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Dear Community,
A quick message to announce the following two new features on our ContaMiner web server for the automated detection of unwantedly crystallised contaminants (https://strube.cbrc.kaust.edu.sa/contaminer/submit)
1) online visualisation of 2FoFc and FoFc maps. In cases of positive results, the ‘UglyMol’ tab allows to inspect 2FoFc and FoFc maps directly in the web browser. Thi
2) life-update. Previously, results were sent to you once all ~2000 MR jobs were finished. Now, the individual results for each potential contaminant will appear as soon as they are finished. This feature should substantially shorten the time for identifying positive results (i.e. contaminant detected), which are terminated faster than negative ones.
3) custom contaminants. In the ‘Advanced’ tab, users can upload own PDB files (more than one is possible) to be included as search models. This feature can be used to include PDB files from your lab bench neighbour’s project to test for potential lab internal contaminations (through bacterial contamination or through mix-up of plasmids or glycerol stocks). This feature could also be ‘abused’ as a means to use the MoRDa pipeline to run molecular replacements with template structures that are not yet deposited in the PDB; for example to run molecular replacement and initial refinement for liganded or complexed versions of an unpublished structure. This might be particularly interesting for crystallographers away from their usual home software environment (e.g. at the beamline).
Finally, a word of warning – Staraniso files might give false positives if they have large anisotropic cuts.
Keep your crystals clean!
With best wishes
The ContaMiner Team