Re: [Chimera-users] Renaming chain directly in Chimera
Hi Damien, For a more reliable response, please send mail to chimera-users@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@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
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@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@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
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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
Damien
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@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@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
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Damien Larivière -
Elaine Meng -
Tom Goddard