[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.
Regards,
Swanand
> 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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