NANs in anomalous_diff.mtz

[biochem-fan]

SIGMAs of some reflections in anomalous_diff.mtz are NaN. Thus, iotbx fails to load the file (e.g. phenix.xtriage and phenix.reflection_file_converter).

To use the file in SHELX, the workaround is as follows:

mtz2sca input.mtz
grep -v nan input.sca > fixed.sca

[helenginn]

Workaround for MTZ files:

sftools << EOF
read input.mtz
select col SIGI = present
select col I = present
purge yes
write input_filtered.mtz
exit
EOF

[helenginn]

NANs were occurring for at least negative intensities. Have attempted to provide a fix for this and remove Friedel pairs where one is missing observations. Single-observation intensities are currently square-rooted to give sigma values until counting sigmas are carried through the experiment (i.e. read/write data to HDF5).

Please close when you are happy with this fix.

[biochem-fan]

Confirmed. ANODE sigma stayed the same, while the completeness slightly improved. Thank you very much for your fix.

[biochem-fan]

anomalous_diff_N.mtz during REFINE_PARTIALITY is OK but anomalous_diff.mtz after MERGE still contains NANs.

[helenginn]

This does not appear to be a problem anymore with the re-written MtzMerger, which replaces MtzGrouper, accessed by adding OLD_MERGE OFF.