Save simulation topology file?

[jacknicoludis]

Is there a way to save the topology file that is generated by Isolde using the Isolde command line?

[tristanic]

I'm afraid not... ISOLDE doesn't actually generate a topology file as such - it does everything in memory, creating an OpenMM Topology object that's used to create the simulation. Given that ISOLDE's simulations are generally meant to be fairly ephemeral things used to tweak the model rather than study its behaviour, I've never really seen the need to add the option to dump it to file. That being said, the OpenMM API does have some built-in tools to write its topology back to file (see http://docs.openmm.org/latest/userguide/application/03_model_building_editing.html), or with a few lines in the ChimeraX Python shell you could easily have it save a PDB file containing only the current portion of the model being simulated. Which approach to take really depends on what you want to do with it.

On Mon, Dec 23, 2024 at 5:58 PM Jack Nicoludis @.***> wrote:

Is there a way to save the topology file that is generated by Isolde using the Isolde command line?

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[jacknicoludis]

Thanks - that makes sense. I'm having trouble figuring out how to access the system and/or topology of the current running Isolde simulation using the ChimeraX python shell. Could you provide some pointers or code for how to access this data object?

[tristanic]

Minimal version (assuming ISOLDE has been started, otherwise session.isolde won't exist):

if session.isolde.simulation_running:
    topology = session.isolde.sim_handler.topology
else:
    topology = None

The session object is always available to the ChimeraX shell, or to any Python file opened in ChimeraX. isolde.simulation_running returns True whenever a simulation is in play (whether actively stepping or paused).