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QChASM / SEQCROW

Plug-in for ChimeraX providing features for building and manipulating organic and organometallic molecules as well as displaying output from quantum chemistry computations.
GNU General Public License v3.0
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Is there a way of visualizing xyz trajectories using SEQCROW on chimera x? #6

Closed Leticia-maria closed 10 months ago

Leticia-maria commented 1 year ago

I have ran a conformational search with crest externally, but when I open the crest_conformers.xyz file, I do not see any place to get an animation of all the conformers.

ajs99778 commented 1 year ago

Running the command coordset slider <model ID> (for example, coordset slider #1) will bring up the animation slider to flip through the conformers. The model ID is shown in the model panel.

The ChimeraX documentation for the coordset command is here: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/coordset.html

ajs99778 commented 1 year ago

There is now a ChimeraX plugin that will automatically run commands when a file is opened. Check it out here on the tool shed: https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxopencommands

You should be able to set it up so it runs coordset slider #X when you open a crest output file. There's more details on how to do this on the tool shed page. The plugin can be installed in probably the same way you installed seqcrow (Tools → More Tools... on the ChimeraX menu, go to the OpenCommands page and click install, and restart ChimeraX).

Let me know if you need any help setting this up