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. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
