2QVO.xds: Difference between revisions

Using "generate_XDS.INP ../../APS/22-ID/2qvo/ACA10_AF1382_1.0???" we obtain:

Now we run xds_par. This runs to completion. We should at least inspect, using XDS-Viewer, the file FRAME.cbf since this shows us the last frame of the dataset, with boxes superimposed which correspond to the expected locations of reflections.  

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]]:

This writes j.hkl, j_fa.hkl and j_fa.ins. However, we overwrite j_fa.ins now:

   

shelxd j_fa

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.  

  shelxe.beta j j_fa -a6 -q -h -s0.55 -m20 -b  

Some important lines in the output: for dataset 2, I get

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 %

for dataset 1, I get

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 CC All/CC Weak 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.

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.  

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.