[Chimera-users] [chimera-dev] Building a multimer model

Benjamin G.S. Horsman benjamin.horsman at utoronto.ca
Sat Apr 7 20:34:01 PDT 2007

Hi Elaine,

Your method worked perfectly.  Thanks for help!


On 4/5/07, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Benjamin,
> There is probably more than one way to do this in Chimera, but I'd
> open the protein of interest six times and match it to the six
> monomers of the related protein. Let's call your protein "A" and the
> similar protein "B" (for which a hexamer is available or can be
> easily constructed from matrices in the PDB file).  Since you didn't
> mention the specifics, I didn't try the whole process outlined below
> (not having a good example to work with), but have used the tools in
> other contexts.
> This is kind of a brute force approach.  Someone else may know of a
> more elegant way...
> Making the hexamer of B:
> If the PDB file doesn't already have a hexamer, it should have matrix
> information that allows it to be constructed.  If BIOMT, use
> Multiscale Models (under Tools... Higher-Order Structure).
> Initially, this doesn't copy all the atoms but just makes surfaces
> for computational expediency.  Since you will need copies of all the
> atoms for matching, using the Multiscale Models GUI: select "All"
> chains, change their style to anything other than surface (e.g.
> Show... Ribbons).  You can see the model IDs of the copies of B in
> the Model Panel (under Favorites).  If SMTRY, CRYST1, or MTRIX you
> could use the Unit Cell tool (under Tools... Higher-Order Structure)
> instead of Multiscale Models.  Relevant manual pages:
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/
> framemulti.html
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/
> unitcell.html
> Matching the 6 copies of A to the monomers of B:
> Options for matching are the "match" command or MatchMaker (GUI under
> Tools... Structure Comparison, also implemented as a command,
> "matchmaker").  If you wanted to name specific atoms to use for
> fitting, you'd use the "match" command.  That can be tedious, and I'd
> try MatchMaker first - if there is some sequence similarity, even
> fairly low, it usually works quite well.  By default, it iterates the
> fit so that only residues that match well in space are ultimately
> used to superimpose the proteins. That means the parts that are
> different should not interfere with a good fit of the parts that are
> the same.  You can adjust several parameters, but for example if B is
> model 0, chains A-F and copies of A are models 1-6, these commands
> would use the matchmaker defaults:
>    matchmaker #0:.a #1 pair ss
>    matchmaker #0:.b #2 pair ss
>    matchmaker #0:.c #3 pair ss
>    matchmaker #0:.d #4 pair ss
>    matchmaker #0:.e #5 pair ss
>    matchmaker #0:.f #6 pair ss
> (pair ss just means to use the specified chains rather than trying
> all chain combinations between the models)  You could specify other
> parameters with various keywords, for example the stringency to use
> when iterating the fit, how much weight secondary structure should
> have vs. the residue types in the sequence, etc.  Relevant manual pages:
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/
> matchmaker.html
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
> I hope this helps,
> Elaine
> -----
> 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
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> On Apr 5, 2007, at 12:10 AM, Benjamin G.S. Horsman wrote:
> > Hello,
> >
> > My name is Benjamin Horsman and I am a student at the University of
> > Toronto.  I have what should be a basic (possibly naive) question
> > regarding protein modelling that I was hoping you might be able to
> > answer for me or point my in the right direction.  I have been
> > studying the structure of a bacterial protein complex, trying to
> > understand how it interacts with several known binding partners.  The
> > complex is known to be a hexameric homomultimer.  Recently the
> > structure of the subunit protein was solved.  However, only the
> > monomeric form of the protein was determined, and the corresponding
> > PDB file does not contain coordinates for the multimer (i.e., no
> > BIOMT1, BIOMT2, BIOMT3 matrix values).  I would like to assemble a
> > model of the hexameric complex for visual inspection and for some
> > docking studies.  What would be the best way to accomplish this?
> >
> > There are several structures in the PDB of hexameric protein complexes
> > composed of subunits with very close structural alignment to my
> > protein of interest, differing in two regions of the protein that are
> > outside of the multimer binding regions.  I believe that my protein
> > complex posses very similar or nearly identical geometry to these
> > known complexes.  Is there any way to basically insert my protein into
> > this geometry?  Can this be done in Chimera?  If not, is there any
> > program or web server that allows this to be done?  Or are you aware
> > of a better way to get this done?
> >
> > Thank you for your time.  Any help is greatly appreciated.
> >
> >
> > Benjamin Horsman
> > _______________________________________________
> > Chimera-dev mailing list
> > Chimera-dev at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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