[phenixbb] atom vdW dictionary for Python

Edward A. Berry BerryE at upstate.edu
Sat Jul 11 08:51:45 PDT 2015

I guess you already looked at this, but wikipedia has values:

"Van der Waals radii taken from
Bondi's compilation (1964).[2]
Values from other sources may
differ significantly (see text)"

On 07/11/2015 05:10 AM, David Shin wrote:
> Hi -
> I'm writing a Python script to measure the volume of pockets within protein structures - plus extra bells and whistles... thus a custom job.
> I was wondering just for speed, if someone could point me to values for van der Waals radii that are somewhat agreed upon for protein atoms, or if there is some dictionary already made that someone could point to that resides in phenix or some other structural biology package that would be ok for me to copy/use.
> Thanks,
> Dave
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