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Simulated-1g1c: Difference between revisions
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→Towards better completeness: using the first two frames
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=== Towards better completeness: using the first two frames === | === Towards better completeness: using the first two frames === | ||
We might want better (anomalous) completeness than what is given by only the very first frame of each dataset. To this end, we change in XDS.INP : | We might want better (anomalous) completeness than what is given by only the very first frame of each dataset. To this end, we change in the XDS.INP part of our script : | ||
DATA_RANGE=1 2 | DATA_RANGE=1 2 | ||
then run the script which reduces the 100 datasets. When this has finished, we insert in XSCALE.INP | |||
NBATCH=2 | NBATCH=2 | ||
after each INPUT_FILE line. The reason for this is that by default, XSCALE establishes scalefactors every | after each INPUT_FILE line (this can be easily done using <pre> awk '{print $0;print "NBATCH=2"}' XSCALE.INP > x </pre>). The reason for this is that by default, XSCALE establishes scalefactors every 5 degrees, but here we want scalefactors for every frame, because the radiation damage is so strong. This gives: | ||
NOTE: Friedel pairs are treated as different reflections. | NOTE: Friedel pairs are treated as different reflections. | ||
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total 165827 42032 43003 97.7% 12.8% 13.3% 162426 8.79 14.7% 15.7% 15% 0.881 16225 | total 165827 42032 43003 97.7% 12.8% 13.3% 162426 8.79 14.7% 15.7% 15% 0.881 16225 | ||
showing that the anomalous completeness, and even the quality of the anomalous signal, can indeed be increased. I doubt, however, that going to three or more frames would improve things even more. | showing that the anomalous completeness, and even the quality of the anomalous signal, can indeed be increased. I doubt, however, that going to three or more frames would improve things even more. | ||
The MTZ files are at [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/1g1c/xds-simulated-1g1c-F-2frames.mtz] and [ftp://turn5.biologie.uni-konstanz.de/pub/xds-datared/1g1c/xds-simulated-1g1c-I-2frames.mtz], respectively. They were of course obtained with XDSCONV.INP: | |||
INPUT_FILE=temp.ahkl | |||
OUTPUT_FILE=temp.hkl CCP4_I | |||
for the intensities, and | |||
INPUT_FILE=temp.ahkl | |||
OUTPUT_FILE=temp.hkl CCP4 | |||
for the amplitudes. In both cases, after xdsconv we have to run | |||
<pre> | |||
f2mtz HKLOUT temp.mtz<F2MTZ.INP | |||
cad HKLIN1 temp.mtz HKLOUT output_file_name.mtz<<EOF | |||
LABIN FILE 1 ALL | |||
END | |||
EOF | |||
</pre> | |||
=== Why this is difficult to solve with SAD phasing === | === Why this is difficult to solve with SAD phasing === | ||