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I have a collection of molecules represented by SMILES codes, along with their corresponding 3D coordinates. I want to efficiently generate figures for these structures using Avogadro. Ideally, I would like to set the visualization parameters (e.g., rendering style, orientation) once and then apply these settings to multiple molecules to ensure consistent and reproducible visualizations. In VMD, I am familiar with using state files to achieve this. How can I achieve a similar reproducibility feature in Avogadro for generating figures of multiple molecules with consistent visualization settings?

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    $\begingroup$ Hi @Hemanth Haridas, have you considered using the Atomic Simulation Environment combined with povray rendering as reported in wiki.fysik.dtu.dk/ase/faq.html ? $\endgroup$
    – Salvios
    Aug 2, 2023 at 11:49

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Yes, this is in the latest development version (1.98) as I discussed on the Avogadro forum.

I shared an example script for exporting screenshots for a folder of *.xyz files.

  • Launch Avogadro2 (latest nightly builds)
  • Run the script in a directory of .xyz files
  • It will load the files one-by-one into Avogadro and save a PNG image

Please share feedback on the Avogadro forum -- we are interested in other automation tasks (e.g., rendering X orbital or surface, etc.)

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