[phenixbb] atom vdW dictionary for Python

[Tim Gruene]

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

GPG Key ID = A46BEE1A


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