Re: [ccp4bb] microscope camera

[Sergei Strelkov]

Moticam 5 has been working well for us for a few years now (installed on a 
Leica binocular)


Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
Pharmaceutical Sciences, KU Leuven O&N2, 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


From: CCP4 bulletin board  on behalf of Dean Derbyshire 

Sent: Wednesday, November 27, 2019 11:35
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] microscope camera

Forgive the off topic subject:

Has anyone got any experience with moticam microscope cameras?
We are looking into cheap cameras for record keeping etc and this supplier 
looks good but...

Cheers in advance

Sent from Mail for Windows 10




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[ccp4bb] EMDB Website Redesign Survey

[James Tolchard]

Dear All,

On behalf of my colleagues at The Electron Microscopy Data Bank (EMDB), 
we would like to invite you to participate in a feedback collection 
survey: https://forms.gle/aagHHoo3fAsoRVoh6


We are currently redesigning the entire EMDB website and we would like 
to gather feedback from the structural biology community in order to 
make it better for all types of users. The results of the survey will be 
used to improve our web pages, search engine, services, and data 
visualisations.


This survey is expected to take around 10 minutes. The survey is 
anonymous, but you can choose to provide your name and e-mail address. 
Any personal information you provide will be confidential and only be 
stored during our redesign process.


If you have any questions about the survey and how the information will 
be used, please direct them to Neli Fonseca (n...@ebi.ac.uk).


Thanks for your help!

Best regards,

James

--
###
James Tolchard
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492647

http://www.pdbe.org
http://www.facebook.com/proteindatabank
http://twitter.com/PDBeurope



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[ccp4bb] EMBO meeting on “Molecular Neurobiology” 8-12 May 2020

[Janssen, B.J.C. (Bert)]

Dear all,



We would like to draw your attention to the EMBO workshop on "Molecular 
Neurobiology", taking place on the beautiful island of Crete on 8-12 May 2020.



The meeting brings together world leading scientists, group leaders and young 
researchers with a keen interest in the latest science occurring at the 
interfaces of structural biology, biophysics, molecular & cellular imaging and 
neuroscience. Given its cross-disciplinary nature, the meeting presents a broad 
overview of molecular neurobiology, ample opportunities for discussions and a 
sneak peak into the latest developments.



See http://meetings.embo.org/event/20-molneuro for more information and 
application guidelines.



Best wishes

Bert





Bert Janssen

Bijvoet Center for biomolecular research

Utrecht University

Padualaan 8, 3584 CH, Utrecht



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Re: [ccp4bb] Xray-dataset usable despite low completeness ?

[Bernhard Rupp]

Sorry for being late on this thread - 

but the completeness myth is one of these conventional wisdoms I am seriously 
questioning and completeness
as a global statistic is almost uninformative, short of telling you 'fewer than 
all recordable reflections up to the reported 
(likely isotropic) resolution limit given whatever (likely isotropic) cutoff 
was applied'. Sounds not very clear to me. 

Kay mentioned already that any information is better than no information, with 
the caveat that you cannot expect
map quality (being an upper limit for model quality - not going into precision 
vs accuracy issue here) corresponding to 
the highest resolution reported, which is in reality frequently anisotropic 
(but not reported or reflected adequately 
in the PDB reports). 
We posted some remarks to this effect recently, pointing out that highly 
incomplete and anisotropic data can still 
yield limited but useful information as long as your claim remains 
correspondingly modest. Section 3.4 in
http://journals.iucr.org/d/issues/2019/12/00/di5032/index.html

Having said that, while random incompleteness is not problematic, systematic 
reciprocal space incompleteness leads
to corresponding systematic real space effects on the map, the simplest being 
anisotropic data reflecting anisotropic
reciprocal map resolution. This is different for example when wedges are 
missing or absence of serial extinctions makes
space group determination more challenging (although we are almost in the age 
where 'record 360 deg of data and 
try every SG' works). James Holton has video examples for incompleteness 
effects and some images are also in my book.
https://bl831.als.lbl.gov/~jamesh/movies/

Cheers & Happy Thanksgiving, BR

PS: A systemic rant regarding data quality representation can be found here
https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2

--
Bernhard Rupp
http://www.hofkristallamt.org/
b...@hofkristallamt.org
--
All models are wrong
but some are useful.
--

-Original Message-
From: CCP4 bulletin board  On Behalf Of Kay Diederichs
Sent: Monday, November 25, 2019 08:07
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Xray-dataset usable despite low completeness ?

