Re: [ccp4bb] Anomalous signal to noise details

Hi all, Thanks for the useful advice. Clemens, I was indeed reminded of the vs / discussion when I started this thread. The reason I brought it up here is because the ratio-of-means form is the way it is described in "Estimation of anomalous signal in diffraction data

Re: [ccp4bb] Anomalous signal to noise details

Dear David, Although this is not exactly a topic of your question, an alternative approach is to use the resolution screening and compare the results. I have implemented this approach to my program SHELIXIR (because it uses SHELX C/D/E), which can be found here: http://kmlinux.fjfi.cvut.cz/~kole

Re: [ccp4bb] Anomalous signal to noise details

Conventionally (e.g. in cryo-EM) the SNR is taken as a ratio of averages, either the ratio of the variance of the signal (average of signal squared) to the variance of the noise, i.e. var(signal) / var(noise), or the square root of that, i.e. sd(signal) / sd(noise). See here: https://en.wikipedia.

Re: [ccp4bb] Anomalous signal to noise details

Hi, I am not sure about the 1.2-1.3 limit, but 0.8 probably comes from sqrt(2/pi), which is the ratio of the mean of a half-normal and its sigma when the mean parameter is 0. Best wishes, Gergely From: CCP4 bulletin board On Behalf Of David Waterman Sent: 18 December, 2020 12:53 To: CCP4BB@

Re: [ccp4bb] Anomalous signal to noise details

> I don't know the justification; maybe just experience? Surely the higher the > better. I've seen George Sheldrick deriving the value of ~0.8 when there is > _no_ anom signal but I forgot the details, sorry ... It is derived from the mean absolute error (cf. p414 in Chapter 8 of BMC, with hel

Re: [ccp4bb] Anomalous signal to noise details

Hi David, On Fri, 18 Dec 2020 11:53:08 +, David Waterman wrote: >Hi folks > >The paper "Substructure solution with SHELXD >" >(Schneider & Sheldrick, 2002) describes how > >data can be truncated at the resolution at which [ΔF t

Re: [ccp4bb] Micro/Macro crystal seeding experience

We recently had a projects where removing the HIS-tag changed an unsolvable crystal form into one where Molecular Replacement worked immediately (and with an NMR ensemble as the search model to boot). In this case the HIS-tag was about 5% of the total domain mass and the tags were probably tangled

Re: [ccp4bb] Anomalous signal to noise details

Dear David, On Fri, Dec 18, 2020 at 11:53:08AM +, David Waterman wrote: > The paper "Substructure solution with SHELXD > " > (Schneider & Sheldrick, 2002) describes how > > data can be truncated at the resolution at which [ΔF to

[ccp4bb] Post-doctoral position in Structural Biology, Paris-Saclay University

Dear All, A post-doctoral position in structural biology is available at the ChemSyBio team (Paris-Saclay University, INRAE, Micalis) headed by Dr Olivier Berteau. The project involves structure determination of novel metalloenzymes by X-ray crystallography, with a focus on enzymes catalyzing

Re: [ccp4bb] Micro/Macro crystal seeding experience

Good morning/afternoon All, I was wondering when the great Scotsman, Patrick, would speak up re: MMS. ;) Patrick gave a seminar at my old institute at the University of Maryland about MMS. I am HUGE fan of MMS and totally drinking the single malt Scotch on this one. I have had success using

[ccp4bb] Anomalous signal to noise details

Hi folks The paper "Substructure solution with SHELXD " (Schneider & Sheldrick, 2002) describes how data can be truncated at the resolution at which [ΔF to its estimated > standard deviation as a function of the resolution] drops to

Re: [ccp4bb] Micro/Macro crystal seeding experience

Hi Rafael Just to amplify Matthew and David's point about random microseed matrix screening - 1. The idea is you add seeds to RANDOM SCREENS - not everyone understands this! People find it very hard to "let go" of the first conditions they see that give them crystals. 2. I now have the oppos

Re: [ccp4bb] Micro/Macro crystal seeding experience

Hi Raphael I can second Tom and Matthews comments. We got crystals only after including an ion exchange column (even though we work with a GST construct cleaved off with thrombin). Well diffracting crystals then only grow by seeding in reduced precipitant concentration. Additionally, the seeds

Re: [ccp4bb] Micro/Macro crystal seeding experience

Hi Raphael Think about simple refinement, differents kits are available additifs kits: - additif, Gras and Silver bullet : from Hampton research - Angstrom and Morpheus from MDL - JBScreen Plus from Jena bioscience detergent kits: - from Hampton resaerch - from Jena bio

[ccp4bb] Project Leader in cryo-EM

Dear all, The Structural Biology Platform at the Friedrich Miescher Institute for Biomedical Research is seeking a highly motivated scientist experienced in cryo-EM, who would like to contribute to the establishment of cryo-ET. The electron microscopy facility is shared with Novartis and equipp