Re: [ccp4bb] To Trim or Not to To Trim

[Manfred S. Weiss]

Dear all,

many views have been expressed in this thread, which I have been
following with great interest. Unfortunately, I have to say that many
of the views are more based on personal preferences, than on the
scientific evidence behind.

Here are some facts, that one may want to consider:

1. When you have crystallized your protein, and collected data
from it, the obvious assumption is that it is still intact. Unless you
have additional information, e.g. from mass spec, that some
side chains are cleaved off, they are there.

2. Absence of evidence (meaning missing electron density)
is NOT evidence of absence 

3. If you trim, you give the impression that the respective atoms
are not there. This means that the solvent model will be incorrect,
because the area will be defined as solvent.

In my view, the best approach is to build the side chains in their
most plausible conformation, or maybe in 2 or 3 or 5 different
conformations, and let the ADPs refine freely.

All the best
Manfred




<http://www.icm.uu.se/structural-biology/griese-lab/>



























































































--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland

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[ccp4bb] Workshop on Crystallographic Fragment Screening, March 01-03, 2023

[Manfred S. Weiss]

Dear friends and colleagues,

within the frame of the iNEXT-Discovery project we are organizing a
three-day workshop  on crystallographic fragment screening from
Mar 01-03, 2023.

The course will take place in presence in Berlin and it is fully booked.
However, we will stream the lectures via Zoom. If you are interested
to listen in, please check out the webpage and register for the stream:
hz-b.de/inext

Please note, that there is a limited number of available spots in the Zoom
session.

Tatjana, Jan, Manfred

--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland

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[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2023

[Manfred S. Weiss]

...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>. 
Support for transnational
fragment-screening experiments is also possible via the EU-project
iNEXT-Discovery. For this, applications have to be submitted through
the iNEXT-Discovery web site.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> in 
order
to obtain updated information about our experimental setup and other
requirements.

Manfred Weiss, Uwe Mueller and the HZB-MX team


--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland

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Re: [ccp4bb] outliers

[Manfred S. Weiss]

a? It
probably
is. If you do this "experiment" millions of times it turns out
seeing at
least one 3-sigma deviate in 1000 tries is very common.
Specifically,
about 93% of the time. It is rare indeed to have every member of a
1000-deviate set all lie within 3 sigmas.  So, we have gone from
one
3-sigma deviate being highly unlikely to being a virtual
certainty if
you look at enough samples.

So, my question is: is a 3-sigma deviate significant?  Is it
significant
only if you have one bond in the structure?  What about angles?
What if
you have 500 bonds and 500 angles?  Do they count as 1000 deviates
together? Or separately?

I'm sure the more mathematically inclined out there will have some
intelligent answers for the rest of us, however, if you are not a
mathematician, how about a vote?  Is a 3-sigma bond length
deviation
significant? Or not?

Looking forward to both kinds of responses,

-James Holton
MAD Scientist




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--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland

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[ccp4bb] Ph.D. position at HZB/BESSY II in Berlin

[Manfred S. Weiss]

The macromolecular crystallography group at the HZB welcomes applications

for a Ph. D. position on the structure and function of plastic degrading 
enzymes.

Within the Helmholtz project FINEST, a doctoral position is available for the

sub-project MICROPLASTICS, which will address the microbial/biochemical 
conversion

of synthetic polymer (plastics) fractions of fine-grained residues 
(microplastics) to

yield valuable products and/or inert residues for safe deposition.

In the PhD project, initially characterized and also novel fungal biocatalysts 
from

FINEST partner UFZ Leipzig acting on synthetic polymers and/or polymer additives

will be biochemically and structurally characterised to enhance their catalytic 
performance

on a structural basis and with bioinformatic tools (in silico protein 
engineering).

FINEST partners UFZ and University of Greifswald will provide strong support in 
the

provision of novel enzymes and their biochemical characterization, respectively.

With FINEST partner HZDR, located in Dresden Rossendorf, an innovative assay for

the detection of micro- and nanoplastic particles will be developed.

For detailed information, please follow this link: 
https://recruitingapp-5181.de.umantis.com/Vacancies/1860/Description/2?lang=eng


--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland

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[ccp4bb] Reminder: Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2022

[Manfred S. Weiss]

...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>. 
Support for transnational
fragment-screening experiments is also possible via the EU-project
iNEXT-Discovery. For this, applications have to be submitted through
the iNEXT-Discovery web site.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> in 
order
to obtain updated information about our experimental setup and other
requirements.

Manfred Weiss, Uwe Mueller and the HZB-MX team


--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland



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[ccp4bb] Deadline extended, NOW July 25, 2022; Helmholtz Workshop on Integrative Structural Biology

[Manfred S. Weiss]

***

The Helmholtz-Zentrum Berlin (HZB) and the Max Delbruck Centre
for Molecular Medicine (MDC) are organizing a one-week training
workshop on methods and applications in Integrative Structural Biology
within the frame of the Helmholtz Cross Cutting Activity
"Structural Biology". The workshop's main focus is on sample preparation
for biophysical studies, X-ray crystallography, cryo-electron microscopy
and NMR including hands-on practical training. Lectures and keynote
presentations will illustrate state-of-the-art examples for the combination
of multiple structural biology techniques to study the structure and dynamics
of biologically important and challenging systems. The workshop will
take place in Berlin-Adlershof and in Berlin-Buch from Oct 08-14, 2022.

The workshop is aimed a PhD students and young postdoctoral researchers
who want to broaden their structural biology experience.

For more information and for application, please visit the site
https://www.helmholtz-berlin.de/events/helmholtz-training-workshop/index_en.html

With best regards
Uwe, Oli, Yvette and Manfred

****

--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland



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[ccp4bb] Helmholtz Workshop on Integrative Structural Biology

[Manfred S. Weiss]

***

The Helmholtz-Zentrum Berlin (HZB) and the Max Delbruck Centre
for Molecular Medicine (MDC) are organizing a one-week training
workshop on methods and applications in Integrative Structural Biology
within the frame of the Helmholtz Cross Cutting Activity
"Structural Biology". The workshop's main focus is on sample preparation
for biophysical studies, X-ray crystallography, cryo-electron microscopy
and NMR including hands-on practical training. Lectures and keynote
presentations will illustrate state-of-the-art examples for the combination
of multiple structural biology techniques to study the structure and dynamics
of biologically important and challenging systems. The workshop will
take place in Berlin-Adlershof and in Berlin-Buch from Oct 08-14, 2022.

The workshop is aimed a PhD students and young postdoctoral researchers
who want to broaden their structural biology experience.

For more information and for application, please visit the site
https://www.helmholtz-berlin.de/events/helmholtz-training-workshop/index_en.html

With best regards
Uwe, Oli, Yvette and Manfred

****

--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland



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[ccp4bb] Job opportunity in Berlin - HZB and Humboldt University advertise a postdoc position

[Manfred S. Weiss]

The Helmholtz Zentrum Berlin für Materialien und Energie, the 
Max-Delbrück-Center for Molecular Medicine, the Freie Universität Berlin, the 
Charite, the Max-Planck-Institute for Colloids and Interfaces  and the Humboldt 
Universität zu Berlin jointly operate three experimental stations for 
bio-macromolecular crystallography at BESSY II, Berlin's modern synchrotron 
radiation source, located in the lovely southeast of Berlin.

(https://www.helmholtz-berlin.de/forschung/oe/ps/macromolecular-crystallography/index_en.html)

The Humboldt University zu Berlin is seeking a

Post Doctoral Research Assistant

to work on and support research topics in the field of structural enzymology 
(e.g. control of chemical reactions in macromolecular crystals, combination of 
UV/Vis absorption spectroscopy and crystallography, etc.) originating from the 
group of Prof. Dr. Holger Dobbek. The successful candidate will also be 
involved in the operation of the BESSY II bio-macromolecular crystallography 
beamlines (headed by Dr. Manfred S. Weiss) including supporting external users 
at the beamlines and will take part in graduate student education.

Initially,  a contract lasting until 31.12.2023 will be offered to the 
successful candidate with the possibility for an extension. The salary will be 
based on German Federal TVöD. The position is available immediately.

Applicants should hold a Ph.D. in the biological, chemical or physical sciences 
and have a solid background in biochemical methods, in bio-macromolecular 
crystallography and/or related fields. The position also requires the 
documented ability to conduct independent research as well as excellent 
communication and interpersonal skills.

Please send applications (CV, list of publications, references, .pdf-file 
format) citing the reference number AN/073/22 in electronic form until 
28.04.2022 to:

Dr. Manfred Weiss 
(mswe...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>)

Here is the link to the job advertisement (in German):

https://www.personalabteilung.hu-berlin.de/de/stellenausschreibungen/wissenschaftliche-r-mitarbeiter-in-m-w-d-befristet-bis-31-12-2023-e-13-tv-l-hu






--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland



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[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2022

[Manfred S. Weiss]

purification (AEKTA)
- nL 96-well crystallization plate formulation and storage at
 5°C and 20°C
- Biophysical characterization with real time PCR (thermofluor assay)
- Contactless compound pipetting using ATS

The HZB-MX group is also providing expert assistance as well as
access to a library of fragments for carrying out crystallographic
fragment-screening experiments. For more information please see
https://www.helmholtz-berlin.de/forschung/oe/ps/macromolecular-crystallography/fragment-screening/index_en.html
or contact mswe...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>. 
Support for transnational
fragment-screening experiments is also possible via the EU-project
iNEXT-Discovery. For this, applications have to be submitted through
the iNEXT-Discovery web site.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> in 
order
to obtain updated information about our experimental setup and other
requirements.

Manfred Weiss, Uwe Mueller and the HZB-MX team


--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Jan Lüning (Sprecher), Prof. Dr. Bernd Rech, Thomas 
Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland



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Re: [ccp4bb] software DS, fconv still available ? contact?

[Manfred S. Weiss]

https://agklebe.pharmazie.uni-marburg.de/

Cheers,
Manfred

Am 14.09.2021 um 14:36 schrieb Guenter Fritz:

Dear all,

does somebody know whom to contact for the software  DSX or fconv of
the former group Klebe in Marburg?

Many thanks and best regards,

Guenter



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--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Jan Lüning (Sprecher), Prof. Dr. Bernd Rech, Thomas 
Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland



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[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2021

[Manfred S. Weiss]

es (separate registration required):
- Protein production and purification (AEKTA)
- nL 96-well crystallization plate formulation and storage at
 5°C and 20°C
- Biophysical characterization with real time PCR (thermofluor assay)
- Contactless compound pipetting using ATS

The HZB-MX group is also providing expert assistance as well as
access to a library of fragments for carrying out crystallographic
fragment-screening experiments. For more information please see
https://www.helmholtz-berlin.de/forschung/oe/ps/macromolecular-crystallography/fragment-screening/index_en.html
or contact mswe...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>. 
Support for transnational
fragment-screening experiments is also possible via the EU-project
iNEXT-Discovery. For this, applications have to be submitted through
the iNEXT-Discovery web site.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> in 
order
to obtain updated information about our experimental setup and other
requirements.

Manfred Weiss, Uwe Mueller and the HZB-MX team


--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Jan Lüning (Sprecher), Prof. Dr. Bernd Rech, Thomas 
Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland



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Re: [ccp4bb] Should Rmerge be reported?

[Manfred S. Weiss]

Dear Graeme,

a better number to look at is Isa. Instead of low resolution Rmerge.
Seriously. We monitor that to assess beamline performance.

Cheers, Manfred

Am 10.06.2021 um 14:42 schrieb Winter, Graeme (DLSLtd,RAL,LSCI):
Once again I find myself jumping to the defence of this rather poor statistic!

Yes, Rmerge is a very poor estimator of "data quality" and has many well published flaws 
related to multiplicity, but the low resolution Rmerge, if combined with a multiplicity > (say) 5, 
is a good indicator of whether the data set is "good" or there is something odd going on.

For example, if you claim a 1.6A structure with an inner shell Rmerge of 0.11, 5-fold 
multiplicity and an overall I/sig(I) of 68 I would "smell a rat"

To me it does have a value, as an unbiased estimator of your true unmerged 
I/sigma as it does not depend on any manipulation you have done to your sigmas. 
It is not a good estimator of where the resolution should be cut or any other 
decisions.

The above situation could be an indicator that there was radiation damage, for 
example

There are better ways of measuring damage - Rd, Rcp, ... but these are not 
commonplace graphs as I understand it. This little number in the middle of the 
table does give you that hint.

So while I would say rejecting a paper because it was not included was very 
heavy handed, I would not like to see it erased from all papers either.

All the best Graeme

From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK> on behalf 
of Manfred S. Weiss 
<mailto:manfred.we...@helmholtz-berlin.de>
Sent: 10 June 2021 13:30
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 
<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Should Rmerge be reported?

Dear Cristy,

this is really hilarious. And it just shows how attached
some ppl are to outdated numbers. Against better
knowledge.

It has been shown many times that Rmerge is flawed
at various levels.

The only reason I can see to report it is to be backwards
compatible. But of course, this is a really weak reason.

I would love to see it disappear.

All the best
Manfred

Am 10.06.2021 um 14:25 schrieb Maria Cristina Nonato:
Dear Colleagues
Hope to find you all well and healthy.

I have a question regarding Rmerge. In recent years, we have published our 
crystallographic structures in highly respected journals using CC1/2, 
I/sigma(I), completeness and multiplicity as quality parameters for our 
diffraction data.

Recently this year, We submitted a paper using the same strategy, but one of 
the reviewers asked us to provide the Rmerge, arguing that providing this data 
was compulsory and it was important to estimate radiation damage.

We replied to the editor arguing that Rmerge should not be used as a quality parameter, as 
suggested by more recent literature, such as the article published by Karplus and 
Diederichs (10.1016/j.sbi.2015.07.003). We also argued that there are modern and efficient 
methods to estimate radiation damage ( 
doi.org/10.1107/S1600576718005241<http://doi.org/10.1107/S1600576718005241>; 
doi.org/10.1107/S0907444909040177<http://doi.org/10.1107/S0907444909040177>). It is 
my opinion that an experienced crystallographer can even  monitor radiation damage over the 
course of data processing.

And our paper was rejected  due to the fact I did not provide 
Rmerge which I certainly could have done If I found necessary.

Journals like Nature ((https://www.nature.com › documents › 
nr-tables-xray<https://www.google.com/url?sa=t=j==s=web==2ahUKEwiigtb19uHwAhWS3YUKHSB1AdkQFjABegQIAxAD=https%3A%2F%2Fwww.nature.com%2Fdocuments%2Fnr-tables-xray.doc=AOvVaw1RbfYvNeiEM07FBEOohMig>)
 and even IUCr Journals (https://journals.iucr.org/f/services/structuralcommunications/) still list Rmerge as a data 
to be reported. I always took this as a suggestion since there are people still using Rmerge for data cutoff, but I 
never took this as if Rmerge was a compulsory data to be reported.

I would like to hear the opinion of this community. Should we compulsorily 
report Rmerge?  If so, Why?

Cheers,

Cristy
--
Cristina Nonato
Associate Professor
Laboratório de Cristalografia de Proteínas
Faculdade de Ciências Farmacêuticas de Ribeirão Preto
University of São Paulo





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--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (Sprecher), Prof. Dr. Jan Lüning, T

Re: [ccp4bb] Should Rmerge be reported?

[Manfred S. Weiss]

Dear Cristy,

this is really hilarious. And it just shows how attached
some ppl are to outdated numbers. Against better
knowledge.

It has been shown many times that Rmerge is flawed
at various levels.

The only reason I can see to report it is to be backwards
compatible. But of course, this is a really weak reason.

I would love to see it disappear.

All the best
Manfred

Am 10.06.2021 um 14:25 schrieb Maria Cristina Nonato:
Dear Colleagues
Hope to find you all well and healthy.

I have a question regarding Rmerge. In recent years, we have published our 
crystallographic structures in highly respected journals using CC1/2, 
I/sigma(I), completeness and multiplicity as quality parameters for our 
diffraction data.

