[phenixbb] reflection file utils : .cif?

Bryan W. Lepore Bryan.Lepore at umassmed.edu
Thu Sep 3 11:06:35 PDT 2009


[ 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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