[Chimera-users] a simple question about multiple sequence alignment

Lan Hua lan.hua at gmail.com
Mon Aug 22 16:31:50 PDT 2011

Hi Elaine,

   Thank you so much for this detailed info.  I will try option B).


On Mon, Aug 22, 2011 at 3:42 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Lan,
> In Chimera, there are several ways to generate the sequence alignment
> needed for comparative modeling.
> Some ways are described in the documentation, with links to related pages:
> <
> http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches
> >
> I'll spell them out here too...
> (A) Do a BLAST search of the PDB using your target sequence as the query.
> For example, choose "Tools... Sequence... Blast Protein" from the Chimera
> menu.  Click the Plain Text tab, paste in your sequence.  Search the "pdb"
> database.  In the list of results, choose the one or more PDBs you want to
> use as template(s), click "Show in MAV" to open as multiple sequence
> alignment aligned to the query, and "Load Structure" to also open those
> structures in Chimera.
> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/blast.html>
> (B) Start with one or more structures you already know you want to use as
> template(s).
> (i) if just one structure, show its sequence by choosing Sequence from the
> Favorites menu in Chimera.
> (ii) if more than one structure, first superimpose them.  There are several
> ways to superimpose structures, but the easiest is usually with MatchMaker
> (under Tools... Structure Comparison):
> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
> <
> http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html
> >
> ...then create a sequence alignment from the superimposed structures using
> Match->Align (also under Tools... Structure Comparison):
> <
> http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html
> >
> Then, use the sequence window's Edit menu to add the sequence of your
> target protein to the alignment.
> <
> http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#editing
> >
> (C) Start with a pre-existing alignment that you made yourself or
> downloaded from some database (HOMSTRAD, Pfam, etc.).
> <http://www.cgl.ucsf.edu/home/meng/sources.html>
> In Chimera, open the alignment file, open your template structure(s) and
> make sure they are are associated to the alignment, and add your target
> sequence to the alignment as in (B).
> Then after (A) (B) or (C) you can use "Structure.... Modeller Tools" in the
> sequence window's menu to run the comparative modeling calculation with
> Modeller.  If you haven't already, you would need to register for Modeller
> use (free for noncommercial users) to get a key code to enter into the
> dialog:
> <
> http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html
> >
> <http://www.salilab.org/modeller/registration.html>
> 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 Aug 22, 2011, at 1:04 PM, Lan Hua wrote:
> > Hi all,
> >
> >     I want to use chimera to create a multiple sequence alignment which
> will be used to build a model.  From elsewhere, I know the pdb id of
> desirable templates, but I don't know how to create the alignment in the
> Chimera.  Any inputs will be very much appreciated.  Thank you!
> >
> >
> > Best,
> > Lan
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