[Chimera-users] Chimera how to question

[Egor Tchesnokov]

Thank you so much for the suggestions. I will try them.

In the meantime what worked for now is generating an alignment from
superposition, saving it as .fasta, then opening .fasta file in text editor
and deleting the extra residues by replacing them with dots. Now this
alignment can be used in Espript for example, and numbering is as desired.

Best
Egor

On Mon, Jun 5, 2017 at 10:55 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

>
>
> > 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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