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

Mon Sep 14 15:44:40 PDT 2020

I'm sorry, I meant I hadn't used the matchmaker tool in my previous email.
I assume this makes molmap unnecessary.

On Mon, Sep 14, 2020 at 6:28 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> The word molmap does not appear in that message, which is also shown here
> in our archive:
>
> <
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2020-September/017196.html
> >
>
> Try following the steps in that message.
>
> Elaine
>
> > On Sep 14, 2020, at 3:19 PM, Tarazkar, Maryam <Maryam.Tarazkar at ucsf.edu>
> wrote:
> >
> > Hmmm, you in the procedure mentioned in the message below from 2:33 pm
> starting with "Open 6eni it was mentioned to use molmap. But you say molmap
> is not needed.....
> > Is there any chance that we set a zoom time to help me figure this out?
> > Maryam
> > From: Elaine Meng <meng at cgl.ucsf.edu>
> > Sent: Monday, September 14, 2020 3:12 PM
> > To: Tarazkar, Maryam <Maryam.Tarazkar at ucsf.edu>
> > Cc: Chimera <chimera-users at cgl.ucsf.edu>
> > Subject: Re: [Chimera-users] Is it possible to make a dimer from a
> monomer protein in chimera?
> >
> > 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
> >
> > > On Sep 14, 2020, at 2:59 PM, Tarazkar, Maryam <
> Maryam.Tarazkar at ucsf.edu> wrote:
> > >
> > > I do have 3D structure of Ebour (monomer protein).
> > > I am sorry but I am a bit confused; So should I follwo the procedure
> explained by Clara?
> > > If yes can you help me how I can Manually fit each monomer into
> density from molmap ?
> > > Thank you
> > > Maryam
> > >
> > > From: Elaine Meng <meng at cgl.ucsf.edu>
> > > Sent: Monday, September 14, 2020 2:42 PM
> > > To: Tarazkar, Maryam <Maryam.Tarazkar at ucsf.edu>
> > > Cc: Chimera <chimera-users at cgl.ucsf.edu>
> > > Subject: Re: [Chimera-users] Is it possible to make a dimer from a
> monomer protein in chimera?
> > >
> > > 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.
> > >
> > > 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.
> > > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative
> >
> > >
> > > 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:
> > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/dor.html>
> > >
> > > Our newer program ChimeraX allows modeling a dimer from a dimer
> template.  There is an example here:
> > > <http://www.rbvi.ucsf.edu/chimerax/features.html#multichain-modeller>
> > >
> > > Elaine
> > >
> > > > On Sep 14, 2020, at 2:33 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > > >
> > > > Hi Maryam,
> > > > 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.
> > > >
> > > > 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!
> > > > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html
> >
> > > >
> > > > 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.
> > > > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html
> >
> > > >
> > > > I hope this helps,
> > > > Elaine
> > > >
> > > >> On Sep 14, 2020, at 2:21 PM, Tarazkar, Maryam <
> Maryam.Tarazkar at ucsf.edu> wrote:
> > > >>
> > > >> Hi Elaine,
> > > >> 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.
> > > >> Given the information above can you expalin me or refer me to a
> reference how I can make a dimer of Ebour using Chimera?
> > > >> Thank you,
> > > >> Maryam
> > > >>
> > > >> From: Elaine Meng <meng at cgl.ucsf.edu>
> > > >> Sent: Monday, September 14, 2020 12:19 PM
> > > >> To: Tarazkar, Maryam <Maryam.Tarazkar at ucsf.edu>
> > > >> Cc: Chimera <chimera-users at cgl.ucsf.edu>
> > > >> Subject: Re: Is it possible to make a dimer from a monomer protein
> in chimera?
> > > >>
> > > >>
> > > >> On Sep 14, 2020, at 12:07 PM, Tarazkar, Maryam <
> Maryam.Tarazkar at ucsf.edu> wrote:
> > > >>>
> > > >>> Hi Elaine,
> > > >>> I am wondering can you refer me to a tutorial in Chimera where it
> explains how to make a dimer protein from a monomer?
> > > >>> Thank you,
> > > >>> Maryam
> > > >>
> > > >> Hi Maryam,
> > > >> 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.
> > > >>
> > > >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/fetch.html>
> > > >>
> > > >> Some files have symmetry information in their files so that you can
> build the multimer with the "sym" command, e.g.
> > > >>
> > > >> open 1fav
> > > >> sym #0 #0
> > > >>
> > > >> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>
> > > >>
> > > >> 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.
> > > >>
> > > >> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> > > >>
> > > >> I hope this helps,
> > > >> Elaine
> > > >> -----
> > > >> Elaine C. Meng, Ph.D.
> > > >> UCSF Chimera(X) team
> > > >> Department of Pharmaceutical Chemistry
> > > >> University of California, San Francisco
> > > >
> > > >
> > > > _______________________________________________
> > > > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > > > Manage subscription:
> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> > >
> > > _______________________________________________
> > > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > > Manage subscription:
> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> >
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription:
> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200914/29c8ec17/attachment-0001.html>