[phenixbb] neighbouring residues with symmetry

Swanand Gore swanand at ebi.ac.uk
Fri Dec 5 10:08:44 PST 2014

Thanks Pavel!

Is there a tool to calculate solvent-accessible surface areas where 
symmetry-related copies are taken into account and any area occluded by 
them is not counted as accessible.


> Hi Swanand,
> yes:
> 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.
> Pavel
> 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

Swanand Gore, wwPDB at PDBe-EMBL-EBI, Cambridge
swanand at ebi.ac.uk ............. http://pdbe.org

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