Re: [ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press

[Vellieux Frédéric]

"how to get grants without papers in Nature. anyone have a solution to that 
one?"

Simple: Once all of us have reviewed enough papers (with the money placed in a 
common pot) we simply buy the Nature Publishing Group. All those having taken 
part get a Nature paper every 4 years to ensure grant money continues to flow 
in.

F.

From: CCP4 bulletin board  on behalf of Hughes, Jon 

Sent: Saturday, June 30, 2018 12:12:50 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press

great idea! 2 hours at €200 per hour makes €1000 - sounds like an eminently 
reasonable starting point for negotiations. if the publishers don't like our 
price, they can do the reviewing themselves - and after a while no one will 
bother to buy the resulting rubbish anyhow! in the mean time we put our stuff 
online directly (without wasting our time, for example, still formatting 
reference lists in the 21st century!). we have them over a barrel. the only 
problem i see is how to get grants without papers in Nature. anyone have a 
solution to that one?
one final aspect is: who gets the money? surely the universities etc. should 
get it, not us: the taxpayer pays us already.
best,
jon

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Keller, 
Jacob
Gesendet: Samstag, 30. Juni 2018 00:00
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] [ccp4bb] Oxford University Press

The one I don't get is why not pay reviewers? $1000 per review? If you look at 
publishers' profit margins, you will see that they can afford it. I actually 
think the scientific community should go on a "review strike" until reviewers 
get paid.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
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-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr 
Leiman
Sent: Friday, June 29, 2018 4:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [ccp4bb] Oxford University Press

Indeed! Scientists in the Soviet Bloc got paid for publishing their scientific 
papers (and maybe for citations as well - not sure about that one)! We need to 
change the current system! Although these changes could be accompanied by many 
other pleasant virtues of the Soviet regime.

Petr


> On Jun 29, 2018, at 8:11 AM, Hughes, Jon  
> wrote:
>
> whose paper? our universities pay subscriptions for these journals and we 
> even pay on top of that for the pages of our publications (even when they're 
> not actually printed!), whilst we review papers for free! sounds like a 
> well-validated way to use taxpayers' money to keep the expensive company cars 
> etc. nice and shiny. why don't universities just require reimbursement for 
> the time we invest to insure that the merchandise is up to standard? €100 per 
> hour would be cheap. seems to me as though some capitalists need to add a few 
> lines to their balance sheets
> best, jon
>
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
> Robbie Joosten
> Gesendet: Freitag, 29. Juni 2018 13:42
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] Oxford University Press
>
> Yes, but think of all the money they miss due to your pirating of their paper 
> ;) It's the typical discussion about whether piracy of copyrighted material 
> leads to loss or gain of revenue. There are a lot of models here, but not 
> necessarily well-validated.
>
> Anyway, if people want to read your papers and cannot get them from
> ResearchGate, I'm sure they can find them on another online
> collection, a hub of some sort ;)
>
> Cheers,
> Robbie
>
>> -Original Message-
>> From: Bernhard Rupp [mailto:hofkristall...@gmail.com]
>> Sent: Friday, June 29, 2018 13:23
>> To: 'Robbie Joosten'; CCP4BB@JISCMAIL.AC.UK
>> Subject: RE: [ccp4bb] Oxford University Press
>>
>> Agreed, but for 10 years old papers this seems a bit of overkill
>>
>>
>>
>> From: CCP4 bulletin board  On Behalf Of Robbie
>> Joosten
>> Sent: Friday, June 29, 2018 12:11
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Oxford University Press
>>
>>
>>
>> Were they open access papers? If they were, than OUP is being too
>> aggressive (IMO), but otherwise it makes sense. I also find the
>> ResearchGate is rather aggressive in bugging you to upload papers
>> that are readily 

[ccp4bb] Announcement: Instruct/CIISB Fragment Screening course in Vestec (Prague area) on April 5 and 6 (arrival on April 4, departure on April 7)

[Vellieux Frédéric]

Dear all,

Just before the end of the year break, before the festive season:

The Centre of Molecular Structure (IBT, Biocev, Vestec, Prague area, Czech 
Republic, one the the two Instruct CZ and CIISB sites) is organising a course 
on April 5 and 6, 2018 (arrival in Vestec on April 4, departure on April 7).

Title: Instruct / CIISB course on fragment screening using crystallography 
laboratory equipment.

