Add a tug command

[Tom Goddard]

Would be nice to have a tug command that would allow tugging specified atoms to target locations for a specified number of time steps. The use case I am thinking of is to place a peptide linker between two fixed ends, for example ferritin (PDB 5n5f) to encapsulin (PDB 7oe2) as done in the encapsulin-ferritin VR demo

https://www.rbvi.ucsf.edu/chimerax/data/vr-nih-feb2022/ferritin.html

It would be powerful if the tug mouse mode could also restrain specified residues to current positions or to positions of other residues from another model. This would allow an interactive loop modeling capability. Currently tugging with no restraints does not provide a way to keep end residues from moving.

ISOLDE has exactly these capabilities. Would be nice to have a simpler standalone capability.

[Tom Goddard]

The current tug mouse mode code looks easy to modify to allow multiple tugging forces. Currently it is using one per-atom parameter, the force constant, and 3 global parameters x0,y0,z0 for the tug anchor point. The anchor point could be changed to per-atom. Currently there is no tug command. Would be pretty simple to add that command which just calls the enhanced mouse mode code.

I am mostly interested in this for interactive modeling uses without density maps. The purpose would be to easily construct hypothetical models.

[Tristan Croll]

Would be happy to offer input into this, but will be a little while. My son brought COVID home from school, and it's currently hitting me pretty hard. One important thing to consider: if you're going to start tugging groups of atoms (e.g. entire domains) then you'll probably also want to be thinking about some form of reinforcement of the core structure - otherwise things tend to end up getting messy quite fast.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 15 March 2022 18:21
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #6381: Add a tug command

#6381: Add a tug command
-------------------------------------------+-------------------------
          Reporter:  Tom Goddard           |      Owner:  Tom Goddard
              Type:  enhancement           |     Status:  assigned
          Priority:  moderate              |  Milestone:
         Component:  MD/Ensemble Analysis  |    Version:
        Resolution:                        |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+-------------------------

Comment (by Tom Goddard):

 The current tug mouse mode code looks easy to modify to allow multiple
 tugging forces.  Currently it is using one per-atom parameter, the force
 constant, and 3 global parameters x0,y0,z0 for the tug anchor point.  The
 anchor point could be changed to per-atom.  Currently there is no tug
 command.  Would be pretty simple to add that command which just calls the
 enhanced mouse mode code.

 I am mostly interested in this for interactive modeling uses without
 density maps.  The purpose would be to easily construct hypothetical
 models.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6381#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Eric Pettersen]

Very sorry to hear that you and your son are sick. First priority is take care of yourself. Then comment on tug mouse mode. :-)

--Eric

[goddard@…]

Thanks for the tug advise.  Get well!

[Tom Goddard]

I added a tug command that allows tugging one set of atoms to the locations of another set of atoms (or markers). Force constant and some other forcefield parameters can be specified. Documentation

​https://plato-test.cgl.ucsf.edu/chimerax/docs/user/commands/tug.html