[Chimera-users] Renaming chain directly in Chimera
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
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.
> 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
>> 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:
>> 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
>> 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
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