The course has two parts: half a day devoted to lectures on April 5 morning, in 
the Biocev auditorium - no registration is needed, everyone is welcome to 
attend the presentations and lectures given by:
Jan Dohnalek (IBT Biocev Vestec)
Andreas Heine (IPC Marburg)
Bohdan Schneider (IBT Biocev Vestec)
Tomas Koval (IBT Biocev Vestec)
Petr Pompach (CMS IBT Biocev Vestec)
Manfred Weiss (Bessy II)
Sameer Velankar (to be confirmed, or another speaker from EBI)
John Darby (Chemistry, U. of York)

The remaining part of the workshop (three half days, April 5 afternoon, April 6 
morning and April 6 afternoon) consist of a "workshop", hands on sessions for 
16 registered participants. This part will be dealing with

-  The initial pre-screening using biophysical methods (Tatsiana 
Charnavets, CMS)

-  Dispensing target protein crystals to a fragment library (Jiri 
Pavlicek, CMS)

-  In situ testing of crystal diffraction, data collection and 
evaluation of the results (Jiri Pavlicek, CMS)

Due to generous Instruct funding, there will be no registration fees for the 16 
registered participants (hands-on sessions), all costs will be covered from the 
first night (April 4 to April 5) in hotel u Krbu in Vestec (ca. 15 minutes walk 
from the Biocev) to the departure from the hotel on April 7 after breakfast. 
For those accepted, of course you are most welcome to arrive earlier and / or 
depart from the Prague area later in order to discover / visit one of Europe's 
most beautiful cities, Prague. There are numerous hotels and "BnB" style 
accomodation available. This isn't part of the course and must be arranged by 
yourselves. Registered participants (and also the people wanting to attend the 
lectures only) must cover the cost of travelling to the venue.

Again, everyone is welcome for the lectures on April 5 morning, in the Biocev 
auditorium

All information (including Course poster) and details can be found on:
http://www.biocev.eu/event/instruct-ciisb-fragment-screening-course/

The deadline for submission of applications is February 9, 2018. Applications 
from laboratories located abroad are especially welcome.

Can you forward this information to anyone you think would be interested ? 
Thanks.

I wish you all a very good festive season.

Fred. Vellieux (Ph.D., HDR)
Centre of Molecular Structure
Institute of Biotechnology
Czech Academy of Sciences, BIOCEV
Prumyslova 595
252 50 Vestec
Czech Republic

Tel +420 325 873 786

-

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nezavazují. Text této zprávy nebo jejích príloh není návrhem na uzavrení 
smlouvy, ani prijetím prípadného návrhu na uzavrení smlouvy, ani jiným právním 
jednáním smerujícím k uzavrení jakékoliv smlouvy a nezakládá predsmluvní 
odpovednost Biotechnologického ústavu AV CR, v. v. i.

Disclaimer: If not expressly stated otherwise, this e-mail message (including 
any attached files) is intended purely for informational purposes and does not 
represent a binding agreement on the part of Institute of Biotechnology CAS. 
The text of this message and its attachments cannot be considered as a proposal 
to conclude a contract, nor the acceptance of a proposal to conclude a 
contract, nor any other legal act leading to concluding any contract; nor does 
it create any pre-contractual liability on the part of Institute of 
Biotechnology CAS

[ccp4bb] Reminder: Open position for a specialist in biological X-ray techniques, especially SAXS plus XRD and crystallisation

[Vellieux Frédéric]

Dear all,

This is a reminder that there is an open position for a specialist in 
biological X-ray techniques (especially SAXS plus X-ray diffraction and 
crystallisation) at the Centre of Molecular Structure (a CIISB and Instruct 
site) in Vestec, Prague region. The deadline for submission of applications is 
December 15, 2017. Since we have been asked the question: the position is open 
to both EU and non-EU nationals.

Feel free to pass along to colleagues who could be interested in the position. 
The advertisement can also be found on the Instruct web site, 
https://www.structuralbiology.eu/jobs/specialist-in-biological-x-ray-techniques-especially-small-angle-x-ray-scattering-saxs-and-single-cr/
 .

