[ccp4bb] How to include in refinement high resolution shells with VERY low completeness ?

[Ivan Shabalin]

Dear CCP4BB,

There seems to be a general consensus for extending data to higher 
resolution to include as much meaningful data as possible. "Meaningful" 
can be defined in different ways. I heard/read opinions such as 0.5 
CC1/2, 0.3 CC1/2, 0.15 CC1/2, and stepped (paired) refinement. The 
latter seems to be one of the most rigorous options according to many 
crystallographers.


Including more data sounds like a good thing, but, it sometimes results 
in low completeness in high resolution shells. As far as i understand, 
this may result from:


a) anisotropic diffraction (if a software cuts of resolution in 
non-isotropic way)


b) sub-optimal data collection (e.g. due to limitations of the 
instrument, such as minimum detector distance allowed, absence of kappa, 
limits on oscillation range)


In the commonly referred paper, the completeness is 96% in the highest 
shell (Karplus, P. A., & Diederichs, K. (2012). Linking crystallographic 
model and data quality. Science (New York, N.Y.), 336(6084), 1030–1033.) 
In other words, these tests were performed for an almost complete dataset.


I used to think that more data is always better, but, as I learned 
recently from Clemens Vonrhein, the resulting low completeness may cause 
model bias in the maps.


Indeed, REFMAC by default tries to restore missing reflections, which 
are approximated as DFc 
(https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html). 



We tried using the keyword "mapcalculate free include" and "mapcalculate 
free exclude" for one of our structures (~1.3A, P1), and it did seem to 
improve the maps a little - we saw more meaningful features.


But, I still have several questions:

1) Does using "mapcalculate free include" in REFMAC represent a sound 
solution to this problem? Does this "no fill-in at all" solution 
constitute a significant problem?


2) Are there any other concerns about using data with low completeness 
in highest shells?


3) STARANISO website suggests a way of handling this problem 
(http://staraniso.globalphasing.org/test_set_flags_about.html). But, 
would not REFMAC "fill-in" all the reflections for map coefficients 
calculation to isotropic completeness anyway?


4) What is your personal approach to handling this issue? Is there 
completeness value in the last shell that is too low to include it in 
Table 1?


Many thanks,

Ivan

With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/









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Re: [ccp4bb] Importance of temperature during initial crystallization screening

[Newman, Janet (Manufacturing, Parkville)]

Interesting topic,

Certainly the two papers suggested by Georg are relevant, and I fully agree 
with the comments from Daniel that it is hard to predict the behaviour of any 
given protein from a statistical analysis of proteins in general.

I find it interesting that even with the use of incubators to store and image 
crystal experiments (which takes away the issue of setting up plates in the 
cold) we still find that our facility users have a strong bias towards 20C over 
8C – for example, our standard initial screen (Shotgun) has been set up just 
over 360 times in the last year, 216 times at 20C and 135 times at 8C. It is 
equally easy to type “20” or “8” into the request for the plate storage 
temperature, so its not ease of crystallisation setup which dictates this. It 
might well be that the thought of harvesting crystals from cold plates puts 
people off the lower temperature?

A quick search through our database shows that of the shotgun screens that were 
set up in the last year, 51% of those set up at 20C were (human) scored as 
containing crystals, and 47% of those set up at 8C were (human) scored as 
containing crystals. So the rate of crystal formation at the two temperature is 
essentially the same.

Patrick, I can’t comment on “unusual” temperatures, as I don’t have any 
significant experience with going outside the 4-20 region.

Cheers, Janet


From: CCP4 bulletin board  On Behalf Of Georg Mlynek
Sent: Friday, 2 August 2019 5:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Importance of temperature during initial crystallization 
screening


Hi Sergei, this publication should be useful for you.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756611/

Additionally it is proposed that when your protein is not so stable (lower Tm), 
one should incubate the screens at 4C.

http://scripts.iucr.org/cgi-bin/paper?S0907444911036225

Br, Georg.


