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2QVO.xds: Difference between revisions
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==XDS data reduction== | ==XDS data reduction== | ||
===dataset 2=== | |||
This is a pared-down XDS.INP (obtained by egrep -v '^ *!' XDS.INP) based upon XDS-MARCDD.INP from the XDS distribution site - it has only those lines that are not commented out (to arrive here, one takes the steps outlined in [[Tutorial(First_Steps)]]): | This is a pared-down XDS.INP (obtained by egrep -v '^ *!' XDS.INP) based upon XDS-MARCDD.INP from the XDS distribution site - it has only those lines that are not commented out (to arrive here, one takes the steps outlined in [[Tutorial(First_Steps)]]): | ||
DETECTOR=CCDCHESS MINIMUM_VALID_PIXEL_VALUE=1 OVERLOAD=65000 | DETECTOR=CCDCHESS MINIMUM_VALID_PIXEL_VALUE=1 OVERLOAD=65000 | ||
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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]]. | 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]]. | ||
===dataset 1=== | |||
This works exactly the same way as dataset 2, except that we have to replace ../../g/040707-8_2_2_1.???? by f/040707-8_2_2_1.???? where f points to the directory with the frames. All .LP files, XPARM.XDS and XDS_ASCII.HKL are [[Media:Xds 2qvo dataset1.tar.bz2.png|here]]. | |||
==Optimization of data reduction== | ==Optimization of data reduction== | ||
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One candidate for optimization is MAXIMUM_ERROR_OF_SPOT_POSITION. By default this is 3.0 . In the case of these data, this default appears to be very small, because the STANDARD DEVIATION OF SPOT POSITION (PIXELS) is quite high (1.5 and more). This prevents XDS from using all the reflections for geometry refinement. | One candidate for optimization is MAXIMUM_ERROR_OF_SPOT_POSITION. By default this is 3.0 . In the case of these data, this default appears to be very small, because the STANDARD DEVIATION OF SPOT POSITION (PIXELS) is quite high (1.5 and more). This prevents XDS from using all the reflections for geometry refinement. | ||
I found that MAXIMUM_ERROR_OF_SPOT_POSITION=6.0 significantly improved the CCmax/CCweak indicators. | I found that MAXIMUM_ERROR_OF_SPOT_POSITION=6.0 significantly improved the CCmax/CCweak indicators (to more than 40). | ||
==SHELXC/D/E structure solution== | ==SHELXC/D/E structure solution== | ||
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but of course this gives much worse statistics. | but of course this gives much worse statistics. | ||
==Limits== | |||
With dataset 2, I tried to use 270 frames but could not solve the structure using the SHELXC/D/E approach. With 315 frames, it was possible. | |||