2,652
edits
1Y13: Difference between revisions
→A solution
No edit summary |
|||
| Line 279: | Line 279: | ||
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 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. For some reason, the beamline software did not write the correct wavelength into the headers. | ||
So this little detective work appears to tell us what happened in the morning of Sunday June 27, 2004 at ALS beamline 821. | So this little detective work appears to tell us what happened in the morning of Sunday June 27, 2004 at ALS beamline 821. | ||
== Further analysis of datasets E1 and E2 == | |||
Here, we try to learn more about the constituents of "firstparts". | |||
Running "[[xdsstat]] > XDSSTAT.LP" in the e1_1-372 and e2_1-369 directories, we obtain statistics output not available from CORRECT. We open XDSSTAT.LP with the CCP4 program "loggraph", and take a look at [[misfits.pck]], [[rf.pck]], and the other files produced by [[xdsstat]], using [[VIEW]] or [[XDS-Viewer]]: | |||
Although | [[File:e1_1-372-xdsstat1.png]] Reflections and misfits, by frame - looks normal | ||
[[File:e1_1-372-xdsstat2.png]] Intensity and sigma by frame - looks normal | |||
[[File:e1_1-372-xdsstat3.png]] "partiality" and profile agreement, by frame - looks good but it's clear that the profiles at high frame number agree worse with the average profiles, possibly due to radiation damage | |||
[[File:e1_1-372-xdsstat4.png]] R_meas, by frame, clearly showing good R_meas in the middle of the dataset. | |||
[[File:e1_1-372-xdsstat-raddam.png]] R_d - an R-factor which directly depends on radiation damage. This is calculated as a function of frame number difference and the linear rise indicates significant radiation damage that should be correctable in [[XSCALE]], using the CRYSTAL_NAME keyword. | |||
[[File:e1_1-372-misfits.png]] misfits mapped on the detector, showing ice rings. | |||
[[File:e1_1-372-rf.png]] R_meas mapped on the detector, showing elevated R_meas at the location of the ice rings. | |||
== Solving the structure == | |||
Although we could now think of using these two files ("firstparts" and "secondparts" merged) and assume that they are peak and inflection wavelengths, it appears more reasonable to try and solve the structure with SAD - which means using "firstparts" only. | |||
To make sure we haven't overlooked anything | |||