Dear Matthias,

Of course, high completeness is better than low completeness.
But as long as your low resolution is pretty much complete, there is no such 
thing as "too low completeness" at high resolution. Each reflection adds 
information to the map, and serves as a restraint in refinement.

best,
Kay 


On Mon, 25 Nov 2019 14:11:52 +0100, Matthias Oebbeke 
 wrote:

>Dear ccp4 Bulletin Board,
>
>I collected a dataset at a synchrotron beamline and got the statistics
>(CORRECT.LP) after processing (using xds) shown in the attached 
>pdf-file.
>
>Do you think this dataset is usable, due to its low completeness? As 
>you can see in the attached file the completeness is just 50% in the 
>highest resolution shell, whereas the I over Sigma is above 2 and also 
>the CC 1/2 (80%) and the R factors (36.8%) have reasonable values.
>Furthermore the overall statistic are good regarding R factor, CC 1/2 
>and I over Sigma. The only problem seems to be the completeness. If I 
>would set the cut-off at a lower resolution to get good completeness, I 
>would throw away nearly half of my reflections.
>
>I'm happy to here your opinion. In Addition to that: The space group is 
>orthorhombic and the dataset was collected over 120° using fine slicing 
>(0.1°).
>
>
>Best regards,
>
>Matthias Oebbeke
>
>
>-- 
>Matthias Oebbeke, M.Sc.
>Research Group of Professor Dr. G. Klebe
>Institute of Pharmaceutical Chemistry
>Philipps-University Marburg
>Marbacher Weg 6, 35032 Marburg, Germany
>Phone: +49-6421-28-21392
>Mail: oebbe...@staff.uni-marburg.de
>www.agklebe.de
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Xray-dataset usable despite low completeness ?

[Jurgen Bosch]

Think of completeness with an analogy to turkey.
Say you happen to find a one-legged turkey (incomplete by conventional 
standard) you could still stuff it and put it in the oven and enjoy 93% of the 
turkey. The 7% missing, who cares? Other than I like both legs of the turkey :-)

Happy Thanksgiving everyone

Jürgen 

P.S. back to my wine & ducks to be roasted. @BR, mit Rotkraut & Kartoffelknödel

> On Nov 28, 2019, at 4:38 PM, Bernhard Rupp  wrote:
> 
> Sorry for being late on this thread - 
> 
> but the completeness myth is one of these conventional wisdoms I am seriously 
> questioning and completeness
> as a global statistic is almost uninformative, short of telling you 'fewer 
> than all recordable reflections up to the reported 
> (likely isotropic) resolution limit given whatever (likely isotropic) cutoff 
> was applied'. Sounds not very clear to me. 
> 
> Kay mentioned already that any information is better than no information, 
> with the caveat that you cannot expect
> map quality (being an upper limit for model quality - not going into 
> precision vs accuracy issue here) corresponding to 
> the highest resolution reported, which is in reality frequently anisotropic 
> (but not reported or reflected adequately 
> in the PDB reports). 
> We posted some remarks to this effect recently, pointing out that highly 
> incomplete and anisotropic data can still 
