failing test with CCP4 7.0.18
Hi, The test libtbx.python $(libtbx.find_in_repositories cctbx/development/run_shelx.py) P31 works with CCP4 7.0.17, but fails when run with SHELXL from CCP4 7.0.18. The test apparently involves creating a small random crystal structure, calculating the structure factors and solving the structure using SHELXL. The updated SHELXL version creates deterministic, but slightly different anisotropic temperature factors. I am not sure if this is a problem with the test or with the SHELXL update. Could anybody have a look into that? -Markus -- 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
I don't understand exactly what Ralf was testing here, but this test dates from the early days of cctbx (2002) and as far as I am aware hasn't caused any problems until now. CCP4 update 18 actually appears to be distributing an older version of shelxl than update 14, is this correct? Hopefully the guys at CCP4 can shed some light on what the difference in the shelxl versions they are distributing might be. I don't see any mention of shelxl updates at http://www.ccp4.ac.uk/updates/ $ /dls_sw/apps/ccp4/64/7.0/update14/ccp4-7.0/bin/shelxl +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXL - CRYSTAL STRUCTURE REFINEMENT - MULTI-CPU VERSION + + Copyright(C) George M. Sheldrick 1993-2014 Version 2014/7 + + started at 14:36:05 on 01-Sep-2016 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ $ /dls_sw/apps/ccp4/64/7.0/update18/ccp4-7.0/bin/shelxl +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXL - CRYSTAL STRUCTURE REFINEMENT - MULTI-CPU VERSION + + Copyright(C) George M. Sheldrick 1993-2016 Version 2016/4 + + started at 14:36:42 on 01-Sep-2016 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Cheers, Richard 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] [[email protected]] on behalf of [email protected] [[email protected]] Sent: 19 August 2016 10:19 To: [email protected] Subject: [cctbxbb] failing test with CCP4 7.0.18 Hi, The test libtbx.python $(libtbx.find_in_repositories cctbx/development/run_shelx.py) P31 works with CCP4 7.0.17, but fails when run with SHELXL from CCP4 7.0.18. The test apparently involves creating a small random crystal structure, calculating the structure factors and solving the structure using SHELXL. The updated SHELXL version creates deterministic, but slightly different anisotropic temperature factors. I am not sure if this is a problem with the test or with the SHELXL update. Could anybody have a look into that? -Markus -- 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] http://phenix-online.org/mailman/listinfo/cctbxbb
It appears to me that update 18 has " 2016/4" ShelXL version whereas update 14 - "2014/7" which is older (and more stable). It worth noting the version "2016/4" has a number of bugs that could easily break tests (in particularly related to symmetry operators and H-bonds). http://www.xrayforum.co.uk/viewtopic.php?f=124&t=2761http://www.xrayforum.co.uk/viewtopic.php?f=122&t=2758 Cheers,Oleg.
From: [email protected] To: [email protected] Date: Thu, 1 Sep 2016 13:39:32 +0000 CC: [email protected] Subject: Re: [cctbxbb] failing test with CCP4 7.0.18
I don't understand exactly what Ralf was testing here, but this test dates from the early days of cctbx (2002) and as far as I am aware hasn't caused any problems until now.
CCP4 update 18 actually appears to be distributing an older version of shelxl than update 14, is this correct? Hopefully the guys at CCP4 can shed some light on what the difference in the shelxl versions they are distributing might be. I don't see any mention of shelxl updates at http://www.ccp4.ac.uk/updates/
$ /dls_sw/apps/ccp4/64/7.0/update14/ccp4-7.0/bin/shelxl
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXL - CRYSTAL STRUCTURE REFINEMENT - MULTI-CPU VERSION + + Copyright(C) George M. Sheldrick 1993-2014 Version 2014/7 + + started at 14:36:05 on 01-Sep-2016 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
$ /dls_sw/apps/ccp4/64/7.0/update18/ccp4-7.0/bin/shelxl
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXL - CRYSTAL STRUCTURE REFINEMENT - MULTI-CPU VERSION + + Copyright(C) George M. Sheldrick 1993-2016 Version 2016/4 + + started at 14:36:42 on 01-Sep-2016 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Cheers,
Richard
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] [[email protected]] on behalf of [email protected] [[email protected]] Sent: 19 August 2016 10:19 To: [email protected] Subject: [cctbxbb] failing test with CCP4 7.0.18
Hi,
The test
libtbx.python $(libtbx.find_in_repositories cctbx/development/run_shelx.py) P31
works with CCP4 7.0.17, but fails when run with SHELXL from CCP4 7.0.18.
The test apparently involves creating a small random crystal structure, calculating the structure factors and solving the structure using SHELXL. The updated SHELXL version creates deterministic, but slightly different anisotropic temperature factors. I am not sure if this is a problem with the test or with the SHELXL update. Could anybody have a look into that?
-Markus
-- 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] http://phenix-online.org/mailman/listinfo/cctbxbb
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Could anyone from the CCP4 team comment on this? Cheers, Richard 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] [[email protected]] on behalf of Oleg Dolomanov [[email protected]] Sent: 01 September 2016 14:58 To: cctbx mailing list Cc: CCP4 Subject: Re: [cctbxbb] failing test with CCP4 7.0.18 It appears to me that update 18 has " 2016/4" ShelXL version whereas update 14 - "2014/7" which is older (and more stable). It worth noting the version "2016/4" has a number of bugs that could easily break tests (in particularly related to symmetry operators and H-bonds). http://www.xrayforum.co.uk/viewtopic.php?f=124&t=2761 http://www.xrayforum.co.uk/viewtopic.php?f=122&t=2758 Cheers, Oleg.
