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

[Jerry Tanoury]

Thank you so much!  I'll look into it.  My script uses  basic build
commands: bond, combine, adjust, delete, open.

Jerry

On Wed, Jul 29, 2020 at 12:16 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Jerry,
> Sorry, no.  The chi angles are built-in definitions for amino acid side
> chains only, and alway use the official definitions of which atoms are used
> for measurement.
>
> You may be able to do what you want using our newer program ChimeraX
> instead of Chimera.
> <http://www.rbvi.ucsf.edu/chimerax/index.html>
>
>  ChimeraX has a "torsion" command that allows you to specify the four
> atoms used to define the angle (again the middle two have to be in a real
> covalent bond) as well as what you want the angle value to be. The manual
> page includes examples:
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html>
>
> ChimeraX command-line atom specification:
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>
>
> ChimeraX may not have all of the Chimera functions used in your current
> script, but it does have "setattr" (and residue attributes phi, psi, chiN),
> a "build" command with some of the structure-building options, and "open"
> command that includes fetching by PDB ID, PubChem ID, SMILES string, etc.:
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html>
> <http://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#residue>
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/build.html>
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch>
>
> 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 8:41 AM, Jerry Tanoury <jerrytanoury at gmail.com>
> wrote:
> >
> > 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 ....
> >
> > Jerry
> >
> > 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
>
>
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