Thank you in advance,

Best regards,

F. Vellieux

Fred. Vellieux (Ph.D., HDR)
Centre of Molecular Structure
Institute of Biotechnology
Czech Academy of Sciences, BIOCEV
Prumyslova 595
252 50 Vestec
Czech Republic

Tel +420 325 873 786


Open position at the Centre of Molecular Structure, Institute of Biotechnology, 
Biocev:

Specialist in biological X-ray techniques, especially small-angle X-ray 
scattering (SAXS) and single crystal X-ray diffraction (plus crystallisation), 
full time

The Centre of Molecular Structure (CMS), part of CIISB (the Czech 
Infrastructure for Integrative Structural Biology) and one of the European 
network ERIC-Instruct sites, is operated by the Institute of Biotechnology CAS 
v.v.i. (Biocev, Vestec, central Bohemia, Czech Republic). The CMS is a 
technology platform providing access to scientific instrumentation and service 
to researchers, mostly working in "life sciences".  Details of the scientific 
equipment and services provided at the CMS can be consulted on 
http://www.biocev.eu/en/corefacilit/centre-of-molecular-structure/ and links 
therein.

We are looking for a specialist in X-ray techniques. The focus of the position 
is to provide excellent service in maintaining and operating a newly acquired 
state-of-the-art SAXS line and partially also the X-ray diffraction and 
crystallisation platform. User support providing training, assistance or 
sometimes full service (depending on the particular case) is also expected.

The successful candidate will also have the opportunity to collaborate in 
exciting research projects involving X-rays (both diffraction and scattering) 
in IBT research groups focused on structural biology. For such additional 
duties (that will represent up to 50% of the time),  practical knowledge of 
protein and nucleic acid purification and crystallisation is a plus. 
Participation to data collection trips at synchrotron radiation beam lines is 
expected.

The applicants (preferably having Ph.D. level experience) must have practical 
experience with bio-SAXS and have a strong interest in providing training and 
assistance to users and students.

The position offered is for an initial period of three years, with the 
possibility of renewal.

Applications (in electronic format, Word document or pdf files preferred) 
including a cover letter, curriculum vitae, and the names and addresses of 
three referees must be sent to the main office of the Institute of 
Biotechnology:

Institute of Biotechnology CAS, v.v.i.
Prumyslova 595
252 50 Vestec
Czech Republic
Phone: +420 325 873 700
E-mail: btu-off...@ibt.cas.cz

Any questions regarding this position can be directed to
Dr Frederic Vellieux, 
frederic.velli...@ibt.cas.cz
or Dr Jan Dohnalek, dohna...@ibt.cas.cz

Application deadline: 15 December 2017

Expected starting date: within the period January - March 2018
-

Upozornení: Není-li v této zpráve výslovne uvedeno jinak, má tato E-mailová 
zpráva nebo její prílohy pouze informativní charakter. Tato zpráva ani její 
prílohy v zádném ohledu Biotechnologický ústav AV CR, v. v. i. k nicemu 
nezavazují. Text této zprávy nebo jejích príloh není návrhem na uzavrení 
smlouvy, ani prijetím prípadného návrhu na uzavrení smlouvy, ani jiným právním 
jednáním smerujícím k uzavrení jakékoliv smlouvy a nezakládá predsmluvní 
odpovednost Biotechnologického ústavu AV CR, v. v. i.

Disclaimer: If not expressly stated otherwise, this e-mail message (including 
any attached files) is intended purely for informational purposes and does not 
represent a binding agreement on the part of Institute of Biotechnology CAS. 
The text of this message and its attachments cannot be considered as a proposal 
to conclude a contract, nor the acceptance of a proposal to conclude a 
contract, nor any other legal act leading to concluding any contract; nor does 
it create any pre-contractual liability on the part of Institute of 
Biotechnology CAS

[ccp4bb] Open position for a specialist in biological X-ray techniques (SAXS, X-ray diffraction, crystallisation)

[Vellieux Frédéric]

Dear all,

Could you pass the following announcement on to suitable candidates (including 
yourselves, of course) ?

Thank you.

Fred. Vellieux

Fred. Vellieux (Ph.D., HDR)
Centre of Molecular Structure
Institute of Biotechnology
Czech Academy of Sciences, BIOCEV
Prumyslova 595
252 50 Vestec
Czech Republic

Tel +420 325 873 786

Open position at the Centre of Molecular Structure, Institute of Biotechnology, 
Biocev:

Specialist in biological X-ray techniques, especially small-angle X-ray 
scattering (SAXS) and single crystal X-ray diffraction (plus crystallisation), 
full time

The Centre of Molecular Structure (CMS), part of CIISB (the Czech 
Infrastructure for Integrative Structural Biology) and one of the European 
network ERIC-Instruct sites, is operated by the Institute of Biotechnology CAS 
v.v.i. (Biocev, Vestec, central Bohemia, Czech Republic). The CMS is a 
technology platform providing access to scientific instrumentation and service 
to researchers, mostly working in "life sciences".  Details of the scientific 
equipment and services provided at the CMS can be consulted on 
http://www.biocev.eu/en/corefacilit/centre-of-molecular-structure/ and links 
therein.

