Dear Gérard,
As being part of the group how has initially raised the issue to Stefan, I
stand out to try clarifying a misinterpretation.
In brief, because we are happy users of StarAniso, it happened that we have
submitted an mtz that it had produced to the ContaMiner server. We were very
surprised to find that almost all contaminants evaluated gave high scores
according to MoRDa. On the contrary, using an "isotropicaly" treated mtz, no
hit could be detected in by ContaMiner.
Being collected on PROXIMA-1 beamline, it coun't be a "badly collected
datasets" ;-)
So, most probably, as you suggested, the issue is linked to some bad
assumptions made by MoRDa or inadequate criteria choices _in_the_cases_ of
"corrected" anisotropic data.
We can probably provide some examples of datasets to the developers willing to
pursue investigations on this.
I completely agree with Tristan! I have to admit having lost several weeks in
my career (if not months) with "contaminated" crystals. And working on an MX
beamline, I can testify that this is unfortunately happening regularly.
I will finish with a big thanks to all the (StarAniso/ContaMiner/MoRDA)
developers how are helping us to untwist the unavoidable experimental
mess/reality.
Kind regards,
Pierre
________________________________________
De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Gerard Bricogne
[g...@globalphasing.com]
Envoyé : jeudi 23 novembre 2017 19:34
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] new ContaMiner features
Dear Stefan,
Regarding your final paragraph: your server carries a warning
with the exact wording:
"Submitting StarAniso files can give you suspicious results. Use
with care!"
It seems rather regrettable that you are posting such a public
warning without ever having contacted the STARANISO developers about
your 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 the
program and offering it to the community through a server, and the
least 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 - who
knows? Or it could be that some particularly badly collected datasets
are made to look worse after their anisotropy analysis.
Could we discuss your observations, and what it is exactly that
you call "suspicious", before they end up being referred to in such an
uninformative manner as some sort of "Government Health Warning"?
I think that would be nice :-) and we would be only too keen to
take whatever extra "care" is needed ourselves. We would all learn
something.
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 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
--
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