Recently this year, We submitted a paper using the same strategy, but one of 
the reviewers asked us to provide the Rmerge, arguing that providing this data 
was compulsory and it was important to estimate radiation damage.

We replied to the editor arguing that Rmerge should not be used as a quality parameter, as 
suggested by more recent literature, such as the article published by Karplus and 
Diederichs (10.1016/j.sbi.2015.07.003). We also argued that there are modern and efficient 
methods to estimate radiation damage ( 
doi.org/10.1107/S1600576718005241<http://doi.org/10.1107/S1600576718005241>; 
doi.org/10.1107/S0907444909040177<http://doi.org/10.1107/S0907444909040177>). It is 
my opinion that an experienced crystallographer can even  monitor radiation damage over the 
course of data processing.

And our paper was rejected  due to the fact I did not provide 
Rmerge which I certainly could have done If I found necessary.

Journals like Nature ((https://www.nature.com › documents › 
nr-tables-xray<https://www.google.com/url?sa=t=j==s=web==2ahUKEwiigtb19uHwAhWS3YUKHSB1AdkQFjABegQIAxAD=https%3A%2F%2Fwww.nature.com%2Fdocuments%2Fnr-tables-xray.doc=AOvVaw1RbfYvNeiEM07FBEOohMig>)
 and even IUCr Journals (https://journals.iucr.org/f/services/structuralcommunications/) still list Rmerge as a data 
to be reported. I always took this as a suggestion since there are people still using Rmerge for data cutoff, but I 
never took this as if Rmerge was a compulsory data to be reported.

I would like to hear the opinion of this community. Should we compulsorily 
report Rmerge?  If so, Why?

Cheers,

Cristy
--
Cristina Nonato
Associate Professor
Laboratório de Cristalografia de Proteínas
Faculdade de Ciências Farmacêuticas de Ribeirão Preto
University of São Paulo





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--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (Sprecher), Prof. Dr. Jan Lüning, Thomas 
Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland



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[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2021

[Manfred S. Weiss]

ment-screening experiments. For more information please see
https://www.helmholtz-berlin.de/forschung/oe/np/gmx/fragment-screening/index_en.html
or contact mswe...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>. 
Support for transnational
fragment-screening experiments is also possible via the EU-project
iNEXT-Discovery. For this, applications have to be submitted through
the iNEXT-Discovery web site.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> in 
order
to obtain updated information about our experimental setup and other
requirements.

Manfred Weiss, Uwe Mueller and the HZB-MX team



--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (Sprecher), Prof. Dr. Jan Lüning, Thomas 
Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin



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Re: [ccp4bb] when does non-isomorphism become a habit?

[Manfred S. Weiss]

Dear James,

let's spin the thought a bit further. What if there is a new program
(Phaser-II) some day,
for which the coordinates in your "new crystal form" are all of a sudden
within the
radius of convergence again? Does this bring your "new crystal form"
back to the old
crystal form again?

I'd say it is neither cell dimensions nor space group that define a new
crystal form. It
is the packing of the molecules. It happens quite often in dehydration
experiments
that molecules in a lattice move a bit and symmetry elements are lost or
new symmetry
elements are created. The space group changes, as well as the unit cell
dimensions. But
the packing remains essentially the same. You can usually infer what
happens, but you
still need molecular replacement to actually solve the "new" form.

Best, Manfred


Am 09.12.2020 um 01:56 schrieb James Holton:

I have a semantics question, and I know how much this forum loves
discussing semantics.

We've all experienced non-isomorphism, where two crystals, perhaps
even grown from the same drop, yield different data. Different enough
so that merging them makes your overall data quality worse. I'd say
that is a fairly reasonable definition of non-isomorphism? Most of the
time unit cell changes are telling, but in the end it is the I/sigma
and resolution limit that we care about the most.

Now, of course, even for non-isomorphous data sets you can usually
"solve" the non-isomorphous data without actually doing molecular
replacement.  All you usually need to do is run pointless using the
PDB file from the first crystal as a reference, and it will re-index
the data to match the model.  Then you just do a few cycles of rigid
body and you're off and running.  A nice side-effect of this is that
all your PDB files will line up when you load them into coot.  No
worries about indexing ambiguities, space group assignment, or origin
choice. Phaser is a great program, but you don't have to run it on
everything.

My question is: what about when you DO have to run Phaser to solve
that other crystal from the same drop?  What if the space group is the
same, the unit cell is kinda-sorta the same, but the coordinates have
moved enough so as to be outside the radius of convergence of
rigid-body refinement?  Does that qualify as a different "crystal
form" or different "crystal habit"?  Or is it the same form, and just
really non-isomorphous?

Opinions?

-James Holton
MAD Scientist



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--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (Sprecher), Prof. Dr. Jan Lüning, Thomas 
Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
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[ccp4bb] Fwd: Call for MX beamtime proposals at HZB, BESSY II, deadline extended to September 06, 2020

[Manfred S. Weiss]

ents. For more information please see
https://www.helmholtz-berlin.de/forschung/oe/np/gmx/fragment-screening/index_en.html
or contact mswe...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>. 
Support for fragment-screening
experiments is also possible via the EU-project iNEXT-Discovery. For
this, applications have to be submitted through the iNEXT-Discovery
web site.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> in 
order
to obtain updated information about our experimental setup and other
requirements.

Manfred Weiss and the HZB-MX team


--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (Sprecher), Prof. Dr. Jan Lüning, Thomas 
Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
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[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2020

[Manfred S. Weiss]

ents. For more information please see
https://www.helmholtz-berlin.de/forschung/oe/np/gmx/fragment-screening/index_en.html
or contact mswe...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>. 
Support for fragment-screening
experiments is also possible via the EU-project iNEXT-Discovery. For
this, applications have to be submitted through the iNEXT-Discovery
web site.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> in 
order
to obtain updated information about our experimental setup and other
requirements.

Manfred Weiss and the HZB-MX team


--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (Sprecher), Prof. Dr. Jan Lüning, Thomas 
Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
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[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2020

[Manfred S. Weiss]

ttps://www.helmholtz-berlin.de/forschung/oe/np/gmx/fragment-screening/index_en.html
or contact mswe...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> in 
order
to obtain updated information about our experimental setup and other
requirements.

Manfred Weiss and the HZB-MX team



--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (Sprecher), Prof. Dr. Jan Lüning, Thomas 
Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
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[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2019

[Manfred S. Weiss]

e>.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> in 
order
to obtain updated information about our experimental setup and other
requirements.

Manfred Weiss and the HZB-MX team

--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta 
Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (Sprecher), Prof. Dr. Jan Lüning, Thomas 
Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
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Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

[Manfred S. Weiss]

Hi Rhys,

all three structures are at modest resolution and they don't seem to
be properly refined. At least they are all below average. I wonder
how this paper made it past the referees.

I haven't checked the paper, but there are ways and means how to
deal with weakly bound ligands in the best possible way. One aspect
is to improve the phases as much as possible without having the ligand
present. This was obviously NOT done. Another way is to use the
PANDDA approach, which relies on having many data sets available.
I suppose that this was also not done.

The best way to check is to delete the ligand and so some extensive
refinement in order to remove the phase bias introduced by the
ligand. Only then you can reliably assess whether something is there
or not.

Cheers, Manfred

Am 19.07.2019 um 15:21 schrieb Rhys Grinter:
Hi All,

I was chatting with a colleague during a recent synchrotron visit and they'd 
recently come across some ligand/drug bound structures associated with a paper 
recently published in a high impact factor journal.

They had pulled the associated SFs from the PDB and found that the electron 
density associated with these ligands didn't match that reported in the paper 
and certainly wasn't sufficient to model the alleged ligand.

I also pulled the structure factors and after refinement in the 
presence/absence of the alleged ligand I also feel that the density present 
does not warrant modelling of the ligand.

I was hoping that the community might be able to give me an outside opinion on 
these datasets (PDB IDs: 6MO0, 6MO1, 6MO2) and if the problem associated with 
the data is verified, provide some advice on how to proceed.

This isn't the first occasion I've seen ligand bound structures with 
questionable density deposited in association with papers in well respected 
journals. Despite improvements to validation I feel that this problem is 
widespread.

Best Regards,

Rhys

--
Dr Rhys Grinter
NHMRC Postdoctoral Researcher
Monash University
+61 (0)3 9902 9213
+61 (0)403 896 767



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Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

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Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (Sprecher), Prof. Dr. Jan Lüning, Thomas 
Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

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[ccp4bb] Last chance to apply: Workshop "Diffraction Data Collection Using Synchrotron Radiation"

[Manfred S. Weiss]

Dear all,

the application deadline for this popular workshop has been
extended to May 08.

Cheers, Manfred



I would hereby like to announce the 6th edition of the workshop
"Diffraction Data Collection Using Synchrotron Radiation", which
will take place from July 04-06, 2019 at the BESSY II storage
ring of the Helmholtz-Zentrum Berlin for Materials and Energy
(HZB) in Berlin.

This workshop is the successor to five previous successful work-
shops, which took place in 2007, 2009, 2011, 2013 and 2016. It is
sponsored by the German Society for Crystallography (DGK) and
organised in cooperation with the DGK Working Group 1 (Biological
Structures).

The workshop comprises a series of basic lectures on the topic
and two extended practical sessions. It is aimed at PhD students
in Biological Crystallography with little or no experience in
diffraction data collection at a synchrotron. The practical sessions
will take place at the MX beamlines located at the electron storage
ring BESSY II.

The workshop fee is 100 EUR for DGK-members and 120 EUR for non-members.
This fee covers all conference material as well as board and lodging
for two nights on the campus in Berlin-Adlershof.

For more information please visit the web page
https://www.helmholtz-berlin.de/events/dgk/index_en.html

The application page is now open. Since the number of students will
have to be limited to 20 in order to ensure that the practical sessions
run efficiently, we expect that the workshop will fill up quickly.
Participants are also expected to present a poster on their own work.
As previously, the best poster will be awarded with an attractive prize.
##

Manfred Weiss

--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. 
Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (kommissarisch), Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Job opportunity in Berlin - HZB and Humboldt University advertise a postdoc position

[Manfred S. Weiss]

The Helmholtz Zentrum Berlin für Materialien und Energie, the 
Max-Delbrück-Center for Molecular Medicine, the Freie Universität Berlin, the 
Chariteand the Humboldt Universität zu Berlin jointly operate three 
experimental stations for bio-macromolecular crystallography at BESSY II, one 
of the world’s most modern synchrotron radiation sources for VUV and soft 
X-rays.
(https://www.helmholtz-berlin.de/forschung/oe/np/gmx/index_en.html)

The Humboldt University zu Berlin is seeking a

Post Doctoral Research Assistant

to work on and support research topics in the field of structural enzymology 
(e.g. control of chemical reactions in macromolecular crystals, combination of 
UV/Vis absorption spectroscopy and crystallography, etc.) originating from the 
group of Prof. Dr. Holger Dobbek. The successful candidate will also be 
involved in the operation of the BESSY II bio-macromolecular crystallography 
beamlines (headed by Dr. Manfred S. Weiss) including supporting external users 
at the beamlines and will take part in graduate student education.

Initially, a contract lasting until 31.12.2020 will be offered to the 
successful candidate with the possibility for an extension. The salary will be 
based on German Federal TVöD. The position is available immediately.

Applicants should hold a Ph.D. in the biological, chemical or physical sciences 
and have a solid background in biochemical methods, in bio-macromolecular 
crystallography and/or related fields. The position also requires the 
documented ability to conduct independent research as well as excellent 
communication and interpersonal skills.

Please send applications (CV, list of publications, two references, .pdf-file 
format) citing the reference number AN/106/19 in electronic form until 
25.04.2019 to:

Dr. Manfred Weiss 
(mswe...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>)

Here is the link to the advertisement (in German):
https://www.personalabteilung.hu-berlin.de/de/stellenausschreibungen/wissenschaftlicher-mitarbeiter-m-w-d-befristet-bis-31-12-2020-e-13-tv-l-hu


--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. 
Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (kommissarisch), Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Reminder: Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2019

[Manfred S. Weiss]

p/gmx/fragment-screening/index_en.html
or contact mswe...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> to 
obtain
updated information about our experimental setup and other
requirements.



--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. 
Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (kommissarisch), Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Workshop "Diffraction Data Collection Using Synchrotron Radiation"

[Manfred S. Weiss]

I would hereby like to announce the 6th edition of the workshop
"Diffraction Data Collection Using Synchrotron Radiation", which
will take place from July 04-06, 2019 at the BESSY II storage
ring of the Helmholtz-Zentrum Berlin for Materials and Energy
(HZB) in Berlin.

This workshop is the successor to five previous successful work-
shops, which took place in 2007, 2009, 2011, 2013 and 2016. It is
sponsored by the German Society for Crystallography (DGK) and
organised in cooperation with the DGK Working Group 1 (Biological
Structures).

The workshop comprises a series of basic lectures on the topic
and two extended practical sessions. It is aimed at PhD students
in Biological Crystallography with little or no experience in
diffraction data collection at a synchrotron. The practical sessions
will take place at the MX beamlines located at the electron storage
ring BESSY II.

The workshop fee is 100 EUR for DGK-members and 120 EUR for non-members.
This fee covers all conference material as well as board and lodging
for two nights on the campus in Berlin-Adlershof.

For more information please visit the web page
https://www.helmholtz-berlin.de/events/dgk/index_en.html<http://www.helmholtz-berlin.de/bessy-mx-workshop/>

The application page is now open. Since the number of students will
have to be limited to 20 in order to ensure that the practical sessions
run efficiently, we expect that the workshop will fill up quickly.
Participants are also expected to present a poster on their own work.
As previously, the best poster will be awarded with an attractive prize.
##

Manfred Weiss

--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. 
Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (kommissarisch), Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2019

[Manfred S. Weiss]

;.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> to 
obtain
updated information about our experimental setup and other
requirements.

Manfred Weiss and the HZB-MX team


--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. 
Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (kommissarisch), Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2018

[Manfred S. Weiss]

Dear all,

the next MX-proposal application deadline: September 01, 2018 is approaching
https://www.helmholtz-berlin.de/user/beamtime/proposals/index_en.html

This time all proposals will be handled with the new version of GATE,
GATE2.0
https://www.helmholtz-berlin.de/pubbin/hzbgate

Hereby we would like to invite the submission of new proposals for
MX-beamtime at the HZB-MX beamlines for the next beam time period
(02/2019-08/2019).

In order to apply for beamtime, please register at the HZB on-line
access tool "GATE" (https://www.helmholtz-berlin.de/pubbin/hzbgate)
and submit a new beam time application proposal.

With the new GATE version, the proposal categories have been
improved. We now expect from each group only ONE BAG proposal.
Each such proposals can contain up to 20 individual projects.

HZB provides MX-beamtime at the three MX-beamlines BL14.1, BL14.2
and BL14.3. The three beamlines are equipped with state-of-the-art
instrumentation and are currently the most productive MX-stations
in Germany with over 300 PDB depositions annually. Beamtime is
granted based on the reviewed proposals and on reports from
previous research activities. Please make sure to include them
if available.