Am 2019-08-01 um 2:54 PM schrieb Patrick Shaw Stewart:

Hi Sergei

We did some data-mining on this way, way back, in 2004.

See the second section in this link

https://www.douglas.co.uk/PDB_data.htm

When you consider the non-standard temps - ie NOT 4C or 20C - it looks as 
though the higher-end temps may work better.  But of course it's hard to make 
sense of the results of a martingale.

Thx Patrick

PS Janet (Newman) do you have anything more up-to-date on this?



On Thu, Aug 1, 2019 at 10:24 AM Sergei Strelkov 
mailto:sergei.strel...@kuleuven.be>> wrote:

Dear all,



I wondered if someone could point me to a recent study on the importance of 
temperature during initial search for crystallization conditions. It would be 
interesting to see any real statistics on this subject.



We typically try to perform screening at at two temperatures, such as 
duplicating a given kit screen at 20C and 4C if there is enough sample. My 'gut 
feeling' is that this is not as important as sampling the chemical space though.



Thank you!

Sergei



Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
Pharmaceutical Sciences, KU Leuven O, Campus Gasthuisberg, Herestraat 49 bus 
822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 32 Lab 
pages: 
http://pharm.kuleuven.be/Biocrystallography



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 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
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Re: [ccp4bb] Importance of temperature during initial crystallization screening

[Daniel M. Himmel, Ph. D.]

Sergei,

That depends heavily on the protein, so I don't know if a statistical study
will accurately reflect the
importance of temperature.  With some proteins, no matter how thoroughly
you sample chemical
space, temperature is critical, and a study would have to focus on such a
protein.  The data available
is probably biased, because it is far easier to do crystallization
experiments close to room temperature,
and most proteins for which structures have actually been determined
probably were not crystallized at
4 degrees C.  I would venture to guess that there is a large protein
structure space that has yet to be explored
comprising proteins that don't normally form highly ordered crystals close
to room temperature (at least in
their native states, i.e., without creative protein redesigns coupling the
structure of interest to an additional
subunit or domain that facilitates crystallization at higher temperatures).

Daniel M. Himmel, Ph. D.

E-mail :  danielmhim...@gmail.com

URL  :  http://www.DanielMhimmel.com/index_Xtal.html


On Thu, Aug 1, 2019 at 5:24 AM Sergei Strelkov 
wrote:

> Dear all,
>
>
> I wondered if someone could point me to a recent study on the importance
> of temperature during initial search for crystallization conditions. It
> would be interesting to see any real statistics on this subject.
>
>
> We typically try to perform screening at at two temperatures, such as
> duplicating a given kit screen at 20C and 4C if there is enough sample. My
> 'gut feeling' is that this is not as important as sampling the chemical
> space though.
>
>
> Thank you!
>
> Sergei
>
>
> Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
> Pharmaceutical Sciences, KU Leuven O, Campus Gasthuisberg, Herestraat 49 
> bus 822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 
> 32 Lab pages: http://pharm.kuleuven.be/Biocrystallography 
> 
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] General interest

[John R Helliwell]

 Dear Colleagues,
The details, including all abstracts, for the IUCr Satellite at ECM32 Vienna on 
Data Science Skills in Publishing for Editors, Authors and Referees can be 
found here:-
https://forums.iucr.org/viewtopic.php?f=39=419 
Best wishes,
John 
Emeritus Professor John R Helliwell DSc
Chairman of the IUCr Committee on Data 


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Re: [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

[Ivan Shabalin]

Ernst,

Depositing images is very easy these days with services like SbGrid, 
proteindiffraction.org (also known as IRRMC), and Zenodo.


For example, for depositing images to proteindiffraction.org (which is 
run by Wladek Minor) you just need to create an account, tar your 
images, upload them to the server, and specify the PDB code. All the 
metadata will be extracted and curated by the server. And you dont even 
need to tell the DOI of the dataset to the PDB - RCSB will automatically 
communicate to proteindiffraction.org  and link the PDB entry to the 
DOI. In this scenario, the deposition to the PDB goes first, and the 
deposition of images goes second.


