smtbx.refine not working correctly?
Not sure who to ask... Tried smtbx.refine from latest phenix & dials builds, both give [gw56@cs03r-sc-serv-16 Refine]$ smtbx.refine lcy.ins lcy.hkl lcy_smtbx.res Traceback (most recent call last): File "/dls_sw/apps/dials/dials-v1-6-4/build/../modules/cctbx_project/smtbx/command_line/refine.py", line 152, in <module> run(args, options) File "/dls_sw/apps/dials/dials-v1-6-4/build/../modules/cctbx_project/smtbx/command_line/refine.py", line 67, in run strictly_shelxl=False) File "/dls_sw/apps/dials/dials-v1-6-4/modules/cctbx_project/smtbx/refinement/__init__.py", line 10, in from_shelx return _(cls, *args, **kwds) File "/dls_sw/apps/dials/dials-v1-6-4/modules/cctbx_project/iotbx/shelx/__init__.py", line 59, in smtbx_refinement_model_from builder.weighting_scheme, AttributeError: 'smtbx_builder' object has no attribute 'weighting_scheme' [gw56@cs03r-sc-serv-16 Refine]$ module load phenix/1.12 Setting up phenix environment and PATH... [gw56@cs03r-sc-serv-16 Refine]$ smtbx.refine lcy.ins lcy.hkl lcy_smtbx.res Traceback (most recent call last): File "/dls_sw/apps/phenix/1.12/phenix-1.12-2829/build/../modules/cctbx_project/smtbx/command_line/refine.py", line 152, in <module> run(args, options) File "/dls_sw/apps/phenix/1.12/phenix-1.12-2829/build/../modules/cctbx_project/smtbx/command_line/refine.py", line 67, in run strictly_shelxl=False) File "/dls_sw/apps/phenix/1.12/phenix-1.12-2829/modules/cctbx_project/smtbx/refinement/__init__.py", line 10, in from_shelx return _(cls, *args, **kwds) File "/dls_sw/apps/phenix/1.12/phenix-1.12-2829/modules/cctbx_project/iotbx/shelx/__init__.py", line 59, in smtbx_refinement_model_from builder.weighting_scheme, AttributeError: 'smtbx_builder' object has no attribute 'weighting_scheme' who's best to ask about this? 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
There was never really much work put in to making the command line interface work slickly - the main interface to probably 99.99% of users is via Olex2. I suspect that error message is telling you that your ins file doesn't have a weighting scheme defined. Where did your ins file come from and what does it look like? 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: 20 July 2017 07:16 To: [email protected] Subject: [cctbxbb] smtbx.refine not working correctly? Not sure who to ask... Tried smtbx.refine from latest phenix & dials builds, both give [gw56@cs03r-sc-serv-16 Refine]$ smtbx.refine lcy.ins lcy.hkl lcy_smtbx.res Traceback (most recent call last): File "/dls_sw/apps/dials/dials-v1-6-4/build/../modules/cctbx_project/smtbx/command_line/refine.py", line 152, in <module> run(args, options) File "/dls_sw/apps/dials/dials-v1-6-4/build/../modules/cctbx_project/smtbx/command_line/refine.py", line 67, in run strictly_shelxl=False) File "/dls_sw/apps/dials/dials-v1-6-4/modules/cctbx_project/smtbx/refinement/__init__.py", line 10, in from_shelx return _(cls, *args, **kwds) File "/dls_sw/apps/dials/dials-v1-6-4/modules/cctbx_project/iotbx/shelx/__init__.py", line 59, in smtbx_refinement_model_from builder.weighting_scheme, AttributeError: 'smtbx_builder' object has no attribute 'weighting_scheme' [gw56@cs03r-sc-serv-16 Refine]$ module load phenix/1.12 Setting up phenix environment and PATH... [gw56@cs03r-sc-serv-16 Refine]$ smtbx.refine lcy.ins lcy.hkl lcy_smtbx.res Traceback (most recent call last): File "/dls_sw/apps/phenix/1.12/phenix-1.12-2829/build/../modules/cctbx_project/smtbx/command_line/refine.py", line 152, in <module> run(args, options) File "/dls_sw/apps/phenix/1.12/phenix-1.12-2829/build/../modules/cctbx_project/smtbx/command_line/refine.py", line 67, in run strictly_shelxl=False) File "/dls_sw/apps/phenix/1.12/phenix-1.12-2829/modules/cctbx_project/smtbx/refinement/__init__.py", line 10, in from_shelx return _(cls, *args, **kwds) File "/dls_sw/apps/phenix/1.12/phenix-1.12-2829/modules/cctbx_project/iotbx/shelx/__init__.py", line 59, in smtbx_refinement_model_from builder.weighting_scheme, AttributeError: 'smtbx_builder' object has no attribute 'weighting_scheme' who's best to ask about this? 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 _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb
HI Richard INS file came from … me CELL 0.68890 20.3603 8.7534 9.6876 90.000 110.056 90.000 ZERR 8.000 0.0000 0.0000 0.0000 0.000 0.000 0.000 LATT 7 SYMM -X, Y, 1/2-Z SFAC C H N O DISP C -0.0067 0.0008 DISP H -0.1092 0.0000 DISP N -0.0076 0.0016 DISP O -0.0073 0.0030 UNIT 28.0 16.0 8.0 24.0 L.S. 10 BOND $H LIST 6 FMAP 2 ANIS PLAN 20 O001 4 0.26988 0.41664 0.45019 11.00000 0.01958 8.09 O002 4 0.30540 0.32022 0.67905 11.00000 0.02024 8.04 O003 4 0.32713 0.95180 0.39555 11.00000 0.02152 7.87 O004 4 0.46583 0.60285 1.08121 11.00000 0.02324 7.77 O005 4 0.51967 0.79968 1.03290 11.00000 0.02525 7.61 O006 4 0.39528 1.07842 0.58282 11.00000 0.02749 7.50 C007 3 0.36481 0.96195 0.52574 11.00000 0.01341 6.92 C008 3 0.47301 0.70190 0.99780 11.00000 0.01326 6.89 C009 1 0.37258 0.82568 0.61751 11.00000 0.01598 6.02 C00A 1 0.34263 0.56664 0.64627 11.00000 0.01542 6.01 C00B 1 0.30223 0.42606 0.58223 11.00000 0.01626 5.99 C00C 1 0.42421 0.70238 0.84566 11.00000 0.01609 5.98 C00D 1 0.38684 0.56889 0.79284 11.00000 0.01596 5.97 C00E 1 0.33615 0.69527 0.55756 11.00000 0.01611 5.97 C00F 1 0.41833 0.83350 0.76309 11.00000 0.01670 5.93 H001 2 0.3087 0.6979 0.4627 11.00000 0.05 1.09 H002 2 0.3915 0.4821 0.8491 11.00000 0.05 1.03 H003 2 0.4391 0.9176 0.8004 11.00000 0.05 0.90 H004 2 0.2834 0.2431 0.6373 11.00000 0.05 0.86 HKLF 4 END no weighting scheme I guess… pointer on how I add one would be awesome :o) Cheers Graeme On 20 Jul 2017, at 09:22, [email protected]mailto:[email protected] wrote: There was never really much work put in to making the command line interface work slickly - the main interface to probably 99.99% of users is via Olex2. I suspect that error message is telling you that your ins file doesn't have a weighting scheme defined. Where did your ins file come from and what does it look like? 