See the "how to manually rotate bonds" explanation in my previous answer. You can rotate any of the bonds in the whole structure that way. Or if you would rather use a command, see "torsion" (also can be used for any rotatable bond in the whole structure): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.html> Tom's answer also applies to moving any parts of the whole structure. Best, Elaine
On Jul 17, 2023, at 3:54 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Dear Tom e Elaine,
Thank you very much for this very useful information ! Actually, I've already tried to play with the Phi command BUT the orientations were still not perfect...
Could you probably suggest a command that would additionally change the torsional angle of the adjacent residue (e.g. selecting i-10 residue, where i is the last residue from the core fragment used for creating of the bond) in order that it could additionally change the orientation of the whole segment ?
Many thanks in advance
Enrico
Il giorno gio 13 lug 2023 alle ore 23:51 Tom Goddard <goddard@sonic.net> ha scritto:
Another approach is just to select the atoms you want to move, choose the "Move Atoms" mouse mode in the Right Mouse toolbar and drag the selected part where you want it (holding the shift key allows you to rotate it). This will create bad bond geometry where the selected piece connects to the station piece. If you make the bond length approximately right when you drag the new piece, then you can use the "Minimize" mouse mode and click on residues near the connection to fix the bond geometry.
Tom
On Jul 13, 2023, at 10:57 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, You could try specifying a phi value (backbone angle) in the "build join peptide" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#join>
... But that one angle is unlikely to get the position that you want, and it is a pain to keep starting over and trying again, so it would probably be more convenient to adjust it and other backbone angles in the linker region "manually" after you have done the join.
Still, it may be a long process and difficult to get exactly what you want. How to manually rotate bonds: first hide ribbons and show all atoms (or at least all the backbone atoms), and then you can use the Build Structure tool, the Adjust Torsions section,
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#adjust>
... and/or the "bond rotation" mouse mode: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode>
There is also a "torsion" command but it is easier to use the GUIs to adjust continuously than to keep entering commands with different values. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/torsion.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 13, 2023, at 8:46 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I need to fuse two models in the entire construction. Precisely having a water soluble domain with a linker in the first model #1 as well as transmembrane alpha helix segment in the #2 I load the both in chimera-x and then use the bond command with the aim to create a peptide bond between the last residue of the #1 and the first residue of the #2.
Here is my command:
# select the last residue from the core and the first residue from the TM helix; build join peptide #1:182@C #2:1@N move large
The problem is that on the text step I will need to add the membrane in the TM part, but the orientation of the created construction is not optimal. How could I easily modify the mutual orientation between #1 and #2 ? I join the both initial pdbs to this message, in order that my model could be checked :-)
Many thanks in advance
Enrico
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