Experimental setup:

BL14.1:
- Photon flux: 1.4x10¹¹ Phot/sx100mAx0.05%BW at sample position
 (0.1-1 sec exposure time per frame)
- User defined beam shaping from 50µm-100µm diameter possible
- Pilatus 6M detector, 141mm-680mm max. distance from the sample
- Microdiffractometer (MD2) with Mini-kappa goniometer
- Automatic sample changer (CATS), 90 sample storage capacity
(SPINE-Pin & EMBL sample magazine compatibility)
- 32-core XEON-CPU server, with 10Gb uplink to Pilatus 6M
- Data collection control via MXCuBE
- EDNA
- Common MX-software installed including XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing with XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- Pressure chamber for noble gas derivatization (Xe, Kr
 available upon request)
- AMPTEK-XRF detector and XFEPLOT software available

We are also offering the hard- and software environment for
carrying out:
- UV-RIP experiments at BL14.1. For further information, please visit:

https://www.helmholtz-berlin.de/forschung/oe/np/gmx/ancillary-facilities/uvrip_en.html

BL14.2:
- Photon flux: 1.9x10¹¹ Phot/sx100mAx0.05%BW at sample position
 (0.1-1 sec exposure time per frame)
- Pilatus 3S-2M detector with 1000 micron Si sensor thickness,
 55mm-600mm distance from the sample
- Nanodiffractometer (DESY P11 design) and on-axis sample microscope
- User defined beam shaping from 30µm-150µm diameter possible
- GROB sample changer for SPINE and UNIPUCK support
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Common MX-software installed including XDS, iMOSFLM, CCP4, Phenix,
 SHELXC-D-E, etc.
- Automated data processing with XDSAPP
- Amptek XRF detector
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpixel CCD-camera
- UV-Microsprectrophotometer offline setup available
- AMPTEK-XRF detector and XFEPLOT software available

BL14.3:
- Photon flux: 4x10exp10 Phot/sx100mAx0.05%BW at sample position
 (3-20 sec exposure time per frame)
- Rayonix MX-225 X-ray detector, 54mm-450mm distance from the
 sample, 30 deg 2-Theta possible
- MD2S microdiffractometer
- REX nozzle changer
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- EDNA installed and available
- Common MX software installed including XDS, iMOSFLM, CCP4, Phenix,
 SHELXC-D-E, etc.
- Automated data processing using XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- HC1lab dehydration device installed (please specify HC1-beamtime
 in your proposal if needed)
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpixel CCD-camera

S1-biolab facilities (separate registration required):
- Protein production and purification
- Nanoliter 96 well crystallization plate formulation and storage at
 5 °C and 20 °C
- Biophysical characterization with real time PCR (thermofluor assay)

The HZB-MX group is also providing expert assistance as well as
access to a library of fragments for carrying out crystallographic
fragment-screening experiments. For more information please contact
mswe...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> to 
obtain
updated information about our experimental setup and other
requirements.

Manfred Weiss and the HZB-MX team

--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie 

[ccp4bb] Reminder: Call for MX beamtime proposals at HZB, BESSY II, deadline extended to Sunday March 04, 2018

[Manfred S. Weiss]

Dear all,

this is a gentle reminder of the current call for MX beamtime
proposals at HZB, BESSY II. The deadline for accepting proposals
has been extended to Sunday, March 04, 2018.

Best wishes

Manfred, on behalf of the HZB-MX team


Next MX-proposal application deadline: March 01, 2018 is approaching
http://www.helmholtz-berlin.de/user/beamtime/proposals/index_en.html

Hereby we would like to invite the submission of new proposals for
MX-beamtime at the HZB-MX beamlines for the next beam time period
(08/2018-01/2019).

In order to apply for beamtime, please register at the HZB on-line
access tool "GATE" (https://www.helmholtz-berlin.de/pubbin/hzbgate)
and submit a new beam time application proposal.

HZB provides MX-beamtime at the three MX-beamlines BL14.1, BL14.2
and BL14.3. The three beamlines are equipped with state-of-the-art
instrumentation and are currently the most productive MX-stations
in Germany with over 300 PDB depositions annually. Beamtime is
granted based on the reviewed proposals and on reports from
previous research activities. Please make sure to include them
if available.

What's new: Due to a planned upgrade of the experimental endstation
   BL14.3 will not be fully available. Details can be 
provided
   upon request.

Experimental setup:

BL14.1:
- Photon flux: 1.4x10¹¹ Phot/sx100mAx0.05%BW at sample position
 (0.1-1 sec exposure time per frame)
- User defined beam shaping from 50µm-100µm diameter possible
- Pilatus 6M detector, 141mm-680mm max. distance from the sample
- Microdiffractometer (MD2) with Mini-kappa goniometer MK3
- Automatic sample changer (CATS), 90 sample storage capacity
(SPINE-Pin & EMBL sample magazine compatibility)
- 32-core XEON-CPU server, with 10Gb uplink to Pilatus 6M
- Data collection control via MXCuBE
- EDNA
- Common MX-software installed including XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing with XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- Pressure chamber for noble gas derivatization (Xe, Kr
 available upon request)
- AMPTEK-XRF detector and XFEPLOT software available

We are also offering the hard- and software environment for
carrying out:
- UV-RIP experiments at BL14.1. For further information, please visit:

https://www.helmholtz-berlin.de/forschung/oe/np/gmx/ancillary-facilities/uvrip_en.html

BL14.2:
- Photon flux: 1.9x10¹¹ Phot/sx100mAx0.05%BW at sample position
 (0.1-1 sec exposure time per frame)
- Pilatus 3S-2M detector with 1000 micron Si sensor thickness,
 55mm-600mm distance from the sample
- Nanodiffractometer (DESY P11 design) and on-axis sample microscope
- User defined beam shaping from 30µm-150µm diameter possible
- GROB sample changer for SPINE and UNIPUCK support
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Common MX-software installed including XDS, iMOSFLM, CCP4, Phenix,
 SHELXC-D-E, etc.
- Automated data processing with XDSAPP
- Amptek XRF detector
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpixel CCD-camera
- UV-Microsprectrophotometer offline setup available
- AMPTEK-XRF detector and XFEPLOT software available

BL14.3:
- Photon flux: 4x10exp10 Phot/sx100mAx0.05%BW at sample position
 (3-20 sec exposure time per frame)
- Rayonix MX-225 X-ray detector, 45mm-380mm distance from the
 sample, 30 deg 2-Theta possible
- MARdtb goniometer
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- EDNA installed and available
- Common MX software installed including XDS, iMOSFLM, CCP4, Phenix,
 SHELXC-D-E, etc.
- Automated data processing using XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- HC1c dehydration device installed (please specify HC1-beamtime
 in your proposal if needed)
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpixel CCD-camera

S1-biolab facilities (separate registration required):
- Protein production and purification
- Nanoliter 96 well crystallization plate formulation and storage at
 5 °C and 20 °C
- Biophysical characterization with real time PCR (thermofluor assay)

The HZB-MX group is also providing expert assistance as well as
access to a library of fragments for carrying out crystallographic
fragment-screening experiments. For more information please contact
mswe...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> to 
obtain
updated information about our experimental setup and other
requirements.

Manfred Weiss and the HZB-MX team

--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany

_

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2018

[Manfred S. Weiss]

Next MX-proposal application deadline: March 01, 2018 is approaching
http://www.helmholtz-berlin.de/user/beamtime/proposals/index_en.html

Hereby we would like to invite the submission of new proposals for
MX-beamtime at the HZB-MX beamlines for the next beam time period
(08/2018-01/2019).

In order to apply for beamtime, please register at the HZB on-line
access tool "GATE" (https://www.helmholtz-berlin.de/pubbin/hzbgate)
and submit a new beam time application proposal.

HZB provides MX-beamtime at the three MX-beamlines BL14.1, BL14.2
and BL14.3. The three beamlines are equipped with state-of-the-art
instrumentation and are currently the most productive MX-stations
in Germany with over 300 PDB depositions annually. Beamtime is
granted based on the reviewed proposals and on reports from
previous research activities. Please make sure to include them
if available.

What's new: Due to a planned upgrade of the experimental endstation
   BL14.3 will not be fully available. Details can be 
provided
   upon request.

Experimental setup:

BL14.1:
- Photon flux: 1.4x10¹¹ Phot/sx100mAx0.05%BW at sample position
 (0.1-1 sec exposure time per frame)
- User defined beam shaping from 50µm-100µm diameter possible
- Pilatus 6M detector, 141mm-680mm max. distance from the sample
- Microdiffractometer (MD2) with Mini-kappa goniometer MK3
- Automatic sample changer (CATS), 90 sample storage capacity
(SPINE-Pin & EMBL sample magazine compatibility)
- 32-core XEON-CPU server, with 10Gb uplink to Pilatus 6M
- Data collection control via MXCuBE
- EDNA
- Common MX-software installed including XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-D-E, etc.
- Automated data processing with XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- Pressure chamber for noble gas derivatization (Xe, Kr
 available upon request)
- AMPTEK-XRF detector and XFEPLOT software available

We are also offering the hard- and software environment for
carrying out:
- UV-RIP experiments at BL14.1. For further information, please visit:

https://www.helmholtz-berlin.de/forschung/oe/np/gmx/ancillary-facilities/uvrip_en.html

BL14.2:
- Photon flux: 1.9x10¹¹ Phot/sx100mAx0.05%BW at sample position
 (0.1-1 sec exposure time per frame)
- Pilatus 3S-2M detector with 1000 micron Si sensor thickness,
 55mm-600mm distance from the sample
- Nanodiffractometer (DESY P11 design) and on-axis sample microscope
- User defined beam shaping from 30µm-150µm diameter possible
- GROB sample changer for SPINE and UNIPUCK support
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Common MX-software installed including XDS, iMOSFLM, CCP4, Phenix,
 SHELXC-D-E, etc.
- Automated data processing with XDSAPP
- Amptek XRF detector
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpixel CCD-camera
- UV-Microsprectrophotometer offline setup available
- AMPTEK-XRF detector and XFEPLOT software available

BL14.3:
- Photon flux: 4x10exp10 Phot/sx100mAx0.05%BW at sample position
 (3-20 sec exposure time per frame)
- Rayonix MX-225 X-ray detector, 45mm-380mm distance from the
 sample, 30 deg 2-Theta possible
- MARdtb goniometer
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- EDNA installed and available
- Common MX software installed including XDS, iMOSFLM, CCP4, Phenix,
 SHELXC-D-E, etc.
- Automated data processing using XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- HC1c dehydration device installed (please specify HC1-beamtime
 in your proposal if needed)
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpixel CCD-camera

S1-biolab facilities (separate registration required):
- Protein production and purification
- Nanoliter 96 well crystallization plate formulation and storage at
 5 °C and 20 °C
- Biophysical characterization with real time PCR (thermofluor assay)

The HZB-MX group is also providing expert assistance as well as
access to a library of fragments for carrying out crystallographic
fragment-screening experiments. For more information please contact
mswe...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> to 
obtain
updated information about our experimental setup and other
requirements.

Manfred Weiss and the HZB-MX team

--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende 

[ccp4bb] Job opportunity in Berlin - HZB and MDC advertise a postdoc position

[Manfred S. Weiss]

The Helmholtz Zentrum Berlin für Materialien und Energie, the 
Max-Delbrück-Center for Molecular Medicine, the Freie Universität Berlin and 
the Humboldt Universität zu Berlin jointly operate three experimental stations 
for bio-macromolecular crystallography at BESSY II, one of the world’s most 
modern synchrotron radiation sources for VUV and soft X-rays.
(http://www.helmholtz-berlin.de/forschung/oe/em/soft-matter/forschung/bessy-mx/index_en.html)

The Max-Delbrück-Center is seeking a

Post Doctoral Research Assistant

to support a structure-based drug discovery project on various GTPase families 
(headed by Dr. Oliver Daumke). The successful candidate will also be involved 
in the operation of the BESSY II bio-macromolecular crystallography beamlines 
(headed by Dr. Manfred S. Weiss) and will take part in graduate student 
education.

Initially, a three-year contract will be offered to the successful candidate 
with the possibility for an extension. The salary will be based on German 
Federal TVöD. The position is available from March, 2018.

Applicants should hold a Ph.D. in the biological, chemical or physical sciences 
and have a background in bio-macromolecular crystallography, biochemistry or 
computational chemistry. The position also requires the documented ability to 
conduct independent research as well as excellent communication and 
interpersonal skills.

The MDC is an equal opportunity employer and supports gender equality.

Please send applications (CV, list of publications, .pdf-file format) in 
electronic form until 30.11.2017 to:


Dr. Manfred Weiss 
(mswe...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>)

and

Dr. Oliver Daumke 
(oliver.dau...@mdc-berlin.de<mailto:oliver.dau...@mdc-berlin.de>)


--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. 
Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (kommissarisch), Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de

[ccp4bb] Reminder: Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2017

[Manfred S. Weiss]

Next MX-proposal application deadline: September 01, 2017 is approaching
http://www.helmholtz-berlin.de/user/beamtime/proposals/index_en.html

Hereby we would like to invite the submission of new proposals for
MX-beamtime at the HZB-MX beamlines for the next beam time period
(02/2018-08/2018).

In order to apply for beamtime, please register at the HZB on-line
access tool "GATE" (https://www.helmholtz-berlin.de/pubbin/hzbgate)
and submit a new beam time application proposal.

What's new: Helical data collection will be possible on BL14.1 !!!

HZB provides MX-beamtime at the three MX-beamlines BL14.1, BL14.2
and BL14.3. The three beamlines are equipped with state-of-the-art
instrumentation and are currently the most productive MX-stations
in Germany with over 500 PDB depositions in 2016 alone. Beamtime
is granted based on the reviewed proposals and on reports from
previous research activities. Please make sure to include them if
available.

Experimental setup:

BL14.1:
- Photon flux: 1.4x10¹¹ Phot/sx100mAx0.05%BW at sample position
 (0.1-1 sec exposure time per frame)
- User defined beam shaping from 50µm-100µm diameter possible
- Pilatus 6M detector, 141mm-680mm max. distance from the sample
- Microdiffractometer (MD2) with Mini-kappa goniometer MK3
- Automatic sample changer (CATS), 90 sample storage capacity
 (SPINE-Pin & EMBL sample magazine compatibility)
- 32-core XEON-CPU server, with 10Gb uplink to Pilatus 6M
- Data collection control via MXCuBE
- EDNA
- Common MX-software installed including XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-E, etc.
- Automated data processing with XDSAPP2.0
- Remotely controlled cryo-shutter for crystal annealing
- Pressure chamber for noble gas derivatization (Xe, Kr
 available upon request)
- AMPTEK-XRF detector and XFEPLOT software available

We are also offering the hard- and software environment for
carrying out:
- UV-RIP experiments at BL14.1. For further information, please visit:

http://www.helmholtz-berlin.de/forschung/funkma/soft-matter/forschung/bessy-mx/ancillary-facilities/uvrip_en.html

BL14.2:
- Photon flux: 1.9x10¹¹ Phot/sx100mAx0.05%BW at sample position
 (0.1-1 sec exposure time per frame)
- Pilatus 3S-2M detector with 1000 micron Si sensor thickness,
 55mm-600mm distance from the sample
- Nanodiffractometer (DESY P11 design) and on-axis sample microscope
- User defined beam shaping from 30µm-150µm diameter possible
- GROB sample changer for SPINE and UNIPUCK support
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Common MX-software installed including XDS, iMOSFLM, CCP4, Phenix,
 SHELXC-E, etc.
- Automated data processing with XDSAPP2.0
- Amptek XRF detector
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpixel CCD-camera
- UV-Microsprectrophotometer offline setup available
- AMPTEK-XRF detector and XFEPLOT software available

BL14.3:
- Photon flux: 4x10exp10 Phot/sx100mAx0.05%BW at sample position
 (3-20 sec exposure time per frame)
- Rayonix MX-225 X-ray detector, 45mm-380mm distance from the
 sample, 30 deg 2-Theta possible
- MARdtb goniometer
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- EDNA installed and available
- Common MX software installed including XDS, iMOSFLM, CCP4, Phenix,
 SHELXC-E, etc.
- Automated data processing using XDSAPP2.0
- Remotely controlled cryo-shutter for crystal annealing
- HC1c dehydration device installed (please specify HC1-beamtime
 in your proposal if needed)
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpixel CCD-camera

S1-biolab facilities (separate registration required):
- Protein production and purification
- Nanoliter 96 well crystallization plate formulation and storage at
 5 °C and 20 °C
- Biophysical characterization with real time PCR (thermofluor assay)

The HZB-MX group is also providing expert assistance as well as
access to a library of fragments for carrying out crystallographic
fragment-screening experiments. For more information please read:
http://www.helmholtz-berlin.de/forschung/oe/em/soft-matter/forschung/bessy-mx/fragment-screening/index_en.html
or contact us at 
mswe...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> to 
obtain
updated information about our experimental setup and other
requirements.