> yield limited but useful information as long as your claim remains 
> correspondingly modest. Section 3.4 in
> http://journals.iucr.org/d/issues/2019/12/00/di5032/index.html
> 
> Having said that, while random incompleteness is not problematic, systematic 
> reciprocal space incompleteness leads
> to corresponding systematic real space effects on the map, the simplest being 
> anisotropic data reflecting anisotropic
> reciprocal map resolution. This is different for example when wedges are 
> missing or absence of serial extinctions makes
> space group determination more challenging (although we are almost in the age 
> where 'record 360 deg of data and 
> try every SG' works). James Holton has video examples for incompleteness 
> effects and some images are also in my book.
> https://bl831.als.lbl.gov/~jamesh/movies/
> 
> Cheers & Happy Thanksgiving, BR
> 
> PS: A systemic rant regarding data quality representation can be found here
> https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2
> 
> --
> Bernhard Rupp
> http://www.hofkristallamt.org/
> b...@hofkristallamt.org
> --
> All models are wrong
> but some are useful.
> --
> 
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Kay Diederichs
> Sent: Monday, November 25, 2019 08:07
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Xray-dataset usable despite low completeness ?
> 
> Dear Matthias,
> 
> Of course, high completeness is better than low completeness.
> But as long as your low resolution is pretty much complete, there is no such 
> thing as "too low completeness" at high resolution. Each reflection adds 
> information to the map, and serves as a restraint in refinement.
> 
> best,
> Kay 
> 
> 
> On Mon, 25 Nov 2019 14:11:52 +0100, Matthias Oebbeke 
>  wrote:
> 
>> Dear ccp4 Bulletin Board,
>> 
>> I collected a dataset at a synchrotron beamline and got the statistics
>> (CORRECT.LP) after processing (using xds) shown in the attached 
>> pdf-file.
>> 
>> Do you think this dataset is usable, due to its low completeness? As 
>> you can see in the attached file the completeness is just 50% in the 
>> highest resolution shell, whereas the I over Sigma is above 2 and also 
>> the CC 1/2 (80%) and the R factors (36.8%) have reasonable values.
>> Furthermore the overall statistic are good regarding R factor, CC 1/2 
>> and I over Sigma. The only problem seems to be the completeness. If I 
>> would set the cut-off at a lower resolution to get good completeness, I 
>> would throw away nearly half of my reflections.
>> 
>> I'm happy to here your opinion. In Addition to that: The space group is 
>> orthorhombic and the dataset was collected over 120° using fine slicing 
>> (0.1°).
>> 
>> 
>> Best regards,
>> 
>> Matthias Oebbeke
>> 
>> 
>> -- 
>> Matthias Oebbeke, M.Sc.
>> Research Group of Professor Dr. G. Klebe
>> Institute of Pharmaceutical Chemistry
>> Philipps-University Marburg
>> Marbacher Weg 6, 35032 Marburg, Germany
>> Phone: +49-6421-28-21392
>> Mail: oebbe...@staff.uni-marburg.de
>> www.agklebe.de
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?

