Dear all, I have a series of pdb files and I would select particular regions that contain specific residues, for example KAYFPG, of which I do not know the exact position in the sequence. Actually I open the sequence window and search for the sequence but this is time consuming if you have multiple pdb. Is there a command to shorten this search? Using the select command seems not possible as I can select all residues of a particular amino acid and not neighbour residues by name. Thanks for your help, Best Marco -- Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 http://stc.uniroma2.it/?page_id=622&cn-entry-slug=marco-sette
Hi Marco, You can use the main Chimera menu: Select... Sequence. However, there is no command. With the dialog opened from the menu, youcan enter the exact sequence, such as KAYFPG, or a Prosite pattern as explained here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/findseq.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 23, 2023, at 3:57 AM, Marco Sette via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear all,
I have a series of pdb files and I would select particular regions that contain specific residues, for example KAYFPG, of which I do not know the exact position in the sequence. Actually I open the sequence window and search for the sequence but this is time consuming if you have multiple pdb. Is there a command to shorten this search? Using the select command seems not possible as I can select all residues of a particular amino acid and not neighbour residues by name. Thanks for your help, Best Marco
Thanks Elaine, Best, Marco Il 23/03/2023 16:44, Elaine Meng ha scritto:
Hi Marco, You can use the main Chimera menu: Select... Sequence. However, there is no command.
With the dialog opened from the menu, youcan enter the exact sequence, such as KAYFPG, or a Prosite pattern as explained here:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/findseq.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 23, 2023, at 3:57 AM, Marco Sette via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear all,
I have a series of pdb files and I would select particular regions that contain specific residues, for example KAYFPG, of which I do not know the exact position in the sequence. Actually I open the sequence window and search for the sequence but this is time consuming if you have multiple pdb. Is there a command to shorten this search? Using the select command seems not possible as I can select all residues of a particular amino acid and not neighbour residues by name. Thanks for your help, Best Marco
-- Dr Marco Sette, PhD. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette@uniroma2.it Tel.: +39-0672594424 -- Questa email รจ stata esaminata alla ricerca di virus dal software antivirus Avast. www.avast.com
participants (2)
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Elaine Meng -
Marco Sette