[chimerax-users] [Chimera-users] Structure Minimization and Molecule Movement (ChimeraX-1.0)?

[Elaine Meng]

Dear Ammar,
For future reference, for ChimeraX questions it is better to use the chimerax-users at cgl.ucsf.edu mailing list instead of this one.  We announced ChimeraX on both "announce" lists, however, because we thought Chimera users would want to know about it.

(1) Moving only a subset of atoms.  In ChimeraX, the way to move only a subset of the models or the atoms with the mouse is to assign the mouse to move only the selected models or atoms, then select the atoms of interest, and then move them with the mouse.

For example, all of the icons in the "Right Mouse" tab of the toolbar represent different modes, and clicking an icon assigns that function to the right mouse button ( = trackpad + Alt on Windows, trackpad +  command key on a Mac).  Click the icon that looks like a blue sphere with arrows around it to assign the right mouse button to "move selected atoms."  Then dragging with the right mouse button (or trackpad equivalent) will translate the selected atoms and additionally pressing Shift will rotate the selected atoms.

Right Mouse icons and what they mean:
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html>

Similar between Chimera and ChimeraX: there are multiple possible ways to select the ligand, e.g. choosing its residue name from menu: Select... Residue... [residue name], or Ctrl-clicking on one of its atoms and then pressing the keyboard up arrow key to promote the selection to the whole residue.
<http://rbvi.ucsf.edu/chimerax/docs/user/menu.html#select>
<http://rbvi.ucsf.edu/chimerax/docs/user/selection.html>

Although the Right Mouse icons only assign functions to the right mouse button, with the "mousemode" command, you can assign any of these functions to any mouse button alone or in combination with modifier keys.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode>

(2) There is no minimize structure tool in ChimeraX currently.  There are limited local "jiggling" calculations with the "tug" and "minimize" mouse modes but only for structures with only standard biopolymer residues and water, not ligands in general:
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html>

.... and more extensive molecular dynamics capabilities with the ISOLDE plugin for refinement/modeling into density maps:
<https://isolde.cimr.cam.ac.uk/what-isolde/>

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

> On Jun 20, 2020, at 6:18 PM, Ammar Jastaniah <ajasta2 at uic.edu> wrote:
> 
> Hi,
> I am not able to find the minimize feature function in ChimeraX-1.0. Is there an equivalent to the regular Chimera version, which is to be found under Tools ==> Structure Editing ===> Minimize Structure?
> 
> Also. Are you able to move a PDB file ligand molecule around while keeping the other receptor PDB structure stationary/in its place in ChimeraX-1.0? Once again, this is achievable in Chimera by clicking on Tools ==> Movement ===> Movement Mouse Mode.
> Thank you.
> Ammar