[Chimera-users] protein sequence editing at sequence level

Eric Pettersen pett at cgl.ucsf.edu
Fri Oct 21 14:21:38 PDT 2011

On Oct 21, 2011, at 11:35 AM, frederick lee wrote:

> hello chimera users,
> i know how to add or delete an entire sequence entry,
> but i can't figure out how to delete a portion of a sequence entry
> or a set of aligned sequences. currently, i have to go to another
> program (e.g., jalview) to accomplish that. is there a way to
> do that within chimera?

Hi Fred,
	Since the sequence/alignment viewer was designed for sequences where  
at least one corresponds to a structure, the desire to delete columns  
hasn't really come up to date.  There is a kludgey way to do this.   
Basically, you can save alignment files restricted to the current  
region.  So you would drag out the region of the alignment you want to  
preserve and then use the viewer's "File->Save As..." to save the  
alignment with "Restrict to active region" checked.  Keep in mind that  
if you need to omit columns in the middle of the sequence/alignment,  
you can use shift-drag to drag a second discontinuous block that will  
still be part of the previous region.
	Then you can open the saved alignment in a new viewer.  You may then  
have to use Structure->Associations... to force structures to  
associate with the appropriate partial sequences.

> also when i edit a protein structure (e.g., remove chains)
> and save the resulting structure, the sequence information of the
> *original* structure is kept in the pdb file. is there a way to only
> save sequence info corresponding to the structure actually saved?

	Right.  Chimera preserves all the original headers except for SHEET/ 
HELIX, which it updates as needed.  For now you're going to have to  
edit the PDB to drop the orphaned SEQRES records.  I will open  
enhancement requests in our bug-tracking database for this improvement  
and for the ability to easily delete alignment columns and put you on  
the recipient list so you'll know when they get implemented.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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