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

Tom Goddard goddard at sonic.net
Thu Jun 5 10:14:14 PDT 2014


Hi Darrell,

  To get smaller step size when opening a density map I’d suggest using the Volume Viewer dialog setting “Adjust step to show at most <N> Mvoxels” under menu Features / Data Display Options.  This is the parameter that is setting the initial step size that you think is too coarse.  If you want to go to a factor of 2 lower step size, then you might multiply the current N Mvoxel limit by 8.  Then you can save that setting in your Chimera preferences using menu Features / Save Default Dialog Settings.

  For adjusting the vertex density of molecular surfaces to scale with number of atoms are you talking about solvent excluded surfaces (menu Actions / Surface or surface command) or grid surfaces (molmap command)?  The solvent excluded surface calculation fails for most large structures so I can’t see that working.  If you mean molmap surfaces, let me know, and I’ll pass on a bit of Python that can do the scaling.

	Tom


On Jun 5, 2014, at 9:55 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:

> 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
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