Manfred Weiss and the HZB-MX group

--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. 

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline September 01, 2017

[Manfred S. Weiss]

Next MX-proposal application deadline: September 01, 2017 is approaching
http://www.helmholtz-berlin.de/user/beamtime/proposals/index_en.html

Hereby we would like to invite the submission of new proposals for
MX-beamtime at the HZB-MX beamlines for the next beam time period
(02/2018-08/2018).

In order to apply for beamtime, please register at the HZB on-line
access tool "GATE" (https://www.helmholtz-berlin.de/pubbin/hzbgate)
and submit a new beam time application proposal.

What's new: Helical data collection will be possible on BL14.1 !!!

HZB provides MX-beamtime at the three MX-beamlines BL14.1, BL14.2
and BL14.3. The three beamlines are equipped with state-of-the-art
instrumentation and are currently the most productive MX-stations
in Germany with over 500 PDB depositions in 2016 alone. Beamtime
is granted based on the reviewed proposals and on reports from
previous research activities. Please make sure to include them if
available.

Experimental setup:

BL14.1:
- Photon flux: 1.4x10¹¹ Phot/sx100mAx0.05%BW at sample position
 (0.1-1 sec exposure time per frame)
- User defined beam shaping from 50µm-100µm diameter possible
- Pilatus 6M detector, 141mm-680mm max. distance from the sample
- Microdiffractometer (MD2) with Mini-kappa goniometer MK3
- Automatic sample changer (CATS), 90 sample storage capacity
 (SPINE-Pin & EMBL sample magazine compatibility)
- 32-core XEON-CPU server, with 10Gb uplink to Pilatus 6M
- Data collection control via MXCuBE
- EDNA
- Common MX-software installed including XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-E, etc.
- Automated data processing with XDSAPP2.0
- Remotely controlled cryo-shutter for crystal annealing
- Pressure chamber for noble gas derivatization (Xe, Kr
 available upon request)
- AMPTEK-XRF detector and XFEPLOT software available

We are also offering the hard- and software environment for
carrying out:
- UV-RIP experiments at BL14.1. For further information, please visit:

http://www.helmholtz-berlin.de/forschung/funkma/soft-matter/forschung/bessy-mx/ancillary-facilities/uvrip_en.html

BL14.2:
- Photon flux: 1.9x10¹¹ Phot/sx100mAx0.05%BW at sample position
 (0.1-1 sec exposure time per frame)
- Pilatus 3S-2M detector with 1000 micron Si sensor thickness,
 55mm-600mm distance from the sample
- Nanodiffractometer (DESY P11 design) and on-axis sample microscope
- User defined beam shaping from 30µm-150µm diameter possible
- GROB sample changer for SPINE and UNIPUCK support
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Common MX-software installed including XDS, iMOSFLM, CCP4, Phenix,
 SHELXC-E, etc.
- Automated data processing with XDSAPP2.0
- Amptek XRF detector
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpixel CCD-camera
- UV-Microsprectrophotometer offline setup available
- AMPTEK-XRF detector and XFEPLOT software available

BL14.3:
- Photon flux: 4x10exp10 Phot/sx100mAx0.05%BW at sample position
 (3-20 sec exposure time per frame)
- Rayonix MX-225 X-ray detector, 45mm-380mm distance from the
 sample, 30 deg 2-Theta possible
- MARdtb goniometer
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- EDNA installed and available
- Common MX software installed including XDS, iMOSFLM, CCP4, Phenix,
 SHELXC-E, etc.
- Automated data processing using XDSAPP2.0
- Remotely controlled cryo-shutter for crystal annealing
- HC1c dehydration device installed (please specify HC1-beamtime
 in your proposal if needed)
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpixel CCD-camera

S1-biolab facilities (separate registration required):
- Protein production and purification
- Nanoliter 96 well crystallization plate formulation and storage at
 5 °C and 20 °C
- Biophysical characterization with real time PCR (thermofluor assay)

The HZB-MX group is also providing expert assistance as well as
access to a library of fragments for carrying out crystallographic
fragment-screening experiments. For more information please read:
http://www.helmholtz-berlin.de/forschung/oe/em/soft-matter/forschung/bessy-mx/fragment-screening/index_en.html
or contact us at 
mswe...@helmholtz-berlin.de<mailto:mswe...@helmholtz-berlin.de>.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx<http://www.helmholtz-berlin.de/bessy-mx> to 
obtain
updated information about our experimental setup and other
requirements.

Manfred Weiss and the HZB-MX group

--
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. 

[ccp4bb] Reminder: Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2017

[Manfred S. Weiss]

Please mark your calendar:

The next MX-proposal application deadline: March 01, 2017 is approaching
http://www.helmholtz-berlin.de/user/beamtime/proposals/index_en.html

Hereby we would like to invite the submission of new proposals for
MX-beamtime at the HZB-MX beamlines for the next beam time period
(08/2017-01/2018).

In order to apply for beamtime, please register at the HZB on-line
access tool "GATE" (https://www.helmholtz-berlin.de/pubbin/hzbgate)
and submit a new beam time application proposal.

What's new: Goniometer upgrade of BL14.1

HZB provides MX-beamtime at the three MX-beamlines BL14.1, BL14.2
and BL14.3. The three beamlines are equipped with state-of-the-art
instrumentation and are currently the most productive MX-stations in
Germany with over 300 PDB depositions annually. Beamtime is granted
based on the reviewed proposals and on reports from previous research
activities. Please make sure to include them if available.

Experimental setup:

BL14.1:
- Photon flux: 1.4x10¹¹ Phot/sx100mAx0.05%BW at sample position
 (0.1-1 sec exposure time per frame)
- User defined beam shaping from 50µm-100µm diameter possible
- PILATUS 6M detector, 141mm-680mm max. distance from the sample
- Microdiffractometer (MD2) with Mini-kappa goniometer MK3
- Automatic sample changer (CATS), 90 sample storage capacity
  (SPINE-Pin & EMBL sample magazine compatibility)
- 32-core XEON-CPU server, with 10Gb uplink to Pilatus 6M
- Data collection control via MXCuBE
- EDNA
- Common MX-software installed including XDS, iMOSFLM, CCP4,
 Phenix, SHELXC-E, etc.
- Automated data processing with XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- Pressure chamber for noble gas derivatization (Xe, Kr
 available upon request)
- AMPTEK-XRF detector and XFEPLOT software available

We are also offering the hard- and software environment for
carrying out:
- UV-RIP experiments at BL14.1. For further information, please visit:

http://www.helmholtz-berlin.de/forschung/funkma/soft-matter/forschung/bessy-mx/ancillary-facilities/uvrip_en.html

BL14.2:
- Photon flux: 1.9x10¹¹ Phot/sx100mAx0.05%BW at sample position
 (0.1-1 sec exposure time per frame)
- PILATUS 3S-2M detector with 1000 micron Si sensor thickness,
 55mm-600mm distance from the sample
- Nanodiffractometer (DESY P11 design) and on-axis sample microscope
- User defined beam shaping from 30µm-150µm diameter possible
- GROB sample changer for SPINE and UNIPUCK support
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- Common MX-software installed including XDS, iMOSFLM, CCP4, Phenix,
 SHELXC-E, etc.
- Automated data processing with XDSAPP
- Amptek XRF detector
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpixel CCD-camera
- UV-Microsprectrophotometer offline setup available
- AMPTEK-XRF detector and XFEPLOT software available

BL14.3:
- Photon flux: 4x10exp10 Phot/sx100mAx0.05%BW at sample position
 (3-20 sec exposure time per frame)
- Rayonix MX-225 X-ray detector, 45mm-380mm distance from the
 sample, 30 deg 2-Theta possible
- MARdtb goniometer
- 60-core XEON-CPU server, with fibre channel SAN up-link data
 processing environment
- EDNA installed and available
- Common MX software installed including XDS, iMOSFLM, CCP4, Phenix,
 SHELXC-E, etc.
- Automated data processing using XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- HC1c dehydration device installed (please specify HC1-beamtime
 in your proposal if needed)
- Pressure chamber for noble gas derivatization (Xe, Kr available
 upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
 8 Mpixel CCD-camera

S1-biolab facilities (separate registration required):
- Protein production and purification
- Nanoliter 96 well crystallization plate formulation and storage at
 5 °C and 20 °C
- Biophysical characterization with real time PCR (thermofluor assay)

The HZB-MX group is also providing expert assistance as well as
access to a library of fragments for carrying out crystallographic
fragment-screening experiments. For more information please visit
http://www.helmholtz-berlin.de/forschung/oe/em/soft-matter/forschung/bessy-mx/fragment-screening/index_en.html
or contact us at 
mswe...@helmholtz-berlin.de.

Please visit our web page 
www.helmholtz-berlin.de/bessy-mx to 
obtain
updated information about our experimental setup and other
requirements.

Manfred Weiss and the HZB-MX group




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. 
Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG 

[ccp4bb] Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, 2017

[Manfred S. Weiss]

Next MX-proposal application deadline: March 01, 2017 is approaching
http://www.helmholtz-berlin.de/user/beamtime/proposals/index_en.html

Hereby we would like to invite the submission of new proposals for
MX-beamtime at the HZB-MX beamlines for the next beam time period
(08/2017-01/2018).

In order to apply for beamtime, please register at the HZB on-line
access tool "GATE" (https://www.helmholtz-berlin.de/pubbin/hzbgate)
and submit a new beam time application proposal.

What's new: In situ-screening in crystallization plates on BL14.1
will be reinstalled from March 2017 onwards!

HZB provides MX-beamtime at the three MX-beamlines BL14.1, BL14.2
and BL14.3. The three beamlines are equipped with state-of-the-art
instrumentation and are currently the most productive MX-stations
in Germany with over 300 PDB depositions annually. Beamtime is
granted based on the reviewed proposals and on reports from
previous research activities. Please make sure to include them
if available.

Experimental setup:

BL14.1:
- Photon flux: 1.4x10¹¹ Phot/sx100mAx0.05%BW at sample position
  (0.1-1 sec exposure time per frame)
- User defined beam shaping from 50µm-100µm diameter possible
- Pilatus 6M detector, 141mm-680mm max. distance from the sample
- Microdiffractometer (MD2) with Mini-kappa goniometer MK3
- Automatic sample changer (CATS), 90 sample storage capacity
 (SPINE-Pin & EMBL sample magazine compatibility)
- 32-core XEON-CPU server, with 10Gb uplink to Pilatus 6M
- Data collection control via MXCuBE
- EDNA
- Common MX-software installed including XDS, iMOSFLM, CCP4,
  Phenix, SHELXC-E, etc.
- Automated data processing with XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- Pressure chamber for noble gas derivatization (Xe, Kr
  available upon request)
- AMPTEK-XRF detector and XFEPLOT software available

We are also offering the hard- and software environment for
carrying out:
- UV-RIP experiments at BL14.1. For further information, please visit:

http://www.helmholtz-berlin.de/forschung/funkma/soft-matter/forschung/bessy-mx/ancillary-facilities/uvrip_en.html

BL14.2:
- Photon flux: 1.9x10¹¹ Phot/sx100mAx0.05%BW at sample position
  (0.1-1 sec exposure time per frame)
- Pilatus 3S-2M detector with 1000 micron Si sensor thickness,
  55mm-600mm distance from the sample
- Nanodiffractometer (DESY P11 design) and on-axis sample microscope
- User defined beam shaping from 30µm-150µm diameter possible
- GROB sample changer for SPINE and UNIPUCK support
- 60-core XEON-CPU server, with fibre channel SAN up-link data
  processing environment
- Common MX-software installed including XDS, iMOSFLM, CCP4, Phenix,
  SHELXC-E, etc.
- Automated data processing with XDSAPP
- Amptek XRF detector
- Pressure chamber for noble gas derivatization (Xe, Kr available
  upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
  8 Mpixel CCD-camera
- UV-Microsprectrophotometer offline setup available
- AMPTEK-XRF detector and XFEPLOT software available

BL14.3:
- Photon flux: 4x10exp10 Phot/sx100mAx0.05%BW at sample position
  (3-20 sec exposure time per frame)
- Rayonix MX-225 X-ray detector, 45mm-380mm distance from the
  sample, 30 deg 2-Theta possible
- MARdtb goniometer
- 60-core XEON-CPU server, with fibre channel SAN up-link data
  processing environment
- EDNA installed and available
- Common MX software installed including XDS, iMOSFLM, CCP4, Phenix,
  SHELXC-E, etc.
- Automated data processing using XDSAPP
- Remotely controlled cryo-shutter for crystal annealing
- HC1c dehydration device installed (please specify HC1-beamtime
  in your proposal if needed)
- Pressure chamber for noble gas derivatization (Xe, Kr available
  upon request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom,
  8 Mpixel CCD-camera

S1-biolab facilities (separate registration required):
- Protein production and purification
- Nanoliter 96 well crystallization plate formulation and storage at
  5 °C and 20 °C
- Biophysical characterization with real time PCR (thermofluor assay)

The HZB-MX group is also providing expert assistance as well as
access to a library of fragments for carrying out crystallographic
fragment-screening experiments. For more information please contact
us at mswe...@helmholtz-berlin.de.

Please visit our web page www.helmholtz-berlin.de/bessy-mx to obtain
updated information about our experimental setup and other
requirements.

Manfred Weiss and the HZB-MX group

--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitz

[ccp4bb] Workshop "Challenges in Data Processing" Announcement

[Manfred S. Weiss]

Dear all,

we would hereby like to announce that on Dec 09, 2016
attached to the  2016 HZB Users Meeting, there will be
a workshop on "Challenges in data processing". This
workshop should be interesting for anybody who has to
process some diffraction data sets now and then, with
an obvious focus on macromolecular diffraction data.

Please have a closer look at the program:

http://www.helmholtz-berlin.de/events/data-processing/index_en.html

Registration for the workshop is free of charge but
the number of participants is limited. So please make
up your minds early and register. First come, first
serve.

Cheers,

Karine + Manfred


--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. 
Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de

Re: [ccp4bb] Another puzzle: 5gnn: SOLVED

[Manfred S. Weiss]

ostly random coil, with only very few and very short
segments of secondary structure.

   In reciprocal space, an oddness of a different kind is that if
one looks at the mtz file, the amplitudes and their sigmas are on a
very small scale. However the STARANISO display shows a smooth and
plausible distribution of I/sig(I) to the full nominal resolution
limit of 1.6A.

   Looking at the publication associated with this entry

   http://www.ncbi.nlm.nih.gov/pubmed/27492925

indicates that the structure was solved by MR from a model obtained
from a structure prediction server (I-TASSER). No further details are
given, even in the Supplemental Material. Table 1 does report a
MolProbity clash score of 103.59, as well as 10% Ramachandran outliers
and 25.51% rotamer outliers. It also contains a mention of a twinning
operator -h, -k, l with a twinning fraction of 0.5, although there is
no mention of it in the text nor in the PDB file.

   I will follow my own advice and resist the temptation of calling
this "the end of civilisation as we know it", but this is startling.
Perhaps we have over-advertised to the non-experts the few successes
of structure prediction programs as reliable sources of MR models and
thus created unwarranted optimism, besides the usual exaggeration of
the degree to which X-ray crystallography has become a push-button
commodity that can deliver results to untrained users. What is also
disconcerting is that the abundant alarm bells that rang along the way
(the MolProbity clash score and geometry reports, the contents of the
PDB validation report, and simple common sense when examining electron
density and model) failed to make anyone involved along the way take
notice that there was something seriously wrong.

   This case seems to bring to the forefront even more vividly than
4nl6 and 4nl7 some collective issues that we face. Here the problem is
not one of contamination of a protein prep resulting in crystals of
"the wrong protein": there is also a more diffuse contamination by
deficiencies of judgement, expertise and vigilance at several
consecutive stages, including refereeing and publication.