We are looking for a specialist in X-ray techniques. The focus of the position 
is to provide excellent service in maintaining and operating a newly acquired 
state-of-the-art SAXS line and partially also the X-ray diffraction and 
crystallisation platform. User support providing training, assistance or 
sometimes full service (depending on the particular case) is also expected.

The successful candidate will also have the opportunity to collaborate in 
exciting research projects involving X-rays (both diffraction and scattering) 
in IBT research groups focused on structural biology. For such additional 
duties (that will represent up to 50% of the time),  practical knowledge of 
protein and nucleic acid purification and crystallisation is a plus. 
Participation to data collection trips at synchrotron radiation beam lines is 
expected.

The applicants (preferably having Ph.D. level experience) must have practical 
experience with bio-SAXS and have a strong interest in providing training and 
assistance to users and students.

The position offered is for an initial period of three years, with the 
possibility of renewal.

Applications (in electronic format, Word document or pdf files preferred) 
including a cover letter, curriculum vitae, and the names and addresses of 
three referees must be sent to the main office of the Institute of 
Biotechnology:

Institute of Biotechnology CAS, v.v.i.
Prumyslova 595
252 50 Vestec
Czech Republic
Phone: +420 325 873 700
E-mail: btu-off...@ibt.cas.cz

Any questions regarding this position can be directed to
Dr Frederic Vellieux, frederic.velli...@ibt.cas.cz
or Dr Jan Dohnalek, dohna...@ibt.cas.cz

Application deadline: 15 December 2017

Expected starting date: within the period January - March 2018

-

Upozornení: Není-li v této zpráve výslovne uvedeno jinak, má tato E-mailová 
zpráva nebo její prílohy pouze informativní charakter. Tato zpráva ani její 
prílohy v zádném ohledu Biotechnologický ústav AV CR, v. v. i. k nicemu 
nezavazují. Text této zprávy nebo jejích príloh není návrhem na uzavrení 
smlouvy, ani prijetím prípadného návrhu na uzavrení smlouvy, ani jiným právním 
jednáním smerujícím k uzavrení jakékoliv smlouvy a nezakládá predsmluvní 
odpovednost Biotechnologického ústavu AV CR, v. v. i.

Disclaimer: If not expressly stated otherwise, this e-mail message (including 
any attached files) is intended purely for informational purposes and does not 
represent a binding agreement on the part of Institute of Biotechnology CAS. 
The text of this message and its attachments cannot be considered as a proposal 
to conclude a contract, nor the acceptance of a proposal to conclude a 
contract, nor any other legal act leading to concluding any contract; nor does 
it create any pre-contractual liability on the part of Institute of 
Biotechnology CAS

Re: [ccp4bb] Help needed finding hit condition

[Vellieux Frédéric]

Hello,

Such pH drifts are rather common with crystallisation screens. Have you tried 
to produce other precipitant solutions with ca. 47% PEG 1000, 80 mM Potassium 
bromide but having a pH of (say) 6.2 ? A pH rangle close to that where your 
crystals were obtained. This would mean changing buffering agent to… MES 
perhaps ?

Cheers,

Fred.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jonathan 
Bailey
Sent: Monday, July 31, 2017 2:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Help needed finding hit condition

Dear CCP4bb community

I apologies for the slightly off topic post.

We have recently had success crystallizing a membrane protein (diffraction > 3 
Å at a synchrotron source) using the in meso method, the hit condition was from 
the Jena Bioscience screen Pi-minimal condition number #57.

Hit condition – 47.1 % w/v PEG1000, 150 mM Tris pH 8.0, 80 mM Potassium bromide

The screen is old and expired 12/20/2013 (lot # JBS00013133), we have tried to 
reproduce the crystals using homemade optimization screens around the hit 
condition but have not had any success. We have tried reproducing the hit using 
a new (not expired) Pi-minimal screen but had no success. We are only able to 
reproduce the crystals using the expired screen and we do not have much of it 
left.

We went back and tested the pH of the condition that had given crystals, the 
expected pH was 7.9 but we found it to be 6 – 6.5 using a pH indicator strip. 
We believe the drop in pH is caused by oxidative degradation of the PEG1000 
resulting in the formation of carboxylic acid species.

We have contacted Jena Bioscience to try and get some of the old screen stock 
but unfortunately they do not have any.

