Hi Yarrow -
1. Yes, according to the wiki<http://www.pymolwiki.org/index.php/Dots>, the
dots are located on the vdW surface unless the `dot_solvent` setting is turned
on (in which case they’re on the solvent accessible surface).
2. Based on the settings listed with “dot” in their names, it doesn’t look like
dot_transparency is currently available.
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Dec 30, 2014, at 6:48 PM, Yarrow Madrona
<acacia.madr...@ucsf.edu<mailto:acacia.madr...@ucsf.edu>> wrote:
Hell Pymolers,
1. Does anyone know what the dot representation for a residue represents? Is it
the van der waals radii?
2. Is there a way to draw transparency for the dots?
-Yarrow
--
Yarrow Madrona, Ph.D.
Postdoctoral Scholar
University of California, San Francisco
Department of Pharmaceutical Chemistry
Rm N551, 600 16th street
San Francisco CA, 94143
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