DIMPLE (CCP4: Supported Program)


DIMPLE - automated difference map calculation


DIMPLE (DIfference Map PipeLinE) an automated software pipeline for rapidly processing crystals that contain a known protein and possibly a ligand bound to this protein. The main goal is to present a user with a quick answer to the question of whether or not they have a bound ligand or drug candidate in their crystal. The software is developed primarily for use at synchrotron beamlines, but can be used also for in-house automation. DIMPLE takes the already known "apo" structure for the target protein and compares it with the electron density map for the same, crystallised structure (and possibly bound ligand) interpreted from the X-ray diffraction images. It then presents the user with a set of snapshot images illustrating the regions where there are large areas of electron density unaccounted for by the protein structure model. Within a few seconds, an experienced user can decipher from these images if any of this unaccounted for density indicates a bound ligand. A positive result can mean that the rest of the batch of crystals for this particular ligand can be discarded allowing for a more efficient use of the beam time and saving the user from lots of potentially unnecessary processing.

It takes in a merged MTZ file containing intensities and a PDB coordinate file containing the already solved protein structure. It outputs an MTZ file containing the calculated electron density map and difference map along with the positioned structure and images of the density blobs.


dimple [options...] input.mtz input.pdb output_dir

optional arguments:
  -h, --help            show this help message and exit
  --hklout out.mtz      output mtz file (default: final.mtz)
  --xyzout out.pdb      output pdb file (default: final.pdb)
  -s, --summary         show refmac summary
  -f {png,jpeg,tiff}    format of generated images (default: png)
  --weight VALUE        refmac matrix weight (default: auto-weight)
  -R MTZ_FILE, --free-r-flags MTZ_FILE
                        reference file with all reflections and freeR flags
  -I ICOL, --icolumn ICOL
                        I column label (default: IMEAN)
  --sigicolumn SIGICOL  SIGI column label (default: SIG<ICOL>)

All files are stored in the specified output directory.
For quick summary (after running the program): dimple info OUTPUT_DIR


Current version: Ronan Keegan, Marcin Wojdyr
Previous versions: Graeme Winter, George Pelios