[Chimera-users] Sequence aligment

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 17 14:38:37 PDT 2011

Hi Simon,
Although Chimera certainly isn't a sequence-aligning machine (intended more for integrated sequence-structure work), it can be done without too much trouble if the sequences are fairly easy to align.

Chimera doesn't read non-aligned multisequence files, so the approach would be to put one sequence in a Fasta file, open that in Chimera, then use Multalign Viewer's (the tool that is showing the sequence) Edit menu to add the other sequence to create a pairwise alignment.


Note that Chimera will use the SEQRES information, if present, in a PDB file.  Thus if you used Sequence (in Favorites menu) to show the sequence for a chain in your PDB structure, it may include residues for which coordinates are missing.  If all the residues are included in the SEQRES but for only one structure, you could show it with Sequence to get the first sequence and then proceed as above.  If all the residues are included in the SEQRES info for both your structures, you could just use the Matchmaker tool (under Tools... Structure Comparison) or matchmaker command with the "show alignment" option to give you the pairwise sequence alignment.  


If the sequences are not easy to align, i.e. quite dissimilar, the alignment with default parameters might not be good enough.  You may need to delete the second sequence (see Multalign Viewer's Edit menu), and re-add after changing parameters, or if you had used the Matchmaker approach, delete the whole alignment and try matchmaker again with different alignment parameters.

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 Jun 17, 2011, at 2:11 PM, Simon Sham wrote:

> Hi,
> Is it possible that to do a sequence alignment in Chimera given only a text file with 2 protein amino acid sequences? I have the pdb files but there are some missing amino acids in them.
> Thanks for your help.
> Simon

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