Thanks,

Ivan


With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/

On 8/1/19 03:48, Schonbrunn, Ernst wrote:
I totally agree with the deposition of raw data along with the 
coordinate set(s).  It is the only way to independently validate a model 
that has been generated by somewhat subjective procedures of data 
reduction and scaling, structure solution and refinement.


More importantly, algorithms and procedures steadily evolve, thanks to 
you folks.   Raw data of important structures re-processed using future 
(or present) algorithms may result in much clearer pictures of 
structure-function relationships than those of original interpretations.


What would be the best way to deposit raw data?  How much would this add 
to the storage and maintenance capabilities of RCSB?  Likely requires 
additional funding.  If grant opportunities exist one could make a 
strong case.


Ernst

*From:* CCP4 bulletin board  *On Behalf Of *Kay 
Diederichs

*Sent:* Thursday, August 1, 2019 1:54 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* EXT: Re: [ccp4bb] [6HR5] collected on an Eiger so Rmerge not 
relevant


First of all, you are of course correct, Rmerge (as Rmeas, Rpim, CC1/2, 
I/sigma ...) is not detector-dependent.


Second, when looking at the "experiment" section of the PDB deposition, 
I note that some Rmerge values are even given there! The statistics 
there are dubious, e.g. seemingly the I/sigma in the high resolution 
shell is 2.2 meaning that they could have used higher resolution data.


Third, look at the sliders on the entry page: the validity of this PDB 
entry is suspicious - quite bad Rfree and geometry.


One more case for the deposition of raw data. In my eyes, the RCSB 
policy should be that raw data must be deposited when accepting such a 
bad entry.


HTH,
Kay

On Wed, 31 Jul 2019 17:49:47 +0100, Weston Lane > wrote:


 >I was looking at the following structure in the PDB: 
http://www.rcsb.org/structure/6HR5 I noticed that the R/Rfree stats were 
pretty high for 2.9A resolution so I followed up by looking for the 
"Table 1" statistics in the journal article. Link to article: 
https://www.nature.com/articles/s41589-019-0311-9 Table is located in 
the supplemental materials "Table 9".

 >
 >From the processing statistics it's clear that the diffraction from 
that crystal wasn't great but I don't want to get hung up on the 
processing or the validity of the structure. What struck me what this 
little explanation the authors included to explain the outlier 
statistics in the table:

 >
 >"Crystal of P36_S1_25 was collected on an Eiger detector, so Rmerge 
data are not relevant."

 >
 >We all know that Rmerge isn't a great metric for data quality but I've 
never heard that it's detector-dependent. This doesn't make sense to me. 
If it's actually true can someone explain, please?

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



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else is unauthorized. Any unauthorized reader is hereby notified that 
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Re: [ccp4bb] [EXTERNAL] [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

[Ivan Shabalin]

Clemens,

I have not looked at the structure, but the issues you described are 
alarming. It is a little sad because the paper itself seems very 
comprehensive and rigorous.


It is great to hear so many voices advocating for depositing raw images. 
I hope more researchers will be convinced to do so, especially because 
depositing images is very easy these days with services like SbGrid, 
proteindiffraction.org (also known as IRRMC), and Zenodo.


Ivan



With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/

On 8/1/19 05:03, Clemens Vonrhein wrote:

Hi Ivan,

On Wed, Jul 31, 2019 at 05:32:24PM -0400, Ivan Shabalin wrote:

And Rfree of 36% seems really high.


If you look at the maps (e.g. after some re-refinement with your
favourite refinement package) it seems as if there are a few sequence
shifts (around and after A78), some poor density and additional
unmodelled density ... which all add to those high R-values I guess.

