[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?


Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)

31 Center Drive, Room 3B62B, MSC 2135
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