Re: [ccp4bb] Xray-dataset usable despite low completeness ?

[Ethan A Merritt]

On Thursday, 28 November 2019 16:51:15 Jurgen Bosch wrote:
> Think of completeness with an analogy to turkey.
> Say you happen to find a one-legged turkey (incomplete by conventional 
> standard) you could still stuff it and put it in the oven and enjoy 93% of 
> the turkey. The 7% missing, who cares? Other than I like both legs of the 
> turkey :-)

Don't forget that it helps to evaluate turkey quality
if you can taste matched samples from both sides. 
The cc1/2 "cooking comparison" test cannot be conducted
properly if one leg is missing.  The turkey is still
just as good but the yumminess is on a subjective scale.

(turkey sampling is still hours away here)

Ethan


> 
> Happy Thanksgiving everyone
> 
> Jürgen 
> 
> P.S. back to my wine & ducks to be roasted. @BR, mit Rotkraut & 
> Kartoffelknödel
> 
> > On Nov 28, 2019, at 4:38 PM, Bernhard Rupp  wrote:
> > 
> > Sorry for being late on this thread - 
> > 
> > but the completeness myth is one of these conventional wisdoms I am 
> > seriously questioning and completeness
> > as a global statistic is almost uninformative, short of telling you 'fewer 
> > than all recordable reflections up to the reported 
> > (likely isotropic) resolution limit given whatever (likely isotropic) 
> > cutoff was applied'. Sounds not very clear to me. 
> > 
> > Kay mentioned already that any information is better than no information, 
> > with the caveat that you cannot expect
> > map quality (being an upper limit for model quality - not going into 
> > precision vs accuracy issue here) corresponding to 
> > the highest resolution reported, which is in reality frequently anisotropic 
> > (but not reported or reflected adequately 
> > in the PDB reports). 
> > We posted some remarks to this effect recently, pointing out that highly 
> > incomplete and anisotropic data can still 
> > yield limited but useful information as long as your claim remains 
> > correspondingly modest. Section 3.4 in
> > http://journals.iucr.org/d/issues/2019/12/00/di5032/index.html
> > 
> > Having said that, while random incompleteness is not problematic, 
> > systematic reciprocal space incompleteness leads
> > to corresponding systematic real space effects on the map, the simplest 
> > being anisotropic data reflecting anisotropic
> > reciprocal map resolution. This is different for example when wedges are 
> > missing or absence of serial extinctions makes
> > space group determination more challenging (although we are almost in the 
> > age where 'record 360 deg of data and 
> > try every SG' works). James Holton has video examples for incompleteness 
> > effects and some images are also in my book.
> > https://bl831.als.lbl.gov/~jamesh/movies/
> > 
> > Cheers & Happy Thanksgiving, BR
> > 
> > PS: A systemic rant regarding data quality representation can be found here
> > https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2
> > 
> > --
> > Bernhard Rupp
> > http://www.hofkristallamt.org/
> > b...@hofkristallamt.org
> > --
> > All models are wrong
> > but some are useful.
> > --
> > 
> > -Original Message-
> > From: CCP4 bulletin board  On Behalf Of Kay 
> > Diederichs
> > Sent: Monday, November 25, 2019 08:07
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Xray-dataset usable despite low completeness ?
> > 
> > Dear Matthias,
> > 
> > Of course, high completeness is better than low completeness.
> > But as long as your low resolution is pretty much complete, there is no 
> > such thing as "too low completeness" at high resolution. Each reflection 
> > adds information to the map, and serves as a restraint in refinement.
> > 
> > best,
> > Kay 
> > 
> > 
> > On Mon, 25 Nov 2019 14:11:52 +0100, Matthias Oebbeke 
> >  wrote:
> > 
> >> Dear ccp4 Bulletin Board,
> >> 
> >> I collected a dataset at a synchrotron beamline and got the statistics
> >> (CORRECT.LP) after processing (using xds) shown in the attached 
> >> pdf-file.
> >> 
> >> Do you think this dataset is usable, due to its low completeness? As 
> >> you can see in the attached file the completeness is just 50% in the 
> >> highest resolution shell, whereas the I over Sigma is above 2 and also 
> >> the CC 1/2 (80%) and the R factors (36.8%) have reasonable values.
> >> Furthermore the overall statistic are good regarding R factor, CC 1/2 
> >> and I over Sigma. The only problem seems to be the completeness. If I 
> >> would set the cut-off at a lower resolution to get good completeness, I 
> >> would throw away nearly half of my reflections.
> >> 
> >> I'm happy to here your opinion. In Addition to that: The space group is 
> >> orthorhombic and the dataset was collected over 120° using fine slicing 
> >> (0.1°).
> >> 
> >> 
> >> Best regards,
> >> 
> >> Matthias Oebbeke
> >> 
> >> 
> > 
> > #

Re: [ccp4bb] Xray-dataset usable despite low completeness ?

[Bernhard Rupp]

It has come to our attention that on this bulletin board insensitive and 
hurtful comments have 
been made towards animals with disability. Particularly concerning is the 
display of white privilege
and racial bias towards a minority individual  given that the turkey is also 
referred to in German as 'Indian'. 
In view of this non-inclusive and divisive display of unwokeness, the faculty 
Bias Response Team 
will contact you shortly and allow you to present your self-critique.
  
We want this board to remain a safe zone inclusive of all animals, complete or 
not.

Stuffed, BR

-Original Message-
From: CCP4 bulletin board  On Behalf Of Jurgen Bosch
Sent: Thursday, November 28, 2019 13:51
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Xray-dataset usable despite low completeness ?

Think of completeness with an analogy to turkey.
Say you happen to find a one-legged turkey (incomplete by conventional 
standard) you could still stuff it and put it in the oven and enjoy 93% of the 
turkey. The 7% missing, who cares? Other than I like both legs of the turkey :-)

