[Chimera-users] mutating residues

[Elaine Meng]

Dear Tatyana,
To mutate amino acids, you can use the command "swapaa" or the  
graphical interface Rotamers (under Tools... Structure Editing).  To  
mutate nucleic acids from one base to another, you can use the command  
"swapna".  Choose Favorites... Command Line to show the command line.

Manual pages for the commands (you can also see these by using the  
commands "help swapaa" and "help swapna"):
<http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/swapaa.html 
 >
<http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/swapna.html 
 >

and for Rotamers (you can also see this by clicking Help on the  
Rotamers dialog):
<http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/rotamers/framerot.html 
 >

Example commands, could be used with PDB structure 10mh :

swapaa leu :41.a
[change residue 41 in chain A, which is a tryptophan, to leucine]

swapna A :406.b
[change residue 406 in chain B from DG to adenine nucleotide]
swapna T :429.c
[change residue 429 in chain C from DC to thymidine nucleotide]

One easy way to figure out a residue number is to hover the mouse  
cursor over an atom in the structure -- that will pop up a "balloon"  
showing the residue name, number, and chain, as well as the atom name.

Swapna only changes the base and swapaa only changes the side chain.   
Swapaa and Rotamers have lots of options, so you may want to look at  
their manual pages; for example, if you have a density map, you can  
choose the conformation that fits it best.  There is some use of  
Rotamers in the "Structure Analysis and Comparison" tutorial:
<http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/squalene.html 
 >

I hope this helps,
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Apr 8, 2009, at 11:15 AM, Tatyana Fedotova wrote:
>
> I have opened pdb file with DNA and protein coordinates. I would  
> like to
> mutate some residues and base pairs.
> Do you know how I can introduce them?