[Chimera-users] Chimera how to question

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 5 09:55:25 PDT 2017



> On Jun 5, 2017, at 5:59 AM, Egor Tchesnokov <tchesnok at ualberta.ca> wrote:
> 
> Hello,
> Is there a way to delete a set of residues in the beginning of the sequence, so these residues disappear from the sequence in the pdb file? 
> I am working on the structure-base alignment and the exogneous residues in the protein sequence (eg. affinity-tag) interfere with the nubmering of the endigenous residues.
> Thank you
> Egor

Hi Egor,
Of course you can delete atoms.  You can select them and then use menu: Actions… Atoms/Bonds… delete, or you can use the “delete” command ...either with selection (delete sel) or with some other kind of specification of what you wanted to delete, e.g.

delete :1-20.A

...to delete residues 1-20 of chain A.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html>

Maybe in your case it would be easiest to use the sequence window (Favories… Sequence) to select the set of residues you want to delete by dragging a box around them, and then using the menu or command.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html>

However, this will not change any sequence numbering.  Chimera just uses the numbers that are in the input file.  Sometimes but not always, affinity-tag residues are given negative residue numbers in the input file.  If you want to renumber residues, see menu: Tools.. Structure Editing… Renumber Residues, or the command “resrenumber”:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/renumber.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/resrenumber.html>

Chimera questions should be sent to chimera-users at cgl.ucsf.edu (CC’d here) to ensure that they will be answered.
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco





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