Hello, I'm trying to move some waters away from a ligand (and eventually some lipids as well) as they overlap too much for minimization to fix it. I can't seem to figure out how to select an entire (water) molecule. The select atom lets me select one atom, but I cannot chain or add more atoms. Some atoms seem to refuse to move even when I try to move one at a time using the "Move atoms" right mouse option. Any help would be appreciated as I can't find much about translating molecules (the bond rotation works perfectly!). Thanks! Eddie
Eddie,
I know shift-clicking on atoms will add them to the selection on desktop, but I'm not sure how that works in VR.
My SEQCROW bundle has a mouse mode for selecting entire fragments. This should let you click on one atom in a molecule to easily select the whole thing. I've never used VR, so I'm not sure if it works with that or what that looks like. If you want to test it out, it's the "select fragment" mode on the "more right mouse" toolbar. After installing SEQCROW, you'll have to restart ChimeraX to see this toolbar.
Best,
Tony ________________________________ From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Dr. Eddie via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: Thursday, October 6, 2022 1:00 PM To: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: [chimerax-users] Moving molecules in VR
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Hello, I'm trying to move some waters away from a ligand (and eventually some lipids as well) as they overlap too much for minimization to fix it. I can't seem to figure out how to select an entire (water) molecule. The select atom lets me select one atom, but I cannot chain or add more atoms. Some atoms seem to refuse to move even when I try to move one at a time using the "Move atoms" right mouse option. Any help would be appreciated as I can't find much about translating molecules (the bond rotation works perfectly!). Thanks! Eddie
Hi Eddie,
In virtual reality to select an entire water press the selection button that you assigned on the hand controller and while holding the button drag upward. That will extend the selection to the next larger group of atoms like the up-arrow key does for a selection on the keyboard. Sorry this trick is not in the ChimeraX VR documentation. The documentation does mention that some modes like contour level adjustment work this way, depress the button, raise or lower the controller then release the button. But it does not describe all the modes that have this unusual up/down dragging behavior that does not work with a mouse.
Tony's suggestion to use a SEQCROW defined mouse mode won't work unless Tony added Python methods to his mouse mode (vr_press, vr_motion, vr_release) which provide support for VR. Mouse modes that don't have those methods do not work in VR.
Tom
On Oct 6, 2022, at 10:00 AM, Dr. Eddie via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello, I'm trying to move some waters away from a ligand (and eventually some lipids as well) as they overlap too much for minimization to fix it. I can't seem to figure out how to select an entire (water) molecule. The select atom lets me select one atom, but I cannot chain or add more atoms. Some atoms seem to refuse to move even when I try to move one at a time using the "Move atoms" right mouse option. Any help would be appreciated as I can't find much about translating molecules (the bond rotation works perfectly!). Thanks! Eddie _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
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Anthony James Schaefer -
Dr. Eddie -
Tom Goddard