[Chimera-users] protein sequence editing at sequence level
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?
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.
UCSF Computer Graphics Lab
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