[Chimera-users] bond rotation

[Elaine Meng]

On Jun 25, 2010, at 10:20 AM, Watson, Lisa wrote:

> Hi Elaine,
> I have changed several nucleotide bases in the DNA structure I am working with so that I can model in cytosine methylation.  Is there a way that I can rotate the changed bases so that they are aligned to base-pair properly?
> Thanks for your help!
> -Lisa

Hi Lisa,
Sure, you can interactively rotate bonds.  If you Ctrl-doubleclick a bond it should show a little menu where one of the choices is to rotate that bond.  After you activate the rotation, the "adjust torsions" dialog will appear, which includes various ways to rotate the bond.  You can have several rotatable bonds at the same time.

Here is more about Adjust Torsions:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#adjust>

Also, the tutorial "Structure Comparison and Analysis" includes measuring distances, finding H-bonds and clashes, and rotating bonds:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

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