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1Y13 (view source)

Revision as of 16:40, 17 March 2011

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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):
[[File:1y13-e1-scales.png]]
[[File:1y13-e1-scales.png]]
demonstrating that "something happens" between frame 372 and 373 (of course one has to look at the table to find the exact numbers).  
demonstrating that "something happens" between frame 372 and 373 (of course one has to look at the table to find the exact numbers).  


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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]]:
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]]:


[[File:e1_1-372-xdsstat1.png]] Reflections and misfits, by frame - looks normal
[[File:e1_1-372-xdsstat1.png]]  
[[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
Reflections and misfits, by frame - looks normal
[[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-xdsstat2.png]]  
[[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.
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 ==
== Solving the structure ==
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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.
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
Let's look at the XSCALE statistics for "firstparts":
 
      NOTE:      Friedel pairs are treated as different reflections.
 
SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
RESOLUTION    NUMBER OF REFLECTIONS    COMPLETENESS R-FACTOR  R-FACTOR COMPARED I/SIGMA  R-meas  Rmrgd-F  Anomal  SigAno  Nano
  LIMIT    OBSERVED  UNIQUE  POSSIBLE    OF DATA  observed  expected                                      Corr
    9.40        6122    844      883      95.6%      2.9%      3.5%    6111  54.76    3.2%    1.4%    79%  2.137    313
    6.64      12037    1611      1621      99.4%      2.9%      3.6%    12035  51.54    3.1%    1.5%    80%  2.259    684
    5.43      15348    2065      2086      99.0%      3.5%      3.7%    15347  47.79    3.7%    1.7%    78%  2.294    908
    4.70      18714    2487      2498      99.6%      3.0%      3.7%    18711  49.55    3.2%    1.5%    72%  1.712    1120
    4.20      21104    2797      2821      99.1%      3.1%      3.7%    21102  47.24    3.3%    1.7%    72%  1.727    1271
    3.84      23316    3095      3117      99.3%      3.8%      4.0%    23313  42.74    4.1%    2.1%    65%  1.617    1420
    3.55      25693    3345      3366      99.4%      4.4%      4.5%    25693  37.93    4.7%    2.6%    50%  1.411    1548
    3.32      28017    3633      3653      99.5%      5.2%      5.2%    28015  32.89    5.6%    3.6%    40%  1.335    1687
    3.13      30266    3842      3848      99.8%      7.2%      7.2%    30264  25.87    7.7%    4.8%    36%  1.158    1797
    2.97      32595    4114      4118      99.9%      10.4%    10.4%    32594  19.26    11.1%    7.7%    30%  1.068    1925
    2.83      34384    4315      4320      99.9%      14.3%    14.8%    34382  14.88    15.3%    10.3%    20%  0.937    2031
    2.71      35654    4475      4478      99.9%      18.3%    19.1%    35652  12.13    19.5%    13.1%    15%  0.891    2110
    2.61      37307    4705      4710      99.9%      27.5%    28.8%    37304    8.44    29.4%    19.8%    11%  0.834    2224
    2.51      38997    4893      4896      99.9%      35.5%    38.0%    38997    6.78    38.0%    26.0%    10%  0.817    2318
    2.43      40036    5026      5027      100.0%      51.3%    55.1%    40032    4.92    54.8%    38.0%    2%  0.738    2387
    2.35      39975    5180      5222      99.2%      71.3%    68.9%    39967    3.78    76.4%    52.7%    21%  0.887    2446
    2.28      42041    5385      5423      99.3%      93.7%    93.1%    42037    2.90  100.3%    66.7%    11%  0.798    2548
    2.21      43012    5538      5541      99.9%      85.7%    88.3%    43011    2.87    91.8%    58.8%    10%  0.818    2644
    2.16      42610    5701      5703      100.0%    113.6%    120.7%    42607    2.13  122.0%    85.4%    4%  0.722    2724
    2.10      38996    5634      5912      95.3%    146.1%    153.9%    38944    1.50  157.8%  122.7%    3%  0.711    2639
    total      606224  78685    79243      99.3%      6.7%      7.2%  606118  16.88    7.2%    12.0%    29%  1.055  36744
 
The anomalous correlation is good at low resolution, though not outstanding. At high resolution it rises again but this is presumably due to the ice rings.
Kay
Bureaucrats
2,652

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