[cctbxbb] Find special positions for a spacegroup in sgtbx

Pavel Afonine pafonine at lbl.gov
Sun Mar 22 08:53:29 PDT 2020

@Steve: if interested, I can send you an example. Otherwise, grepping in 
cctbx code base for 'spacial position' will yield a ton of examples.

On 3/22/20 08:51, Pavel Afonine wrote:
> Hi Tristan,
> in CCTBX you can find if an atom (or, generally, a point in space) 
> belongs to a special position.
> Pavel
> On 3/22/20 05:49, Tristan Croll wrote:
>> If there isn't already a pre-existing method in CCTBX, I recently did 
>> something along these lines using ChimeraX and Clipper (drawing all 
>> the symmetry axes in a unit cell - see attached example). The source 
>> code is at 
>> https://github.com/tristanic/chimerax-clipper/blob/master/src/geometry/symmetry_axes.py 
>> - should be fairly straightforward to port the logic to CCTBX.
>> On 2020-03-22 12:00, Collins, Steve (DLSLtd,RAL,SCI) wrote:
>>> Hello,
>>> I'm trying to find something I can run from Python to get all the 
>>> special (high-symmetry) positions and usual (e.g. Wyckoff) labels 
>>> for a particular space group. I can't find this in the sgtbx 
>>> documentation. Does anyone know if it can be done? Or maybe a 
>>> different package?
>>> Thanks - and stay safe!
>>> Steve Collins
>>> -- 
>>> This e-mail and any attachments may contain confidential, copyright 
>>> and or privileged material, and are for the use of the intended 
>>> addressee only. If you are not the intended addressee or an 
>>> authorised recipient of the addressee please notify us of receipt by 
>>> returning the e-mail and do not use, copy, retain, distribute or 
>>> disclose the information in or attached to the e-mail.
>>> Any opinions expressed within this e-mail are those of the 
>>> individual and not necessarily of Diamond Light Source Ltd.
>>> Diamond Light Source Ltd. cannot guarantee that this e-mail or any 
>>> attachments are free from viruses and we cannot accept liability for 
>>> any damage which you may sustain as a result of software viruses 
>>> which may be transmitted in or with the message.
>>> Diamond Light Source Limited (company no. 4375679). Registered in 
>>> England and Wales with its registered office at Diamond House, 
>>> Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 
>>> 0DE, United Kingdom
>>> _______________________________________________
>>> cctbxbb mailing list
>>> cctbxbb at phenix-online.org <mailto:cctbxbb at phenix-online.org>
>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>> _______________________________________________
>> cctbxbb mailing list
>> cctbxbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/cctbxbb

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20200322/4bef7a7f/attachment.htm>

More information about the cctbxbb mailing list