[phenixbb] neighbouring residues with symmetry

[Pavel Afonine]

Hi Swanand,

what we have readily available is the tool to calculate bulk-solvent 
mask: is a binary map (0 in protein region and 1 in bulk-solvent 
region). Definitions and calculation algorithm are described in

Jiang, J.-S. & Brünger, A. T. (1994). J. Mol. Biol. 243, 100-115.

Perhaps other can point something else (if any) but this is all I'm 
aware of.

Pavel

On 12/5/14 10:08 AM, 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

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