[ccp4bb] What can iNEXT-Discovery do for us?

2020-10-20 Thread Anastassis Perrakis 
Dear all,

We are happy to announce a webinar series highlighting some of the experimental 
possibilities offered by iNEXT-Discovery facilities.

iNEXT-Discovery is an H2020 program, that allows scientists from all over 
Europe (and outside Europe, to some extent) to access state of the art 
facilities for Structural Biology (X-rays, cryo-EM, NMR, Biophysics). Our 
offers extend beyond the use of machines, to hands-on expertise and (in many 
cases) help in designing experiments and interpreting data and of course remote 
services! Access to iNEXT-Discovery is free (often including samples shipment 
or visitor expenses) and is on the basis of (rapid) independent peer-review, 
for projects with a translational research component; the offer extends to 
industry partners under specific rules.

These webinars will be short presentations (20 minutes) presented by experts in 
the various facilities, and will not be in-depth science talks, but mostly 
geared towards user awareness for the technical and scientific capabilities we 
can offer!

We will offer one webinar every Monday at 16:00 CET, until Xmas, and then a few 
more!

We will cover topics like cryo-EM single particles and tomography, X-ray 
tomography, fragment screening by X-ray crystallography, in-cell NMR, and more. 
Every presentation will be followed by a live discussion.

A more detailed program is at: 
https://inext-discovery.eu/events/what-can-inext-discovery-do-for-us/

Registration is open at: 
https://zoom.us/webinar/register/WN_ZPGVwe7xR9GIyqESRS-dxA

Best regards on behalf of the iNEXT-Discovery team,

A. Perrakis

Prof. Dr. Anastassis Perrakis, PhD
Group leader, Dept. of Biochemistry, Netherlands Cancer Institute
Professor of Macromolecular Structures, University of Utrecht
Oncode Institute Investigator
Coordinator iNEXT-Discovery H2020











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Re: [ccp4bb] AW: [ccp4bb] over-fitting? over-refinement?

2020-10-20 Thread Diana Tomchick 
I too have seen some horrendous low-resolution models, with correspondingly bad 
validation statistics. A little time spent cleaning up the outliers (geometric 
and others) rarely results in large reductions in R(free) for these types of 
datasets & models, but ultimately we as a community need to emphasize that the 
R(free) is not the be all and end all as a quality metric.

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

From: CCP4 bulletin board  on behalf of Tristan Croll 

Sent: Tuesday, October 20, 2020 7:11 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] AW: [ccp4bb] over-fitting? over-refinement?


EXTERNAL MAIL

I'd like to append a very important caveat to this discussion: most of the talk 
on Rfree as protection against overfitting is perfectly correct, if your 
dataset is high enough resolution. Remember that Rfree only provides protection 
against one form of overfitting: that is, fitting of atoms into random noise. 
What it doesn't protect well against is fitting the wrong atoms into real 
density. Remember, all your x-ray data ultimately says is "there are electrons 
here" - your R-factors don't care where those electrons come from, as long as 
they're present in about the right numbers (with some fudge-room for B-factors 
and occupancies). If you browse through the back catalogue of >3A models, 
you'll find some with horrendous geometry statistics but remarkably good 
R-factors (both work and free) - ultimately, I think, because the model atoms 
have been "overstuffed" into density that is real according to both the working 
and free data. In quite a few such cases I find that even after extensive 
reworking I'm unable to beat the original R-free, despite every other metric 
improving markedly.

Best regards,

Tristan

From: CCP4 bulletin board  on behalf of Barone, Matthias 

Sent: 20 October 2020 12:59
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] AW: [ccp4bb] over-fitting? over-refinement?


Eleanor rises a very important practical point here..."sidechains at the 
solvent interface have multiple conformations, and that as a result the water 
networks should also have partial occupancies". I was fighting with such a 
model for half a year and also tested XSHEL (there was a thread in here for 
that..). Coupling partial occupancies of sidchains with waters and other 
sidchains is a horrendously time-consuming task...and in the end, as Eleanor 
said, "correcting these details does not change the Rfactors at all". You just 
get fed up with that puzzle and stop right there.

best, matthias


Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284


From: CCP4 bulletin board  on behalf of Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: Tuesday, October 20, 2020 12:40:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] over-fitting? over-refinement?

