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2QVO.xds: Difference between revisions
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→XDS data reduction
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REFINE(CORRECT)=DISTANCE BEAM ORIENTATION CELL AXIS | REFINE(CORRECT)=DISTANCE BEAM ORIENTATION CELL AXIS | ||
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000 30000 !Used by DEFPIX for excluding shaded parts of the detector. | VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000 30000 !Used by DEFPIX for excluding shaded parts of the detector. | ||
INCLUDE_RESOLUTION_RANGE=50.0 | INCLUDE_RESOLUTION_RANGE=50.0 0 !Angstroem; used by DEFPIX,INTEGRATE,CORRECT | ||
MINIMUM_ZETA=0.1 !Defines width of 'blind region' (XPLAN,INTEGRATE,CORRECT) | MINIMUM_ZETA=0.1 !Defines width of 'blind region' (XPLAN,INTEGRATE,CORRECT) | ||
WFAC1=1.5 !This controls the number of rejected MISFITS in CORRECT; a larger value leads to fewer rejections. | WFAC1=1.5 !This controls the number of rejected MISFITS in CORRECT; a larger value leads to fewer rejections. | ||
STRONG_PIXEL=6.0 !used by: COLSPOT | STRONG_PIXEL=6.0 !used by: COLSPOT | ||
The resulting output files are XYCORR.LP, INIT.LP, COLSPOT.LP, IDXREF.LP, DEFPIX.LP, INTEGRATE.LP and CORRECT.LP. Data files are XPARM.XDS (from IDXREF | The resulting output files are XYCORR.LP, INIT.LP, COLSPOT.LP, IDXREF.LP, DEFPIX.LP, INTEGRATE.LP and CORRECT.LP. Data files are XPARM.XDS (from IDXREF), and the XDS_ASCII.HKL file all of which can be downloaded from [[Media:Xds_2qvo.tar.bz2.png|here]]. | ||
==SHELXC/D/E structure solution== | |||
generate XDSCONV.INP (a trick is to use MERGE=TRUE, for some reason the results are better that way) and run xdsconv and shelxc: | |||
#!/bin/csh -f | |||
cat > XDSCONV.INP <<end | |||
INPUT_FILE=../XDS_ASCII.HKL | |||
OUTPUT_FILE=temp.hkl SHELX | |||
MERGE=TRUE | |||
FRIEDEL'S_LAW=FALSE | |||
end | |||
xdsconv | |||
shelxc j <<end | |||
SAD temp.hkl | |||
CELL 53.10 53.10 40.90 90 90 90 | |||
SPAG P42 | |||
MAXM 2 | |||
end | |||
This writes j_fa.ins, j.hkl, j_fa.hkl . However, we overwrite j.ins now: | |||
cat > j_fa.ins <<end | |||
TITL j_fa.ins SAD in P42 | |||
CELL 0.98000 53.10 53.10 40.90 90.00 90.00 90.00 | |||
LATT -1 | |||
SYMM -Y, X, 1/2+Z | |||
SYMM -X, -Y, Z | |||
SYMM Y, -X, 1/2+Z | |||
SFAC S | |||
UNIT 128 | |||
SHEL 999 3.0 | |||
FIND 3 | |||
NTRY 100 | |||
MIND -1.0 2.2 | |||
ESEL 1.3 | |||
TEST 0 99 | |||
SEED 1 | |||
PATS | |||
HKLF 3 | |||
END | |||
end | |||
shelxd j_fa | |||
This gives best CC All/Weak of 35.61 / 26.03 . Next we run G. Sheldrick's beta-Version of shelxe Version 2009/4: | |||
shelxe.beta -a6 -q j j_fa -h -s0.55 -m20 -b | |||
Some important lines in the output: | |||
79 residues left after pruning, divided into chains as follows: | |||
A: 20 B: 22 C: 37 | |||
CC for partial structure against native data = 50.42 % | |||
<wt> = 0.300, Contrast = 0.731, Connect. = 0.817 for dens.mod. cycle 20 | |||
Estimated mean FOM = 0.659 Pseudo-free CC = 68.71 % | |||
'''clearly indicating that the structure is solved.''' | |||
For completeness, we run the inverse hand: | |||
shelxe.beta -a6 -q j j_fa -h -s0.55 -m20 -b -i | |||
but of course this gives much worse statistics. | |||