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2QVO.xds: Difference between revisions
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and run xds_par for the last time. | and run xds_par for the last time. | ||
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]] (right-click with the mouse, and then save the file to your disk). | ||
===dataset 1=== | ===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]] | 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]] (right-click). | ||
==SHELXC/D/E structure solution== | ==SHELXC/D/E structure solution== | ||
This is done in a subdirectory of the XDS data reduction directory. Here, we generate XDSCONV.INP ( | This is done in a subdirectory of the XDS data reduction directory. Here, we generate XDSCONV.INP (I used MERGE=TRUE, sometimes the results are better that way) and run xdsconv and [[ccp4com:SHELX_C/D/E|SHELXC]]: | ||
#!/bin/csh -f | #!/bin/csh -f | ||
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shelxd j_fa | shelxd j_fa | ||
This gives best CC All/Weak of 35.61 / 26.03 . Next we run G. Sheldrick's beta-Version of [[ccp4com:SHELX_C/D/E|SHELXE]] Version 2009/4: | This gives best CC All/Weak of 35.61 / 26.03 for dataset 2, and best CC All/Weak of 36.74 / 21.55 for dataset 1. | ||
Next we run G. Sheldrick's beta-Version of [[ccp4com:SHELX_C/D/E|SHELXE]] Version 2009/4: | |||
shelxe.beta j j_fa -a6 -q -h -s0.55 -m20 -b | shelxe.beta j j_fa -a6 -q -h -s0.55 -m20 -b | ||
Some important lines in the output: | Some important lines in the output: for dataset 2, I get | ||
79 residues left after pruning, divided into chains as follows: | 79 residues left after pruning, divided into chains as follows: | ||
A: 20 B: 22 C: 37 | A: 20 B: 22 C: 37 | ||
CC for partial structure against native data = 50.42 % | CC for partial structure against native data = 50.42 % | ||
... | |||
<wt> = 0.300, Contrast = 0.731, Connect. = 0.817 for dens.mod. cycle 20 | <wt> = 0.300, Contrast = 0.731, Connect. = 0.817 for dens.mod. cycle 20 | ||
... | |||
'''clearly indicating that the structure | Estimated mean FOM = 0.659 Pseudo-free CC = 68.71 % | ||
for dataset 1, I get | |||
80 residues left after pruning, divided into chains as follows: | |||
A: 23 B: 57 | |||
CC for partial structure against native data = 45.79 % | |||
... | |||
<wt> = 0.300, Contrast = 0.711, Connect. = 0.812 for dens.mod. cycle 20 | |||
... | |||
Estimated mean FOM = 0.611 Pseudo-free CC = 63.70 % | |||
'''clearly indicating that the structure can be solved with each of the two datasets individually.''' | |||
For completeness, we run the inverse hand: | For completeness, we run the inverse hand: | ||
| Line 133: | Line 143: | ||
but of course this gives much worse statistics. | but of course this gives much worse statistics. | ||
==Optimization of data reduction== | |||
The only safe way to optimize the data reduction is to look at external quality indicators. Internal R-factors, and even the correlation coefficient of the anomalous signal are of comparatively little value. A readily available external quality indicator is CCmax/CCweak as obtained by [[ccp4com:SHELX_C/D/E|SHELXD]]. | |||
WFAC1 was already discussed above. Another 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 too small, because the STANDARD DEVIATION OF SPOT POSITION (PIXELS) (as reported by IDXREF, INTEGRATE and CORRECT after refinement) 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 internal statistics (mostly the r-factors, but not so much the correlation coefficient of the anom signal), and improved CCmax/CCweak indicators (to more than 40). SHELXE then produces significantly better and more complete models. Try for yourself! | |||
There are some parameters in the SHELXC/D/E approach above that could be optimized as well: first of all, MERGE=TRUE in XDSCONV.INP turned later out to be the wrong choice (using the default MERGE=FALSE turns out to give a model with 85 consecutive residues for dataset 1). Then of course, the resolution limit for SHELXD could be varied, and the solvent content for SHELXE. For SHELXE in particular, many things could be tried. | |||
==Limits== | ==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. | |||
With dataset 2, I tried to use 270 frames but could not solve the structure using the above SHELXC/D/E approach (not even with MAXIMUM_ERROR_OF_SPOT_POSITION=6.0). With 315 frames, it was possible. | |||