[phenixbb] neighbouring residues with symmetry

[Gabor Bunkoczi]

Hi Swanand,

there is code to calculate solvent accessible surface area (per atom) in 
mmtbx.geometry.asa, but this does not take symmetry into account, and 
calculate ASA for chains in isolation. On the other hand, it may not be 
very difficult to amend to do what you want. Please feel free to get in 
touch if you need more information.

BW, Gabor

On 2014-12-05 18:08, Swanand Gore wrote:
> 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 [1]
> 
> 
> 
> Links:
> ------
> [1] http://pdbe.org
> 
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