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XDSGUI: Difference between revisions
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→tools: Reason for possible failure: the spot2pdb program expects SPOT.XDS to have 7 columns, as IDXREF attaches 3 columns with indices to the 4 columns that COLSPOT wrote. So you cannot visualize SPOT.XDS from COLSPOT - it has to be written by IDXREF.
m (better wording in 2nd paragraph) |
m (→tools: Reason for possible failure: the spot2pdb program expects SPOT.XDS to have 7 columns, as IDXREF attaches 3 columns with indices to the 4 columns that COLSPOT wrote. So you cannot visualize SPOT.XDS from COLSPOT - it has to be written by IDXREF.) |
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* The third item ("Optimizing data quality") offers commands that manipulate [[XDS.INP]] in several ways. Please note: the popup "XDS.INP has been changed externally" is emitted by the Qt system and cannot be switched off. It appears if one of the scripts changes XDS.INP while it is opened by XDSGUI (which is always the case) . Thus, one should simply press the "Reload" button. The user-definable command may be used e.g. for <pre>echo RELRAD=7 ! default is 5 >x; grep -v BEAM_DIVERGENCE XDS.INP >>x; cat x > XDS.INP; rm x</pre> This provides more pixels to the background estimation (for another INTEGRATE), and is useful for weakly exposed data sets which have mostly pixels with zero counts. | * The third item ("Optimizing data quality") offers commands that manipulate [[XDS.INP]] in several ways. Please note: the popup "XDS.INP has been changed externally" is emitted by the Qt system and cannot be switched off. It appears if one of the scripts changes XDS.INP while it is opened by XDSGUI (which is always the case) . Thus, one should simply press the "Reload" button. The user-definable command may be used e.g. for <pre>echo RELRAD=7 ! default is 5 >x; grep -v BEAM_DIVERGENCE XDS.INP >>x; cat x > XDS.INP; rm x</pre> This provides more pixels to the background estimation (for another INTEGRATE), and is useful for weakly exposed data sets which have mostly pixels with zero counts. | ||
* The last item ("Further analyses") offers useful commands. "determine spacegroup with pointless" runs [[pointless]] against the XDS_ASCII.HKL file. The button "show spots in reciprocal space" runs [[spot2pdb]] to show you the reflections of SPOT.XDS in reciprocal space, with coot. You see the reflections that could be indexed in IDXREF in yellow, the not-indexed ones in pink, the rotation axis in blue and the origin as a blue cross. Ice rings and additional lattices can be easily identified - see [[spot2pdb]] for examples! | * The last item ("Further analyses") offers useful commands. "determine spacegroup with pointless" runs [[pointless]] against the XDS_ASCII.HKL file. The button "show spots in reciprocal space" runs [[spot2pdb]] to show you the reflections of SPOT.XDS in reciprocal space, with coot. You see the reflections that could be indexed in IDXREF in yellow, the not-indexed ones in pink, the rotation axis in blue and the origin as a blue cross. Ice rings and additional lattices can be easily identified - see [[spot2pdb]] for examples! Reason for possible failure: the spot2pdb program expects SPOT.XDS to have 7 columns, as IDXREF attaches 3 columns with indices to the 4 columns that COLSPOT wrote. So you cannot visualize SPOT.XDS from COLSPOT - it has to be written by IDXREF. | ||
* Useful scripts for user tools are shared in [[XDSGUI User tools]] | * Useful scripts for user tools are shared in [[XDSGUI User tools]] | ||