Hello everyone. I have a question about Chimera: I want to put two monomers (of a dimer) in simmetry. I tried to do this with mouse, with poor results.I would like to know if there is a method or a script that can help me. Thanks to all.Francesco
Hi Francesco, It depends on the information in the PDB file: it may include matrices describing operations to generate the biological multimer (BIOMT), or copies related by crystallographic symmetry (SMTRY or CRYST1), or copies related by noncrystallographic symmetry (MTRIX). If this information is already present in the PDB file you can just use the command "sym" (or depending on the type of information, the Unit Cell or Multiscale Models tool) to make the corresponding multimers. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemul...> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.h...> If the PDB file does not contain such information, then possible approaches are: - use File... Fetch by ID to get the PQS-predicted multimer for this structure (however, not all structures are available from this site) - specify the dimer axis and center yourself manually in the "sym" command (but it may be hard to figure those out) - if there is a closely related protein with dimer of known structure, and you expect your protein to dimerize the same way, you can open the other protein, open two copies of your protein, and match them to the monomers of the other protein (for example, with MatchMaker) <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmak...> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 25, 2011, at 10:59 AM, Francesco Biagi wrote:
Hello everyone. I have a question about Chimera: I want to put two monomers (of a dimer) in simmetry. I tried to do this with mouse, with poor results. I would like to know if there is a method or a script that can help me. Thanks to all. Francesco
Hi Elaine,Thank you very much, I will try the methods you have described me. Indeed there is a closely related dimer, so i'll try to match it with my protein, using MatchMaker. With command "sym", Chimera returns me an error, probably it depends on the PDB files.Anyway I'll try other methods. Thanks again for the precious help,F. Biagi
Subject: Re: [Chimera-users] how to make simmetric dimer From: meng@cgl.ucsf.edu Date: Mon, 25 Apr 2011 13:55:44 -0700 CC: chimera-users@cgl.ucsf.edu To: francescobiagi@live.it
Hi Francesco, It depends on the information in the PDB file: it may include matrices describing operations to generate the biological multimer (BIOMT), or copies related by crystallographic symmetry (SMTRY or CRYST1), or copies related by noncrystallographic symmetry (MTRIX).
If this information is already present in the PDB file you can just use the command "sym" (or depending on the type of information, the Unit Cell or Multiscale Models tool) to make the corresponding multimers.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemul...> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.h...>
If the PDB file does not contain such information, then possible approaches are:
- use File... Fetch by ID to get the PQS-predicted multimer for this structure (however, not all structures are available from this site)
- specify the dimer axis and center yourself manually in the "sym" command (but it may be hard to figure those out)
- if there is a closely related protein with dimer of known structure, and you expect your protein to dimerize the same way, you can open the other protein, open two copies of your protein, and match them to the monomers of the other protein (for example, with MatchMaker) <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmak...>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 25, 2011, at 10:59 AM, Francesco Biagi wrote:
Hello everyone. I have a question about Chimera: I want to put two monomers (of a dimer) in simmetry. I tried to do this with mouse, with poor results. I would like to know if there is a method or a script that can help me. Thanks to all. Francesco
Hi Francesco, If you tell me the PDB ID I could take a look at it. Just send it to me if you didn't want to include everybody on this mailing list. Elaine On Apr 25, 2011, at 5:32 PM, Francesco Biagi wrote:
Hi Elaine, Thank you very much, I will try the methods you have described me. Indeed there is a closely related dimer, so i'll try to match it with my protein, using MatchMaker. With command "sym", Chimera returns me an error, probably it depends on the PDB files. Anyway I'll try other methods. Thanks again for the precious help, F. Biagi
Subject: Re: [Chimera-users] how to make simmetric dimer From: meng@cgl.ucsf.edu Date: Mon, 25 Apr 2011 13:55:44 -0700 CC: chimera-users@cgl.ucsf.edu To: francescobiagi@live.it
Hi Francesco, It depends on the information in the PDB file: it may include matrices describing operations to generate the biological multimer (BIOMT), or copies related by crystallographic symmetry (SMTRY or CRYST1), or copies related by noncrystallographic symmetry (MTRIX).
If this information is already present in the PDB file you can just use the command "sym" (or depending on the type of information, the Unit Cell or Multiscale Models tool) to make the corresponding multimers.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemul...> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.h...>
If the PDB file does not contain such information, then possible approaches are:
- use File... Fetch by ID to get the PQS-predicted multimer for this structure (however, not all structures are available from this site)
- specify the dimer axis and center yourself manually in the "sym" command (but it may be hard to figure those out)
- if there is a closely related protein with dimer of known structure, and you expect your protein to dimerize the same way, you can open the other protein, open two copies of your protein, and match them to the monomers of the other protein (for example, with MatchMaker) <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmak...>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 25, 2011, at 10:59 AM, Francesco Biagi wrote:
Hello everyone. I have a question about Chimera: I want to put two monomers (of a dimer) in simmetry. I tried to do this with mouse, with poor results. I would like to know if there is a method or a script that can help me. Thanks to all. Francesco
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Francesco Biagi