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2QVO.xds: Difference between revisions
→Optimization of data reduction
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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! | 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! | ||
One thing I noticed that if I specify the known spacegroup in IDXREF then the results are worse than if the integration is performed in P1. Likewise, [[optimization]] did not work: recycling of GXPARM.XDS to use as XPARM.XDS, and thus imposing the lattice symmetry in the geometry refinement in INTEGRATE. These findings my correspond to the fact that in P1 the angles do not refine to 90.0xx or 89.9xx degrees. In other words, the metric symmetry is not as well fulfilled as it should be. This results in fairly large deviations from the ideal P42 positions; the refinement of cell parameters in P1 partly compensates for this. I have however no idea why this deviation from metric symmetry could occur. | |||
==Optimization of structure solution== | |||
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. | 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 above SHELXC/D/E approach (not even with MAXIMUM_ERROR_OF_SPOT_POSITION=6.0). 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. | ||