Dear Stefan,
Just a couple of thoughts:
- first of all I think that Gerard is absolutely right, it would have been
nice to raise such issues first with the developers. In my experience,
Staraniso does a fantastic job if used correctly.
- but if you're OK with public trials, may I ask: why on Earth would anybody
need ContaMiner? Are you trying to offer some sort of computational cure for
sloppy biochemistry? There is zero point in crystallizing crap samples, sorry
to say this. In my 17 or so years in Strubi I've never heard of anybody
crystallizing a "contaminant", being it a purification tag or whatever.
I suppose this might have happened to somebody you know, hence the motivation
to spend time on the bizarre ContaMiner. Which is a pity, a silly outcome
would only teach people to do their job (or train their robots) properly.
Best wishes,
Radu
--
Radu Aricescu
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44-(0)1223-267049
fax: +44-(0)1223-268305
www: http://www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/radu-aricescuDear Stefan,Regarding your final paragraph: your server carries a warningwith the exact wording:"Submitting StarAniso files can give you suspicious results. Usewith care!"It seems rather regrettable that you are posting such a publicwarning without ever having contacted the STARANISO developers aboutyour observations, nor giving any information about what you call"suspicious" or what the "care" you recommend would consist of.We have taken a great deal of care ourselves in developing theprogram and offering it to the community through a server, and theleast we would have expected is that any pattern of "suspicious"results would be referred to us so that we could investigate them.There may be some assumptions made in MoRDa that we are not aware of,that might be incompatible with assumptions made in STARANISO - whoknows? Or it could be that some particularly badly collected datasetsare made to look worse after their anisotropy analysis.Could we discuss your observations, and what it is exactly thatyou call "suspicious", before they end up being referred to in such anuninformative manner as some sort of "Government Health Warning"?I think that would be nice :-) and we would be only too keen totake whatever extra "care" is needed ourselves. We would all learnsomething.With best wishes,Gerard.(on behalf of the STARANISO developers)--On Thu, Nov 23, 2017 at 05:02:39PM +0100, Stefan Arold wrote:Dear Community,A quick message to announce the following two new features on ourContaMiner web server for the automated detection of unwantedlycrystallised contaminants (https://strube.cbrc.kaust.edu.sa/contaminer/submit)1) online visualisation of 2FoFc and FoFc maps. In cases of positiveresults, the ‘UglyMol’ tab allows to inspect 2FoFc and FoFc mapsdirectlyin the web browser. Thi2) life-update. Previously, results were sent to you once all ~2000 MR jobswere finished. Now, the individual results for each potential contaminantwill appear as soon as they are finished. This feature should substantiallyshorten the time for identifying positive results (i.e. contaminantdetected), which are terminated faster than negative ones.3) custom contaminants. In the ‘Advanced’ tab, users can upload own PDBfiles (more than one is possible) to be included as search models. Thisfeature can be used to include PDB files from your lab bench neighbour’sproject to test for potential lab internal contaminations (throughbacterial contamination or through mix-up of plasmids or glycerol stocks).This feature could also be ‘abused’ as a means to use the MoRDa pipelinetorun molecular replacements with template structures that are not yetdeposited in the PDB; for example to run molecular replacement and initialrefinement for liganded or complexed versions of an unpublished structure.This might be particularly interesting for crystallographers away fromtheir usual home software environment (e.g. at the beamline).Finally, a word of warning – Staraniso files might give false positives ifthey have large anisotropic cuts.Keep your crystals clean!With best wishesThe ContaMiner Team--===============================================================* ** Gerard Bricogne [log in to unmask] ** ** Global Phasing Ltd. ** Sheraton House, Castle Park Tel: +44-(0)1223-353033 ** Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 ** *===============================================================