[Chimera-users] Chimera - Question

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 13 15:50:35 PDT 2007

Hi Peter,
No problem - the features are documented, but there is no tutorial  
that includes adding a sequence.  I tested the following with the  
most recent snapshot (1.2352, March 2007).

(1) Open your sequence alignment in Chimera.   I just found the  
following problem when testing the procedure:  *if you created the  
sequence alignment with Match->Align, it is necessary to save it to a  
file (File... Save As from the Multalign Viewer menu, pick any  
format), quit from the alignment, and reopen it in Chimera (File...  
Open in the main menu) before you can add a sequence to it*  ...this  
will be fixed in the next release, however.  If the sequence  
alignment was already read from a file, no extra step is needed.

(2) Choose "Edit... Add Sequence" from the Multalign Viewer menu and  
paste the new sequence in the dialog.  Enter a name for the sequence,  
adjust the alignment parameters as desired, and click OK.  Look at  
the alignment and decide whether it seems reasonable.  If not, you  
can use "Edit... Delete Sequences/Gaps" to remove the sequence and  
try realigning it with "Edit... Add Sequence" and different alignment  
parameters.  For example, if the sequence is fairly distantly related  
to the others, you may have better luck with blosum-30 than  
blosum-62.  Editing is described here

(3) If they are not already open, open one or more structures that  
associate with the sequence alignment.

(4) Once your new sequence is aligned with the others to your  
satisfaction, you can draw out boxes on the alignment using the  
mouse.  If the boxes enclose parts of the sequence(s) that are  
associated with the structure(s), the corresponding parts of the  
structures will be highlighted (selected).  Or, you can go the other  
direction by selecting parts of the structures and seeing where they  
are in the alignment. These forms of crosstalk are described here
and in the "Sequences and Structures" tutorial.   You can also show  
the secondary structure assignments on the alignment with  
"Structure... Secondary Structure... show actual" (for those  
sequences associated with
structures) or "show predicted" (for sequences without structures)

Alternatively, if you already have a sequence alignment that includes  
your sequence of interest plus others that will associate with  
structures, you can just open them all in Chimera and skip straight  
to #4.  Sometimes I get alignments from databases such as Pfam.

I hope this helps,
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

On Mar 13, 2007, at 2:27 PM, Peter Murphy wrote:

> Thanks for the quick response Dr. Meng,
>     Thanks to your helpful tutorial, I now know how to align two  
> structures and get an alignment. But I am interested in the ability  
> to add a sequence (that
> doesn't have a structure) to the alignment and see if/where parts  
> of it map onto the structures. Is there such a tutorial on your  
> website, or might you be able to give me a quick rundown :P
> Thanks again
> -- 
> Peter Murphy, B.Sc., M.Sc Candidate
> Atlantic Research Center
> Dalhousie University
> Halifax, Nova Scotia,
> Canada

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