From: [email protected] To: [email protected] Date: Thu, 1 Sep 2016 13:39:32 +0000 CC: [email protected] Subject: Re: [cctbxbb] failing test with CCP4 7.0.18
I don't understand exactly what Ralf was testing here, but this test dates from the early days of cctbx (2002) and as far as I am aware hasn't caused any problems until now.
CCP4 update 18 actually appears to be distributing an older version of shelxl than update 14, is this correct? Hopefully the guys at CCP4 can shed some light on what the difference in the shelxl versions they are distributing might be. I don't see any mention of shelxl updates at http://www.ccp4.ac.uk/updates/
$ /dls_sw/apps/ccp4/64/7.0/update14/ccp4-7.0/bin/shelxl
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXL - CRYSTAL STRUCTURE REFINEMENT - MULTI-CPU VERSION + + Copyright(C) George M. Sheldrick 1993-2014 Version 2014/7 + + started at 14:36:05 on 01-Sep-2016 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
$ /dls_sw/apps/ccp4/64/7.0/update18/ccp4-7.0/bin/shelxl
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXL - CRYSTAL STRUCTURE REFINEMENT - MULTI-CPU VERSION + + Copyright(C) George M. Sheldrick 1993-2016 Version 2016/4 + + started at 14:36:42 on 01-Sep-2016 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Cheers,
Richard
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] [[email protected]] on behalf of [email protected] [[email protected]] Sent: 19 August 2016 10:19 To: [email protected] Subject: [cctbxbb] failing test with CCP4 7.0.18
Hi,
The test
libtbx.python $(libtbx.find_in_repositories cctbx/development/run_shelx.py) P31
works with CCP4 7.0.17, but fails when run with SHELXL from CCP4 7.0.18.
The test apparently involves creating a small random crystal structure, calculating the structure factors and solving the structure using SHELXL. The updated SHELXL version creates deterministic, but slightly different anisotropic temperature factors. I am not sure if this is a problem with the test or with the SHELXL update. Could anybody have a look into that?
-Markus
-- 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] http://phenix-online.org/mailman/listinfo/cctbxbb
_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb
Oleg is correct regarding the version numbers, that is, update 18 delivers the latest version of SHELXL. Regarding the bugs, they should be reported to the developer. CCP4 is mainly a distribution body, and we distribute what (external) developers instruct us to do. Eugene ________________________________ From: [email protected] [[email protected]] on behalf of [email protected] [[email protected]] Sent: Friday, September 16, 2016 11:34 AM To: [email protected] Cc: CCP4 Subject: [ccp4]: RE: [cctbxbb] failing test with CCP4 7.0.18 Could anyone from the CCP4 team comment on this? Cheers, Richard 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] [[email protected]] on behalf of Oleg Dolomanov [[email protected]] Sent: 01 September 2016 14:58 To: cctbx mailing list Cc: CCP4 Subject: Re: [cctbxbb] failing test with CCP4 7.0.18 It appears to me that update 18 has " 2016/4" ShelXL version whereas update 14 - "2014/7" which is older (and more stable). It worth noting the version "2016/4" has a number of bugs that could easily break tests (in particularly related to symmetry operators and H-bonds). http://www.xrayforum.co.uk/viewtopic.php?f=124&t=2761 http://www.xrayforum.co.uk/viewtopic.php?f=122&t=2758 Cheers, Oleg.
From: [email protected] To: [email protected] Date: Thu, 1 Sep 2016 13:39:32 +0000 CC: [email protected] Subject: Re: [cctbxbb] failing test with CCP4 7.0.18
I don't understand exactly what Ralf was testing here, but this test dates from the early days of cctbx (2002) and as far as I am aware hasn't caused any problems until now.
CCP4 update 18 actually appears to be distributing an older version of shelxl than update 14, is this correct? Hopefully the guys at CCP4 can shed some light on what the difference in the shelxl versions they are distributing might be. I don't see any mention of shelxl updates at http://www.ccp4.ac.uk/updates/
$ /dls_sw/apps/ccp4/64/7.0/update14/ccp4-7.0/bin/shelxl
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXL - CRYSTAL STRUCTURE REFINEMENT - MULTI-CPU VERSION + + Copyright(C) George M. Sheldrick 1993-2014 Version 2014/7 + + started at 14:36:05 on 01-Sep-2016 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
$ /dls_sw/apps/ccp4/64/7.0/update18/ccp4-7.0/bin/shelxl
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + SHELXL - CRYSTAL STRUCTURE REFINEMENT - MULTI-CPU VERSION + + Copyright(C) George M. Sheldrick 1993-2016 Version 2016/4 + + started at 14:36:42 on 01-Sep-2016 + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Cheers,
Richard
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] [[email protected]] on behalf of [email protected] [[email protected]] Sent: 19 August 2016 10:19 To: [email protected] Subject: [cctbxbb] failing test with CCP4 7.0.18
Hi,
The test
libtbx.python $(libtbx.find_in_repositories cctbx/development/run_shelx.py) P31
works with CCP4 7.0.17, but fails when run with SHELXL from CCP4 7.0.18.
The test apparently involves creating a small random crystal structure, calculating the structure factors and solving the structure using SHELXL. The updated SHELXL version creates deterministic, but slightly different anisotropic temperature factors. I am not sure if this is a problem with the test or with the SHELXL update. Could anybody have a look into that?
-Markus
-- 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] http://phenix-online.org/mailman/listinfo/cctbxbb
_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb
participants (4)
-
eugene.krissinel＠stfc.ac.uk -
markus.gerstel＠diamond.ac.uk -
Oleg Dolomanov -
richard.gildea＠diamond.ac.uk