[phenixbb] neighbouring residues with symmetry
pafonine at lbl.gov
Fri Dec 5 10:13:47 PST 2014
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
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.
>> 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.
> Swanand Gore, wwPDB at PDBe-EMBL-EBI, Cambridge
> swanand at ebi.ac.uk .............http://pdbe.org
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