On 2 December 2017 at 00:31, Ivan Shabalin
wrote:
> Instead, we just used the search of the
> unit cell parameters in the PDB, which is much faster (but works only if the
> structure of this particular artifact in the same SpGr is in PDB! otherwise,
> one should use ContaMiner or similar service
It is also possible that it co-purifies via a nickel IMAC column purification
step. The affinity of many E. coli proteins for such columns is well known.
Diana
**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of
Dear All,
To add my voice to those who wrote crystallization artifacts happen - we
just witnessed one today. A postdoc from another lab tried crystallizing
a protein for months. Today, during data collection from his poorly
diffracting crystals, one of our guys (Dr. Porebski) scaled the data a
Hi Radu
thank you for your nice message - it is indeed unclear how often these
cases happen. From our side it was nice to hear that people acknowledged
the usefulness of our tool - which can also be used to rule out (known)
contaminant crystals.
Given that our ContaMiner will (by its design) not be
Hi Stefan,
I also owe you an apology for my bad choice of words. One can debate about
usefulness, but Pavel is right, the software is not "bizarre". And, as several
people pointed out, it certainly addresses a need (which I didn't know about).
Mea culpa.
Best wishes,
Radu
> Dear Gerard
>
> I a
Dear Stefan,
Thank you for your message. I am sure that we will figure out
what caused the spurious results described by Pierre, now that we know
about them ;-) .
Perhaps my reaction to your message was a little too loaded with
tension, and if so I regret it. The fact is that we are en
Dear Gerard
I am really sorry that my badly formulated 'final word of warning' has made
you and others spend much time for composing well-formulated replies. I was
at PX1 yesterday, and Leo reminded me of the issue, hence I included it
into my message.
You are absolutely right that reports of anom
Dear Radu,
I would not want to take undue advantage of this already
voluminous thread, but your PS takes us into a different direction,
namely the whole myth-ridden topic of "weak data" - but that will be
for another thread, another time ;-) .
With best wishes,
Gerard.
ral 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 (Sta
Ian's words need to emblazoned over all CCP4 distributions.
Users are an essential part of any development work..
As a developer I would never consider constructive user feedback as a
complaint. Feedback is a critical component of the software development
process and I think I speak for all dev
Hi Graeme
On 24 November 2017 at 06:33, Graeme Winter
wrote:
>
> Despite appearances people do not like to contact authors of software
> packages to complain.
>
As a developer I would never consider constructive user feedback as a
complaint. Feedback is a critical component of the software dev
stan! 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
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 approp
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 (which
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) leads
taMiner/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
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 th
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 discus
ity.
>
> 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]
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 cont
lmb.cam.ac.uk
> Sent: Friday, 24 November 2017 6:36 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] new ContaMiner features
>
> Dear Stefan,
>
> Just a couple of thoughts:
>
> - first of all I think that Gerard is absolutely right, it would have been
> nice to r
ubject: Re: [ccp4bb] new ContaMiner features
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&
17 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
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 jus
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 Ear
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 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
re
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