[Chimera-users] Changing DNA sequence

gren at lbl.gov gren at lbl.gov
Mon Jul 26 11:38:52 PDT 2021

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




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






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




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:  <mailto:gren at lbl.gov> gren at lbl.gov; 

 <https://rengroup.lbl.gov/> https://rengroup.lbl.gov/


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