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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 e.g. the following parameters may need adjustment (typical values are given): most importantly for INTEGRATE: | 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 e.g. the following parameters may need adjustment (typical values are given): most importantly for [[INTEGRATE]]: | ||
* DELPHI=45 ! 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#DELPHI= DELPHI]=45 ! to base reflection profiles and refinements on more reflections - try this first if yo get error messages in the INTEGRATE step | ||
* 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. | ||
and you may also try for CORRECT: | and you may also try for [[CORRECT]]: | ||
* NBATCH=4 ! to reduce the number of scale factors | * [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html#NBATCH= NBATCH]= 4 ! to reduce the number of scale factors | ||
* CORRECTIONS= ABSORB ! don't try to correct for MODULATION and DECAY in scaling | * [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 | ||
Furthermore, you may try to recycle GXPARM.XDS to XPARM.XDS, and to grab the lines e.g. | Furthermore, you may try to recycle GXPARM.XDS to XPARM.XDS, and to grab the lines e.g. | ||
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mv x XDS.INP | mv x XDS.INP | ||
or similar. | or similar. | ||
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. | |||