Thank you for this information, Elaine! Would you plan to integrate the MD engine in chimera-X in the same way as it was in Chimera ? Yours with thanks, Enrico Il giorno dom 29 set 2024 alle ore 21:57 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:

There is no "motion blur" special effect, if that is what you meant.

You could try manually making a different conformation manually (e.g. by rotating a bunch of bonds by hand) as and then morphing from the modified model to the original model with "morph" command, but that may not be anything like what you want.

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html>

Alternatively you could try using the "tug" command, but it won't work on structures containing nonstandard residues (most ligands) unless you also install a separate plugin bundle from the toolshed as described in the help links. I have not tried that.

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/tug.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#openmm> <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxtugligands>

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

...

On Sep 29, 2024, at 8:41 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX users!

I noticed that in ChimeraX there is no built-in molecular dynamics simulation engine as opposed to the older UCSF Chimera. Is it possible to use some visualization trick to deform slightly static coordinates of atomic selection introducing (visually) the impression that they move during movie recording ?

Many thanks in advance

Enrico

Well… this is, in essence, what the ISOLDE plugin is at its heart (it uses the AMBER14 forcefield with a few tweaks and additions). It does like to set its own display style which may not be ideal for situations like this, but most of that can be overridden with ChimeraX commands if you need to. On Mon, 30 Sep 2024 at 21:40, Eric Pettersen via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

On Sep 29, 2024, at 1:37 PM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Would you plan to integrate the MD engine in chimera-X in the same way as it was in Chimera ?

The MD Simulation tool in Chimera was developed by a team at the Universitat Autònoma de Barcelona and generously given to us for inclusion in Chimera. We tweaked some interface elements to somewhat improve ease of use, but none of the work to get the molecular dynamics simulation to run was done by us (though the tool does leverage some Chimera capabilities like Dock Prep).

The ChimeraX programming team does not have the deep expertise needed to write an MD simulation tool, so the most likely route to having such a tool would be if a third party wrote one and put it on the Toolshed. We have considered adding simplified and extremely localized simulations to help with problems like fitting a small part of a structure into a map, but that has not happened so far.

So there is no plan to add an MD Simulation tool, though some related possibilities could happen eventually.

--Eric

Eric Pettersen UCSF Computer Graphics Lab

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