[Chimera-users] editing selected dihedral angles

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 13 10:03:39 PDT 2014


Hi Francesco,
There are several possible ways to change peptide backbone (psi, phi) angles:

(A) select the residues, use Selection Inspector:  after selecting the residues whose angles you want to change, click the green magnifying glass icon near the bottom right of the Chimera window to open the Selection Inspector, inspect: Residue, change "phi" and "psi" to the desired values.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>

(B) use the "setattr" command, because phi and psi are residue attributes.  You could specify which residues directly by residue number and chain, or select them as in (A) and then use the word "sel" in the command.  Examples:

setattr r phi -60 :10-15.a 
setattr r psi -50 sel

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

( C) interactively rotate bonds.  Hide ribbon, show backbone atoms, for example:
~ribbon
show protein&@n,ca,c,o
...and then Ctrl-doubleclick on the bond you want to rotate, choose Rotate bond from the pop-up menu, use the resulting Adjust Torsions dialog.  You may have to change the Near and/or Far atoms if you want the value shown in the dialog to be phi or psi.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust>

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 13, 2014, at 2:43 AM, Francesco Pietra <chiendarret at gmail.com> wrote:

> 
> Hello:
> I would appreciate receiving instructions on changing selected dihedral angles in a peptide. Imagine that the initial and final stretches are alpha-helices, while in the middle, dihedral angles are such that two alpha-helix coiled portions make an angle different from 180 degrees. In all that, all dihedrals in the alpha-helix portions should not be modified.
> 
> Thanks
> francesco pietra




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