[phenixbb] atom vdW dictionary for Python
Tim Gruene
tg at shelx.uni-ac.gwdg.de
Sat Jul 11 04:40:04 PDT 2015
Dear David,
you could write a minimalistic shelxl ins-file and use the covalent
radii from there. You can call them 'agreed on' ;-)
TITL insulin
CELL 0.82657 78.580 78.580 78.580 90.00 90.00 90.00
ZERR 24 0.079 0.079 0.079 0.00 0.00 0.00
LATT -1
SFAC C H N O S P Mg Pt
UNIT 6144 13248 1560 3336 144 0 0 0
MORE 3
HKLF4
END
I did not check how much you could reduce further before shelxl stops
printing the radii.
Best,
Tim
On 07/11/2015 11:10 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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--
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149
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