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imgCIF of _b4_1_master.h5 #42

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kroon-lab opened this issue Feb 9, 2023 · 1 comment
Open

imgCIF of _b4_1_master.h5 #42

kroon-lab opened this issue Feb 9, 2023 · 1 comment

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@kroon-lab
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I used creator to generate an imgCIF from b4_1_master.h5. In addition to my mail of 03-02-2023 I have some comments:
loop

_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1]
_axis.vector[2]
_axis.vector[3]
_axis.offset[1]
_axis.offset[2]
_axis.offset[3]
chi rotation goniometer detx -0.0046 0.0372 -0.9993 0 0 0
omega rotation goniometer . 1 0 0 0 0 0
two_theta rotation goniometer . 1 0 0 0 0 0
phi rotation goniometer chi 1 -0.0037 0.002 0 0 0
detx translation detector dety -1 0 0 -166.87357 172.49715 0
dety translation detector trans 0 1 0 0 0 0
trans translation detector omega 0 0 -1 0 0 -287.22243

==> chi should depend on omega
==> in the publication (he4557) _axis.equipment for two_theta was detector, not goniometer
==> trans should depend on two_theta
==> detx should depend on trans
==> dety depends on detx
==> detx vector should be [1 0 0]
==> dety vector should be [0 -1 0]

loop_
_array_structure_list_axis.axis_id
_array_structure_list_axis.axis_set_id
_array_structure_list_axis.displacement
_array_structure_list_axis.displacement_increment
array_x 1 0.0375 0.075
array_y 2 0.0375 0.075

==> _array_structure_list_axis.axis.id is a pointer to _axis.id above. So I think that array_x should be detx, and likewise for array_y

loop_
_diffrn_detector_axis.axis_id
_diffrn_detector_axis.detector_id
det_z det1

==> again _diffrn_detector_axis.axis.id is a pointer to axis.id, and thus should be trans
loop

_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_increment
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.angle_range
SCAN1 chi . . . 0.0 0 0
SCAN1 omega . . . 0.0 0.1 360.0
SCAN1 phi . . . 0.0 0 0
SCAN1 detx . . . 0.0 0 0
SCAN1 dety . . . 0.0 0 0
SCAN1 trans 287.2224260231453 0 0 . . .

==> only omega is scanned. Leave the other _axis.id out?? I don't mind if they stay in, but normally we use only one scan-axis

The construction with _diffrn_scan_axis and diifrn_scan_frame is different from the one we published (he5447) but seems OK to me.
loop

_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
frm1 ELEMENT01 IMAGE01 1
frm2 ELEMENT01 IMAGE01 2
==> I have a question to @jamesrhester : _diffraction_data_frame.id should be a pointer to _array_structure.id but that data name is never given. Is that a problem?

==> Then, _diffrn_data_frame.array_id is also a pointer to _array_structure.id, so should be the same as _diffraction_data_frame.id ?
Now they are IMAGE01 and frm1 respectively.
==> I cannot find _array_data.id in the dictionary?

@jamesrhester can you please look if the construction with pointers to data is complete, not redundant and does not contain unnecessary data items

@julianhoersch
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To disentangle this a bit I've created two new issues to answer your points
#45 and #46

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