[ccp4bb] Help us design PDBe-KB's aggregated views of small molecules

PDBe-KB is a community-driven resource managed by the Protein Data Bank in Europe (PDBe) team, integrating functional annotations and structure data in the PDB archive. Recently, we started providingaggregated views of available structure data and annotations for ind

Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?

Hi Colin, Yes I agree, see eg page 7 of https://www2.physics.ox.ac.uk/sites/default/files/2011-06-08/optics_notes_and_slides_part_5_pdf_63907.pdf (and there maybe better weblinks). The resolution of cryoEM imaging varies locally and so the “local scaling in a complex way” is what we have to ge

Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?

Dear Colin Great that you mention the Rose equation and its consequences for cryo-EM! I have actually written a paper on that topic some 40 years ago [Marin van Heel: Detection of object in quantum-noise limited images. Ultramicroscopy 8 (1982) 331-342]. I honestly have not thought about it for a

Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?

Hi John I agree that neutrons have a role to increase the contrast for certain atoms. The “water window” for x-ray imaging also fulfils a similar role. The “locally scaled in a complex way” is a bit beyond me. The relationship between “ diffraction” errors and “imaging” errors is based on Pars

[ccp4bb] FW: [ccp4bb] [3dem] Which resolution?

Dear Marin For electron microscopy, the Rose criterion (a measure of contrast/noise) is sometime used to distinguish low contrast features within polymers (see for example Libera, M. & Egerton, R. (2010). Polymer Reviews. 50, 321-339.). A particular value of the Rose criterion implies a partic

Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?

Hi Colin, Neutrons are applied to the uranyl hydrides so as to make their scattering lengths much more equal than with X-rays, and so side step ripple effects of the uranium in the Xray case, which obscures those nearby hydrogens. In terms of feature resolvability the email exchange (and there ma

[ccp4bb] EMBO meeting on “Molecular Neurobiology” 8-12 May 2020, deadline registration 29 Feb.

Dear all, a gentle reminder of the upcoming EMBO workshop on Molecular Neurobiology on the beautiful island of Crete. The extended deadline for registration, 29 Feb., is approaching fast. Last chance to sign up! Please see https://meetings.embo.org/event/20-molneuro for further details. Best w

Re: [ccp4bb] FW: [ccp4bb] [3dem] Which resolution?

Hi John I agree that if I truncate the data at a high information content threshold (e.g. 2 bits) series termination errors might hide the lighter atoms (e.g. the hydrogens in uranium hydride crystal structures). However, I think this is purely a limitation of producing electron density maps vi

[ccp4bb] PhD position available

Dear all, There is an opening for a PhD position in my group. The Beck group recently moved to Hamburg, where we have labs well-equipped for chemistry, biochemistry and molecular biology. Moreover, state-of-the-art facilities for structural characterizations such as PETRA III are close by. The pr

Re: [ccp4bb] [3dem] Which resolution?

Dear Petrus Zwart (and all other X-ray crystallographers and EM-ers) Resolution in the sense of the Abbe Diffraction Limit or the Rayleigh *Criterion are part of what we would now call the theory of linear systems, and are described by a “transfer function”. “Fourier Optics” covers the theory of

[ccp4bb] FW: [ccp4bb] [3dem] Which resolution?

Dear all. Would it help to separate out the issue of the FSC from the value of the threshold? My understanding is that the FSC addresses the spatial frequency at which there is a reliable information content in the image. This concept should apply to a wide variety of types of image. The issue