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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A

Hi Dave, this is what's used in cctbx for mask calculation: cctbx_project/cctbx/eltbx/van_der_waals_radii.py Pavel On 7/11/15 02:10, 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