But given the poor data quality and no raw images (to check and maybe
improve upon that), I didn't feel the urge to delve into that any
further ;-)

Cheers

Clemens







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Re: [ccp4bb] [EXTERNAL] [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

[Kay Diederichs]

Hi Clemens,

thank you for looking into this! To me, a "structure" that has a few sequence 
shifts does not appear useful at all - rather, it taints the PDB. This one 
should be blacklisted, like 6MO[0,1,2]. It's painful to learn that despite all 
the validation that is performed before and at deposition, such entries slip 
into the PDB !

Can PDB_REDO or validation tools identify or even correct such errors? I guess 
they cannot, currently. Probably it's difficult to diagnose the real problem 
underlying Ramachandran outliers and bad density.

Could  the RCSB, as part of validation, run a pipeline (like ARP/wARP, 
phenix.autobuild, Buccaneer/refmac) that uses the submitted model only to 
generate starting phases, and iteratively builds a new model that is then 
compared to the submitted model? I guess that could be done, at least as long 
as the resolution is high enough - how high is high enough?.

In my experience, in cases where one can correct errors based on the deposited 
structure factors, also the raw data are often suboptimally processed  - the 
existence of expert-visible errors in the end result suggests that many 
upstream decisions can and should be improved as well. The only way to improve 
the situation would be deposition of raw data (Zenodo, SBGrid, 
proteindiffraction.org, ...), with a link in the PDB. 

best,
Kay

On Thu, 1 Aug 2019 10:03:49 +0100, Clemens Vonrhein 
 wrote:

>Hi Ivan,
>
>On Wed, Jul 31, 2019 at 05:32:24PM -0400, Ivan Shabalin wrote:
>> And Rfree of 36% seems really high.
>
>If you look at the maps (e.g. after some re-refinement with your
>favourite refinement package) it seems as if there are a few sequence
>shifts (around and after A78), some poor density and additional
>unmodelled density ... which all add to those high R-values I guess.
>
>But given the poor data quality and no raw images (to check and maybe
>improve upon that), I didn't feel the urge to delve into that any
>further ;-)
>
>Cheers
>
>Clemens
>
>--
>
>*--
>* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
>* Global Phasing Ltd., Sheraton House, Castle Park
>* Cambridge CB3 0AX, UK   www.globalphasing.com
>*--
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Importance of temperature during initial crystallization screening

[Patrick Shaw Stewart]

Hi Sergei

We did some data-mining on this way, way back, in 2004.

See the second section in this link

https://www.douglas.co.uk/PDB_data.htm


When you consider the *non-standard *temps - ie NOT 4C or 20C - it *looks*
as though the higher-end temps *may *work better.  But of course it's hard
to make sense of the results of a martingale.

Thx Patrick

PS Janet (Newman) do you have anything more up-to-date on this?



On Thu, Aug 1, 2019 at 10:24 AM Sergei Strelkov 
wrote:

> Dear all,
>
>
> I wondered if someone could point me to a recent study on the importance
> of temperature during initial search for crystallization conditions. It
> would be interesting to see any real statistics on this subject.
>
>
> We typically try to perform screening at at two temperatures, such as
> duplicating a given kit screen at 20C and 4C if there is enough sample. My
> 'gut feeling' is that this is not as important as sampling the chemical
> space though.
>
>
> Thank you!
>
> Sergei
>
>
> Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
> Pharmaceutical Sciences, KU Leuven O, Campus Gasthuisberg, Herestraat 49 
> bus 822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 
> 32 Lab pages: http://pharm.kuleuven.be/Biocrystallography 
> 
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36



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Re: [ccp4bb] [EXTERNAL] [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

[Clemens Vonrhein]

Hi Ivan,

On Wed, Jul 31, 2019 at 05:32:24PM -0400, Ivan Shabalin wrote:
> And Rfree of 36% seems really high.

If you look at the maps (e.g. after some re-refinement with your
favourite refinement package) it seems as if there are a few sequence
shifts (around and after A78), some poor density and additional
unmodelled density ... which all add to those high R-values I guess.

