[Chimera-users] Changing DNA sequence

[gren at lbl.gov]

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 <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!!

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

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

 

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