Problem related to the "Near" atom in the "Adjust Torsions" tool of UCSF chimera
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@CA,140.a@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
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@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@CA,140.a@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
This helped enormously!!! Thank you sooo much. On Sun, Dec 26, 2021 at 1:18 AM Elaine Meng <meng@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.h...
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@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@CA,140.a@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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Prathvi Singh