[Chimera-users] Renaming chain directly in Chimera

Tom Goddard goddard at cgl.ucsf.edu
Fri Feb 27 13:26:23 PST 2009

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.



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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