[Chimera-users] Problem related to the "Near" atom in the "Adjust Torsions" tool of UCSF chimera

Prathvi Singh prathvi at iitk.ac.in
Sun Dec 26 23:01:10 PST 2021

This helped enormously!!! Thank you sooo much.

On Sun, Dec 26, 2021 at 1:18 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Prathvi,
> I don't know of a way to control which end atoms are used by activating a
> torsion with the "rotation" command.  If you're using the Adjust Torsions
> panel, however, you can just change it there.
> <
> https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust
> >
> Or if you just want to change the value of one of the standard defined
> peptide torsion angles (e.g. phi, psi, chi1, chi2, ...) in a command
> without using Adjust Torsions, you can do that with "setattr," e.g.
> setattr r chi1 -85.0 :140.A
> setattr:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
> If you select a peptide residue and then inspect: Residue in the Selection
> Inspector (e.g. from clicking the green magnifying glass icon near the
> lower right corner of the Chimera window) you can see various residue
> attributes and their values, including these torsion angles.  You can also
> change the value in the Selection Inspector.  If you mouse over the entries
> in the dialog it shows the attribute name that could be used in the setattr
> command.
> Selection Inspector:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>
> ChimeraX also has a Selection Inspector and a setattr command.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Dec 25, 2021, at 5:34 AM, Prathvi Singh via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Hi Elaine,
> > I have one more query. I have a residue (its ID is #0:140.a) in a
> protein model. I want to change the torsion angle between its backbone N,
> backbone C-alpha, sidechain C-beta & sidechain C-gamma. In order to do
> that, I execute the following command:
> >
> > rotation 1 :140.a at CA,140.a at CB
> >
> > The execution activates the torsion & lists it in the "Adjust Torsions"
> tool. However, I have noticed that the "near" atom in the "Adjust Torsions"
> tool is sometimes assigned to backbone N & other times is assigned to
> backbone C. This is messing up my calculations. Is there a way to fix the
> "near" atom to backbone N so that it does not change to backbone C?
> > Thanks again

Prathvi Singh,
Research Fellow,
Department of Biological Sciences & Bioengineering,
Indian Institute of Technology, Kanpur-208016
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