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Difficult datasets: Difference between revisions
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The following suggestions apply not only to small-molecule datasets, but also to very weak or low-resolution, or otherwise difficult macromolecular datasets. | The following suggestions apply not only to small-molecule datasets, but also to very weak or low-resolution, or otherwise difficult macromolecular datasets. | ||
These datasets have few (or few strong) reflections per frame. Therefore, the multitude of parameters describing the diffraction experiment needs to be reduced (in refinement one would say: to avoid overfitting). This means that | These datasets have few (or few strong) reflections per frame. Therefore, the multitude of parameters describing the diffraction experiment needs to be reduced (in refinement one would say: to avoid overfitting). This means that some parameters may need adjustment. | ||
* [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#DELPHI= DELPHI]=45 ! to base reflection profiles and refinements on more reflections - try this first if yo get error messages in the INTEGRATE step | == optimizing the parameters for INTEGRATE == | ||
* [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#DELPHI= DELPHI]=45 ! (or 60, or even 90; the default is 5) to base reflection profiles and refinements on more reflections - try this first if yo get error messages in the INTEGRATE step | |||
* [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#REFINE(INTEGRATE)= REFINE(INTEGRATE)]= ! do not refine anything in INTEGRATE; be sure to recycle GXPARM.XDS to XPARM.XDS. Also try REFINE(INTEGRATE)=ORIENTATION CELL ! maybe add BEAM, but probably AXIS or DISTANCE should not be refined. | * [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#REFINE(INTEGRATE)= REFINE(INTEGRATE)]= ! do not refine anything in INTEGRATE; be sure to recycle GXPARM.XDS to XPARM.XDS. Also try REFINE(INTEGRATE)=ORIENTATION CELL ! maybe add BEAM, but probably AXIS or DISTANCE should not be refined. | ||
Furthermore, you may grab the lines e.g. | |||
Furthermore, you may | |||
BEAM_DIVERGENCE= 2.067 BEAM_DIVERGENCE_E.S.D.= 0.207 | BEAM_DIVERGENCE= 2.067 BEAM_DIVERGENCE_E.S.D.= 0.207 | ||
REFLECTING_RANGE= 2.303 REFLECTING_RANGE_E.S.D.= 0.329 | REFLECTING_RANGE= 2.303 REFLECTING_RANGE_E.S.D.= 0.329 | ||
from INTEGRATE.LP and | from INTEGRATE.LP, and insert them into XDS.INP . The latter is accomplished easily with | ||
grep _E INTEGRATE.LP | tail -2 > x | grep _E INTEGRATE.LP | tail -2 > x | ||
grep -v _E.S.D XDS.INP >> x | grep -v _E.S.D XDS.INP >> x | ||
mv x XDS.INP | mv x XDS.INP | ||
or similar. | or similar. These values then serve as a Bayesian prior for the values that will actually be used for integrating. | ||
If you used larger OSCILLATION_RANGE than 1°, you should increase [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#MAXIMUM_ERROR_OF_SPINDLE_POSITION= MAXIMUM_ERROR_OF_SPINDLE_POSITION=] (default is 2°) because you expect larger deviations of experimentally determined and calculated phi positions of reflections. Same might apply to MAXIMUM_ERROR_OF_SPOT_POSITION= ; the default is 3 pixels which may be too low to account for broad reflections. If you don't do this, many reflections that violate these limits will not be used for geometry refinement, which may turn out to be unstable. | |||
== optimizing the parameters for CORRECT == | |||
* [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#NBATCH= NBATCH]= (total rotation range)/45 ! to reduce the number of scale factors; the value of NBATCH is shown as NXBIN in CORRECT.LP for the ABSORB and DECAY correction; default is (total rotation range)/5. Other values, like (total rotation range)/60 or (total rotation range)/90 might also be tried. | |||
* [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#CORRECTIONS= CORRECTIONS]= ABSORB ! don't try to correct for MODULATION and DECAY in scaling | |||
== optimizing the parameters for XSCALE == | |||
If you use XSCALE to merge several XDS datasets, you should make sure that you specify in XSCALE.INP the same values for NBATCH and CORRECTIONS as you do, in XDS.INP, for the CORRECT step. | If you use XSCALE to merge several XDS datasets, you should make sure that you specify in XSCALE.INP the same values for NBATCH and CORRECTIONS as you do, in XDS.INP, for the CORRECT step. | ||