[ccp4bb] Prato cryoEM course 2019 (Tuscany) - few sits still available

Dear all, I would like to highlight the fact that we still have a few places available for the second edition of the “*Prato cryoEM course*” from* 31st to 6th of April 2019*. We will be taking applications until the end of the year. The course aims at PhD students and researchers with little

Re: [ccp4bb] Experimental phasing vs molecular replacement

>>That said, model phases are not so bad.  In fact, in all my experiments with >>fake data the model-phased 2mFo-DFc map always has the best correlation to >>the "true" map.  If you substitute the "true" phases and use the 2mFo-DFc >>coefficients you actually make things worse. Counter-intuitive

Re: [ccp4bb] Experimental phasing vs molecular replacement

It is true that MAD phasing can give you hyper-accurate phases. This is because you are measuring the heavy atom signal in both directions on the Harker diagram, allowing the phase to be solved analytically.  The phasing signal is noisy, of course, but you can fix that either with a bigger heav

Re: [ccp4bb] Sir Prof. Aaron Klug 1926 - 2018

Dear Miri: Thanks very much for your very thoughtful CCP4 post. Since I was one of his last (and perhaps least) postdocs, I felt a bit self-conscious and inadequate initiating discussion. I am very grateful to you for doing so. I would like to point out, for those who are interested, that Ken H

Re: [ccp4bb] ccp4 release 7.0 update 061

On Wed, Dec 05, 2018 at 08:48:59AM -0800, Steven Rees wrote: > The link for the latest CCP4 downloads seems to be down ( > http://www.ccp4.ac.uk/download/). The Cached version loads fine (from Dec > 3), but no server can be found for the download links from this version. Is > anyone else having thi

Re: [ccp4bb] ccp4 release 7.0 update 061

The link for the latest CCP4 downloads seems to be down ( http://www.ccp4.ac.uk/download/). The Cached version loads fine (from Dec 3), but no server can be found for the download links from this version. Is anyone else having this issue? Regards, Steve On Wed, Aug 15, 2018 at 8:12 AM Charles Bal

Re: [ccp4bb] pyruvoyl modification and coot

On 05/12/2018 00:44, Jungwook Kim wrote: I am about to refine a structure containing an N-terminal pyruvoyl residue (naturally derived from serine), which is commonly seen in many decarboxylases. File -> Get Monomer -> PYR Edit -> Merge Molecules -> [Merge the PYR molecule into your protein mo

[ccp4bb] Sir Prof. Aaron Klug 1926 - 2018

Weds., Dec. 5th 2018 London Prof. Klug died November 20th, 2018, and was buried on November 26th in Cambridge, UK. https://www2.mrc-lmb.cam.ac.uk/aaron-klug-1926-2018/ He was among the founders of Structural Biology as we know it today. The title of his 1982 Nobel Prize lecture 'From Macro

Re: [ccp4bb] Experimental phasing vs molecular replacement

Hello, I think what you are alluding to is model bias in (macromolecular) crystallography. What you should consult are the publications associated with this topic, and those on the map coefficients used to compute electron density maps (e.g. SIGMAA weighting), OMIT maps, current refinement te

[ccp4bb] New PDB archive reference paper now in NAR 2019 Database issue

An important new publication describing the activities and development of the Protein Data Bank (PDB), and authored by the whole wwPDB consortium, has been recently released in the 2019 Database issue of Nucleic Acids Research. Please see the following news re

[ccp4bb] Experimental phasing vs molecular replacement

Dear all, It is my understanding that experimental phasing (e.g. Se-SAD), in principle, yields better electron density maps than molecular replacement for protein regions with weak electron densities (partially disordered or flexible). I would appreciate if someone could provide comments on wh