Hi Gary, You need to specify the residue in the command, e.g. the ":18.C" in Tom's example command is residue 18 in chain C. Maybe you made a mistake in that part, so it did not find the residue? There is no command to change both residues in the basepair at the same time, but you can just use "swapna" two times, once for each residue you want to change. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jul 26, 2021, at 11:38 AM, gren--- via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi Tom Thanks a lot. It showed that “No residues specific for swapping” when I work on my pdf, what should I do? By the way, the DNA is dsDNA, is there any way to replace the pair of DNA together? Best regards Gary

From: Tom Goddard <goddard@sonic.net> Sent: Monday, July 26, 2021 11:21 AM To: gren@lbl.gov Cc: Azad, Roksana via Chimera-users <chimera-users@cgl.ucsf.edu> Subject: Changing DNA sequence

Hi Gary, The swapna command lets you change a nucleic acid base, for example, to change residue 18 in chain C from a T to a G use

open 1rsb swapna G :18.C

Documentation for swapna

https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/swapna.html

Tom

...

On Jul 26, 2021, at 1:31 AM, <gren@lbl.gov> <gren@lbl.gov> wrote:

Dear Tom Thanks for many answers to our previous questions.

I have one more question to our loved Chimera program.

I have a NDA model (PDB), but the sequence is not right. Is there any way to use this DNA model to generate a new model with a right order of sequence? In other word, if is there an automatic/ simple method (by comment lines) to replace the sequence by the correct one in Chimera?

Thanks a lot!! Gary

Gang (Gary) Ren, PhD Lawrence Berkeley National Laboratory Molecular Foundry, Room: 2220 1 Cyclotron Road, MS 67R2206 Berkeley CA 94720-8197 Phone: (510) 495-2375; Fax: (510) 486-7268 Email: gren@lbl.gov; https://rengroup.lbl.gov/