   Validation is a hot topic at the moment, and this may serve as a
concrete example that some joined-up thinking and action is indeed a
matter of urgency, and that extreme scenarios of things going wrong do
not exist solely in the imaginations of obsessive-compulsive/paranoid
validators.

   I am grateful to several colleagues for correspondance and
discussions on the matters touched upon on this message.


   With best wishes,

Gerard

--

   ===
   * *
   * Gerard Bricogne g...@globalphasing.com  *
   * *
   * Global Phasing Ltd. *
   * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
   * Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
   * *
   ===


--
Paul Adams
Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence 
Berkeley Lab
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Laboratory Research Manager, ENIGMA Science Focus Area

Building 33, Room 347
Building 80, Room 247
Building 978, Room 4126
Tel: 1-510-486-4225, Fax: 1-510-486-5909
http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 33R0345
Berkeley, CA 94720, USA.

Executive Assistant: Louise Benvenue [ lbenve...@lbl.gov ][ 1-510-495-2506 ]
--


--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. 
Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de

[ccp4bb] ECM-29 - Abstract Deadline is Fast Approaching

[Manfred S. Weiss]

Dear all,

at the ECM-29 in Rovinj, Croatia, there will be a microsymposium with the title
Structure solution on the fly - parallel data collection and structure 
analysis

The description of the MS reads like this:
Recent developments at synchrotron beamlines are enabling users to collect 
very large
numbers of diffraction data sets within a short time. This results in a 
downstream bottleneck
and necessitates the development of software solutions for automated data 
processing and
automated structure solution on the fly. In this microsymposium recent software 
developments
allowing data processing and evaluation, as well as structure determination in 
parallel to data
acquisition will be presented and discussed.

If you would like to consider submitting a contribution to this MS, either oral 
or as a
poster, please do so by Monday, March 23, which is the abstract deadline.

Best wishes

Manfred Weiss + Victor Lamzin
MS Chairs


--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.demailto:mswe...@helmholtz-berlin.de




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. 
Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de

[ccp4bb] 2014 HZB User Meeting and fragment screening workshop

[Manfred S. Weiss]

This year's HZB/BESSY user meeting will take place from Dec 03-05, 2014
in Berlin. The meeting will be accompanied by a one-day workshop titled
Fragment Screening by Crystallography. Registration is free for both
events, but workshop participation is limited to about 100.

More information can be found under:

Users Meeting:
http://www.helmholtz-berlin.de/user/usermeetings/user-meeting-2014/index_en.html

Fragment screening-workshop:
http://www.helmholtz-berlin.de/events/fragment-screening/index_de.html

With best wishes

Manfred  Uwe

--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. 
Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de

[ccp4bb] Postdoc position available

[Manfred S. Weiss]

The Helmholtz Zentrum Berlin für Materialien und Energie, the 
Max-Delbrück-Center for Molecular Medicine Berlin, the Freie Universität 
Berlin, the Humboldt Universität zu Berlin and the Leibniz-Institute for 
Molecular Pharmacology jointly operate three experimental stations for 
bio-macromolecular crystallography within the Joint Berlin MX-Laboratory 
cooperation at BESSY II, one of the world's most modern synchrotron radiation 
sources for VUV and soft X-rays.

The Macromolecular Structure and Interaction Group of the Max-Delbrück-Center 
is seeking a

Post Doctoral Research Assistant

to conduct research on various structural biology / biochemistry projects of the 
MDC Macromolecular Structure and Interaction Group (headed by Prof. Dr. Udo 
Heinemann, 
https://www.mdc-berlin.de/1154162/de/research/research_teams/macromolecular_structure_and_interaction).
 According to research interests and qualifica­tions, the candidate may also 
participate in instrumental and/or computa­tion­al projects of the HZB-MX group. 
The successful candidate will also be involved in the operation of the BESSY II 
bio-macromolecular crystal­lo­graphy beamlines (headed by Dr. Uwe Müller  Dr. 
Manfred S. Weiss, http://www.helmholtz-berlin.de/bessy-mx) and will take part in 
graduate student education.

Initially, a two-year contract will be offered to the successful candidate with 
the possibility for an extension. The salary will be based on German federal 
TvÖD. The position is available immediately, and applications will be 
considered until the position is filled. The MDC is an equal-opportunity 
employer committed to excellence through diversity. Applications of women are 
explicitly encouraged.

Applicants should hold a Ph.D. in the biological, chemical or physical sciences 
and have a background in bio-macromolecular crystallography, biochemistry or 
computational sciences. The position also requires the documented ability to 
conduct independent research as well as excellent communication and 
interpersonal skills.

Please send applications (CV, list of publications, in one combined .pdf-file) 
in electronic form, with the Code MDC-MX-2014/1 to:
Dr. Uwe Müller (u...@helmholtz-berlin.demailto:u...@helmholtz-berlin.de)


--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.demailto:mswe...@helmholtz-berlin.de




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. 
Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de

Re: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)

[Manfred S. Weiss]

That's not quite correct. If N goes to infinity, i.e. at high or very high
data multiplicity Rmerge approaches Rmeas (Rrim).

At this point it does not matter whether you write Rmerge or Rmeas
equals 0.8 * sd(I) / I

For low multiplicity

Rrim (or Rmeas) = 0.8*sd(i)/I

is the correct expression.

Cheers, Manfred

On 16.04.2014 22:16, Bernhard Rupp wrote:

The 2006 Weiss expression - I guess from the context-  is for a single 
reflection h measured N times (and then is identical to my 8-23) while (8-24) 
is valid for the Rmerge (defined in 8-15) of averaging over a shell with h 
reflections each measured N times , which also explains why the two related 
expressions in aimless necessarily have to be different.

Somehow crystallographers historically invented their own linear merging 
statistics instead of 'standard' descriptive statistics like the standard error 
of the mean...still an unresolved mess see the papers/threads on cc1/2, cc* 
etc...

Best, BR

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roberto 
Battistutta
Sent: Wednesday, April 16, 2014 5:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)

Hi,
in the Rupp book the following relation is reported (on pag 415):
Rmerge   0.8/I/s(I)
referring to a relation of the linear merging R-value with the signal-to-noise 
ratio.

in a 2006 CCP4bb, Manfred Weiss reported:
Rrim (or Rmeas) = 0.8*sd(i)/I

so,

First question: is it Rmerge or Rmeas (Rrim) that we are dealing with?

Second question: at the denominator (of the Rupp way to write), it is the 
aimless Mn(I/sd) (usually indicated as the real signal-to-noise ratio) or the 
aimless I/sigma (very different from Mn(I/sd) with high redundancy)?

Thank you very much for the clarification.

Best,
Roberto.

Roberto Battistutta
Associate Professor
Department of Chemistry
University of Padua
via Marzolo 1, 35131 Padova - ITALY
tel. +39.049.827.5262
fax. +39.049.827.5829
roberto.battistu...@unipd.it
www.chimica.unipd.it/roberto.battistutta/
VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - 
ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it


--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   
https://urldefense.proofpoint.com/v1/url?u=http://www.helmholtz-berlin.de/bessy-mxk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=Bmb9nN0eEAg0yI3N0xkQkdpD%2BJyOWQhem2L9N7BX%2FS0%3D%0Am=ioF%2FNBln5i1F4HBuWvTEg%2FjRX8MQaGIyGtlimw4%2BUFg%3D%0As=b513370ad6484d4580d21215cd51c8bb1ac2ad1e55740901cdf35e0d4931d54a
Email: mswe...@helmholtz-berlin.de




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. 
Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

https://urldefense.proofpoint.com/v1/url?u=http://www.helmholtz-berlin.de/k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=Bmb9nN0eEAg0yI3N0xkQkdpD%2BJyOWQhem2L9N7BX%2FS0%3D%0Am=ioF%2FNBln5i1F4HBuWvTEg%2FjRX8MQaGIyGtlimw4%2BUFg%3D%0As=f425d33eab53ef7b63ca749f304cfbf564c480fc2f375df073d9130c31781bd7

Re: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)

[Manfred S. Weiss]

That's not quite correct. If N goes to infinity, i.e. at high or very high
data multiplicity Rmerge approaches Rmeas (Rrim).

At this point it does not matter whether you write Rmerge or Rmeas
equals 0.8 * sd(I) / I

For low multiplicity

Rrim (or Rmeas) = 0.8*sd(i)/I

is the correct expression.

Cheers, Manfred

On 16.04.2014 22:16, Bernhard Rupp wrote:

The 2006 Weiss expression - I guess from the context-  is for a single 
reflection h measured N times (and then is identical to my 8-23) while (8-24) 
is valid for the Rmerge (defined in 8-15) of averaging over a shell with h 
reflections each measured N times , which also explains why the two related 
expressions in aimless necessarily have to be different.

Somehow crystallographers historically invented their own linear merging 
statistics instead of 'standard' descriptive statistics like the standard error 
of the mean...still an unresolved mess see the papers/threads on cc1/2, cc* 
etc...

Best, BR

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roberto 
Battistutta
Sent: Wednesday, April 16, 2014 5:09 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Rmerge, Rmeas, I/sigma, Mn(I/sd)

Hi,
in the Rupp book the following relation is reported (on pag 415):
Rmerge   0.8/I/s(I)
referring to a relation of the linear merging R-value with the signal-to-noise 
ratio.

in a 2006 CCP4bb, Manfred Weiss reported:
Rrim (or Rmeas) = 0.8*sd(i)/I

so,

First question: is it Rmerge or Rmeas (Rrim) that we are dealing with?

Second question: at the denominator (of the Rupp way to write), it is the 
aimless Mn(I/sd) (usually indicated as the real signal-to-noise ratio) or the 
aimless I/sigma (very different from Mn(I/sd) with high redundancy)?

Thank you very much for the clarification.

Best,
Roberto.

Roberto Battistutta
Associate Professor
Department of Chemistry
University of Padua
via Marzolo 1, 35131 Padova - ITALY
tel. +39.049.827.5262
fax. +39.049.827.5829
roberto.battistu...@unipd.it
www.chimica.unipd.it/roberto.battistutta/
VIMM (Venetian Institute of Molecular Medicine) via Orus 2, 35129 Padova - 
ITALY tel. +39.049.7923.236 fax +39.049.7923.250 www.vimm.it


--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. 
Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de

Re: [ccp4bb] Validity of Ion Sites in PDB

[Manfred S. Weiss]

There is another paper out there, which describes the use of long
wavelengths
to define anomalously scattering substructures. This method certainly
helps to
distinguish water molecules from something else, such as chloride for
instance.

http://journals.iucr.org/d/issues/2007/03/00/dz5094/index.html

Cheers, Manfred

On 07.03.2014 11:12, Murray, James W wrote:

Dear all,

It is well known that  you can look at anomalous difference maps to see heavier 
atoms - although I think not enough people do it. One technique that I think is 
powerful, but under-used is to calculate element-specific maps by taking the 
difference of anomalous difference data from just above and below the 
absorption edge. This paper introduces the technique and explains it well 
http://journals.iucr.org/d/issues/2005/05/00/he5321/index.html. I suspect if 
this method were more used, many mis-labeled metals in proteins would come to 
light.

James

--
Dr. James W. Murray
Lecturer in Biotechnology
Dept. Life Sciences
Imperial College, London
Tel: +44 (0)20 759 48895

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene 
[t...@shelx.uni-ac.gwdg.de]
Sent: Friday, March 07, 2014 9:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Validity of Ion Sites in PDB

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Jacob,

the 'check-my-metal' server at http://csgid.org/csgid/metal_sites/
lists a couple of references which might be of interest.

As usual in crytallography one must understand the science in order to
understand the reliability of the models from the PDB. They are not
the truth but only models to explain the data from a diffraction
experiment.

Best,
Tim



On 03/06/2014 08:45 PM, Keller, Jacob wrote:

Dear Crystallographers,

I was curious whether there has been a rigorous evaluation of ion
binding sites in the structures in the pdb, by PDB-REDO or
otherwise. I imagine that there is a considerably broad spectrum of
habits and rigor in assigning solute blobs to ion X or water, and
in fact it would be difficult in many cases to determine which ion
a given blob really is, but there should be at least some fraction
of ions/waters which can be shown from the x-ray data and known
geometry to be X and not Y. This could be by small anomalous
signals (Cl and H2O for example), geometric considerations, or
something else. Maybe this does not even matter in most cases, but
it might be important in others...

All the best,

Jacob Keller


*** Jacob Pearson Keller,
PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr,
Ashburn, VA 20147 email: kell...@janelia.hhmi.org
***


- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Icedove - http://www.enigmail.net/

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Yj2NVdKiYBq9O28v9eCQWDA=
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--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. 
Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de

[ccp4bb] Soft X-rays in MX session at the IUCr conference 2014

[Manfred S. Weiss]

Dear all,

at the 23rd IUCr congress (http://www.iucr2014.org/), which will take
place in August this year in lovely Montreal, John Rose and I are
organizing the microsymposium MS-40 titled S-SAD and other
applications of soft X-rays in MX.

If you happen to have an exciting story, which you would like to bring
to a wide audience, John and I would like to encourage you to submit
an abstract to our session. Some of them will be selected for an oral
presentation, the remaining ones will become part of our exciting
poster session.

We are looking forward to receiving your contributions. If you have
any  questions regarding whether your stuff will fit into the topics
covered by the MS, please don't hesitate to contact either John or
myself.

Hope to see you all in Montreal.

Best wishes

Manfred Weiss

--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. 
Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de

[ccp4bb] 2013 HZB User Meeting and HC1 workshop

[Manfred S. Weiss]

This year's HZB/BESSY user meeting will take place from Dec 04-06, 2013
in Berlin. The meeting will be accompanied by a one-day workshop titled
Crystal dehydration as a new method in MX. Registration is free for both
events, but workshop participation is limited to about 50.

More information can be found under:

Users Meeting:
http://www.helmholtz-berlin.de/user/usermeetings/user-meeting-2013/index_en.html


HC1-workshop:
http://www.helmholtz-berlin.de/events/satelite-workshop-2013/

With best wishes

Manfred  Uwe

--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. 
Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de

Re: [ccp4bb] AW: [ccp4bb] str solving problem

[Manfred S. Weiss]

:


I have a crystal data diffracted  around 2.9 A*,
during the data reduction HKL2000 not convincingly showed the space group 
(indexed in lower symmetry p1), while the mosflm given C-centered Orthorhombic, 
and again with little play around HKL2000 given CO







no ice ring is appeared, diffraction pattern looks ok, misindexing in any 
direction is not conclusive to me (plz see the imj attachment)


The diffraction does not look ok... there's hints of multiple lattices... which 
is not a problem if the two lattice orientations do not perfectly overlap (i.e. 
their spots are separable).

Last I remember, HKL2000 bases its indexing on the 'strongest' spots on an 
image (though you could manually select spots). It could result in a misindex 
if the strongest spots come from separate lattices (and even worse if you have 
twinning/pseudosymmetry issues).

Try a program that uses all spots for indexing, across all images (XDS for 
example) and you might get the true space group.

Or if the crystal is big enough, you could try shooting it in different areas 
and 'searching' for a better spot to collect data.

Or 'grow a better crystal'.

F



-
Francis E. Reyes PhD
215 UCB
University of Colorado at Boulder



--
Dr Eugene Valkov
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.

Email: eval...@mrc-lmb.cam.ac.ukmailto:eval...@mrc-lmb.cam.ac.uk
Tel: +44 (0) 1223 407840tel:%2B44%20%280%29%201223%20407840




--

Pramod Kumar.
Graduate Student.
Crystallography lab.
Department Of Biotechnology.
Indian Institute Of Technology Roorkee
Uttranchal.247667
India
+919359189657.



--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.demailto:mswe...@helmholtz-berlin.de




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. 
Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de

[ccp4bb] Reminder: Announcement of the Workshop Diffraction Data Collection Using Synchrotron Radiation

[Manfred S. Weiss]

This is a reminder of the announcement of the Data Collection Workshop,
which will take place at the BESSY II synchrotron in Berlin from June
13-15, 2013.

