Re: [ccp4bb] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy

Yes, to the uninitiated, that's an easily-overlooked massivefeature of modern MX... Question:  has anybody given Randy's KL information gain treatment to the inclusion (or tightening) of restraints? On 09/10/2024 19:36, James Holton wrote: Sometimes I wonder where we got this idea that "res

Re: [ccp4bb] Commercial storage of biological samples

Thanks, Jonathan. That would certainly be a compact and very portable storage solution for plasmids! Bests, Alexandra Alexandra Deaconescu, B.E., Ph.D. Assistant Professor Brown University Office: (401) 863-3215 Wet Lab: (401) 863-6729 Computational Lab: (401) 863-7031 For Mail: Laboratories

Re: [ccp4bb] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy

Randy, what a beautiful paper! I love it. I’m also a huge fan of the you guys’ resolve_cryo_em density modification paper, which had a major impact on my group’s ability to interpret several challenging structures. Many moons ago when I was a postdoc with Niko Grigorieff, I got interested in th

[ccp4bb] AW: [ccp4bb] Commercial storage of biological samples

dear alexandra, DNA at least is extremely stable, so i'd just spot the plasmids onto filter paper (labelled with a pencil)... and send the spots to a trusted (young!) friend somewhere far away. at least i'd trust that more than any profit-oriented company. best jon -- Prof. Dr. Jon Hughes Depar

Re: [ccp4bb] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy

Sometimes I wonder where we got this idea that "resolution" is somehow an error bar on position. Perhaps we can blame astronomers? And yet, every day we use stereochemical restraints with "sigma" on bond lengths set around 0.005 A.  Ever wonder how this distance was so accurately measured?  Mus

[ccp4bb] Commercial storage of biological samples

Hello US-based structure enthusiasts: I would be interested in storing some of my biological samples (plasmids, cells, purified proteins) using a commercial storage service. I have looked at several options online, but I was hoping that perhaps someone out there has some first-hand experience t

Re: [ccp4bb] AlphaFold3

Thank you to all who replied and for the tip off about the prize - all very newsworthy ;-0 Will try to summarise everything in a para or two. Congrats to the winners!! Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android Original Message On 07/10

Re: [ccp4bb] Nobel prize for Alpha fold and protein design!

Oh, we can just badge ourselves as what the LHC is to Peter Higg's Prize. On 09/10/2024 14:06, Subramanian, Ramaswamy wrote: Dear All, I am sure many of you saw the announcement of the Nobel Prizes. I am glad for the recipients. This would not have been possible but for PDB and the other str

Re: [ccp4bb] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy

So Randy, what should we be saying/using, and where do we find it... and (not least!), /when/ in the experiment-to-final-model process? By "what" I mean, the specific words - since as Ian points out, the words "resolution limit" and "diffraction limit" are quite different, whatever we thoughtl

[ccp4bb] Nobel prize for Alpha fold and protein design!

Dear All, I am sure many of you saw the announcement of the Nobel Prizes. I am glad for the recipients. This would not have been possible but for PDB and the other structural databases (they should have been one of the recipients) and all those who contributed structures to these databases;

Re: [ccp4bb] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy

Even within the domain of crystallography 'resolution' is used (correctly) to mean exactly the same thing as it does in other fields where imaging finds application (such as astronomy and microscopy, as you mention). This is even true in certain applications of crystal diffraction, for example in

Re: [ccp4bb] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy

Dear all Thanks all for these interesting discussions. My view is that the issues arise from a convention adopted many years ago to use the word "resolution" in crystallography to describe the visibility of features in an electron density map and/or the limit in reciprocal space where the diffr

[ccp4bb] Annotation of Protein Modifications in the PDB

Dear all, The PDB archive is now including annotation of protein chemical modifications (PCMs) and post-translational modifications (PTMs) in a standardized way. As previously announced , thePDBx/mmCIF dictionary