[cctbxbb] smtbx.refine not working correctly?

Graeme.Winter at diamond.ac.uk Graeme.Winter at diamond.ac.uk
Thu Jul 20 02:20:41 PDT 2017


@R thank you for

+WGHT 1.0

Cheers G

On 20 Jul 2017, at 10:13, Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at diamond.ac.uk> 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, richard.gildea at diamond.ac.uk<mailto:richard.gildea at diamond.ac.uk><mailto:richard.gildea at diamond.ac.uk> 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: cctbxbb-bounces at phenix-online.org<mailto:cctbxbb-bounces at phenix-online.org><mailto:cctbxbb-bounces at phenix-online.org> [cctbxbb-bounces at phenix-online.org<mailto:cctbxbb-bounces at phenix-online.org><mailto:cctbxbb-bounces at phenix-online.org>] on behalf of Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at diamond.ac.uk><mailto:Graeme.Winter at diamond.ac.uk> [Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at diamond.ac.uk><mailto:Graeme.Winter at diamond.ac.uk>]
Sent: 20 July 2017 07:16
To: cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org><mailto:cctbxbb at phenix-online.org>
Subject: [cctbxbb] smtbx.refine not working correctly?

Not sure who to ask...

Tried smtbx.refine from latest phenix & dials builds, both give


[gw56 at 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 at cs03r-sc-serv-16 Refine]$ module load phenix/1.12

Setting up phenix environment and PATH...

[gw56 at 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

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