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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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Loading Cluster Growth Files #8

Closed Cdc95 closed 1 year ago

Cdc95 commented 1 year ago

Hello,

Grimmes new QCG docking algorithm (https://doi.org/10.1021/acs.jctc.2c00239) produces an XYZ ensemble file (example attached below) where each structure has one more solvent molecule than the previous. To the best of my knowledge, there is currently no convenient way to load all of these structures. As such, I am just wondering if it would be possible to support loading this type of file? Maybe the extension 'growxyz' could be used to distinguish these files from other ensemble files?

Thanks a bunch, Colton

qcg_grow.txt

ajs99778 commented 1 year ago

Colton,

Do these files have an XYZ extension by default? The new XYZ parser in SEQCROW 1.5.11+ should load all the structures as different models if the elements or number of atoms changes from one structure to the next in the XYZ file. It's not possible in ChimeraX to have a structure change elements or number of atoms, so they have to be separate models.

ChimeraX has a built-in command mseries that can flip through different models in a series. You should just be able to do something like mseries slider #1 to open a slider to flip through the different structures.

I could potentially make it so the mseries command is run by default if you open an XYZ file with a name like "qcg_grow". That should be relatively easy to do. I might also just update my new OpenCommands bundle to let users define these types of rules themselves. Currently, it will only run commands for the child models (i.e. #X.1-150) and not the parent (#X), so the mseries commands won't work with it.

Best,

Tony

ajs99778 commented 1 year ago

I've updated OpenCommands to allow commands to run for parent models. These criteria seem to work for me: image

There's installation instructions for OpenCommands here: https://github.com/ajs99778/ChimeraX_OpenCommands#installation and also more details on the tool shed page. Let me know if this fits with your workflow or if there's anything that would make these types of files easier to process.

Cdc95 commented 1 year ago

Sorry for the late response - I must have missed the email for the first comment. That works perfectly!!

Thanks a bunch for all your help :) Colton