Dear Madam/Sir, I was wondering if it possible to "mutate" a base pair in nucleic acid (e..g A-->C), in the same way as can very elegantly be done for proteins with the rotamere function. Thank you and best regards, Samo
Dear Samo, There is a "swapna" command to mutate nucleic acids, see <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html> It does not give choices of different conformations, it just makes the substitution. Also it wouldn't change both bases in the pair at the same time. You would need to mutate one and then the other, using the command twice. It is analogous to the "swapaa" command implementation of rotamers for mutating amino acids. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 30, 2024, at 5:50 AM, Samo Lešnik via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Madam/Sir,
I was wondering if it possible to "mutate" a base pair in nucleic acid (e..g A-->C), in the same way as can very elegantly be done for proteins with the rotamere function.
Thank you and best regards,
Samo
Dear Dr. Meng, this is perfect, thank you! Samo On Tue, Jan 30, 2024 at 5:51 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Samo, There is a "swapna" command to mutate nucleic acids, see
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html>
It does not give choices of different conformations, it just makes the substitution. Also it wouldn't change both bases in the pair at the same time. You would need to mutate one and then the other, using the command twice.
It is analogous to the "swapaa" command implementation of rotamers for mutating amino acids.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 30, 2024, at 5:50 AM, Samo Lešnik via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Dear Madam/Sir,
I was wondering if it possible to "mutate" a base pair in nucleic acid (e..g A-->C), in the same way as can very elegantly be done for proteins with the rotamere function.
Thank you and best regards,
Samo
participants (2)
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Elaine Meng -
Samo Lešnik