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and ran xds again. | and ran xds again. | ||
=== | === What's the problem? === | ||
This is the excerpt from [[CORRECT.LP]] : | This is the excerpt from [[CORRECT.LP]] : | ||
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which is much worse than the spacegroup 19 statistics (compare the ISa values - they differ by a factor of 2 !) so there may be something wrong with some assumptions we were making ... | which is much worse than the spacegroup 19 statistics (compare the ISa values - they differ by a factor of 2 !) so there may be something wrong with some assumptions we were making ... | ||
=== Identifying a possible cause | === Identifying a possible cause === | ||
The easiest thing one can do is to inspect INTEGRATE.LP - this lists scale factor, beam divergence and mosaicity for every reflection. There's a [[jiffies|jiffy]] called "scalefactors" which grep's the relevant lines from INTEGRATE.LP ("scalefactors > scales.log"). This shows the scale factor (column 3): | The easiest thing one can do is to inspect INTEGRATE.LP - this lists scale factor, beam divergence and mosaicity for every reflection. There's a [[jiffies|jiffy]] called "scalefactors" which grep's the relevant lines from INTEGRATE.LP ("scalefactors > scales.log"). This shows the scale factor (column 3): | ||
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'''It should be noted that any abrupt change in conditions during the experiment is going to spoil the resulting data in one way or another. This is most true for a SAD experiment which is supposed to give accurate values for the tiny differences in intensities between Friedel-related reflections.''' | '''It should be noted that any abrupt change in conditions during the experiment is going to spoil the resulting data in one way or another. This is most true for a SAD experiment which is supposed to give accurate values for the tiny differences in intensities between Friedel-related reflections.''' | ||
=== | === A solution === | ||
At this point it is good to look at the data for experiment E2. | At this point it is good to look at the data for experiment E2. Here, we find exactly the same problems of bad ISa and high "STANDARD DEVIATION OF SPOT POSITION (PIXELS)" when reducing frames 1-591 in one run of xds. | ||
With this knowledge, we are lead, for E1, to reduce frames 1-372 and 373-592 separately, in spacegroup 96. For E2, we use frames 1-369 and 371-591, respectively. Frame E2-370 has a very high | With this knowledge, we are lead, for E1, to reduce frames 1-372 and 373-592 separately, in spacegroup 96. For E2, we use frames 1-369 and 371-591, respectively. Frame E2-370 has a very high scale factor so we leave it out altogether. | ||
This is also a good time to closely inspect the headers of the frames: | This is also a good time to closely inspect the headers of the frames: | ||
% grep --binary-files=text DATE | % grep --binary-files=text DATE j1603b3PK_1_E1_37?.img | ||
gives | gives | ||
j1603b3PK_1_E1_370.img:DATE=Sun Jun 27 08:55:51 2004; | |||
j1603b3PK_1_E1_371.img:DATE=Sun Jun 27 08:56:00 2004; | |||
j1603b3PK_1_E1_372.img:DATE=Sun Jun 27 08:56:08 2004; | |||
j1603b3PK_1_E1_373.img:DATE=Sun Jun 27 09:19:45 2004; | |||
j1603b3PK_1_E1_374.img:DATE=Sun Jun 27 09:19:54 2004; | |||
j1603b3PK_1_E1_375.img:DATE=Sun Jun 27 09:20:02 2004; | |||
j1603b3PK_1_E1_376.img:DATE=Sun Jun 27 09:20:10 2004; | |||
j1603b3PK_1_E1_377.img:DATE=Sun Jun 27 09:20:58 2004; | |||
j1603b3PK_1_E1_378.img:DATE=Sun Jun 27 09:21:08 2004; | |||
j1603b3PK_1_E1_379.img:DATE=Sun Jun 27 09:21:17 2004; | |||
and | and | ||
% grep --binary-files=text DATE | % grep --binary-files=text DATE j1603b3PK_1_E2_3[67]?.img | ||
gives | gives | ||
j1603b3PK_1_E2_366.img:DATE=Sun Jun 27 08:55:15 2004; | |||
j1603b3PK_1_E2_367.img:DATE=Sun Jun 27 08:55:23 2004; | |||
j1603b3PK_1_E2_368.img:DATE=Sun Jun 27 08:55:32 2004; | |||
j1603b3PK_1_E2_369.img:DATE=Sun Jun 27 08:56:19 2004; | |||
j1603b3PK_1_E2_370.img:DATE=Sun Jun 27 08:56:28 2004; | |||
j1603b3PK_1_E2_371.img:DATE=Sun Jun 27 09:19:26 2004; | |||
j1603b3PK_1_E2_372.img:DATE=Sun Jun 27 09:19:34 2004; | |||
j1603b3PK_1_E2_373.img:DATE=Sun Jun 27 09:20:22 2004; | |||
j1603b3PK_1_E2_374.img:DATE=Sun Jun 27 09:20:30 2004; | |||
j1603b3PK_1_E2_375.img:DATE=Sun Jun 27 09:20:38 2004; | |||
j1603b3PK_1_E2_376.img:DATE=Sun Jun 27 09:20:47 2004; | |||
thus proving that both datasets were interrupted for 20 minutes around frame 370. | thus proving that both datasets were interrupted for 20 minutes around frame 370. | ||
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proving that the second parts of datasets E1 and E2 should be treated separately from the first parts. | proving that the second parts of datasets E1 and E2 should be treated separately from the first parts. | ||
Upon inspection of the cell parameters, we find that the cell axes of the second "halfs" are shorter by a factor of 0.9908 when compared with the first parts. This suggests that they were collected at a longer wavelength! But then the wavelength values in the headers are most likely completely wrong: we can speculate that the two first parts were collected at the SeMet peak wavelength, and the two second parts at the inflection wavelength. | Upon inspection of the cell parameters, we find that the cell axes of the second "halfs" are shorter by a factor of 0.9908 when compared with the first parts. This suggests that they were collected at a longer wavelength! But then the wavelength values in the headers are most likely completely wrong: we can speculate that the two first parts were collected at the SeMet peak wavelength, and the two second parts at the inflection wavelength. | ||
The almost-simultaneous DATEs in the headers may be explained by an inverse-beam measuring strategy which alternatingly collects 4 frames in one orientation as E1, then rotates the spindle by 180° and collects 4 frames into E2. The beamline software | |||
So this little detective work appears to tell us what happened in the morning of Sunday June 27, 2004 at ALS beamline 821. | |||