But given the poor data quality and no raw images (to check and maybe
improve upon that), I didn't feel the urge to delve into that any
further ;-)

Cheers

Clemens

-- 

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



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[ccp4bb] Improve your previously released coordinates with OneDep

[David Armstrong]

Dear CCP4BB,

The wwPDB are pleased to announce the availability of PDB versioning, 
allowing depositors to update their entries while retaining the same PDB 
accession code.


Depositors can now submit new coordinates for existing entries. 
Initially, this is limited to PDB entries that were submitted via the 
OneDep system, which was introduced in 2014. The wwPDB plans to extend 
this functionality to entries deposited in the legacy systems (ADIT and 
Autodep) in future, and will announce a timeline for this in due course.


Requests should be initiated using the OneDep communication panel within 
the deposition session for the entry in question. Once submitted, the 
revised model will be processed by wwPDB biocurators and a new version 
released. Versioning of PDB entries will be limited to changes in the 
coordinate files, with no changes permitted to the deposited 
experimental data. PDB versioning will be limited to one replacement per 
PDB entry per year, and three entries per Principal Investigator per year.


For more, please visit the wwPDB news pages 
.



--
David Armstrong
Outreach and Training Coordinator
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492544




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Re: [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

[Loes Kroon-Batenburg]

Dear Ernst,

There are several ways to deposit raw data, such as IRRMC, SBGrid and 
Zenodo. The data are findable through a doi. During the depostion in the 
PDB the doi linking to the raw data can be provided. See e.g.  
http://www.ebi.ac.uk/pdbe/entry/pdb/5cy2 where is link to the raw data 
in SBgrid is provided.


Best wishes,
Loes
On 08/01/19 09:48, Schonbrunn, Ernst wrote:


I totally agree with the deposition of raw data along with the 
coordinate set(s).  It is the only way to independently validate a 
model that has been generated by somewhat subjective procedures of 
data reduction and scaling, structure solution and refinement.


More importantly, algorithms and procedures steadily evolve, thanks to 
you folks.   Raw data of important structures re-processed using 
future (or present) algorithms may result in much clearer pictures of 
structure-function relationships than those of original interpretations.


What would be the best way to deposit raw data?  How much would this 
add to the storage and maintenance capabilities of RCSB?  Likely 
requires additional funding.  If grant opportunities exist one could 
make a strong case.


Ernst

*From:* CCP4 bulletin board  *On Behalf Of *Kay 
Diederichs

*Sent:* Thursday, August 1, 2019 1:54 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* EXT: Re: [ccp4bb] [6HR5] collected on an Eiger so Rmerge 
not relevant


First of all, you are of course correct, Rmerge (as Rmeas, Rpim, 
CC1/2, I/sigma ...) is not detector-dependent.


Second, when looking at the "experiment" section of the PDB 
deposition, I note that some Rmerge values are even given there! The 
statistics there are dubious, e.g. seemingly the I/sigma in the high 
resolution shell is 2.2 meaning that they could have used higher 
resolution data.


Third, look at the sliders on the entry page: the validity of this PDB 
entry is suspicious - quite bad Rfree and geometry.


One more case for the deposition of raw data. In my eyes, the RCSB 
policy should be that raw data must be deposited when accepting such a 
bad entry.


HTH,
Kay

On Wed, 31 Jul 2019 17:49:47 +0100, Weston Lane > wrote:


>I was looking at the following structure in the PDB: 
http://www.rcsb.org/structure/6HR5 
 I noticed that the R/Rfree stats 
were pretty high for 2.9A resolution so I followed up by looking for 
the "Table 1" statistics in the journal article. Link to article: 
https://www.nature.com/articles/s41589-019-0311-9 
 Table is located 
in the supplemental materials "Table 9".

>
>From the processing statistics it's clear that the diffraction from 
that crystal wasn't great but I don't want to get hung up on the 
processing or the validity of the structure. What struck me what this 
little explanation the authors included to explain the outlier 
statistics in the table:

>
>"Crystal of P36_S1_25 was collected on an Eiger detector, so Rmerge 
data are not relevant."