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]mailto:[email protected] [[email protected]mailto:[email protected]] on behalf of [email protected]mailto:[email protected] [[email protected]mailto:[email protected]] Sent: 20 July 2017 07:16 To: [email protected]mailto:[email protected] Subject: [cctbxbb] smtbx.refine not working correctly? Not sure who to ask... Tried smtbx.refine from latest phenix & dials builds, both give [gw56@cs03r-sc-serv-16 Refine]$ smtbx.refine lcy.ins lcy.hkl lcy_smtbx.res Traceback (most recent call last): File "/dls_sw/apps/dials/dials-v1-6-4/build/../modules/cctbx_project/smtbx/command_line/refine.py", line 152, in <module> run(args, options) File "/dls_sw/apps/dials/dials-v1-6-4/build/../modules/cctbx_project/smtbx/command_line/refine.py", line 67, in run strictly_shelxl=False) File "/dls_sw/apps/dials/dials-v1-6-4/modules/cctbx_project/smtbx/refinement/__init__.py", line 10, in from_shelx return _(cls, *args, **kwds) File "/dls_sw/apps/dials/dials-v1-6-4/modules/cctbx_project/iotbx/shelx/__init__.py", line 59, in smtbx_refinement_model_from builder.weighting_scheme, AttributeError: 'smtbx_builder' object has no attribute 'weighting_scheme' [gw56@cs03r-sc-serv-16 Refine]$ module load phenix/1.12 Setting up phenix environment and PATH... [gw56@cs03r-sc-serv-16 Refine]$ smtbx.refine lcy.ins lcy.hkl lcy_smtbx.res Traceback (most recent call last): File "/dls_sw/apps/phenix/1.12/phenix-1.12-2829/build/../modules/cctbx_project/smtbx/command_line/refine.py", line 152, in <module> run(args, options) File "/dls_sw/apps/phenix/1.12/phenix-1.12-2829/build/../modules/cctbx_project/smtbx/command_line/refine.py", line 67, in run strictly_shelxl=False) File "/dls_sw/apps/phenix/1.12/phenix-1.12-2829/modules/cctbx_project/smtbx/refinement/__init__.py", line 10, in from_shelx return _(cls, *args, **kwds) File "/dls_sw/apps/phenix/1.12/phenix-1.12-2829/modules/cctbx_project/iotbx/shelx/__init__.py", line 59, in smtbx_refinement_model_from builder.weighting_scheme, AttributeError: 'smtbx_builder' object has no attribute 'weighting_scheme' who's best to ask about this? 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 _______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb
@R thank you for +WGHT 1.0 Cheers G On 20 Jul 2017, at 10:13, [email protected]mailto:[email protected] wrote: HI Richard INS file came from … me CELL 0.68890 20.3603 8.7534 9.6876 90.000 110.056 90.000 ZERR 8.000 0.0000 0.0000 0.0000 0.000 0.000 0.000 LATT 7 SYMM -X, Y, 1/2-Z SFAC C H N O DISP C -0.0067 0.0008 DISP H -0.1092 0.0000 DISP N -0.0076 0.0016 DISP O -0.0073 0.0030 UNIT 28.0 16.0 8.0 24.0 L.S. 10 BOND $H LIST 6 FMAP 2 ANIS PLAN 20 O001 4 0.26988 0.41664 0.45019 11.00000 0.01958 8.09 O002 4 0.30540 0.32022 0.67905 11.00000 0.02024 8.04 O003 4 0.32713 0.95180 0.39555 11.00000 0.02152 7.87 O004 4 0.46583 0.60285 1.08121 11.00000 0.02324 7.77 O005 4 0.51967 0.79968 1.03290 11.00000 0.02525 7.61 O006 4 0.39528 1.07842 0.58282 11.00000 0.02749 7.50 C007 3 0.36481 0.96195 0.52574 11.00000 0.01341 6.92 C008 3 0.47301 0.70190 0.99780 11.00000 0.01326 6.89 C009 1 0.37258 0.82568 0.61751 11.00000 0.01598 6.02 C00A 1 0.34263 0.56664 0.64627 11.00000 0.01542 6.01 C00B 1 0.30223 0.42606 0.58223 11.00000 0.01626 5.99 C00C 1 0.42421 0.70238 0.84566 11.00000 0.01609 5.98 C00D 1 0.38684 0.56889 0.79284 11.00000 0.01596 5.97 C00E 1 0.33615 0.69527 0.55756 11.00000 0.01611 5.97 C00F 1 0.41833 0.83350 0.76309 11.00000 0.01670 5.93 H001 2 0.3087 0.6979 0.4627 11.00000 0.05 1.09 H002 2 0.3915 0.4821 0.8491 11.00000 0.05 1.03 H003 2 0.4391 0.9176 0.8004 11.00000 