Data Analysis

The datasets tab in XCE is only populated after importing data from your beamline visit.

If you restart XCE this will no longer be populated (although the autoprocessed files retrieved previously can still be worked on) and you will need to pull data again from the beamline visit(s).

It is likely the connection has dropped, try restarting XCE and launching the job again.

Open your local bashrc configuration file by entering "gedit ~/.bashrc_local" into terminal.

If your bashrc config file does not contain a line with "source /dls/science/groups/i04-1/software/XChem/xchempaths.sh" then enter this command into a terminal window.

This only needs to be ran once, usually during your first XChem visit.

Check the terminal window.

If you see an error referencing a file in the .../processing/reference directory then please remove this file.

Otherwise, check you have permissions to edit files in this directory and if not, please contact itsupport@diamond.ac.uk

DIMPLE run through XCE sometimes crashes due to issues with restraints or atom type.

Reference models should be sanitised to remove any "unknown" (UNK) residues, or non-standard residues.

Additional reference files should be hidden to prevent DIMPLE running with the wrong files.

We suggest re-running PanDDA in a separate directory and then merging on the pandda.export step. 

Check the log files for any suggestions of issues in your model, fix in pandda.analyse, save and export selected dataset.

Refinement likely failed and XCE is calling the dimple model and maps.

Check the refinement log files and amend any errors in ..cootOut/Refine_#/multi-state-model.pdb and run the refmac.csh shell script.

Sometimes these jobs fail on the cluster, try running again.

Check no illegal characters (e.g. "/") in ligand IDs.

Check software package being used. If error is with GRADE your FedID may be associated with an industrial visit that cannot access the necesary licence files.

XCE cannot find models in your specified PanDDA directory that are more recent than the latest refinement runs.

You can try saving the models again in pandda.inspect or editing the timestamps in your database file.