Folks, For reading shelxl .res files I need to define a cls parameter - it is not _used_ for anything though - so 0 works fine e.g. from iotbx import shelx import sys s = shelx.cctbx_xray_structure_from(0, filename=sys.argv[1]) will work fine. I based this on the documentation at https://cci.lbl.gov/cctbx_docs/iotbx/iotbx.shelx.html What have I missed? Thanks Graeme -- 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
That function isn't supposed be called directly, but via cctbx.xray.structure.from_shelx():
https://github.com/cctbx/cctbx_project/blob/0385ba220080aebda3b9a2b0be51169d...
Dr Richard Gildea
Data Analysis Scientist
Tel: +441235 77 8078
Diamond Light Source Ltd.
Diamond House
Harwell Science & Innovation Campus
Didcot
Oxfordshire
OX11 0DE
________________________________
From: [email protected]
That is a bit opaque, since it (i) does exactly what I wanted (ii) is included in iotbx.shelx which is exactly what I wanted to do (I/O with SHELX files) and (iii) gives no indication whatsoever (docstring or similar) that it should not be used directly. Anyhow, possibly something which one could add to this “discussing documentation” thread? Thanks Graeme
On 22 Aug 2019, at 15:59, [email protected] wrote:
That function isn't supposed be called directly, but via cctbx.xray.structure.from_shelx():
https://github.com/cctbx/cctbx_project/blob/0385ba220080aebda3b9a2b0be51169d...
Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078
Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: [email protected]
on behalf of [email protected] Sent: 22 August 2019 15:53:25 To: cctbx mailing list Subject: [cctbxbb] cls parameter Folks,
For reading shelxl .res files I need to define a cls parameter - it is not _used_ for anything though - so 0 works fine e.g.
from iotbx import shelx import sys
s = shelx.cctbx_xray_structure_from(0, filename=sys.argv[1])
will work fine. I based this on the documentation at
https://cci.lbl.gov/cctbx_docs/iotbx/iotbx.shelx.html
What have I missed?
Thanks Graeme
-- 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
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Hi, Fair enough. I wrote cctbx_xray_structure_from on the same template as smtbx_refinement_model_from. The latter needs that cls parameter but not the former. So it could be made usable straight from iotbx.shelx indeed. A simple change to make, which should not break anything. Best wishes, Luc
On 22 Aug 2019, at 17:04, [email protected]
wrote: That is a bit opaque, since it (i) does exactly what I wanted (ii) is included in iotbx.shelx which is exactly what I wanted to do (I/O with SHELX files) and (iii) gives no indication whatsoever (docstring or similar) that it should not be used directly.
Anyhow, possibly something which one could add to this “discussing documentation” thread?
Thanks Graeme
On 22 Aug 2019, at 15:59, [email protected] wrote:
That function isn't supposed be called directly, but via cctbx.xray.structure.from_shelx():
https://github.com/cctbx/cctbx_project/blob/0385ba220080aebda3b9a2b0be51169d...
Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078
Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: [email protected]
on behalf of [email protected] Sent: 22 August 2019 15:53:25 To: cctbx mailing list Subject: [cctbxbb] cls parameter Folks,
For reading shelxl .res files I need to define a cls parameter - it is not _used_ for anything though - so 0 works fine e.g.
from iotbx import shelx import sys
s = shelx.cctbx_xray_structure_from(0, filename=sys.argv[1])
will work fine. I based this on the documentation at
https://cci.lbl.gov/cctbx_docs/iotbx/iotbx.shelx.html
What have I missed?
Thanks Graeme
-- 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
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participants (3)
-
Graeme.Winter@Diamond.ac.uk
-
Luc Bourhis
-
richard.gildea@diamond.ac.uk