputpage.html>
>> Best,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
>> UCSF Computer Graphics Lab and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>                       http://www.cgl.ucsf.edu/home/meng/index.html
>> On Feb 27, 2009, at 9:40 AM, Damien Larivière wrote:
>>> Dear Elaine,
>>> If a PDB structure contains 2 chains A and B, is it possible to  
>>> rename chain B as for example chain A directly in Chimera in order  
>>> to get one only chain ? Also, is it possible to rename part of  
>>> residues of a chain A (residues 256 to 312 for example) as chain B ?
>>> I ask this question because I often export low resolution surfaces  
>>> (obtained with Multiscale Models tool) in the vrml format or obj  
>>> format. However, I often have to color all the model (chains A and  
>>> B) in only one color and highlight a set of residues in another color.
>>> I know that I can do this by selecting the residues of interest,  
>>> coloring them by using Color zone, but the result is not exportable  
>>> in VRML (problem of vertex color or something like that). To avoid  
>>> export problem, it is very simple to rather rename chains and/or  
>>> reassign a letter to part of chain, which I do by using  
>>> SwissPDBviewer. So, can I do this in Chimera ?
>>> Thanks for your help
>>> Damien
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