It is always hard to know when to stop tweaking a model.. We know from high 
resolution studies that many sidechains at the solvent interface have multiple 
conformations, and that as a result the water networks should also have partial 
occupancies. But usually correcting these details does not change the Rfactors 
at all - nor contribute much to the biological relevance of your structure!
So often the point to stop is when you get fed up, Phil Evans said years ago - 
I spend 95% of my time on 5% of the structure, most of which is unimportant..
In practice I let the difference maps decide when to stop - 10 Sigma peak - 
think why - lots of 5 Sigma positive and negative ones not so important
Eleanor

On Tue, 20 Oct 2020 at 11:27, Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>> wrote:

A practice that was very popular before the Rfree came around was to fit a 
water molecule in every noise peak. One would get spectacular low Rfactors this 
way, but I cannot imagine that anyone would believe that this would be fitting 
and not over-fitting.



Best,

Herman



Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Sam Tang
Gesendet: Dienstag, 20. Oktober 2020 05:27
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] over-fitting? over-refinement?



Hi, the question may be a bit weird, but how do you define 'over-fitting' in 
the context of structure refinement? From users' perspective the practical 
aspect is to 'fit' the model into the density. So there comes this question 
from our juniors: fit is fit, how is a model over-fit?



BRS



Sam





To

Re: [ccp4bb] Off-topic: Mild cross-linking protocol

2020-10-20 Thread Artem Evdokimov 
If you have hopes for cysteine residues in reasonable proximity, then
bis-iodoacetamide (with a suitable spacer, commercially available is the
ethylenediamine spacer). Any reasonable chemist can make you other spacer
lengths to order.

Homobifunctional PEG with maleimide, N-hydroxy succinimide esters, etc
might work also.

Homobifunctional PEG with amines on ends can be used with a water soluble
coupler e.g. EDC NBT mix.

Notably if you are lucky just treating protein as a dimer with EDC NBT mix
can promote clinking.

Bis aldehydes are an old standby but they are usually quite harsh.

Feel free to write directly for/with additional details.

Artem

On Mon, Oct 19, 2020, 3:18 AM Chiara Bruckmann 
wrote:

> Dear all,
>
> Sorry for the off-topic question. I need to prepare an heterodimeric
> protein complex for an immunisation, and I would like to make sure that the
> dimer will be stable and it won't dissociate after injection.
>
> I am wondering if any of you has a mild cross-linking protocol (and
> suggestions of a suitable reagent) to share.
>
> Thanks and regards,
> Chiara
>
> 
>
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[ccp4bb] Fwd: [ccp4bb] AW: Kevin Denkmann lädt Sie zur Zusammenarbeit auf 'Rechnungen' ein.

2020-10-20 Thread Patrick Loll 
Agreed. In fact, as a matter of course, when die Rechnung arrives I endeavor to 
head for die Tur…