My question is does anyone out there happen to have any expired screen stocks 
of this Pi-minimal condition (#57), ideally from the same lot (lot # 
JB200013133), that they would be willing to send us.

Does anyone have any advice as to how to reproduce the condition? We’ve 
considered bubbling oxygen through and heating the sample to accelerate the 
oxidation process.

King Regards

Jonathan Bailey (PhD student)

Professor Martin Caffrey Lab MS group Trinity College Dublin
-

Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato E-mailová 
zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její 
přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu 
nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření 
smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním 
jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní 
odpovědnost Biotechnologického ústavu AV ČR, v. v. i.

Disclaimer: If not expressly stated otherwise, this e-mail message (including 
any attached files) is intended purely for informational purposes and does not 
represent a binding agreement on the part of Institute of Biotechnology CAS. 
The text of this message and its attachments cannot be considered as a proposal 
to conclude a contract, nor the acceptance of a proposal to conclude a 
contract, nor any other legal act leading to concluding any contract; nor does 
it create any pre-contractual liability on the part of Institute of 
Biotechnology CAS

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

[Vellieux Frédéric]

Hello again,

Back in 2001 people still remembered the difference between Rsym and Rmerge. 16 
years later people seem to have forgotten. I will try to dig even more ancient 
references… Archaeology is the name of the game.

http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html

Cheers,

Fred.

From: James Foadi [mailto:james_fo...@yahoo.co.uk]
Sent: Tuesday, July 11, 2017 10:03 AM
To: Vellieux Frédéric <frederic.velli...@ibt.cas.cz>; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

Hello Frederic. Interesting. Have you got some reference on this to share?

James

Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science and 
Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: 
james.fo...@diamond.ac.uk<mailto:james.fo...@diamond.ac.uk> alternative email: 
j.fo...@imperial.ac.uk<mailto:j.fo...@imperial.ac.uk> personal web page: 
http://www.jfoadi.me.uk

On Tuesday, 11 July 2017, 7:15, Vellieux Frédéric 
<frederic.velli...@ibt.cas.cz<mailto:frederic.velli...@ibt.cas.cz>> wrote:

Hello,

I think this needs a little bit of crystarchaeology.

Rmerge and Rsym used to be different. This was at a time when data sets were 
typically collected from several crystals. Pre-cryo cooling, with data recorded 
on photographic film (Arndt-Wonacott cameras).

Rmerge = agreement R-factor from data from several crystals;
Rsym = agreement R-factor from symmetry-equivalents within one crystal.

[I just type "agreement R-factor" in order not to have to type the formulae]

At that time, people were confused about these two terms.

Nowadays both are (used as) synonyms.

Cheers,

Fred.

-Original Message-
From: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of Phil 
Evans
Sent: Monday, July 10, 2017 5:43 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

What is the difference between Rmerge and Rsym - I thought they were the same?
Rrim == Rmeas I think

Phil



> On 10 Jul 2017, at 15:18, John Berrisford 
> <j...@ebi.ac.uk<mailto:j...@ebi.ac.uk>> wrote:
>
> Dear Herman
>
> The new PDB deposition system (OneDep) allows you to enter values for Rmerge, 
> Rsym, Rpim, Rrim and / or CC half. If, during deposition, you do not provide 
> a value for any of these metrics then we will ask you for a value for one of 
> them.
>
> Also, PDB format is a legacy format for the PDB. In 2014 mmCIF became the 
> archive format for the PDB and some large entries are no longer distributed 
> in PDB format. mmCIF is not limited by the constraints of punch cards.
>
> Please see
> https://www.wwpdb.org/documentation/file-formats-and-the-pdb
>
> Regards
>
> John
>
> PDBe
>
>
>
> On 10/07/2017 09:26, 
> herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com> wrote:
>> Dear All,
>>
>> For me this whole discussion is an example of a large number of people 
>> barking at the wrong tree. The real issue is not whether data processing 
>> programs print amongst many quality indicators an Rmerge as well, but the 
>> fact that the PDB and many journals still insist on using the Rmerge as 
>> primary quality indicator. As long as this is true, novice scientist might 
>> be led to believe that Rmerge is the most important quality indicator. As 
>> soon as the PDB and the journals request some other indicator, this will be 
>> over. So that is where we should direct our efforts to.
>>
>> I don't understand at all, why the PDB still insists on an obsolete quality 
>> indicator. However, the PDB format for the coordinates also dates back to 
>> the 1960's to be used with punch cards.
>>
>> My 2 cents.
>> Herman
>>
>>
>>
>> -Ursprüngliche Nachricht-
>> Von: CCP4 bulletin board 
>> [mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] Im Auftrag
>> von Edward A. Berry
>> Gesendet: Samstag, 8. Juli 2017 22:31
>> An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
>> Betreff: Re: [ccp4bb] Rmergicide Through Programming
>>
>> But R-merge is not really narrower as a fraction of the mean value- it just 
>> gets smaller proportionantly as all the numbers get smaller:
>> RMSD of .0043 for R-meas multiplied by factor of 0.022/.027 gives 0.0035 
>> which is the RMSD for Rmerge. The same was true in the previous example. You 
>> could multiply R-meas by .5 or .2 and get a sharper distribution yet! And 
>> that factor would be constant, where this only applies for super-low 
>> redundancy.
>>
>> On 07/08/2017 03:23 PM, James Holton wrote:
>>> The ex

