Re: [Chimera-users] Chimera how to question
On Jun 5, 2017, at 5:59 AM, Egor Tchesnokov <tchesnok@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@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
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@cgl.ucsf.edu> wrote:
On Jun 5, 2017, at 5:59 AM, Egor Tchesnokov <tchesnok@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@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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Egor Tchesnokov -
Elaine Meng