[Chimera-users] Changing DNA sequence

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 26 11:55:19 PDT 2021

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 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 at 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 at sonic.net> 
> Sent: Monday, July 26, 2021 11:21 AM
> To: gren at lbl.gov
> Cc: Azad, Roksana via Chimera-users <chimera-users at 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 at lbl.gov> <gren at 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 at lbl.gov; 
>> https://rengroup.lbl.gov/

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