0.05 0.90 H004 2 0.2834 0.2431 0.6373 11.00000 0.05 0.86 HKLF 4 END no weighting scheme I guess… pointer on how I add one would be awesome :o) Cheers Graeme On 20 Jul 2017, at 09:22, [email protected]mailto:[email protected]mailto:[email protected] wrote: There was never really much work put in to making the command line interface work slickly - the main interface to probably 99.99% of users is via Olex2. I suspect that error message is telling you that your ins file doesn't have a weighting scheme defined. Where did your ins file come from and what does it look like? 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]mailto:[email protected]mailto:[email protected] [[email protected]mailto:[email protected]mailto:[email protected]] on behalf of [email protected]mailto:[email protected]mailto:[email protected] [[email protected]mailto:[email protected]mailto:[email protected]] Sent: 20 July 2017 07:16 To: [email protected]mailto:[email protected]mailto:[email protected] Subject: [cctbxbb] smtbx.refine not working correctly? Not sure who to ask... Tried smtbx.refine from latest phenix & dials builds, both give [gw56@cs03r-sc-serv-16 Refine]$ smtbx.refine lcy.ins lcy.hkl lcy_smtbx.res Traceback (most recent call last): File "/dls_sw/apps/dials/dials-v1-6-4/build/../modules/cctbx_project/smtbx/command_line/refine.py", line 152, in <module> run(args, options) File "/dls_sw/apps/dials/dials-v1-6-4/build/../modules/cctbx_project/smtbx/command_line/refine.py", line 67, in run strictly_shelxl=False) File "/dls_sw/apps/dials/dials-v1-6-4/modules/cctbx_project/smtbx/refinement/__init__.py", line 10, in from_shelx return _(cls, *args, **kwds) File "/dls_sw/apps/dials/dials-v1-6-4/modules/cctbx_project/iotbx/shelx/__init__.py", line 59, in smtbx_refinement_model_from builder.weighting_scheme, AttributeError: 'smtbx_builder' object has no attribute 'weighting_scheme' [gw56@cs03r-sc-serv-16 Refine]$ module load phenix/1.12 Setting up phenix environment and PATH... [gw56@cs03r-sc-serv-16 Refine]$ smtbx.refine lcy.ins lcy.hkl lcy_smtbx.res Traceback (most recent call last): File "/dls_sw/apps/phenix/1.12/phenix-1.12-2829/build/../modules/cctbx_project/smtbx/command_line/refine.py", line 152, in <module> run(args, options) File "/dls_sw/apps/phenix/1.12/phenix-1.12-2829/build/../modules/cctbx_project/smtbx/command_line/refine.py", line 67, in run strictly_shelxl=False) File "/dls_sw/apps/phenix/1.12/phenix-1.12-2829/modules/cctbx_project/smtbx/refinement/__init__.py", line 10, in from_shelx return _(cls, *args, **kwds) File "/dls_sw/apps/phenix/1.12/phenix-1.12-2829/modules/cctbx_project/iotbx/shelx/__init__.py", line 59, in smtbx_refinement_model_from builder.weighting_scheme, AttributeError: 'smtbx_builder' object has no attribute 'weighting_scheme' who's best to ask about this? 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 _______________________________________________ cctbxbb mailing list [email protected]mailto:[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 _______________________________________________ cctbxbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/cctbxbb
participants (2)
-
Graeme.Winter＠diamond.ac.uk -
richard.gildea＠diamond.ac.uk