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

[Vellieux Frédéric]

Hello,

I think this needs a little bit of crystarchaeology.

Rmerge and Rsym used to be different. This was at a time when data sets were 
typically collected from several crystals. Pre-cryo cooling, with data recorded 
on photographic film (Arndt-Wonacott cameras).

Rmerge = agreement R-factor from data from several crystals;
Rsym = agreement R-factor from symmetry-equivalents within one crystal.

[I just type "agreement R-factor" in order not to have to type the formulae]

At that time, people were confused about these two terms.

Nowadays both are (used as) synonyms.

Cheers,

Fred.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Evans
Sent: Monday, July 10, 2017 5:43 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

What is the difference between Rmerge and Rsym - I thought they were the same?
Rrim == Rmeas I think

Phil



> On 10 Jul 2017, at 15:18, John Berrisford  wrote:
>
> Dear Herman
>
> The new PDB deposition system (OneDep) allows you to enter values for Rmerge, 
> Rsym, Rpim, Rrim and / or CC half. If, during deposition, you do not provide 
> a value for any of these metrics then we will ask you for a value for one of 
> them.
>
> Also, PDB format is a legacy format for the PDB. In 2014 mmCIF became the 
> archive format for the PDB and some large entries are no longer distributed 
> in PDB format. mmCIF is not limited by the constraints of punch cards.
>
> Please see
> https://www.wwpdb.org/documentation/file-formats-and-the-pdb
>
> Regards
>
> John
>
> PDBe
>
>
>
> On 10/07/2017 09:26, herman.schreu...@sanofi.com wrote:
>> Dear All,
>>
>> For me this whole discussion is an example of a large number of people 
>> barking at the wrong tree. The real issue is not whether data processing 
>> programs print amongst many quality indicators an Rmerge as well, but the 
>> fact that the PDB and many journals still insist on using the Rmerge as 
>> primary quality indicator. As long as this is true, novice scientist might 
>> be led to believe that Rmerge is the most important quality indicator. As 
>> soon as the PDB and the journals request some other indicator, this will be 
>> over. So that is where we should direct our efforts to.
>>
>> I don't understand at all, why the PDB still insists on an obsolete quality 
>> indicator. However, the PDB format for the coordinates also dates back to 
>> the 1960's to be used with punch cards.
>>
>> My 2 cents.
>> Herman
>>
>>
>>
>> -Ursprüngliche Nachricht-
>> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
>> von Edward A. Berry
>> Gesendet: Samstag, 8. Juli 2017 22:31
>> An: CCP4BB@JISCMAIL.AC.UK
>> Betreff: Re: [ccp4bb] Rmergicide Through Programming
>>
>> But R-merge is not really narrower as a fraction of the mean value- it just 
>> gets smaller proportionantly as all the numbers get smaller:
>> RMSD of .0043 for R-meas multiplied by factor of 0.022/.027 gives 0.0035 
>> which is the RMSD for Rmerge. The same was true in the previous example. You 
>> could multiply R-meas by .5 or .2 and get a sharper distribution yet! And 
>> that factor would be constant, where this only applies for super-low 
>> redundancy.
>>
>> On 07/08/2017 03:23 PM, James Holton wrote:
>>> The expected distribution of Rmeas values is still wider than that of 
>>> Rmerge for data with I/sigma=30 and average multiplicity=2.0. Graph 
>>> attached.
>>>
>>> I expect that anytime you incorporate more than one source of information 
>>> you run the risk of a noisier statistic because every source of information 
>>> can contain noise.  That is, Rmeas combines information about multiplicity 
>>> with the absolute deviates in the data to form a statistic that is more 
>>> accurate that Rmerge, but also (potentially) less precise.
>>>
>>> Perhaps that is what we are debating here?  Which is better? accuracy or 
>>> precision?  Personally, I prefer to know both.
>>>
>>> -James Holton
>>> MAD Scientist
>>>
>>> On 7/8/2017 11:02 AM, Frank von Delft wrote:
 It is quite easy to end up with low multiplicities in the low resolution 
 shell, especially for low symmetry and fast-decaying crystals.

