Dimple - DIfference Map PipeLinE

The difference map pipeline Dimple is a useful tool for quickly finding regions of unmodelled density in diffraction data - ideal for locating ligands. Dimple takes a known protein structural model and fits it to processed diffraction data to provide a refined structure and electron density maps, including a difference map showing unmodelled electron density.

At Diamond, Dimple will automatically run upon the completion of any successful upstream data-reduction pipelines if a structural model is provided in PDB format for the protein. The protein strcuture can either be uploaded protein in ISPyB as a PDB file or code or saved as a pdb file in the `tmp/pdb/` or `processing/pdb/` directories within the visit directory. Multiple structures can be provided and Dimple will select the one with the most similar unit-cell to run against. If the observed unit cell is significantly different to the model, Dimple will run molecular replacement before refinement.

Upon success, Dimple results will display in the ISPyB web interface under the downstream processing tab. A separate set of results will be displayed for each data-reduction pipeline (e.g. fast_dp, xia2-dials) that dimple was run from.

For each run of Dimple, a table indicating the initial and final refinement statistics is shown, along with a graph showing the change in R factors over the refinement cycles. A downward trend in the R factors with each cycle is a good indication that the refinement has been successful.

Dimple generates snapshots of the unmodelled electron density blobs, the largest of which will be diplayed in the web interface.

An interactive visualisation of the Dimple results can be viewed in UglyMol by clicking on the Map/Model Viewer button. The viewer shows the refined structural model along with the 2Fo - Fc map (estimation of true electron density) in blue and the Fo - Fc difference map in Green/Red, showing differences between the observed and modelled electron density (Green = unmodelled, Red = overmodelled). The coordinates of any significant unmodelled blobs will be displayed at the top left of the viewer and clicking on them will focus the view on the blob.

As part of the Dimple pipeline, the software package ANODE from the SHELX suite is also run. ANODE uses the known structural model along with the anomalous diffraction data to generate a density map corresponding to the locations of anomalous scatterers (i.e. heavy atoms) in the structure. A table showing the coordinates, peak height and nearest atoms of peaks in the anomalous density are displayed.

A graph showing the peak height vs peak number is also displayed.

The Interactive Viewer button opens a Mol* visualisation showing the locations of the anomalous peaks within the protein structure.

The data files and logs output by Dimple can be accessed via the *Logs & Files* button.

The primary results files are the final.mtz and final.pdb files, which contain the density maps and refined model coordinates respectively. The most significant results and log files are summarised in the table below:

Please remember to cite the appropriate autoprocessing pipeline used prior to Dimple, the programs that Dimple calls (see dimple.log file to see which programs were called) as well as the following reference for Dimple itself:

• Wojdyr, M., Keegan, R., Winter, G., Ashton, A. (2013) DIMPLE - a pipeline for the rapid generation of difference maps from protein crystals with putatively bound ligands. Acta Cryst. A69: s299.