Dimple
Dimple is an automatic pipeline to calculate a difference map in ascertaining the presence of a bound ligands to a target protein.
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 dimple.sh 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 dimple.sh
- 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 dimple.sh
Known issues: there might be some problem with H3/R3 space groups