Changes between Initial Version and Version 1 of Ticket #7905, comment 6


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Timestamp:
Oct 28, 2022, 2:58:37 PM (3 years ago)
Author:
Tom Goddard

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  • Ticket #7905, comment 6

    initial v1  
    11Oh!  We told you the secret "grid" option in Chimera.  Yes that is using the same reliable SES calculation that is used in ChimeraX.  Even though I wrote the code I can not predict what a grid size of 2 Angstroms will do.  The default is 0.5 Angstroms, and such a large value as 2.0 when you are rolling a probe sphere of radius 1.4 Angstroms over the molecule may behave badly.  I guess I wouldn't expect the code to fail, but the resulting surface may be very ugly.  But I guess you chose the value after lots of testing so it can work.  At any rate, I would still suggest skipping SES surfaces on large atomic models and use Gaussian surfaces at low resolution.
    22
    3 Eric said his NIH 3D script was using large grid values, like 2, probably copied from your code, and it still crashed or ran over an hour.  I tried grid 2 on the 2cse capsid.  Initial memory use is 4 GB which is much lower.  It completed in 34 minutes, ChimeraX was using 8 Gbytes of memory, the surface has 73 million triangles, and a saved GLTF file had a size of 2.2 Gbytes.  The surface is not too pretty and probably much more detail than desired for NIH 3D use cases.  I'll attach an image.
     3Eric said his NIH 3D script was using large grid values, like 2, probably copied from your code, and it still crashed or ran over an hour.  I tried grid 2 on the 2cse capsid.  Initial memory use is 4 GB which is much lower.  It completed in 34 minutes, ChimeraX was using 8 Gbytes of memory, the surface has 73 million triangles, and a saved GLTF file had a size of 2.2 Gbytes.  The surface is not too pretty and probably much more detail than desired for NIH 3D use cases.  I'll attach an image.  This was on a MacBook Pro M1 Max, has 10 cores, only used one, CPU usage was about 9% (ie 1 of 10 cores at about max usage) throughout.