Hi Charlie - that's quite a technical question, so I suggest you ask the
question on the xchembb (use The Google to find it), in case someone has
that script to hand.
(But if you need to do any scripting, chances are you'll need to spend a
few days on the Google anyway, even if someone can send you an example.
The good news is that bash is really simple.)
The PanDDA algorithm does not work if maps are not carefully coordinated
around which reflections are included, especially at low resolution -
though I'm not aware that anybody has carefully analysed what happens
with very anisotropic data.
Frank
On 27/09/2022 10:26, Nichols, Charlie wrote:
Dear All,
Having some difficulty running PANDDA with a large batch of structures
with significantly anisotropic data:
1. We have to use Autoproc / Staraniso processing for all datasets.
2. The default Dimple (Refmac) pipeline gives weird maps with large
areas of -ve density for no apparent reason which then really mess
up the difference-difference map calculations critical for PANDDA
success.
3. Test refinements showed that Buster refinement of the Staraniso
output gave better maps which we hope will improve the
interpretability of the PANDDA maps.
4. Pipedream run on 1000 datasets but PANDDA fails as it requires
complete datasets with any missing reflections filled in from Fcalc
5. Unfortunately PANDDA does not have the correct structure factor
names in the check list – It looks for these pairs: FWT and PHWT,
2FOFCWT_fill and PH2FOFCWT_fill and 2FOFCWT and PH2FOFCWT
6. Pipedeam/Buster outputs iso and aniso filled data so it has
2FOFCWT-iso-fill/PH2FOFCWT_iso-fill and
2FOFCWT-aniso-fill/PH2FOFCWT_aniso-fill which PANDDA does not see
so crashes out.
My scripting is not great so I wondered if anyone could hep me with a
short script to recursively look for ‘refine.mtz’ within
subdirectories from the top-level ‘model-building’ directory and then
run CAD to change the column names from 2FOFCWT-iso-fill and
PH2FOFCWT_iso-fill to 2FOFCWT_fill and PH2FOFCWT_fill so PANDDA can
‘see’ the correct data columns
NB: output .mtz name must still be ‘refine.mtz’ as PANDDA only checks
the top-level directory for each refinement and ‘pipedream.mtz’
symlinks pointing to ‘pipedream/pipedreamDir/refine/refine.mtz’ are
already in place.
Full path:
model_building/target_x####/pipedream/pipedreamDir/refine/refine.mtz
Thanks for your help,
Take care, Charlie.
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