It's amusing how a seemingly innocent ad for a new tool can ignite a rather
prickly thread.. I see two keys to this.
Firstly, for those who are not familiar with the issue the add could be
better structured by providing a clearer statement of what the problem is
or why it is important (with
Dear All,
As someone who is both a user of external software and supports internally
developed software to external users, I am quite familiar with both sides of
this argument. From time to time someone will notice a "weird feature" in
software - sometimes this is a bug, sometimes misuse
Hi Leo,
I agree that the horror beamline stories you describe are far too common.
Unfortunately, they start earlier, in the wet lab or even before. Exactly the
same attitude (careless construct design, crystallising whatever "dirty"
samples, not bothering optimising cryoprotection and so on)
Dear Gerard
I should certainly be the one to blame, as I was the one spotting this
behaviour to Stefan. Telling this, it could indeed be a problem with the data
set, yet submitting the original mtz to ContaMiner provided with the strangely
hoped and expected ContaMiner negative result. I made
Dear all,
to join Pierre's comments on what 'strange' things happen at the beamlines...
yet not too strange for (too) many people: huge screening of salt crystals,
complete data collection of dramatically low resolution data, full power
coupled with 360Deg data collection etc. etc. etc. We do
Hi All,
To add, on couple of occasions I re-determined the structure of so-called
"contaminants". Once, the structure of Secreted Ferritin (PDB 1Z6O) from
crystals that were supposedly that of TNF ligand:receptor complex (proteins
expressed in Tni cells), and in the second instant re-determined
My 2 cents worth:
I think contaminer is an extremely useful service. I may be a sloppy biochemist,
but I am not the only one. There are multiple structures in the database of say
bacterioferritin or AcrB that were solved from crystals that were supposed to
be something else. I remember in a
Dear Pierre,
Thank you for throwing some light on the circumstances under
which the "suspicious" results cropped up :-) . Was the "Government
Heatlh Warning" based on this one and only mtz file, then?
We would certainly be interested in examining this dataset for
any anomalies in the
Dear Radu,
here's an example from 11 years ago.
https://www.ncbi.nlm.nih.gov/pubmed/16929094
ContaMiner would have been useful here in that it would terminated the
crystallographic endeavour earlier
(In this case, however, serendipitous crystallization and structure solution of
the trace
Hi Tom, Tristan, Pierre,
So long that some people find ContaMiner useful, than fair enough :-) But I
still find it really hard to believe that this is a "common" occurrence. Maybe
"regular" at beamlines (who are not to blame of course), but I doubt that
frequency is high. Otherwise, they should
I agree with Tristan, it can be quite easy to crystallise a contaminant even
when one is trying to be careful during the purification process.
Before everyone had a mass spec, looking at gels didn't tell you as much as you
needed to know, as many proteins don't stain well, so are hard to see on
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
Dear Radu,
I think this is a little harsh. Biology is a fabulously messy thing, and very
prone to doing the unexpected. See the excellent paper by Niedzialkowska et al.
at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815408/#!po=13.6905 for some
examples. Sometimes unexpected things (which
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
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
Dear all,
a postdoctoral position is available in a joint project between my group
and the group of Julia Fritz-Steuber. The position is at the University
of Stuttgart Hohenheim, where I have moved recently. The position is
available immediately with preferred starting date 1.1.2018.
The
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
There are now only 50 spaces available for the CCP4 Study Weekend being held in
Nottingham between 10-12 January 2018.
Register now at
https://eventbooking.stfc.ac.uk/news-events/ccp4-study-weekend-2018-384 before
it's too late!
Regards
Karen McIntyre
Science & Technology Facilties Council
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