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

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 22 15:42:07 PDT 2011

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:

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.

(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): 
...then create a sequence alignment from the superimposed structures using Match->Align (also under Tools... Structure Comparison):   
Then, use the sequence window's Edit menu to add the sequence of your target protein to the alignment.

(C) Start with a pre-existing alignment that you made yourself or downloaded from some database (HOMSTRAD, Pfam, etc.).

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:

I hope this helps,
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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