 It is this scenario where Rmerge (lowres) is more misleading than Reas.

 phx


 On 08/07/2017 17:31, James Holton wrote:
> What does Rmeas tell us that Rmerge doesn't?  Given that we know the 
> multiplicity?
>
> -James Holton
> MAD Scientist
>
> On 7/8/2017 9:15 AM, Frank von Delft wrote:
>> Anyway, back to reality:  does anybody still use R statistics to 
>> evaluate anything other than /strong/ data?  Certainly I never look at 
>> it except for the low-resolution bin (or strongest reflections). 
>> Specifically, a "2%-dataset" in that bin is probably healthy, while a 
>> "9%-dataset" probably Has Issues.
>>
>> In which case, back to Jacob's question:  what does 

Re: [ccp4bb] Incorrect Structure in the PDB

[Vellieux Frédéric]

Hello,

I think it makes sense to have a look at the policy of the PDB concerning 
obsoleting structures:

The publication is retracted. The associated PDB entry will be obsoleted if 
requested by the journal. If a request has not been received, the wwPDB will do 
its best to contact the depositor and co-authors, (former) PIs, journal 
editors, etc. when made aware of the retraction. If the reason(s) for 
retraction were such that the associated PDB entry needs to be made obsolete, 
the wwPDB will obsolete the entry. The citation in the obsoleted entry is the 
published journal retraction.
The structure is incorrect, and the entry author obsoletes the entry. The entry 
must contain a statement as to the reason for obsoleting the structure.
A third-party (such as the employer) requests that the entry is obsoleted 
(e.g., in case of malfeasance). The citation in the obsoleted entry must be a 
published explanation and retraction in a peer-reviewed journal.

Source: https://www.wwpdb.org/documentation/policy

Cheers,

Fred.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Trevor 
Sewell
Sent: Tuesday, June 27, 2017 8:35 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Incorrect Structure in the PDB


I have come across a key paper in my field that describes an enzyme mechanism. 
Their work is based on a deposited structure – by other authors - that is 
incorrectly interpreted.

Is there a process for removing a demonstrably wrong structure (deposited by 
others) from the PDB and replacing it with a correctly interpreted structure 
based on the original data? Or is there an alternative, and generally 
recognized, way of getting the correct structure in the public domain?

Many thanks for your advice on this matter.

Trevor Sewell

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Re: [ccp4bb] Why Does Detwinning Not Work?

[Vellieux Frédéric]

Hello Jacob,

Quoting you, "Please let me know if you have a case where detwinning saved the 
day".

Well you asked for it so here is one example where twinning saved the day: 
"Crystal structure of pb9..." by Flayhan et al. (2014), J. Virol. 88 (2), 
820-828. Without detwinning I think there would have been no crystal structure 
in the end...

Cheers,

Fred.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, 
Jacob
Sent: Tuesday, October 11, 2016 2:15 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Why Does Detwinning Not Work?

Dear Crystallographers,

Based on some data sets I have looked at and anecdotal-type evidence here and 
there I have gotten the impression that detwinning does not help in structure 
solution. (Please let me know if you have a case where detwinning saved the 
day.) Is there a clear answer to this enigma anywhere, to anyone's knowledge? 
Wouldn't it seem that *any* detwinning would be better than *no* detwinning? I 
understand that the errors explode as one approaches 50% twins and does 
detwinning, but still, I don't think one *loses* information by detwinning, 
right? Take the case of a 33% twin: since the twin-reflections are on average 
about half the intensity of the non-twin, and since they are generally not 
correlated in intensity, isn't this like having noise added at 50% of the 
measured intensity? So why does detwinning make things worse generally? Is 
there something wrong in the assumptions underlying the detwinning algorithm, 
or perhaps something about the calculation that throws things off?

A related sub-enigma: why is MR generally immune to twinning, but anomalous 
methods are susceptible?

