[phenixbb] reflection file utils : .cif?

Pavel Afonine PAfonine at lbl.gov
Thu Sep 3 11:12:15 PDT 2009


Hi Bryan,

there is a specific tool to do this Just type in the command line:

phenix.cif_as_mtz

and hit Enter. This will give you the instructions about how to use it.

Please let me know if you have any questions or problems using it.

Pavel.


On 9/3/09 11:06 AM, Bryan W. Lepore wrote:
> [ phenix 1.4r3 cctbx tag: 2008_12_07_1353 intel-linux-2.6 redhat-e4.7 ]
>
> i obtained a recent .cif from the PDB, then run :
>
> phenix.reflection_file_converter --mtz=output.mtz test.cif
>
> file_name: test.cif
> file_type: None
>
> No reflection data found in input file.
>
> .... not sure where to go from here (a clip of the file is below, hope not 
> too much) - i know i can run ccp4:cif2mtz, but are .cif part of 
> phenix.reflection_file_converter?
>
> -bryan
>
> (sample of test.cif):
>
> data_testsf
>
> #
> _diffrn_radiation.id   1
> _diffrn_radiation.pdbx_wavelength    1.00600
> #
> _audit.revision_id    1_0
> _audit.creation_date  2009-07-07
> _audit.update_record    'Initial release'
> #
> _symmetry.Int_Tables_number  1
> _symmetry.space_group_name_H-M  'P 1'
> #
> _cell.length_a  79.6610
> _cell.length_b  104.1490
> _cell.length_c  154.0250
> _cell.angle_alpha  81.9570
> _cell.angle_beta  75.9250
> _cell.angle_gamma  73.7280
> #
> _reflns.d_resolution_high  2.967
> _reflns.d_resolution_low  46.392
> _reflns.limit_h_max  26
> _reflns.limit_h_min  -25
> _reflns.limit_k_max  34
> _reflns.limit_k_min  -34
> _reflns.limit_l_max  51
> _reflns.limit_l_min  0
> _reflns.number_all  93210
> _reflns.number_obs  85990
> #
> loop_
> _symmetry_equiv.id
> _symmetry_equiv.pos_as_xyz
> 1  'X,  Y,  Z'
> #
> loop_
> _refln.crystal_id
> _refln.wavelength_id
> _refln.scale_group_code
> _refln.status
> _refln.index_h
> _refln.index_k
> _refln.index_l
> _refln.F_meas_au
> _refln.F_meas_sigma_au
> 1 1 1 o  -25  -16    1    218.4   77.9
> 1 1 1 o  -25  -15    1    250.7   87.9
> 1 1 1 o  -25  -15    2    217.9   78.8
> (... etc... here is a free set hkl :)
> 1 1 1 f  -25   -7    3    315.6   89.7
> (... etc... until the end :)
> #END OF REFLECTIONS
>
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