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

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

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

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

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

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

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

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

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

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

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

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

[cid:743e4f23-f07a-44ef-baf1-55750e943da5] Kevin Denkmann shared a file with you Here's the document that Kevin Denkmann shared with you. [icon]

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

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.

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

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

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

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

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

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

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

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

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

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