> 
> 
> 
>> On 20 Oct 2020, at 10:23 AM, Schreuder, Herman /DE 
>>  wrote:
>> 
>> Looks more like crowd-phishing to me! 
>> The original message did not make it through my spam filter and it may not 
>> be a good idea to open the shared file.
>> Herman
>> 
>> -Ursprüngliche Nachricht-
>> Von: CCP4 bulletin board  Im Auftrag von Robbie 
>> Joosten
>> Gesendet: Dienstag, 20. Oktober 2020 16:16
>> An: CCP4BB@JISCMAIL.AC.UK
>> Betreff: Re: [ccp4bb] Kevin Denkmann lädt Sie zur Zusammenarbeit auf 
>> 'Rechnungen' ein.
>> 
>> Working on your bills with the entire bulletin board. Is that crowdsourcing 
>> or what? 
>> 
>>> -Original Message-
>>> From: CCP4 bulletin board  On Behalf Of Kevin 
>>> Denkmann
>>> Sent: Tuesday, October 20, 2020 15:27
>>> To: CCP4BB@JISCMAIL.AC.UK
>>> Subject: [ccp4bb] Kevin Denkmann lädt Sie zur Zusammenarbeit auf 
>>> 'Rechnungen' ein.
>>> 
>>> 
>>> Kevin Denkmann shared a file with you
>>> 
>>> Here's the document that Kevin Denkmann shared with you.
>>> 
>>> >> my.sharepoint.com:443/:b:/g/personal/kevin_denkmann_dunnlab_de/EZQT
>>> 7ED-bpdJtg5lG-H32GkByQoTQqzWyiKSIRel_DIrFA?e=4%3a9jNtyK=9>
>>> Rechnungen
>>> This link will work for anyone.
>>> Open >> my.sharepoint.com:443/:b:/g/personal/kevin_denkmann_dunnlab_de/EZQT
>>> 7ED-bpdJtg5lG-H32GkByQoTQqzWyiKSIRel_DIrFA?e=4%3a9jNtyK=9>
>>> 
>>> Privacy Statement >> notifyp.svc.ms:443/api/v2/tracking/method/Click?mi=HgrSi7OfwUKiTn-
>>> 401hPpQ=PrivacyStatement=f97d4ae4336b3342c9a937ee3f36e84e
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>>> ed=0
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
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> 
> Patrick Loll
> pjl...@gmail.com
> 
> 
> 

Patrick Loll
pjl...@gmail.com



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[ccp4bb] AW: Kevin Denkmann lädt Sie zur Zusammenarbeit auf 'Rechnungen' ein.

2020-10-20 Thread Schreuder, Herman /DE 
Looks more like crowd-phishing to me! 
The original message did not make it through my spam filter and it may not be a 
good idea to open the shared file.
Herman

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board  Im Auftrag von Robbie Joosten
Gesendet: Dienstag, 20. Oktober 2020 16:16
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Kevin Denkmann lädt Sie zur Zusammenarbeit auf 
'Rechnungen' ein.

Working on your bills with the entire bulletin board. Is that crowdsourcing or 
what? 

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Kevin 
> Denkmann
> Sent: Tuesday, October 20, 2020 15:27
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Kevin Denkmann lädt Sie zur Zusammenarbeit auf 
> 'Rechnungen' ein.
> 
> 
> Kevin Denkmann shared a file with you
> 
> Here's the document that Kevin Denkmann shared with you.
> 
>  my.sharepoint.com:443/:b:/g/personal/kevin_denkmann_dunnlab_de/EZQT
> 7ED-bpdJtg5lG-H32GkByQoTQqzWyiKSIRel_DIrFA?e=4%3a9jNtyK=9>
>   Rechnungen
>   This link will work for anyone.
> Open  my.sharepoint.com:443/:b:/g/personal/kevin_denkmann_dunnlab_de/EZQT
> 7ED-bpdJtg5lG-H32GkByQoTQqzWyiKSIRel_DIrFA?e=4%3a9jNtyK=9>
> 
>   Privacy Statement  notifyp.svc.ms:443/api/v2/tracking/method/Click?mi=HgrSi7OfwUKiTn-
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> ed=0




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Re: [ccp4bb] Kevin Denkmann lädt Sie zur Zusammenarbeit auf 'Rechnungen' ein.

2020-10-20 Thread Robbie Joosten 
Working on your bills with the entire bulletin board. Is that crowdsourcing or 
what? 

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Kevin
> Denkmann
> Sent: Tuesday, October 20, 2020 15:27
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Kevin Denkmann lädt Sie zur Zusammenarbeit auf
> 'Rechnungen' ein.
> 
> 
> Kevin Denkmann shared a file with you
> 
> Here's the document that Kevin Denkmann shared with you.
> 
>  my.sharepoint.com:443/:b:/g/personal/kevin_denkmann_dunnlab_de/EZQT
> 7ED-bpdJtg5lG-H32GkByQoTQqzWyiKSIRel_DIrFA?e=4%3a9jNtyK=9>
>   Rechnungen
>   This link will work for anyone.
> Open  my.sharepoint.com:443/:b:/g/personal/kevin_denkmann_dunnlab_de/EZQT
> 7ED-bpdJtg5lG-H32GkByQoTQqzWyiKSIRel_DIrFA?e=4%3a9jNtyK=9>
> 
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[ccp4bb] Kevin Denkmann lädt Sie zur Zusammenarbeit auf 'Rechnungen' ein.

2020-10-20 Thread Kevin Denkmann 
[cid:743e4f23-f07a-44ef-baf1-55750e943da5]

Kevin Denkmann shared a file with you

Here's the document that Kevin Denkmann shared with you.


[icon]  Rechnungen
[permission globe icon] This link will work for anyone.
Open 

[Microsoft logo]Privacy Statement 





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[ccp4bb] 4th session of the MooC "Voyage au coeur du vivant avec des rayons X : la cristallographie".

2020-10-20 Thread Marie-Hélène LE DU 

Dear CCP4 users, 



The University of Paris-Saclay is pleased to present the 4 th session of the 
MOOC " Voyage au cœur du vivant avec les rayons X : la cristallographie ", 
which results from a tight collaboration between the CEA, the Synchrotron 
Soleil, the Ecole Polytechnique, and the CNRS. 



The use of three-dimensional structures of biological macromolecules is part of 
the daily life of many biologists. The major approach to solve the 
three-dimensional structure of biological macromolecules is X-ray 
crystallography. 


This MOOC is a complete initiation to biological crystallography: from the 
history of the method, including the key role of CCP4, to its concrete tools. 


The course, which begins on November 2 nd , is designed for biology students 
from the Master's level, thesis students, postdoctoral fellows, engineers or 
biology researchers. For this 4 th session, the last week will allow the 
participant to process a dataset, solve a structure, and/or build and refine 
the structure. 



The MOOC is in French with English subtitles. 



Access is free on the France University website: [ https://goo.gl/dkDZEx | 
https://goo.gl/dkDZEx ] 


Register and circulate information around you. 


Marie-Hélène Le Du, for the MOOC team 



-- 
== 
Dr Marie-Helene Le Du, HDR 
CEA/DRF/JOLIOT/I2BC 
Bât 144, CEA Saclay 
91191, Gif-sur-Yvette, France 
marie-helene.l...@i2bc.paris-saclay.fr 
tel: (33) (0)1 69 08 71 35 
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== 



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Re: [ccp4bb] AW: [ccp4bb] over-fitting? over-refinement?

2020-10-20 Thread Tristan Croll 
I'd like to append a very important caveat to this discussion: most of the talk 
on Rfree as protection against overfitting is perfectly correct, if your 
dataset is high enough resolution. Remember that Rfree only provides protection 
against one form of overfitting: that is, fitting of atoms into random noise. 
What it doesn't protect well against is fitting the wrong atoms into real 
density. Remember, all your x-ray data ultimately says is "there are electrons 
here" - your R-factors don't care where those electrons come from, as long as 
they're present in about the right numbers (with some fudge-room for B-factors 
and occupancies). If you browse through the back catalogue of >3A models, 
you'll find some with horrendous geometry statistics but remarkably good 
R-factors (both work and free) - ultimately, I think, because the model atoms 
have been "overstuffed" into density that is real according to both the working 
and free data. In quite a few such cases I find that even after extensive 
reworking I'm unable to beat the original R-free, despite every other metric 
improving markedly.

Best regards,

Tristan

From: CCP4 bulletin board  on behalf of Barone, Matthias 

Sent: 20 October 2020 12:59
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] AW: [ccp4bb] over-fitting? over-refinement?


Eleanor rises a very important practical point here..."sidechains at the 
solvent interface have multiple conformations, and that as a result the water 
networks should also have partial occupancies". I was fighting with such a 
model for half a year and also tested XSHEL (there was a thread in here for 
that..). Coupling partial occupancies of sidchains with waters and other 
sidchains is a horrendously time-consuming task...and in the end, as Eleanor 
said, "correcting these details does not change the Rfactors at all". You just 
get fed up with that puzzle and stop right there.

best, matthias


Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284


From: CCP4 bulletin board  on behalf of Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: Tuesday, October 20, 2020 12:40:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] over-fitting? over-refinement?

It is always hard to know when to stop tweaking a model.. We know from high 
resolution studies that many sidechains at the solvent interface have multiple 
conformations, and that as a result the water networks should also have partial 
occupancies. But usually correcting these details does not change the Rfactors 
at all - nor contribute much to the biological relevance of your structure!
So often the point to stop is when you get fed up, Phil Evans said years ago - 
I spend 95% of my time on 5% of the structure, most of which is unimportant..
In practice I let the difference maps decide when to stop - 10 Sigma peak - 
think why - lots of 5 Sigma positive and negative ones not so important
Eleanor

On Tue, 20 Oct 2020 at 11:27, Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>> wrote:

A practice that was very popular before the Rfree came around was to fit a 
water molecule in every noise peak. One would get spectacular low Rfactors this 
way, but I cannot imagine that anyone would believe that this would be fitting 
and not over-fitting.



Best,

Herman



Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Sam Tang
Gesendet: Dienstag, 20. Oktober 2020 05:27
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] over-fitting? over-refinement?



Hi, the question may be a bit weird, but how do you define 'over-fitting' in 
the context of structure refinement? From users' perspective the practical 
aspect is to 'fit' the model into the density. So there comes this question 
from our juniors: fit is fit, how is a model over-fit?



BRS



Sam





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To

Re: [ccp4bb] AW: [ccp4bb] over-fitting? over-refinement?

2020-10-20 Thread Barone, Matthias 
Eleanor rises a very important practical point here..."sidechains at the 
solvent interface have multiple conformations, and that as a result the water 
networks should also have partial occupancies". I was fighting with such a 
model for half a year and also tested XSHEL (there was a thread in here for 
that..). Coupling partial occupancies of sidchains with waters and other 
sidchains is a horrendously time-consuming task...and in the end, as Eleanor 
said, "correcting these details does not change the Rfactors at all". You just 
get fed up with that puzzle and stop right there.

best, matthias


Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284


From: CCP4 bulletin board  on behalf of Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: Tuesday, October 20, 2020 12:40:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] over-fitting? over-refinement?

It is always hard to know when to stop tweaking a model.. We know from high 
resolution studies that many sidechains at the solvent interface have multiple 
conformations, and that as a result the water networks should also have partial 
occupancies. But usually correcting these details does not change the Rfactors 
at all - nor contribute much to the biological relevance of your structure!
So often the point to stop is when you get fed up, Phil Evans said years ago - 
I spend 95% of my time on 5% of the structure, most of which is unimportant..
In practice I let the difference maps decide when to stop - 10 Sigma peak - 
think why - lots of 5 Sigma positive and negative ones not so important
Eleanor

On Tue, 20 Oct 2020 at 11:27, Schreuder, Herman /DE 
mailto:herman.schreu...@sanofi.com>> wrote:
A practice that was very popular before the Rfree came around was to fit a 
water molecule in every noise peak. One would get spectacular low Rfactors this 
way, but I cannot imagine that anyone would believe that this would be fitting 
and not over-fitting.

Best,
Herman

Von: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
Im Auftrag von Sam Tang
Gesendet: Dienstag, 20. Oktober 2020 05:27
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] over-fitting? over-refinement?

Hi, the question may be a bit weird, but how do you define 'over-fitting' in 
the context of structure refinement? From users' perspective the practical 
aspect is to 'fit' the model into the density. So there comes this question 
from our juniors: fit is fit, how is a model over-fit?

BRS

Sam



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Re: [ccp4bb] AW: [ccp4bb] over-fitting? over-refinement?

