[Chimera-users] Setting a unique torsion to a specified value

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 29 08:02:33 PDT 2020

Hi Jerry,
No, it won't work to try to define an attribute and then change it.  Also, you cannot just name any 4 atoms in the structure; the bond to rotate must be a real covalent bond.

Instead you would use either
(A)  the "Adjust Torsions" graphical interface (in menu under Tools... Structure Editing), in which you can specify all 4 atoms to be used for the measurement:

... or (B) the command "rotation" in which you specify only the two atoms in the bond to be rotated to define the rotation, and then the change in angle relative to the current position, see:

For example, something like this to rotate 40 degrees around the CA-CB bond of residue 1 in chain A:

rotation 1 :1.A at CA  :1.A at CB
rotation 1 40

Although with the "angle" command you can measure an angle using any 4 atoms (even if they are not directly bonded), you can't specify changing this angle because how to modify the structure to accomplish that change is undefined.

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

> On Jul 29, 2020, at 6:32 AM, Jerry Tanoury <jerrytanoury at gmail.com> wrote:
> Dear forum,
> I am new to chimera.  I have been building and modifying several structures using command-line, and have been successful except for setting a specific torsion to a specified angle.  The torsion is not phi, psi, etc.  I thought I could define the torsion as a specific attribute using an attribute assignment file and defattr.  In my model, the torsion is ":1.A at O3 :1.A at S1 :1.B at O2 :1.B at S2", and I would like to set it to a value of 15.  So, my assignment file would be (?):
> attribute: MyTors
> match mode: any
> recipient: atoms
>             :1.A at O3 :1.A at S1 :1.B at O2 :1.B at S2 15
> Then from command-line I would use: defattr MyTors
> Is this correct?
> Thank you for the help,
> Jerry

More information about the Chimera-users mailing list