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 Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu