More details on Dimple can be found here.

Dimple automatic run

It is linked to EDNA autoprocessing. There are two ways to give the pdb files to EDNA autoprocessing,

  • by uploading a pdb file associate with a sample in ISPyB, and link samples in mxCuBE (see here)
  • by copying the pdb file in PROCESSED_DATA/your_image_directory_name/autoprocessing_imagePrefix_run#_#/EDNA_proc/

pdb files uploaded to ISPyB have priority and will be used.

Note that DIMPLE requires a valid PDB file. Make sure in particulary that the definition of the Hermann-Mauguin space group is properly described without parenthesis and with the screw axis as a two digit number as in the exemple here :

CRYST1   50.000   50.000  200.000  90.00  90.00  90.00 P 43 21 2

Output files

Output from Dimple are written with EDNA autoprocessing results in PROCESSED_DATA/your_image_directory_name/autoprocessing_imagePrefix_run#_#/EDNA_proc/results/dimple/ and are named :

  • ep_imagePrefix_run#_#_dimple.pdb : refined pdb
  • ep_imagePrefix_run#_#_dimple.mtz

  • ep_imagePrefix_run#_#_refmac5restr_dimple.log

  • ep_imagePrefix_run#_#_findblobs_dimple.log

  • ep_imagePrefix_run#_#_results_dimple.pdf : overall summary of all DIMPLE steps results

  • ep_imagePrefix_run#_#_dimple.log

Dimple manual run

At the end of EDNA autoprocessing a script name is create in the directory PROCESSED_DATA/your_image_directory_name/xds_your_run/. There are two option to run dimple manually:

  • If you uploaded a pdb files in the meantime into ISPyB, linked to a sample, just run
  • If you prefer not to upload any pdb to ISPyB, copy the pdb file somewhere in PROCESSED_DATA/your_image_directory_name/autoprocessing_imagePrefix_run#_#/EDNA_proc/ then run

Known issues: there might be some problem with H3/R3 space groups