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

Jerry Tanoury jerrytanoury at gmail.com
Wed Jul 29 08:41:24 PDT 2020

Thank you Elaine.  I was aware of the rotation command.  However, my
starting torsion angle will not be the same for all the structures, and I
will have at least 100 structures to manipulate.
Would it be possible to redefine a chi angle to be the four atoms I have
noted, for example, then use:

 settattr r chi1 80 ....


On Wed, Jul 29, 2020 at 11:02 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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:
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust
> >
> ... 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:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rotation.html>
> 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.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>
> I hope this helps,
> Elaine
> -----
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200729/19d96efb/attachment.html>

More information about the Chimera-users mailing list