Auto-Rickshaw at MX

Owned by MX Cluster (Unlicensed)
Last updated: Sept 06, 2021
3 min read

This page outlines the use of Auto-Rickshaw to quickly find and visualise electron density in structures that may correspond to ligands. 

If you’re on site/using an on-site machine, follow the below instructions. Otherwise, see: http://webapps.embl-hamburg.de/cgi-bin/Auto-Rick/arinitAR1_sp.cgi

 

1) Start Auto-Rickshaw and navigate to MR

Go to AR homepage at http://autorickshaw:5000/ (Either from MX1 or from MX2 ) 

  • Select orange Auto-Rickshaw button

  • Check listed EPN corresponds to your experiment

  • Select your name / relevant PI's name from the drop-down list

  • Select relevant datafile suffix

  • Select relevant datafile prefix

FOR SINGLE DATASET SUBMISSION:

  • On Auto-Rickshaw Phasing page, click Advanced-version on left-hand side (AR PROTEIN only, Single dataset evaluation) and select MR from the drop-down menu. 

  • The MR phasing page will open; fill in empty fields. All fields need to be filled in for AR to run!

  • For PDB search model, select your receptor/ apo-protein of interest

  • Click 'Submit your AR job", this will start the pipeline.

FOR MULTIPLE DATASET SUBMISSION:

  • On Auto-Rickshaw Phasing page, click Advanced-version on left-hand side (AR PROTEIN only, Multiple dataset evaluation already scaled) and select MR from the drop-down menu.

  • Click 'MR' to go to the MR phasing page. All the datasets will be listed; select all required datasets.

  • Complete all required fields.

  • In this case, 'Submit your AR job" will launch a job for each dataset. Please be patient while it is submitting the multiple jobs. Wait for the next page to appear with the information on the data submission and a unique link for each AR job. 



2) Check results in job summary

To check your job process/results:

  • Select 'Auto-Rickshaw' button in the header to return to the Auto-Rickshaw Phasing page

  • Click 'ARJob summary', under the 'AR utility' header. This brings up a table of submissions to the pipeline sorted by time submitted

  • Click on the hyperlink the 'AR_ID' column to go to the job page for that ID. This page outlines where in the pipeline the process is up to.

4) Visualize results in UglyMol 

  • Select 'Auto-Rickshaw' button in the header to return to the Auto-Rickshaw Phasing page

  • Click 'Evaluate ligands from ARrun' button under 'AR utility' header. This brings up a similar table to the job summary page, but with coloured text:

    • GREEN text → substantial difference electron density has been found for ligand or missing part

    • ORANGE text → ambiguous or AR jobs still running. 

    • RED text → no ligand density present. 

The above traffic signal system only makes sense if your model has been refined below 35% Rfree. (Rfac/Rfree is indicated in the first column below each AR-ID) 

Click on the diffraction image in the 'STATUS' column for the relevant AR_ID, then click "from Auto-Rickshaw". This opens an UglyMol rendering of the model and electron density. All green/orange/red text IDs will have the mtz available for viewing from this platform.

Hit 'H' to open the keyboard shortcuts help window in UglyMol.

  • The view will jump to the first "dumbbell". These dumbbells are just indicators of nearby density peaks (eg. they are not really present in the model!) Spacebar will change view to the next dumbbell (you'll have to move through both "atoms" of the dumbbell before you jump to the next).

  • Press 'C' to toggle to B-factor colouring. Ignore the label 'B-factor'! This is actually colouring by most likely ligand positions; red (100%) is highest sigma → best quality peak; blue (0%) is lowest → the worst. As you toggle through dumbbells, you will move from highest quality to lowest.