There is only about 10 days left to the deadline.

For details concerning the program, please see:

http://www.helmholtz-berlin.de/bessy-mx-workshop/


Manfred Weiss  Uwe Mueller



We would hereby like to announce the 4th edition of the workshop
Diffraction Data Collection Using Synchrotron Radiation, which will take
place from June 13-15, 2013 at the BESSY II storage ring of the Helmholtz-
Zentrum Berlin for Materials and Energy (HZB) in Berlin.

This workshop is the successor to three previous successful workshops,
which took place in 2007, 2009 and 2011. It is sponsored by the German
Society for Crystallography (DGK) and organised by the DGK Working
Group 1 (Biological Structures) in cooperation with Dr. Manfred Weiss
and Dr. Uwe Mueller.

The workshop comprises a series of basic lectures on the topic and two
extended practical sessions. It is aimed at PhD students in Biological
Crystallography with little or no experience in diffraction data collection
at a synchrotron. The practical sessions will take place at the MX
beamlines
located at the electron storage ring BESSY II.

The workshop fee is 60 EUR for DGK-members and 75 EUR for non-members.
This fee covers all conference material as well as board and lodging for
two
nights on the campus in Berlin-Adlershof.

For more information please visit the web page
http://www.helmholtz-berlin.de/bessy-mx-workshop/

Registration is now open. Since the number of students will have to be
limited
to 20 in order to ensure that the practical sessions run efficiently, we
expect that
the workshop will fill up quickly. Participants are also expected to
present a poster
on their own work. As previously, the best poster will be awarded with
an attractive
prize.
##

Manfred Weiss  Uwe Mueller

--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de


--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de






Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. 
Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

[Manfred S. Weiss]

Dear all,

I find this discussion most amazing. Here, we are dealing with the most
serious issue
that happened to Macromolecular Crystallography since the Alabama case,
and the
whole discussion is centered around singular and plural and Greek and
Latin words
and what not.

In psychology such phenomenon is referred to as displacement activity.

If you are interested, here is the MacMillon definition of it:

http://www.macmillandictionary.com/dictionary/british/displacement-activity

Cheers,

Manfred


On 01.04.2012 19:35, Gerard Bricogne wrote:

On Sun, Apr 01, 2012 at 01:18:15PM -0400, David Schuller wrote:

On 04/01/12 10:18, Gerard Bricogne wrote:

Dear Paul,

   May I join the mostly silent chorus of Greek/Latin-aware grumps who
wince when seeing data treated as singular when it is plural.

When it are plural?

  Good nit-picking :-) . In my mind the quotes around data would have
had the same effect as writing 'the word data', and referring to that word
by the 'it'. So there is only one word, while its grammatical number is
plural.



At any rate, I heard a Nobel laureate use it incorrectly just two days ago.

  We shouldn't learn to write by imitating Nobel laureates, then.


  With best wishes,

   Gerard.


--
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu


--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. 
Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführerin: Prof. Dr. Anke Rita Kaysser-Pyzalla

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de

[ccp4bb] Workshop Diffraction Data Collection Using Synchrotron Radiation - Deadline approaching

[Manfred S. Weiss]

Please note that there is only a few more days left to register for the 
workshop

announced below.

Manfred



After the successful first two workshops on Diffraction Data Collection
Using Synchrotron Radiation, which took place in 2007 and 2009, a third
edition of the workshop will be held from July 07-09, 2011 at the Helmholtz
Zentrum Berlin fuer Materialien und Energie (HZB) in Berlin.

The workshop is sponsored by the German Society for Crystallography
(DGK) and organised by the DGK Working Group 1 (Biological Structures)
in cooperation with Dr. Manfred Weiss and Dr. Uwe Mueller.

The workshop comprises a series of basic lectures on the topic and two
extended practical sessions. It is aimed at PhD students in Biological
Crystallography with little or no experience in diffraction data collection
at a synchrotron. The practical sessions will take place at the MX
beamlines
located at the electron storage ring BESSY II.

The workshop fee is 50 EUR for DGK-members and 60 EUR for non-members.
This fee covers all conference material as well as board and lodging for
two
nights on the campus in Berlin-Adlershof.

For more information please visit the web page
http://www.helmholtz-berlin.de/bessy-mx-workshop/

Registration is now open. Since the number of students will have to be
limited
to 20 in order to ensure that the practical sessions run efficiently, we
expect that
the workshop will fill up quickly. Participants are also invited to
present a poster.
As last time, the best poster will receive an attractive prize.
##

Manfred Weiss  Uwe Mueller


--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de

Helmholtz-Zentrum Berlin für Materialien und Energie GmbH
Hahn-Meitner-Platz 1, 14109 Berlin
Vorsitzender des Aufsichtsrats: Prof. Dr. Dr. h.c. mult. Joachim Treusch
Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph
Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c.
Wolfgang Eberhardt, Dr. Ulrich Breuer
Sitz der Gesellschaft: Berlin
Handelsregister: AG Charlottenburg, 89 HRB 5583

[ccp4bb] Application deadline for MX-beamtime at HZB-BESSY is approaching soon at March 1, 2011 !

[Manfred S. Weiss]

*Next MX-proposal application deadline: March 1, 2011 *

We kindly invite new MX-proposals for beamtime applications for the next
beamtime period.

In order to apply for beamtime, please register at the HZB on-line access
tool BOAT (http://www.bessy.de/boat/). HZB provides beamtime at the
MX-beamlines 14.1, 14.2 and 14.3. The requested beamtime is  granted
based on the peer-reviewed proposal and reports from previous research
activities. Reported results from previous beamtimes stated in the 
Experimental

Reports form will affect the chances for future beamtimes significantly.
Please make sure to include them if available.


NEWS: HC1c crystal device is now operational on BL14.3


Experimental setup:

BL14.1 setup:
- Photon flux: 1.4x10¹¹ Phot/sx100mAx0.05%BW at sample position (0.1-20 
sec exposure time per frame)

- User defined beam shaping from 30µm-100µm diameter possible
- MX-225 X-ray detector, 92mm-720mm max. distance from the sample
- Microdiffractometer (MD2) with Mini-kappa goniometer MK3 (STAC controlled)
- Automatic sample changer (CATS), 90 sample storage capacity (SPINE-Pin 
 EMBL sample magazine compatibility)

- 96-well crystallization plate scanning operational upon request
- Dedicated eight-core XEON-CPU server, with fibre channel SAN up-link 
data processing environment

- EDNA installed and available
- Common MX software installed including HKL2000, XDS, IMOSFLM, CCP4, 
Phenix, SHELXC-E, etc.

- Automated data processing with ixds and xdsi available
- Remotely controlled cryo-shutter for crystal annealing
- Bruker AXS X-Flash XRF detector
We are offering the hard- and software environment for carrying out
UVRIP experiments at BL14.1. For further information, please visit:
http://www.helmholtz-berlin.de/forschung/funkma/soft-matter/forschung/bessy-mx/ancillary-facilities/uvrip_en.html

BL14.2 setup:
- Photon flux: 1.9x10¹¹ Phot/sx100mAx0.05%BW at sample position (3-20 
sec exposure time per frame)
- MX-225 X-ray detector, 45mm-380mm distance from the sample, 30 deg 
2-Theta possible

- mardtb goniometer installed
- Dedicated eight-core XEON-CPU server, with fibre channel SAN up-link 
data processing environment

- EDNA installed and available
- Common MX software installed including HKL2000, XDS, IMOSFLM, CCP4, 
Phenix, SHELXC-E, etc.

- Automated data processing with ixds and xdsi available
- Remotely controlled cryo-shutter for crystal annealing
- Bruker AXS X-Flash XRF detector
- Pressure chamber for noble gas derivatization (Xe, Kr available upon 
request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom, 8 
Mpixel CCD-camera


BL14.3 setup:
- Photon flux: 4x10exp10 Phot/sx100mAx0.05%BW at sample position (3-20 
sec exposure time per frame)
- SX-165 X-ray detector, 45mm-380mm distance from the sample, 30 deg 
2-Theta possible

- mardtb goniometer installed
- Dedicated eight-core XEON-CPU server, with fibre channel SAN up-link 
data processing environment

- EDNA installed and available
- Common MX software installed including HKL2000, XDS, IMOSFLM, CCP4, 
Phenix, SHELXC-E, etc.

- Automated data processing with ixds and xdsi available
- Remotely controlled cryo-shutter for crystal annealing
- HC-1c dehydration device installed, HC1-beamtime upon request
- Pressure chamber for noble gas derivatization (Xe, Kr available upon 
request)
- Ultra high performance stereo microscope Leica M205A, 20-255x zoom, 8 
Mpixel CCD-camera


Please visit our web page www.helmholtz-berlin.de/bessy-mx to gain updated
information about our experimental setup and other requirements.

Uwe Mueller, Manfred Weiss and the HZB BESSY-MX group

--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (BESSY-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de

iHelmholtz-Zentrum Berlin für Materialien und Energie GmbH
Hahn-Meitner-Platz 1, 14109 Berlin
Vorsitzender des Aufsichtsrats: Prof. Dr. Dr. h.c. mult. Joachim Treusch
Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph
Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c.
Wolfgang Eberhardt, Dr. Ulrich Breuer
Sitz der Gesellschaft: Berlin
Handelsregister: AG Charlottenburg, 89 HRB 5583/i

[ccp4bb] Workshop Diffraction Data Collection Using Synchrotron Radiation

[Manfred S. Weiss]

After the successful first two workshops on Diffraction Data Collection
Using Synchrotron Radiation, which took place in 2007 and 2009, a third
edition of the workshop will be held from July 07-09, 2011 at the Helmholtz
Zentrum Berlin fuer Materialien und Energie (HZB) in Berlin.

The workshop is sponsored by the German Society for Crystallography
(DGK) and organised by the DGK Working Group 1 (Biological Structures)
in cooperation with Dr. Manfred Weiss and Dr. Uwe Mueller.

The workshop comprises a series of basic lectures on the topic and two
extended practical sessions. It is aimed at PhD students in Biological
Crystallography with little or no experience in diffraction data collection
at a synchrotron. The practical sessions will take place at the MX 
beamlines

located at the electron storage ring BESSY II.

The workshop fee is 50 EUR for DGK-members and 60 EUR for non-members.
This fee covers all conference material as well as board and lodging for 
two

nights on the campus in Berlin-Adlershof.

For more information please visit the web page
http://www.helmholtz-berlin.de/bessy-mx-workshop/

Registration is now open. Since the number of students will have to be 
limited
to 20 in order to ensure that the practical sessions run efficiently, we 
expect that
the workshop will fill up quickly. Participants are also invited to 
present a poster.

As last time, the best poster will receive an attractive prize.
##

Manfred Weiss  Uwe Mueller

--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (BESSY-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de

iHelmholtz-Zentrum Berlin für Materialien und Energie GmbH
Hahn-Meitner-Platz 1, 14109 Berlin
Vorsitzender des Aufsichtsrats: Prof. Dr. Dr. h.c. mult. Joachim Treusch
Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph
Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c.
Wolfgang Eberhardt, Dr. Ulrich Breuer
Sitz der Gesellschaft: Berlin
Handelsregister: AG Charlottenburg, 89 HRB 5583/i

[ccp4bb] misdirected email

[Manfred S. Weiss]

Dear all,

I am terribly sorry about my mis-directed email.

Please accept my sincere apologies.

Manfred.

--


*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: mswe...@embl-hamburg.de *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *

[ccp4bb] Workshop Diffraction Data Collection Using Synchrotron Radiation (fwd)

[Manfred S. Weiss]

After the successful first workshop on Diffraction Data
Collection Using Synchrotron Radiation, which took place
in 2007, a second edition of the workshop will be held from
August 13-15, 2009 at the Helmholtz Zentrum Berlin fuer
Materialien und Energie (HZB) in Berlin.

The workshop is sponsored by the German Society for Crystallography
(DGK) and organised by the DGK Working Group 1 (Biological Structures)
in cooperation with Dr. Uwe Mueller (BESSY, Berlin).

The workshop comprises a series of basic lectures on the topic
and two extended practical sessions. It is aimed at PhD students
in Biological Crystallography with little or no experience in
diffraction data collection at a synchrotron. The practical
session will take place at the MX beamlines located at the
electron storage ring BESSY II.

The workshop fee is 50 EUR. This fee covers all conference
material as well as board and lodging for two nights on the
campus in Berlin-Adlershof.

For more information please visit the web page
www.embl-hamburg.de/workshops/2009/diffraction

Registration will be open soon. Since the number of students
will have to be limited to 20 in order to ensure that the
practical sessions run efficiently, we expect that the
workshop will fill up quickly.
##


Manfred Weiss  Uwe Mueller

--


*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: mswe...@embl-hamburg.de *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *

Re: [ccp4bb] unit cell flags in mtz files and refmac

[Manfred S. Weiss]

Dear Bart and Howard,

let's assume that the paper is novel. Without asking
too much, however, I think it would be fair to ask
why they used a homology model for molecular
replacement, when they claimed successful structure
solution two years ago.

Also, since they claim successful structure solution,
I think it is not too far-fetched to ask them for a
preliminary coordinate file for reviewing purposes.

Let's give them the freedom of doubt, but let's watch
how they respond to the obvious question. I do agree
completely with the two of you that in its present
form the paper is not acceptable. But if we reject it,
they will submit it elsewhere. At least we have the
chance of catching something if it is there.

Cheers, Manfred.



On Thu, 26 Feb 2009, Jan Abendroth wrote:


Thanks a lot, Garib,
as always, there is a new version of refmac just out that fixes all the
problems.

Cheers
Jan

2009/2/26 Garib Murshudov ga...@ysbl.york.ac.uk


I think we have fixed this problem just recently. The problem was related
with refmac not being able to pick correct dataset from mtz. IF there was
one dataset in mtz then there was no problem

 Please have a look:
www.ysbl.york.ac.uk/refmac/latest_refmac.html

Garib


On 26 Feb 2009, at 21:52, Jan Abendroth wrote:

Hi all,
I am trying to follow good practices and keep my set of free reflections
between data sets, eg. in this case between an in-house low resolution and a
synchrotron high resolution data set. High resolution data from hkl2000 were
imported through the ccp4i task, keeping the low resolution FreeRs. This mtz
file contains both unit cells, see below. The refined data set contains only
one unit cell description, unfortunately the one from the FreeR
(refmac5.5.72 and refmac5.5.70). As the two unit cells are sufficiently
different, coot displays the model towards the edge of the density, real
space refinement pulls the model back in the middle, refmac then starts with
really high Rs and pulls the model back out.

When using rather ancient refmac5.2.0019, the mtz file has the correct unit
cell description.

Btw. both refinements look about the same. The only difference is a rather
annoying shift of the electron density that is displayed in coot based on
different unit cell in the mtz file.

Is there a way to tell refmac which of the two unit cells to put in the
output mtz file? Intuitively, it should be the one from which the amplitudes
originate?

Cheers
Jan


*mtz file after import*
1 myprotein
  high_reso
  synchrotron
 79.0610   79.0610  311.7950   90.   90.   90.
 1.0
2 myprotein
  low_resol
  rotating_anode
 78.5860   78.5860  311.1900   90.   90.   90.
 1.54180


*refmac5.5.0072*
2 myprotein
  low_reso
  rotating_anode
 78.5860   78.5860  311.1900   90.   90.   90.
 1.54180

*refmac5.2.0019:*
1 myprotein
  high_reso
  synchrotron
 79.0610   79.0610  311.7950   90.   90.   90.
 1.0


--
--
Jan Abendroth
deCODE biostructures
Seattle / Bainbridge Island, WA, USA
work: JAbendroth_at_decode.com
home: Jan.Abendroth_at_gmail.com









--


*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: mswe...@embl-hamburg.de *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *

Re: [ccp4bb] R pim and Rmeans

[Manfred S. Weiss]

Hi Frank,

of course R_pim is just one number and it may not be discriminatory
enough to decide when to stop including images. But I can say from
my own experience that R_pim will not drop forever. I have seen
data sets with R_pim values of 0.5% to 2.0 A or better resolution,
but never R_pim values significantly smaller than that (even with
the redundancy approaching 100). You may try this out yourself.
I bet you that R_pim will eventually go up again after a few
revolutions when radiation damage kicks in. The real question in
my opinion is, when is the deviation from the 1/(N-1) drop such,
that you would want to stop including more images.

