[Chimera-users] mutation DNA base pairs

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 11 09:51:50 PDT 2015


Dear Urszula,
The command for mutating a DNA base is “swapna” - you would have to use it twice, one time for each member of the pair.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html>

For example, if your base pair was between residue 2 in chain A named DG and residue 23 in chain B named DC, to change them into DA-DT it would be something like:

swapna A :2.A preserve true
swapna T :23.B preserve true

Or you could omit “preserve true” … see the manual page linked above for details.  The pairing geometry might not be that good after the swap, but you could rotate the bonds manually if you wanted (see Build Structure tool, Adjust Torsions section):
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>

To get the heteroatom color-coding on the new bases (red oxygen and blue nitrogen) you could use command “color byhet” 

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 11, 2015, at 7:25 AM, Urszula Uciechowska <urszula.uciechowska at biotech.ug.edu.pl> wrote:

> Dear chimera users,
> 
> I was wondering if its possible to mutate DNA base pair (G-C etc.)in
> chimera using swapa command?
> 
> Thank you in advance for any suggestions
> Urszula Uciechowska
> 




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