Re: [ccp4bb] Automated refinement convergence

2024-01-18 Thread Nigel Moriarty
I, too, love the smell of cooking (or cooked?) jobs in the morning. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : nwmoria...@lbl.gov Web : CCI.LBL.gov ORCID :

[ccp4bb] Introducing the UNTANGLE Challenge

2024-01-18 Thread James Holton
Greetings Everybody, I present to you a Challenge. Structural biology would be far more powerful if we can get our models out of local minima, and together, I believe we can find a way to escape them. tldr: I dare any one of you to build a model that scores better than my "best.pdb" model

[ccp4bb] Crystal imagers?

2024-01-18 Thread Olga Moroz
Dear All, Does anyone use Jansci PS256 imager? And if yes, what do you think about it? Is it reliable, easy to use, or has some problems? We are thinking of buying it to replace our Rigaku Minstrel, which has been out of action for more than a year... Thanks a lot! Olga Dr Olga Moroz York

Re: [ccp4bb] Automated refinement convergence

2024-01-18 Thread James Holton
Hey there Robert, Refmac has a keyword called "kill" that I think is what you are looking for.  It is documented here: https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html   You can specify a conditional exit based on R factor, etc. Or you can just create a

[ccp4bb] Updated links - Phenix version 1.21 released

2024-01-18 Thread Paul Adams
The Phenix developers are pleased to announce that version 1.21 of Phenix is now available (build 1.21-5207). Binary installers for Linux, Mac OSX, and Windows (under Windows Subsystem for Linux), and the source installer, are available at the download site:

[ccp4bb] Postdoctoral position in Structural Biology at the University of Toronto

2024-01-18 Thread Jeffrey Lee
Postdoctoral position in Structural Biology at the University of Toronto We are seeking an enthusiastic and self-motivated Postdoctoral Fellow to study the mechanisms of fertilization in the Lee Lab at the University of Toronto, Department of Laboratory Medicine and Pathobiology. The

Re: [ccp4bb] Automated refinement convergence

2024-01-18 Thread Robbie Joosten
Hi Robert, I see your point but extending the number of cycles to reach convergence has a big risk of going into infinite loops (which you point out). In the case of Refmac stopping early is not really needed as it is very fast anyway; a few unnecessary cycles won't take that long. Generally

[ccp4bb] Automated refinement convergence

2024-01-18 Thread Robert Oeffner
Hi, I am wondering if authors of refinement programs would like to consider putting on their users wish list the ability of refinement programs to automatically terminate once the refinement has reached convergence. Various refinement metrics such as R factors, CC or RMS values typically will

Re: [ccp4bb] Phenix version 1.21 released

2024-01-18 Thread Randy John Read
For anyone who is confused: Unfortunately, the link given here (https://phenix-online.org/download/) says that the latest release is 1.19.2-4158! That’s very odd because the same URL without the trailing slash (https://phenix-online.org/download) gets to a different page with the right