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nglviewer / ngl

WebGL protein viewer
http://nglviewer.org/ngl/
MIT License
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SAS surface and SES surface look the same #800

Open DAlvGar opened 3 years ago

DAlvGar commented 3 years ago

Hi all,

I detected a potential bug. SES surface (Solvent excluded surface) looks exactly the same as the SAS (solvent accessible surface). Reproducible in http://nglviewer.org/ngl/ molecular surface example. They should be different: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/surface.html

How could I fix this?

Thank you all!

Dani

fredludlow commented 3 years ago

So I think the bug is in SES. It should look approximately the same as tehe av method (but calculated differently)...

DAlvGar commented 3 years ago

Hi Fred, thanks for checking this. Is anything I could help with? I took a look to the calcualtion but, being honest, I am a bit lost in there to know what to modify, any tips would be helpful.

fredludlow commented 3 years ago

I just had another quick look and I'm not really any the wiser.

I checked out version 0.9.0-dev.0 (the oldest tag I could easily build) just in case it was a regression during some of the typescript conversion or in case I'd broken marching cubes (I made a few changes when adding the 'av' surface type) - anyway, the behaviour is the same there too, so whatever it is it's been like that a while.

https://fredludlow.com/ngl/v0.9.0-dev.0/examples/webapp.html

How badly do you want SAS? (I think SES and AV are equivalent (and AV looks nicer)). From that diagram I guess it's "just" a case of following the VWS code and adding a constant to all the atom radii...

Sorry, that's probably not super helpful...