Hi Jerry, Unfortunately ChimeraX does not yet have "adjust" "bond" or "combine" ... the latter one is mentioned in the missing features section of the ChimeraX download page. For now, you might have to do only the torsion part of your workflow in ChimeraX, if that is possible. Elaine
On Jul 29, 2020, at 9:20 AM, Jerry Tanoury <jerrytanoury@gmail.com> wrote:
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@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@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@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.ht...>
... 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@CA :1.A@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@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@O3 :1.A@S1 :1.B@O2 :1.B@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@O3 :1.A@S1 :1.B@O2 :1.B@S2 15
Then from command-line I would use: defattr MyTors
Is this correct? Thank you for the help, Jerry
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