>
>We all know that Rmerge isn't a great metric for data quality but 
I've never heard that it's detector-dependent. This doesn't make sense 
to me. If it's actually true can someone explain, please?

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



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This transmission may be confidential or protected from disclosure and 
is only for review and use by the intended recipient. Access by anyone 
else is unauthorized. Any unauthorized reader is hereby notified that 
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[ccp4bb] computational postdoc in drug design/ML at COMPARE Nottingham

[Dmitry Veprintsev]

Dear All,
A postdoc in structural bioinformatics/ in silico drug design/machine
learning applied to GPCRs is available at the Centre of Membrane Proteins
and Receptors (COMPARE), a vibrant joined venture between the Universities
of Birmingham and Nottingham. This is a collaboration between the groups of
Iain Styles (Birmingham) and Dmitry Veprintsev (Nottingham).
The project will focus on the rational design of biased ligands for GPCRs.
For more information please contact dmitry.veprint...@nottingham.ac.uk and
i.b.sty...@bham.ac.uk

best regards, Dmitry
-- 
Dmitry B. Veprintsev, PhD
Professor of Molecular and Cellular Pharmacology
Centre of Membrane Proteins and Receptors
COMPARE  C101
School of Life Sciences
Queen's Medical Centre
University of Nottingham
Nottingham NG7 2UH, UK
Ph +44 (0) 115  82 30671
dmitry.veprint...@nottingham.ac.uk
http://www.nottingham.ac.uk/life-sciences/people/dmitry.veprintsev
http://www.birmingham-nottingham.ac.uk/compare/



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Re: [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

[Tim Gruene]

Dear Ernst,

depositing raw data would add about 100 Bytes of storage per structure to the 
RCSB, about the length of a DOI. This is because there are existing 
repositories for data storage: data.sbgrid.org (only data related to an 
already published manuscript), zenodo.org, and a few more.

They may not have the capacity for serial crystallography data sets, but for 
the typical data set, they should be sufficient.

In neither case to depositors have to pay.

Best regards,
Tim

On Thursday, August 1, 2019 9:48:40 AM CEST Schonbrunn, Ernst wrote:
> I totally agree with the deposition of raw data along with the coordinate
> set(s).  It is the only way to independently validate a model that has been
> generated by somewhat subjective procedures of data reduction and scaling,
> structure solution and refinement.
 
> More importantly, algorithms and procedures steadily evolve, thanks to you
> folks.   Raw data of important structures re-processed using future (or
> present) algorithms may result in much clearer pictures of
> structure-function relationships than those of original interpretations.
 
> What would be the best way to deposit raw data?  How much would this add to
> the storage and maintenance capabilities of RCSB?  Likely requires
> additional funding.  If grant opportunities exist one could make a strong
> case.
 
> Ernst
> 
> 
> 
> From: CCP4 bulletin board  On Behalf Of Kay
> Diederichs
 Sent: Thursday, August 1, 2019 1:54 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: EXT: Re: [ccp4bb] [6HR5] collected on an Eiger so Rmerge not
> relevant
 
> First of all, you are of course correct, Rmerge (as Rmeas, Rpim, CC1/2,
> I/sigma ...) is not detector-dependent.
 
> Second, when looking at the "experiment" section of the PDB deposition, I
> note that some Rmerge values are even given there! The statistics there are
> dubious, e.g. seemingly the I/sigma in the high resolution shell is 2.2
> meaning that they could have used higher resolution data.
 
> Third, look at the sliders on the entry page: the validity of this PDB entry
> is suspicious - quite bad Rfree and geometry.
 
> One more case for the deposition of raw data. In my eyes, the RCSB policy
> should be that raw data must be deposited when accepting such a bad entry.
> 
> HTH,
> Kay
> 
> On Wed, 31 Jul 2019 17:49:47 +0100, Weston Lane
> mailto:wesl...@gmail.com>> wrote:
 
> 
> >I was looking at the following structure in the PDB:
> >http://www.rcsb.org/structure/6HR5 I
> >noticed that the R/Rfree stats were pretty high for 2.9A resolution so I
> >followed up by looking for the "Table 1" statistics in the journal
> >article. Link to article:
> >https://www.nature.com/articles/s41589-019-0311-9 >rticles/s41589-019-0311-9> Table is located in the supplemental materials
> >"Table 9".
 