Cheers, Manfred.


*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: [EMAIL PROTECTED] *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *



On Tue, 9 Dec 2008, Frank von Delft wrote:

 Hi Manfred


  thanks a lot for your comments, since they raise some interesting
  points.
 
  R_pim should give the precision of the averaged measurement,
  hence the name. It will decrease with increasing data redundancy,
  obviously. The decrease will be proportional to the square root
  of the redundancy if only statistical errors or counting errors
  are present. If other things happen, such as for instance
  radiation damage, then you are introducing systematic errors,
  which will lead to either R_pim decreasing less than it should,
  or R_pim even increasing.
 
  This raises an important issue. As more and more images keep
  being added to a data set, could one decide at some point,
  when to add any further images?

 This really is the point:  in these days of fast data collection, I
 assume that most people collect more frames than necessary for
 completeness.  At least, I always do.  So the question is no longer is
 this data good enough -- that you can test quickly enough with
 downstream programs.

 Rather, it is, how many of the frames that I have should I include, so
 that you don't have to run the same combination of downstream programs
 for 20 combinations of frames.

 Radiation damage is the key, innit.  Sure, I can pat myself on the
 shoulder by downweighting everything by 1/1-N -- so after 15 revolutions
 of tetragonal crystal that'll give a brilliant Rpim, but the crystal
 will be a cinder and the data presumably crap.

 But it's the intermediate zone (1-2x completeness) where I need help,
 but I don't see how Rpim is discriminatory enough.

 phx.

Re: [ccp4bb] R pim and Rmeans

[Manfred S. Weiss]

Hi Frank,

thanks a lot for your comments, since they raise some interesting
points.

R_pim should give the precision of the averaged measurement,
hence the name. It will decrease with increasing data redundancy,
obviously. The decrease will be proportional to the square root
of the redundancy if only statistical errors or counting errors
are present. If other things happen, such as for instance
radiation damage, then you are introducing systematic errors,
which will lead to either R_pim decreasing less than it should,
or R_pim even increasing.

This raises an important issue. As more and more images keep
being added to a data set, could one decide at some point,
when to add any further images? I have done a little work
in that direction but nothing exhaustive.

Cheers,

Manfred.


*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: [EMAIL PROTECTED] *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *



On Sun, 7 Dec 2008, Frank von Delft wrote:

 Hi Manfred

 I've been using and thinking Rmeas ever since I first saw it; but
 (embarrassingly) I've only just woken up to Rpim -- so thanks for the
 prompt. So I trawled the original references (Weiss and Hilgenfeld,
 1997) to find out why it has the form it does, but I must have skimmed
 too quickly, because I couldn't find the explanation.

 Rpim, as I understand it, is trying to do two things (See Eq 3 in link
 below):
 1) penalise me for bad data
 2) reward me for high redundancy

 But why that *particular* balance of redundancy vs badness? And how do
 we know that it was the best one?

 And is this really waterproof? Since the redundancy factor (1/(N-1))
 tends to zero for large N, does it not dominate for large redundancy?
 For instance, for terrible data (e.g. wrong symmetry) but very high
 redundancy, then Rpim will still tend to zero, won't it?

 So to counteract that, N might be downweighted it turn by the data
 badness. Which could in its turn again be I don't think I like where
 this is going :)

 Cheers
 phx.








 Manfred S. Weiss wrote:
  Dear Deb,
 
  R_meas or R_rim is a merging R-factor which is independent of the
  redundancy or multiplicity of the data (hence its name), R_pim
  stands for precision indicating merging R-factor. R_pim
  gives you the precision of the averaged measurement, which is
  the one you are actually using for structure solution and refinement.
 
  SCALA will calculate both R_rim (R_meas) and R_pim, XDS/XSCALE
  will calculate R_rim (R_meas) only, and SCALEPACK neither of the
  two. However, you may produce a file from SCALEPACK with scaled
  but unmerged intensities (option NO MERGE ORIGINAL INDEX)
  and then download a program from my site called RMERGE or
  RMERGE_4LINUX, which will do the job for you.
 
  If you have further questions, please see the page
  http://www.embl-hamburg.de/~msweiss/projects/msw_qual.html
  or ask me.
 
  Cheers, Manfred
 
  
  *  *
  *Dr. Manfred S. Weiss  *
  *  *
  * Team Leader  *
  *  *
  * EMBL Hamburg OutstationFon: +49-40-89902-170 *
  * c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
  * D-22603 Hamburg   Email: [EMAIL PROTECTED] *
  * GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
  *  *
  
 
 
  On Sat, 6 Dec 2008, Debajyoti Dutta wrote:
 
 
   �
 
  Dear members,
 
  I have a little query hare about Rpim and Rmeans. How these are used to 
  mark data quality, and how can one calculate it.
 
  Thak you for your reply in advance.
 
  Sincerely
  Deb
 

[ccp4bb] Tutorial for Learning and Teaching Macromolecular Crystallography

[Manfred S. Weiss]

Dear colleageus,

I would like to bring to your attention that as a result of a
workshop on Diffraction Data Collection Using Synchrotron
Radiation held last year, we have developed a tutorial for
X-ray crystallography. The tutorial consists of five experiments,
and contains all relevant information needed to reproduce the
experiments. The sources of the chemicals are given, the
procedures described in detail, the diffraction images provided
and the path to structure solution outlined.

One may use the tutorial to teach X-ray crystallography within
a practical course or in class, or interested students can work
independently with the material to learn all the steps of structure
determination by various methods.

The five experiments are:

1) S-SAD on cubic insulin
2) Br-MAD on thaumatin
3) Molecular replacement on monoclinic lysozyme
4) Solvent ion identification in tetragonal lysozyme
5) Identification of a weakly bound ligand in lysozyme

Except for experiment 2, data collection may also be performed on
home sources.

The tutorial has been described in a paper (open access) in the
most recent issue of J. Appl. Cryst.

See: http://dx.doi.org/10.1107/S0021889808032494

All material can be downloaded from either one of the two sites:

http://www.embl-hamburg.de/Xray_Tutorial/

http://www.mx.bessy.de/bessy-ws/bessy.html

In case you want to use it or have used it already, I would of
course appreciate any feedback, so that we can continue to
improve it.

With best wishes,

Manfred Weiss (on behalf of the tutorial team)

Annette Faust, Santosh Panjikar, Uwe Mueller, Venkat Parthasarathy,
Andea Schmidt  Victor Lamzin.


*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: [EMAIL PROTECTED] *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *

Re: [ccp4bb] Anion binding sites in proteins

[Manfred S. Weiss]

I should like to point out here that almost ANY protein will pick
up something from the crystallization solution (cations, anions).
Unfortunately, in the majority of cases these partially occupied
ions will not be seen or will be mistakenly interpreted as water
molecules. One way to 'see' such things is to carefully inspect
an anomalous difference Fourier electron density map from good
quality data collected at longer wavelength (even CuKa is good
enough for that.

See: Mueller-Dieckmann et al (2007). Acta Cryst D63, 366-380.

A most spectacular example is the recent PDB entry 2RKP, where
at least 16 chlorides have been identified based on a data set
collected at a wavelength of 2.0 A.

Cheers, Manfred.


*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: [EMAIL PROTECTED] *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *

[ccp4bb] New Deadline - EMBO World Lecture Course

[Manfred S. Weiss]

Dear all,

there are still a few places left in the

 EMBO World Lecture Course on

  RECENT DEVELOPMENTS IN MACROMOLECULAR CRYSTALLOGRAPHY

which I had announced earlier (see below).

Check out the web page http:/cwp.embo.org/wpc08-02/
or contact me for further information.

The NEW DEADLINE is Monday, June 23, 2008.

It's a great opportunity.

Cheers,

Manfred.


   EMBO World Lecture Course on

 RECENT DEVELOPMENTS IN MACROMOLECULAR CRYSTALLOGRAPHY

 We would like to announce an EMBO World Lecture Course on
 RECENT DEVELOPMENTS IN MACROMOLECULAR CRYSTALLOGRAPHY, which
 will take place from Nov 09-14, 2008 in the town in Pune in
 India, on the premises of the National Chemical Laboratory
 NCL. This course consists of various lectures describing recent
 methodological developments in the field from crystallization, to
 diffraction data collection, structure determination and function
 prediction from structure as well as lectures on recent
 achievements in biology using X-ray diffraction techniques.

 Pune is located abour 150 km south of Mumbai (Bombay) on the
 foothills of the Western valley of Maharashtra in Western
 India. It is a city of great culture and is rich in tradition
 and history as well as having a balanced climate.

 Due to space limitations, we can only accommodate up to 100 participants.
 Preference will be given to applicants who wish to present their
 own work. From the submitted abstracts a number of short talks
 will be selected. Also, the three best posters will be awarded a
 poster price.

 REGISTRATION for the course is now open.

 For more information and registration, please check the course
 homepage http:/cwp.embo.org/wpc08-02/ or contact the organizers

Manfred S. Weiss ([EMAIL PROTECTED])
Paul A. Tucker ([EMAIL PROTECTED])
Santosh Panjikar ([EMAIL PROTECTED])
C. G. Suresh ([EMAIL PROTECTED])
Sanjay N. Nene ([EMAIL PROTECTED])

 Best regards,

 Manfred

 
 *  *
 *Dr. Manfred S. Weiss  *
 *  *
 * Team Leader  *
 *  *
 * EMBL Hamburg OutstationFon: +49-40-89902-170 *
 * c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
 * D-22603 Hamburg   Email: [EMAIL PROTECTED] *
 * GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
 *  *
 

[ccp4bb] Reminder - EMBO World Lecture Course

[Manfred S. Weiss]

Dear all,

this is to remind you of the upcoming deadline for the

 EMBO World Lecture Course on

  RECENT DEVELOPMENTS IN MACROMOLECULAR CRYSTALLOGRAPHY

which I had announced earlier (see below).

Check out the web page http:/cwp.embo.org/wpc08-02/
or contact me for further information.

Best wishes,

Manfred.


   EMBO World Lecture Course on

 RECENT DEVELOPMENTS IN MACROMOLECULAR CRYSTALLOGRAPHY

 We would like to announce an EMBO World Lecture Course on
 RECENT DEVELOPMENTS IN MACROMOLECULAR CRYSTALLOGRAPHY, which
 will take place from Nov 09-14, 2008 in the town in Pune in
 India, on the premises of the National Chemical Laboratory
 NCL. This course consists of various lectures describing recent
 methodological developments in the field from crystallization, to
 diffraction data collection, structure determination and function
 prediction from structure as well as lectures on recent
 achievements in biology using X-ray diffraction techniques.

 Pune is located abour 150 km south of Mumbai (Bombay) on the
 foothills of the Western valley of Maharashtra in Western
 India. It is a city of great culture and is rich in tradition
 and history as well as having a balanced climate.

 Due to space limitations, we can only accommodate up to 100 participants.
 Preference will be given to applicants who wish to present their
 own work. From the submitted abstracts a number of short talks
 will be selected. Also, the three best posters will be awarded a
 poster price.

 REGISTRATION for the course is now open.

 For more information and registration, please check the course
 homepage http:/cwp.embo.org/wpc08-02/ or contact the organizers

Manfred S. Weiss ([EMAIL PROTECTED])
Paul A. Tucker ([EMAIL PROTECTED])
Santosh Panjikar ([EMAIL PROTECTED])
C. G. Suresh ([EMAIL PROTECTED])
Sanjay N. Nene ([EMAIL PROTECTED])

 Best regards,

 Manfred

 
 *  *
 *Dr. Manfred S. Weiss  *
 *  *
 * Team Leader  *
 *  *
 * EMBL Hamburg OutstationFon: +49-40-89902-170 *
 * c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
 * D-22603 Hamburg   Email: [EMAIL PROTECTED] *
 * GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
 *  *
 

Re: [ccp4bb] Spacegroup choices, reindexing and so on

[Manfred S. Weiss]

Dear Graeme,

here is what I would do, or what I would like to have.

If you are able to identify the Laue group of the data with
some degree of certainty, then all of the processing and
scaling should be carried out in this Laue group.

Then, by looking at systematic absences you may give probabilities
for each of the possible space groups, i.e. each of the eight
possibilities in P-orthorhombic. Typically one option will
have the highest probability and this is the one which should
be written out. In a second run, the user should be given the
choice of overriding this.

Now, for space groups such as P222_1, this should always be
reindexed to standard setting, if it turns out to be the one
with the highest probability.

Hope that helps,

Manfred.


*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: [EMAIL PROTECTED] *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *



On Mon, 21 Jan 2008, Winter, G (Graeme) wrote:

 Hi All,

 A user question about the xia2 behaviour has opened a pot of worms, and
 I thought I would ask the community for opinions. If (for example) you
 are using an automated data processing or analysis tool, and the
 systematic absences suggest a spacegroup choice, what would you like to
 do:

 (1) nothing - just mention this in the output
 (2) assign the base version of this spacegroup (e.g. P41212 to
 represent that or it's enantiomorph)
 (3) create multiple copies of the reflection file with all of the
 spacegroup options

 As a further question, if the spacegroup looks like P 2 21 21 (say)
 would you like this to be reindexed to the standard setting?

 Now, I suspect that there will be a wide range of opinions on this.

 Following #1 will give possibly strange effects if truncate tries to
 inflate systematically absent reflections
 Following #2 will result in reflections being removed by truncate
 #3 gives lots of reflection files and lots of mess

 Currently I follow #2 with reindexing to the standard setting.

 There have been discussions in the past of being able to flag or
 enantiomorph in the spacegroup definition in the mtz file. This would
 be useful here, but would not really help with the reindex or no
 question...

 Thanks!

 Graeme

Re: [ccp4bb] Spacegroup choices, reindexing and so on

[Manfred S. Weiss]

Dear Ian,

I thought that in cases of for instance P-orthorhombic where
you can have a screw axis along a, b, or c or any combination
of it, the standard is always to make the unique axis the
c-axis. I.e. the longest axis in P222, and P2(1)2(1)2(1), but
the 2(1)-axis in P222(1) or P2(1)22 or P22(1)2 and the 2-axis
in P22(1)2(1) or P2(1)22(1) or P2(1)2(1)2. I am not sure
if all programs (even within CCP4) understand any of the
non-conventional settings.

Best regards,

manfred.



*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: [EMAIL PROTECTED] *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *



On Mon, 21 Jan 2008, Ian Tickle wrote:


 Hi Manfred

 I agree with everything you say except the last bit about re-indexing!
 For those space groups with alternate settings, e.g. those with standard
 names C2 or P2221 or P21212, why is it necessary to re-index to the
 'standard setting' when the data will have been already indexed
 correctly by Mosflm or whatever according to the ITC Vol A convention
 (e.g. a  b  c for the oI lattice)?  It's not clear to me what you gain
 by re-indexing in that situation (presumably at the heavy-atom solution
 or translation function stage), and I know from experience that what you
 lose is the risk of causing endless confusion by having datasets around
 indexed in both ways.

 This becomes particularly problematic when the data is stored in some
 kind of database, because then you really want to have one definitive
 space group name per crystal which is defined right at the outset and
 cannot be changed.  Changing the space group in mid-stream is then not
 an option, except by deleting all the database entries for that crystal
 and starting all over again with the new space group name.  Of course if
 the initial choice of space group was really wrong (e.g. the wrong
 Bravais lattice assignment) then you have no option but to start over
 and re-process the data.

