Re: [Chimera-users] Is it possible to make a dimer from a monomer protein in chimera?

14 Sep 2020


      Hi Clara, 
I don't think Maryam has a map, or at least she never said anything about a map.
Elaine
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On Sep 14, 2020, at 3:25 PM, Clara Gilda Altomare <ca2574@columbia.edu> wrote:
Hi Maryam,
To manually fit your monomer just activate only for each copy opened in the model panel and move them with the mouse. But to clarify, when you say you have a 3D structure, is that a pdb or a map (.map or .mrc)?
I’ve never used the modeler tool, but that will likely be an easier method.
Elaine,
I apologize, I always respond directly to questions to limit the amount of message board emails. The method I suggested is pretty much the same as yours, I just gave the steps as they would go directly into the command line and said how to do it for pdb and map of the monomer because the word structure can be used for both.
On Mon, Sep 14, 2020 at 6:13 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Maryam,
Use the procedure in the message below from 2:33 pm starting with "Open 6eni."  I don't know what Clara said, as I didn't get that message, but as far as I know there is no reason to use molmap.
Elaine
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On Sep 14, 2020, at 2:59 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
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I do have 3D structure of Ebour (monomer protein).
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I am sorry but I am a bit confused; So should I follwo the procedure explained by Clara?
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If yes can you help me how I can Manually fit each monomer into density from molmap ?
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Thank you
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Maryam
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From: Elaine Meng <meng@cgl.ucsf.edu>
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Sent: Monday, September 14, 2020 2:42 PM
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To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu>
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Cc: Chimera <chimera-users@cgl.ucsf.edu>
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Subject: Re: [Chimera-users] Is it possible to make a dimer from a monomer protein in chimera?
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Oops, I thought you meant you already had a 3D structure of a monomer protein.  Now I think you meant you didn't have any 3D structure.
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You cannot use Chimera's Modeller tool to model a dimer, even if the template is a dimer.  This is mentioned in the manual page.
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<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative>
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You can use it to model a monomer (see the link above for help), and then starting with the monomer structure from Modeller, you can perform the steps described in my previous message to build a dimer.  If you need a tutorial, there is one that uses the Chimera Modeller tool here, but it is more complicated than your situation:
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<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html>
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Our newer program ChimeraX allows modeling a dimer from a dimer template.  There is an example here:
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<http://www.rbvi.ucsf.edu/chimerax/features.html#multichain-modeller>
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Elaine
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On Sep 14, 2020, at 2:33 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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Hi Maryam,
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Open 6eni.  Open your structure two times so that you have two copies of the same thing.  Superimpose one copy of your structure on one monomer of 6eni, superimpose the other copy of your structure on the other monomer of 6eni.
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You can use the Matchmaker tool (menu: Tools... Structure Comparison... Matchmaker) to superimpose.  You probably should set options to choose "chain pairing" by specific chain, and you use the tool twice, once for one copy of your structure and once for the other.  Just try it, I think you can figure it out, even if it takes a little trial and error!
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<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>
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Then you can close 6eni, then you will just have the "dimer" of your structure.  If you want to combine the two copies into one model before saving that as PDB, see the "combine" command.
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<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
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I hope this helps,
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Elaine
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On Sep 14, 2020, at 2:21 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
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Hi Elaine,
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So I have a protein that is monomer (Ebour). I want to make it as a dimer based on the template of 6eni. (in fact 6eni is the closet hit to Ebour based on what Modeler predicts). Note that 6eni is dimer.
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Given the information above can you expalin me or refer me to a reference how I can make a dimer of Ebour using Chimera?
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Thank you,
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Maryam
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From: Elaine Meng <meng@cgl.ucsf.edu>
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Sent: Monday, September 14, 2020 12:19 PM
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To: Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu>
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Cc: Chimera <chimera-users@cgl.ucsf.edu>
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Subject: Re: Is it possible to make a dimer from a monomer protein in chimera?
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On Sep 14, 2020, at 12:07 PM, Tarazkar, Maryam <Maryam.Tarazkar@ucsf.edu> wrote:
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Hi Elaine,
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I am wondering can you refer me to a tutorial in Chimera where it explains how to make a dimer protein from a monomer?
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Thank you,
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Maryam
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Hi Maryam,
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Yes, of course you can do it, but there is no specific tutorial:  how to do it really depends what information is in the input file, what you know about the structure, etc.  If it is an entry in the PDB database you could just try fetching the biounit directly and seeing if it  is a dimer.  E.g. menu File... Fetch by ID, use the "PDB (biounit)" choice.
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<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/fetch.html>
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Some files have symmetry information in their files so that you can build the multimer with the "sym" command, e.g.
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open 1fav
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sym #0 #0
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<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>
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If it is not yet a deposited structure, but you already have a related structure that is a dimer, you can just open two copies of your protein and match it onto the two monomers of that other structure, e.g. with the Matchmaker tool.
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<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
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I hope this helps,
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Elaine
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-----
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Elaine C. Meng, Ph.D.
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UCSF Chimera(X) team
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Department of Pharmaceutical Chemistry
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University of California, San Francisco
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Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users