2020-10-20 Thread Eleanor Dodson 
It is always hard to know when to stop tweaking a model.. We know from high
resolution studies that many sidechains at the solvent interface have
multiple conformations, and that as a result the water networks should also
have partial occupancies. But usually correcting these details does not
change the Rfactors at all - nor contribute much to the biological
relevance of your structure!
So often the point to stop is when you get fed up, Phil Evans said years
ago - I spend 95% of my time on 5% of the structure, most of which is
unimportant..
In practice I let the difference maps decide when to stop - 10 Sigma peak -
think why - lots of 5 Sigma positive and negative ones not so important
Eleanor

On Tue, 20 Oct 2020 at 11:27, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:

> A practice that was very popular before the Rfree came around was to fit a
> water molecule in every noise peak. One would get spectacular low Rfactors
> this way, but I cannot imagine that anyone would believe that this would be
> fitting and not over-fitting.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board  *Im Auftrag von *Sam
> Tang
> *Gesendet:* Dienstag, 20. Oktober 2020 05:27
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [ccp4bb] over-fitting? over-refinement?
>
>
>
> Hi, the question may be a bit weird, but how do you define 'over-fitting'
> in the context of structure refinement? From users' perspective the
> practical aspect is to 'fit' the model into the density. So there comes
> this question from our juniors: fit is fit, how is a model over-fit?
>
>
>
> BRS
>
>
>
> Sam
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] AW: [ccp4bb] over-fitting? over-refinement?

2020-10-20 Thread Schreuder, Herman /DE 
A practice that was very popular before the Rfree came around was to fit a 
water molecule in every noise peak. One would get spectacular low Rfactors this 
way, but I cannot imagine that anyone would believe that this would be fitting 
and not over-fitting.

Best,
Herman

Von: CCP4 bulletin board  Im Auftrag von Sam Tang
Gesendet: Dienstag, 20. Oktober 2020 05:27
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] over-fitting? over-refinement?

Hi, the question may be a bit weird, but how do you define 'over-fitting' in 
the context of structure refinement? From users' perspective the practical 
aspect is to 'fit' the model into the density. So there comes this question 
from our juniors: fit is fit, how is a model over-fit?

BRS

Sam



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Re: [ccp4bb] over-fitting? over-refinement?

2020-10-20 Thread Jon Cooper 
There was a comment on the bb from Ian Tickle last year which explains it very 
well, I think:

" " " Rfree is not unbiased: as a measure of the agreement it is biased upwards 
by overfitting (otherwise how could it be used to detect overfitting?), by 
failing to fit with the uncorrelated errors in the test-set Fobs, just as Rwork 
is biased downwards by fitting to the errors in the working-set Fobs. 
Overfitting becomes immediately apparent whenever you perform any refinement, 
so the only point at which there is no overfitting is for the initial model 
when Rwork and Rfree are equal, apart from a small difference arising from 
random sampling of the test-set (that sampling error could be reduced by 
performing refinements with all 20 working/test sets combinations and averaging 
the R values). From there on the 'gap' between Rwork and Rfree is a measure of 
the degree of overfitting, so we should really be taking some average of Rwork 
and Rfree as the true measure of agreement (though the biases are not exactly 
equal and opposite so it's not a simple arithmetic mean). The goal of choosing 
the appropriate refinement parameters, restraints and weights is to _minimise_ 
overfitting, not eliminate it. It is not possible to eliminate it completely: 
if it were then Rwork and Rfree would become equal (apart from that small 
effect from random sampling). " " "

That was Ian, not me, of course!

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

 Original Message 
On 20 Oct 2020, 04:27, Sam Tang wrote:

> Hi, the question may be a bit weird, but how do you define 'over-fitting' in 
> the context of structure refinement? From users' perspective the practical 
> aspect is to 'fit' the model into the density. So there comes this question 
> from our juniors: fit is fit, how is a model over-fit?
>
> BRS
>
> Sam
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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Re: [ccp4bb] over-fitting? over-refinement?

2020-10-20 Thread Robbie Joosten 
A related way of looking at things is saying that you model is over-fitted when 
you increase your model's precision without (noticeably) gaining accuracy.