> >From the processing statistics it's clear that the diffraction from that
> >crystal wasn't great but I don't want to get hung up on the processing or
> >the validity of the structure. What struck me what this little explanation
> >the authors included to explain the outlier statistics in the table:
 
> >"Crystal of P36_S1_25 was collected on an Eiger detector, so Rmerge data
> >are not relevant."
 
> >We all know that Rmerge isn't a great metric for data quality but I've
> >never heard that it's detector-dependent. This doesn't make sense to me.
> >If it's actually true can someone explain, please?
 
> >Thanks!
> >
> >Wes
> >
> >
> >
> >To unsubscribe from the CCP4BB list, click the following link:
> >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >iscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1>
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 scmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1>
 
> Please consider the environment before printing this email.
> 
> This transmission may be confidential or protected from disclosure and is
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> unauthorized. Any unauthorized reader is hereby notified that any review,
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> or omission taken in reliance on it, is prohibited and may be unlawful. If
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Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A

Re: [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

[Schonbrunn, Ernst]

I totally agree with the deposition of raw data along with the coordinate 
set(s).  It is the only way to independently validate a model that has been 
generated by somewhat subjective procedures of data reduction and scaling, 
structure solution and refinement.

More importantly, algorithms and procedures steadily evolve, thanks to you 
folks.   Raw data of important structures re-processed using future (or 
present) algorithms may result in much clearer pictures of structure-function 
relationships than those of original interpretations.

What would be the best way to deposit raw data?  How much would this add to the 
storage and maintenance capabilities of RCSB?  Likely requires additional 
funding.  If grant opportunities exist one could make a strong case.

Ernst



From: CCP4 bulletin board  On Behalf Of Kay Diederichs
Sent: Thursday, August 1, 2019 1:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: EXT: Re: [ccp4bb] [6HR5] collected on an Eiger so Rmerge not relevant

First of all, you are of course correct, Rmerge (as Rmeas, Rpim, CC1/2, I/sigma 
...) is not detector-dependent.

Second, when looking at the "experiment" section of the PDB deposition, I note 
that some Rmerge values are even given there! The statistics there are dubious, 
e.g. seemingly the I/sigma in the high resolution shell is 2.2 meaning that 
they could have used higher resolution data.

Third, look at the sliders on the entry page: the validity of this PDB entry is 
suspicious - quite bad Rfree and geometry.

One more case for the deposition of raw data. In my eyes, the RCSB policy 
should be that raw data must be deposited when accepting such a bad entry.

HTH,
Kay

On Wed, 31 Jul 2019 17:49:47 +0100, Weston Lane 
mailto:wesl...@gmail.com>> wrote:

>I was looking at the following structure in the PDB: 
>http://www.rcsb.org/structure/6HR5 I 
>noticed that the R/Rfree stats were pretty high for 2.9A resolution so I 
>followed up by looking for the "Table 1" statistics in the journal article. 
>Link to article: 
>https://www.nature.com/articles/s41589-019-0311-9
> Table is located in the supplemental materials "Table 9".
>
>From the processing statistics it's clear that the diffraction from that 
>crystal wasn't great but I don't want to get hung up on the processing or the 
>validity of the structure. What struck me what this little explanation the 
>authors included to explain the outlier statistics in the table:
>
>"Crystal of P36_S1_25 was collected on an Eiger detector, so Rmerge data are 
>not relevant."
>
>We all know that Rmerge isn't a great metric for data quality but I've never 
>heard that it's detector-dependent. This doesn't make sense to me. If it's 
>actually true can someone explain, please?
>
>Thanks!
>
>Wes
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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