[Chimera-users] Setting the vertex density in a script

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Thu Jun 5 09:55:07 PDT 2014


Hi Chimera friends,

To save memory and reduce exported geometry sizes, I want to use a script to automatically scale the vertex density of generated molecular surfaces by the size of the molecule. Is there a way to grab the size (number of atoms?) of the loaded molecule(s) and use that with some simple math to set the vertex density value? I know this will reduce surface fidelity, but for very large molecules, the mesh size becomes unwieldy.

On a separate, but related note, when loading a volumetric file like electron microscopy data, the "step" size in the Volume Viewer automatically adjusts (1, 2, 4, 8, 16) to optimize visual performance and memory. I'm using a script to import volumetric data and then "Export Scene…". For that export, I want to drop down the step to the next lowest step to get a smoother mesh. I can just set the step value to the minimum with something like "volume #0 step 1 limitVoxelCount false", but this risks maxing out the memory and crashing for very large data sets. Is there a way to use a script to get the current step value and then lower by one step for my export?

Thanks,
Darrell

--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

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