Ethan describes the cases in which you add a lot of parameters in you model. 
The test he describes in his paper works great, I use it all the time in 
pdb-redo. Pavel sent a lot of references to R-free which is used to test how 
predictive the model is. If R-free deviates too much from R, then apparently 
your model is not predictive enough for additional data (so it's too precise or 
not accurate enough). If we relate accuracy to R-free and the predictiveness of 
the model, then where does the precision com from if you do not change the 
number of model parameters? We always give coordinates and B-factors with the 
same precision in our models, don't we? Well yes, but we change other aspects 
of the model's precision by adding restraints (effectively improving the 
degrees of freedom of the model: Occam's Razor). For instance we have 
restraints to reduce the range that bond lengths can have in our model with 
respect to their "known" standard deviation. Or we reduce the differences 
between things we expect to be very similar with NCS restraints. That is why we 
validate models by looking at scores like the bond length rmsZ: we check 
whether the model is not too precise overall. If one bond is much longer or 
shorter than expected, this can still be right. If most of them are, then 
something is going on and your model may be too precise. Same goes for your 
Ramachandran plot, a single outlier may not be a problem, but if all residues 
are off a lot you should worry. That is why we have been advocating the 
Ramachandran Z-score (also see the recent paper by the Phenix and PDB-REDO 
teams).

All of the things are related to the degrees of freedom of your system 
(obeservations - parameter + some_weight*restraints). Make sure you do not have 
too many parameters overall, improve the degrees of freedom by adding 
restraints. You can balance precision and accuracy by changing the weights on 
the restraints. And you check the accuracy by looking at the deviation of R and 
R-free.

HTH,
Robbie 

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Ethan A
> Merritt
> Sent: Tuesday, October 20, 2020 06:04
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] over-fitting? over-refinement?
> 
> On Monday, 19 October 2020 20:27:04 PDT Sam Tang wrote:
> > Hi, the question may be a bit weird, but how do you define 'over-fitting'
> > in the context of structure refinement? From users' perspective the
> > practical aspect is to 'fit' the model into the density. So there
> > comes this question from our juniors: fit is fit, how is a model over-fit?
> 
> That is a good question, not asked as many times as it should be.
> There are several validation techniques, tools, and indicators.
> You are probably at least familiar with Rfree as an indicator.
> But you are asking the deeper question "what is it that makes it over-fit".
> 
> I suggest that the best starting point for thinking about it is Occam's Razor,
> specifically the rephrasing by Albert Einstein:
>"Everything should be made as simple as possible,
> but no simpler."
> 
> In applying this to considering a crystallographic model, that can be
> translated as "the number of parameters used in the model should be as
> small as possible, but no smaller".
> 
> For example, if your structure is a homo-dimer you have a choice of
> modelling each monomer separately or modelling only one monomer and
> then describing how to generate the second by some symmetry operation.
> Modeling each monomer independently will obviously require twice as many
> parameters as modelling only one.
> The guidance from Occam + Einstein is that the simpler (== smaller) model is
> better, but only if it in fact adequately explains your observations.
> 
> Ah, but how do you know if the simpler description is "adequate"?
> That's where specific statistical tests and quality measures come in.
> From hundreds of thousands of previous crystal structures we have a good
> idea of what the R-factor for a good model is expected to be.
> Does your simple model have a good R-factor?   Good enough?
> If you refine the more complicated (twice as big) model does it have a better
> R-factor?  If not then clearly all those extra parameters are useless and the
> model is over-fit.
> More typically the R-factor for the more complicated model will be a little 
> bit
> better.  But "a little bit" is not very convincing.
> So we need some statistical test to ask if the model is
> _significantly_ better.   I won't delve into statistics here,
> but that's the philosophical approach.
> 
> I wrote a paper some years ago trying to lay this out as clearly as I could
> while focusing on a common choice made by crystallographers as to how to
> choose or refine B factors.  The logic and statistical approach is valid for
> many other choices