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

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Hi Steve, check this website: http://cci.lbl.gov/cctbx/cctbx_web.cgi It demonstrates what information you can extract from a space group using cctbx. Cheers, Oleg. ________________________________ From: [email protected] on behalf of Collins, Steve (DLSLtd,RAL,SCI) Sent: 23 March 2020 09:40 To: cctbx mailing list ; Tristan Croll Subject: Re: [cctbxbb] Find special positions for a spacegroup in sgtbx Thanks Both, What I really need is, for a given spacegroup (e.g. by number), the set of symmetry operators and a list of special positions with Wyckoff symbols. I guess it’s not too hard to calculate them but then I need to understand the definition of the Wyckoff symbols, so I just wondered it if it was already available to save me the job (and chance of errors!). Some machine-readable version of the International Tables would be ideal. Cheers! Steve From: [email protected] On Behalf Of Pavel Afonine Sent: 22 March 2020 15:53 To: cctbx mailing list ; Tristan Croll Subject: Re: [cctbxbb] Find special positions for a spacegroup in sgtbx @Steve: if interested, I can send you an example. Otherwise, grepping in cctbx code base for 'spacial position' will yield a ton of examples. Pavel 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/symme... - 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 [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb _______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb -- 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