[phenixbb] neighbouring residues with symmetry

Pavel Afonine pafonine at lbl.gov
Fri Dec 5 09:32:19 PST 2014

Hi Swanand,


iotbx.show_distances your.pdb > all_distances

will show long list of all distances between pairs including symmetry 
related. For symmetry related it will also show the symmetry operator 
the relates involved atoms.

Look implementation for underlying code.

Type iotbx.show_distances without arguments to see all options.


On 12/5/14 8:41 AM, Swanand Gore wrote:
> Hi All,
> I am sure this has been asked and answered a lot of times...
> Is there a python script somewhere that reads a mmcif file and for any 
> residue in it, returns a list of residues within a certain distance of 
> it. And it returns any symmetry-related copies of residues too within 
> that distance.
> Any pointer greatly appreciated.
> Thanks,
> Swanand

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