 The only other situation where re-indexing may be necessary is where you
 know the correct Bravais lattice and approximate cell parameters
 *before* processing the data, e.g. where you have a previously solved
 isomorphous or near-isomorphous structure, but where the alternate
 indexings have similar cell parameters so the initial automatic choice
 of cell orientation may not have been correct.

 Cheers

 -- Ian

  -Original Message-
  From: [EMAIL PROTECTED]
  [mailto:[EMAIL PROTECTED] On Behalf Of Manfred S. Weiss
  Sent: 21 January 2008 09:34
  To: Winter, G (Graeme)
  Cc: CCP4BB@JISCMAIL.AC.UK
  Subject: Re: [ccp4bb] Spacegroup choices, reindexing and so on
 
  Dear Graeme,
 
  here is what I would do, or what I would like to have.
 
  If you are able to identify the Laue group of the data with
  some degree of certainty, then all of the processing and
  scaling should be carried out in this Laue group.
 
  Then, by looking at systematic absences you may give probabilities
  for each of the possible space groups, i.e. each of the eight
  possibilities in P-orthorhombic. Typically one option will
  have the highest probability and this is the one which should
  be written out. In a second run, the user should be given the
  choice of overriding this.
 
  Now, for space groups such as P222_1, this should always be
  reindexed to standard setting, if it turns out to be the one
  with the highest probability.
 
  Hope that helps,
 
  Manfred.
 
  
  *  *
  *Dr. Manfred S. Weiss  *
  *  *
  * Team Leader  *
  *  *
  * EMBL Hamburg OutstationFon: +49-40-89902-170 *
  * c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
  * D-22603 Hamburg   Email: [EMAIL PROTECTED] *
  * GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
  *  *
  
 
 
  On Mon, 21 Jan 2008, Winter, G (Graeme

[ccp4bb] Announcement - EMBO World Lecture Course

[Manfred S. Weiss]

  EMBO World Lecture Course on

RECENT DEVELOPMENTS IN MACROMOLECULAR CRYSTALLOGRAPHY

We would like to announce an EMBO World Lecture Course on
RECENT DEVELOPMENTS IN MACROMOLECULAR CRYSTALLOGRAPHY, which
will take place from Nov 09-14, 2008 in the town in Pune in
India, on the premises of the National Chemical Laboratory
NCL. This course consists of various lectures describing recent
methodological developments in the field from crystallization, to
diffraction data collection, structure determination and function
prediction from structure as well as lectures on recent
achievements in biology using X-ray diffraction techniques.

Pune is located abour 150 km south of Mumbai (Bombay) on the
foothills of the Western valley of Maharashtra in Western
India. It is a city of great culture and is rich in tradition
and history as well as having a balanced climate.

Due to space limitations, we can only accommodate up to 100 participants.
Preference will be given to applicants who wish to present their
own work. From the submitted abstracts a number of short talks
will be selected. Also, the three best posters will be awarded a
poster price.

REGISTRATION for the course is now open.

For more information and registration, please check the course
homepage http:/cwp.embo.org/wpc08-02/ or contact the organizers

   Manfred S. Weiss ([EMAIL PROTECTED])
   Paul A. Tucker ([EMAIL PROTECTED])
   Santosh Panjikar ([EMAIL PROTECTED])
   C. G. Suresh ([EMAIL PROTECTED])
   Sanjay N. Nene ([EMAIL PROTECTED])

Best regards,

Manfred


*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: [EMAIL PROTECTED] *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *

Re: [ccp4bb] differences between Rsym and Rmerge

[Manfred S. Weiss]

Dear Mohd and all others,

Well, I guess it is time again to define and talk about R-factors.

The term R_sym goes back to the times, when X-ray data were
recorded by precession photography on film. Except for the central
cone, each reflection was observed only once and R_sym described
the agreement strictly between symetry-related reflections, hence
R_sym.

In diffractometer times, when reflections were measured one by one,
only for a subset of reflections (typically a plane in reciprocal
space) were symmetry-related reflections measured two times. R_sym
became R_int, where int stands for internal agreement. These
additional reflections were just measured to calculate R_int,
later on they were discarded.

Nowadays, where a diffraction data set typically consists of dozens
or hundreds of images recorded from some sort of an area detector,
multiple measurements of the same reflection AND symmetry-related
reflections are merged together to calculate the mean intensity
for a given reflection. Hence, the agreement factor becomes R_merge
or merging R-factor.

As you can see, R_merge is more general than R_sym, and is (as Kay
pointed out) the preferred term.

However, when talking about R-factor I can never refrain from
mentioning that R_merge should actually NEVER EVER be used,
because it is inherently flawed. As the redundancy or the
multiplicity of the data increases, R_merge will also increase,
although the mean intensity will be more precisely determined.
As was postulated by Kay and myself about 10 years ago, R_merge
should be replaced by a redundancy-independent merging R-factor
(termed R_rim or R_meas). Unfortunately, only SCALA and XDS
produce this R-factor, SCALEPACK does not (not yet, I hope --
pun to Dallas). If you want to calculate R_rim or R_meas based
on scaled but unmerged data, I have my own program, which you
can download from my web site, as does Kay.

I hope this clarifies things.

Cheers, Manfred.


*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: [EMAIL PROTECTED] *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *



On Fri, 18 Jan 2008, Salameh, Mohd A., Ph.D. wrote:

 Hi everybody!
 I will appreciate it if anybody can clarify to me the differences
 between Rmerge and Rsym. Many thanks, M

 
 Mohammed A. Salameh, Ph.D.
 Mayo Clinic Cancer Center
 Griffin Cancer Research Building
 4500 San Pablo Road
 Jacksonville, FL 32224
 Tel:(904) 953-0046
 Fax:(904) 953-0277
 [EMAIL PROTECTED]
 

Re: [ccp4bb] Poinless and space group P 4 3 2

[Manfred S. Weiss]

Dear Kristof,

I recently had lots of trouble with molrep in space group
F432. Both Phaser and Molrep failed, only Amore produced
a solution.

Hope that helps.

Manfred.



*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: [EMAIL PROTECTED] *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *



On Tue, 13 Nov 2007, Kristof Van Hecke wrote:

 Dear all,

 When running Pointless 1.2.0 (see summary below), I get the cubic
 space group P 4 3 2
 (mosflm gave P 2 3 or P 4 3 2)

 !--SUMMARY_BEGIN--

 Best Solution space group P 4 3 2
 Reindex operator: [h,k,l]
 Laue group probability: 1.000
 Systematic absence probability: 0.975
 Total probability:  0.975
 Space group confidence: 0.964
 Laue group confidence   1.000

 !--SUMMARY_END--

 However, although I have multiple models (ensemble) with
 approximately 30% sequence identity (44% homology), I'm not able to
 get any reasonable solution with Phaser.
 As we know the protein can form dimers and even trimers, is it
 possible that Poinless is giving a higher space group because of
 pseudo-symmetry in this case..?

 Does anyone has got experience with Pointless and this kind of space
 group please..?

 Many thanks

 Kristof


 --
 Kristof Van Hecke, PhD
 Biomoleculaire Architectuur
 Celestijnenlaan 200 F
 B-3001 Heverlee (Leuven)
 Tel: +32(0)16327477
 --





 Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

[ccp4bb] MOLREP for space group F432

[Manfred S. Weiss]

Dear CCP4ers,

has anybody ever noticed a strange behaviour of MOLREP in space
group F432 (no. 209)? It seems as if the rotation function works
ok, but translation functions take about 100 times the time they
should.

Cheers, Manfred.


*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: [EMAIL PROTECTED] *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *

Re: [ccp4bb] Solving structure of protein-protein complexes using MR

[Manfred S. Weiss]

Hi Joe,

I think you are wasting your time pursueing molrep.

Go for some experimental phases. Try a bromide soak or xenon
derivatisation. Provided your molrep solution is correct,
you don't need a lot of extra phase information.

Cheers, Manfred.



*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: [EMAIL PROTECTED] *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *



On Fri, 6 Jul 2007, Joe Smith wrote:

 Hi all,

 We have been trying to solve a structure of protein-protein complexes using
 3.1A data (one of the proteins is of 120kDa whereas the other is of 20kDa).
 The structure of smaller protein is known (individually-100% sequence
 identity) whereas the bigger protein does not share more than 10% sequence
 identity with the similar proteins solved from other sources.

 Due to some problem in getting Seleno-labelled protein, we have also been
 trying to use molecular replacement (MR) to solve the structure. We want to
 find out the correct position of smaller protein using MR and then plan to
 extend the phases to the whole asymmetric unit (we hope it could be done but
 not sure). We are more or less sure about the fold of bigger protein and
 expect it to be similar to the other known related structures.
 In one of the solution obtained using phaser, the map looks really good, but
 this solution doesn't provide good packing of the complex inside the unit
 cell. Due to low scattering contribution of the smaller protein, we are
 unable to refine any possible solutions using REFMAC.

 We welcome any kind of suggestions in this regard.

  Thanking you in advance.

  Joe

[ccp4bb] REMINDER - Murnau conference on STRUCTURAL BIOLOGY OF DISEASE MECHANISMS

[Manfred S. Weiss]

Dear colleagues,

Please let us remind you of the International Murnau Conference on
STRUCTURAL BIOLOGY OF DISEASE MECHANISMS, which will take place
from Sep 05-08, 2007 in the small and beautiful Bavarian town of
Murnau, about one hour south of Munich. Murnau is located right
at the Staffelsee with a beautiful view on the Bavarian alps.

The deadline for registration is approaching and there are only
few places left, so if you would like to participate and become
part of the meeting, please register soon.

You may find all relevant details, including the exciting program
with many internationally renowned speakers and the registration
page on the conference web page http://www.murnauconference.de.

We strongly believe that the success of the 2005-conference will
be continued in 2007 and would be delighted to welcome you in
Murnau. Please do not hesitate to contact us in case of further
queries.

With best regards,

Manfred Weiss

on behalf of the Murnau organization committee



*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: [EMAIL PROTECTED] *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *

[ccp4bb] Standards for the publication of macromolecular NMR structures

[Manfred S. Weiss]

To: CCP4 Bulletin Board

Dear All

I am attaching a message concerning a workshop on Standards for the
publication of macromolecular NMR structures to be held at this year's
ACA meeting. I think that this will be of interest to many of you,
especially if you are planning to attend the ACA meeting anyways.

Best wishes

Manfred.


NMR workshop


From: Howard Einspahr [EMAIL PROTECTED]

The IUCr is sponsoring a workshop on updating publication standards for NMR
structures on July 21 in Salt Lake City UT, the day before the 2007 American
Crystallographic Association (ACA) meeting. The workshop is organized by
Mitchell Guss, Manfred Weiss and Howard Einspahr with the help of Guy
Montelione, John Markley, Eldon Ulrich, Luciano Mueller and others from the
NMR community. Acta Cryst. F published an NMR structure paper in 2006 and
was advised by referees at the time that the 1998 IUPAC standards, which
were used as a basis for review, were in need of an update. The workshop
dovetails nicely with NMR community efforts on standards and a Task Force
under the aegis of BMRB and RCSB launching their work in the coming months.
Several members of the Task Force including its chair, Rob Kaptein, will make
presentations at the workshop and the workshop will serve as a preliminary to
the Task Force's work. Also presenting on aspects of publication standards
will be Manfred Weiss and Howard Einspahr.

If you are planning to attend the ACA meeting this summer, please consider
to participate in the workshop. After a morning of presentations and lunch,
the workshop will hold a series of breakout sessions to draft the updates
that arise from the meeting and review those in a final joint session at
the end of the day. This is a chance for early input into the evolution of
new standards for publication of NMR structures. Registration for the workshop
is $75 for students and postdoctoral fellows, $125 for all others. For further
details, see the web pages at http://www.biochem.utah.edu/aca2007/index.html,
which provides a registration form PDF under the appropriate tab. Deadline for
advance registration is June 1.

Re: [ccp4bb] extra high B factor

[Manfred S. Weiss]

Dear all,

Frankly speaking I am having some doubts about this whole
discussion.

1. Apparently, it does not make a difference in R and Rfree
   whether the peptide is in the structure or not. This does
   suggest that there is very little (if any) information about
   the peptide in the data. Right?

2. You stated that you can unambiguously trace the peptide
   from N- to C-terminus. If you assume atomic B-factors of
   100 or larger and calculate the density, I really can't
   see how this is possible. Maybe you could produce an
   omit S. A. difference electron density map to show this.

3. You said the affinity between protein and peptide is
   10^-7 or 10^-8 M. This means that something is a bit
   strange in any case. With this affinity you should get
   100% occupancy. Of course, it is possible that your
   buffer/cryo-solvent/etc. reduce the affinity. Have you
   considered this?

Cheers, Manfred.


*  *
*Dr. Manfred S. Weiss  *
*  *
* Team Leader  *
*  *
* EMBL Hamburg OutstationFon: +49-40-89902-170 *
* c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 *
* D-22603 Hamburg   Email: [EMAIL PROTECTED] *
* GERMANY   Web: www.embl-hamburg.de/~msweiss/ *
*  *



On Mon, 30 Apr 2007, Jiamu Du wrote:

 Does anyone know a program can perform the ocupancy refinement?
 Or we always only refine B factor to reflect the occupancy?

 Thanks


 On 4/30/07, Eleanor Dodson [EMAIL PROTECTED] wrote:
 
  Well - it is extremely likely that the peptide is partially occupied and
  the occupancy may well be  0.5..
 
  But at this resolution you are going to have great difficulty deciding
  whether you should have
  Occ=1.0 B = 130
 
  Occ = 0.5  B = 100
 
  Occ = 0.33  B = ??? 80???
 
  As your Rfactors show it makes very little difference to any scoring
  system..
 
  You can look at difference maps and try to see if one looks flatter than
  the other ..
 
  Even the overall Wilson plot B is not very well determined, so I wouldnt
  worry too much..
 
  Eleanor
 
  Jiamu Du wrote:
   Dear All:
   According to your suggestion, I have set the peptide's occupency to
   0.5. Two strategies were employed.
   1. Direct using Refmac restrained refinement for 10 cycles. The B
   factor only drops to around 100. R/Rf did not change, either.
   2. Direct CNS B-fator refinemen. The B factor drops to a moderate
   level 60-80, and the R/Rf each increases about 2%.
   3. First using CNS B-fator refinemen nad next Refmac restrained
   refinement. The B factor drops to 60-80, and the R/Rf did not change.
  
   I think next step TLS refinement should be carried out.
  
  
   On 4/30/07, *Philippe DUMAS* [EMAIL PROTECTED]
   mailto:[EMAIL PROTECTED] wrote:
  
   Jiamu
  
   According to the numbers you have mentioned I conclude that you
   peptide occupancy should be around  60-64 %
   I am interested to know what will be the value that you will
   obtain after refinement...
  
  
   Philippe Dumas
   IBMC-CNRS, UPR9002
   15, rue Ren? Descartes 67084 Strasbourg cedex
   tel: +33 (0)3 88 41 70 02
   [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
  
  
   -Message d'origine-
   *De :* CCP4 bulletin board [mailto: CCP4BB@JISCMAIL.AC.UK
   mailto:CCP4BB@JISCMAIL.AC.UK]*De la part de* Jiamu Du
   *Envoy? :* lundi 30 avril 2007 05:57
   *? :* CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
   *Objet :* [ccp4bb] extra high B factor
  
   Dear All:
   I am refining a protein-peptide complex struture at 2.6
   angstrom resolution.
   The data was obtain from a co-crystal and the wilson B factor
   of the data is about 70.
   The affinity between protein and peptide is about 10E-7 to
   10E-8 molar.
   Protein fragment of the structure has a common B facor about 50.
   But surprisingly, the average B factor of the peptide is as
   high as 130, although the peptide can be clearly traced from
   the the electron density map. All residues of the peptide have
   such a high B factor.
   My question is how can I reduce the abnormal high B factor to
   a common level or if this high B factor acceptable.
   And another question is if this high B fator will influence
   the final refiment level.
  
   Thanks.
  
   --
   Jiamu Du
   State Key Laboratory