All the best,

Jacob Keller

***
Jacob Pearson Keller, PhD
Research Scientist
HHMI Janelia Research Campus / Looger lab
Phone: (571)209-4000 x3159
Email: kell...@janelia.hhmi.org
***

-

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Re: [ccp4bb] Off topic: textbook proteins for crystallization

[Vellieux Frédéric]

Xylose Isomerase is another one.

Cheers,

Fred.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of WENHE 
ZHONG
Sent: Wednesday, April 20, 2016 11:39 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Off topic: textbook proteins for crystallization

Dear CCP4 members,

We would like to choose some proteins that are “extremely” easy to grow good 
crystals. There is only one protein I can think of which is lysozyme. Do you 
have other candidates that you use as a textbook protein in crystallization?

Thank you.

Kind regards,
Wenhe
-

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Re: [ccp4bb] New crystallization technique

[Vellieux Frédéric]

Hi Bernhard,

We've been thinking along the same lines over here (but then our approach was 
far more "Sci Fi" like than yours, that is truly applicable in a real 
laboratory environment): we were devising ways here to crystallise in space, in 
black holes. Too bad, you beat us at it. Congratulations, really, well 
deserved. I foresee a trip to Stockholm for you in the future.

Anyway now that we have been scooped, we won't be able to publish our 
preliminary results (carried out at CERN): the method indeed works. However, 
crystal growth slows down when approaching the "center" of the black hole (this 
is what our preliminary experiments at CERN have shown), and our mathematical 
modelling indicates that all the macromolecule will have aggregated together to 
form a single "perfect" crystal when gravity is infinite (but then time has 
stopped and we were trying to find innovative ways to solve this time barrier 
of eternity). Strangely enough, modelling has also shown that in the case of 
crystallisation in plates, all the drops would be able to cross the adhesive 
tape to gather into one giant droplet, in which a single perfect giant crystal 
would appear. These crystals would be of sufficient volume even for the latest 
pocket-sized neutron sources. But then, again, too bad: you beat us at it.

Fred.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von 
Delft
Sent: Friday, April 1, 2016 7:36 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] New crystallization technique

Sounds awesome.  How do you get the crystals out again?

On 01/04/2016 03:33, Bernhard Rupp (Hofkristallrat a.D.) wrote:
> Hi Fellows,
>
> after quite some tinkering we finally got an exciting new
> crystallization technique to work that has produced exciting results
> in the few cases tested so far.
>
> I attach the first page of the paper. The theory is somewhat involved
> (supplemental material) but the complete letter is available from
> http://www.hofkristallamt.org/Rupp_2016_Phys_Rev_Letters_116(13)_Hyper
> gravit
> y.pdf
>
>
> Best regards, BR
> -
> Bernhard Rupp
> 001 (925) 209-7429
> +43 (676) 571-0536
> b...@ruppweb.org
> http://www.ruppweb.org/
> -
> Physicist are there to find the laws of nature.
> Engineers are there to work around them.
> -
>
-

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Re: [ccp4bb] cryo for crystals with CTAB as precipitant

[Vellieux Frédéric]

Hi there,

What about trying the ''olde'' method of a thin layer of oil around the 
crystal? No guarantee whatsoever that this will work but if you don't try it 
you won't know.

Fred.

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Alejandro 
Madrigal Carrillo [amadri...@email.ifc.unam.mx]
Sent: Monday, February 22, 2016 11:00 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] cryo for crystals with CTAB as precipitant

Dear All,


I got crystals using CTAB 10mM as precipitant, but I have had problems with the 
cryoprotectant solution which freezes.  Has anybody collected crystallographic 
data with crystals grown in this detergent? What cryoprotectant do you 
recommend to test?


Two papers report use of glycerol as cryoprotectant (Brown MA et al., 2005; 
glycerol 40% Ren A et al, 2010 ). But at -20oC the reservoir solution plus 
cryoprotectant freezes. I tried with many cryoprotectants  (glycerol 40%, EG 
35%, PEG 400 35%, hexanediol 50%, Sucrose 28%, Xylitol 30%, etc) but solution 
at -20oC looks cloudy or frozen.


Any suggestion will be appreciated.


Thanks in advance,

Alejandro Madrigal Carrillo, M.Sc.
Laboratorio de Biofísica de Biomacromoléculas, 205 sur
Departamento de Bioquímica y Biología Estructural
Instituto de Fisiología Celular
Universidad Nacional Autónoma de México
Circuito Exterior S/N. Ciudad Universitaria
México, D.F., México, 04510
Teléfono: +52 55 5622 5640
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