Happy Thanksgiving everyone

Jürgen 

P.S. back to my wine & ducks to be roasted. @BR, mit Rotkraut & Kartoffelknödel

> On Nov 28, 2019, at 4:38 PM, Bernhard Rupp  wrote:
> 
> Sorry for being late on this thread -
> 
> but the completeness myth is one of these conventional wisdoms I am 
> seriously questioning and completeness as a global statistic is almost 
> uninformative, short of telling you 'fewer than all recordable reflections up 
> to the reported (likely isotropic) resolution limit given whatever (likely 
> isotropic) cutoff was applied'. Sounds not very clear to me.
> 
> Kay mentioned already that any information is better than no 
> information, with the caveat that you cannot expect map quality (being 
> an upper limit for model quality - not going into precision vs 
> accuracy issue here) corresponding to the highest resolution reported, which 
> is in reality frequently anisotropic (but not reported or reflected 
> adequately in the PDB reports).
> We posted some remarks to this effect recently, pointing out that 
> highly incomplete and anisotropic data can still yield limited but 
> useful information as long as your claim remains correspondingly 
> modest. Section 3.4 in 
> http://journals.iucr.org/d/issues/2019/12/00/di5032/index.html
> 
> Having said that, while random incompleteness is not problematic, 
> systematic reciprocal space incompleteness leads to corresponding 
> systematic real space effects on the map, the simplest being 
> anisotropic data reflecting anisotropic reciprocal map resolution. 
> This is different for example when wedges are missing or absence of serial 
> extinctions makes space group determination more challenging (although we are 
> almost in the age where 'record 360 deg of data and try every SG' works). 
> James Holton has video examples for incompleteness effects and some images 
> are also in my book.
> https://bl831.als.lbl.gov/~jamesh/movies/
> 
> Cheers & Happy Thanksgiving, BR
> 
> PS: A systemic rant regarding data quality representation can be found 
> here
> https://www.cell.com/structure/fulltext/S0969-2126(18)30138-2
> 
> --
> Bernhard Rupp
> http://www.hofkristallamt.org/
> b...@hofkristallamt.org
> --
> All models are wrong
> but some are useful.
> --
> 
> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Kay 
> Diederichs
> Sent: Monday, November 25, 2019 08:07
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Xray-dataset usable despite low completeness ?
> 
> Dear Matthias,
> 
> Of course, high completeness is better than low completeness.
> But as long as your low resolution is pretty much complete, there is no such 
> thing as "too low completeness" at high resolution. Each reflection adds 
> information to the map, and serves as a restraint in refinement.
> 
> best,
> Kay
> 
> 
> On Mon, 25 Nov 2019 14:11:52 +0100, Matthias Oebbeke 
>  wrote:
> 
>> Dear ccp4 Bulletin Board,
>> 
>> I collected a dataset at a synchrotron beamline and got the 
>> statistics
>> (CORRECT.LP) after processing (using xds) shown in the attached 
>> pdf-file.
>> 
>> Do you think this dataset is usable, due to its low completeness? As 
>> you can see in the attached file the completeness is just 50% in the 
>> highest resolution shell, whereas the I over Sigma is above 2 and 
>> also the CC 1/2 (80%) and the R factors (36.8%) have reasonable values.
>> Furthermore the overall statistic are good regarding R factor, CC 1/2 
>> and I over Sigma. The only problem seems to be the completeness. If I 
>> would set the cut-off at a lower resolution to get good completeness, 
>> I would throw away nearly half of my reflections.
>> 
>> I'm happy to here your opinion. In Addition to that: The space group 
>> is orthorhombic and the datase

[ccp4bb] DIALS 2.0: from images to MTZ files with DIALS

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Dear ccp4bb

We are pleased to announce the release of - DIALS 2.0: a complete toolkit for 
processing of X-ray diffraction data from area detector images through to 
scaled intensities - free to all users and every line of code available for 
inspection at https://github.com/dials/dials. 

Thanks to the efforts of everyone in the team we are please to announce the 
release of DIALS 2.0 for processing of crystallographic rotation data. This 
includes a large number of changes in particular:

• symmetry determination and scaling - used by default in xia2
• flexible workflows for challenging data
• improvements in speed across for all main steps in the analysis
• more consistent output file naming
• multi-crystal analysis with cosym and xia2.multiplex
• Python 3 compatible code (experimental: will be fully supported in 
2.1)

As always we are constantly working on bug fixes and improvements so the 
current release is version 2.0.2. The binaries for download can be found at:

Downloads: https://dials.github.io/installation.html

With the tutorial documentation at:

Documentation at: https://dials.github.io 

If you have any problems please feel free to log issues at:

Issues: https://github.com/dials/dials/issues 

Or drop us a line at dials-supp...@lists.sourceforge.net. DIALS 2 will be 
included in the forthcoming CCP4 7.1 release. 

This work is only possible thanks to the support of institutions and funding 
agencies:

Diamond Light Source
CCP4 
Biostruct-X project No. 283570 (EU FP7)
Wellcome Trust (Grant No. 202933/Z/16/Z) 
US National Institutes of Health grants GM095887 and GM117126

Which in turn reflects the support offered from the community for our efforts, 
so thank you. 

Sent on behalf of the DIALS development group.
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