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 : orcid.org/0000-0001-8857-9464 On Thu, Jan 18, 2024 at 1:16 PM James Holton <jmhol...@lbl.gov> wrote: > 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 specified file containing "stop Y" from an external > process. I use it when running refmac on a cluster that has run time > limits but difficult-to-predict CPU speeds. > > Phenix, I don't think has a checkpointing feature. Not that I know of. > > Amber does support checkpointing and now counts as a refinement program > since support for structure factor restraints was added in 22. > > Personally, when I do refinements I do dozens to hundreds of > macro-macro-cycles. As in, take the pdb file output by one run and feed > it into another run. There is an instantiation overhead to doing this, > as you note, but I like my models to be super converged. I define > convergence as the x,y,z,B and occ values in the pdb file are not > changed by the refinement program. This does not happen quickly, but it > does eventually happen. Yes, you can get oscillations, but one way to > deal with those is to add a bit more damping, or to adjust the x-ray > weight down and then up and then back to auto again. This "weight snap" > tends to take things that were dangling from a cliff in the energy > landscape and knock them to the ground. After that, the oscillations are > less common. > > And like an equilibrated chromatography column, an xyz-converged model > is the best way to know that when you edit and re-refine, everything you > see is due to the edit, and not some other process that just wasn't > finished yet. > > That's what I do. Maybe I just want to feel like I've got something > cooking while I sleep... > > Cheers, > > -James Holton > MAD Scientist > > On 1/18/2024 3:04 AM, Robert Oeffner wrote: > > 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 reach a plateau once the refinement of a macromolecular structure with > X-ray or EM-data has converged and further macro-cycles of refinement will > no longer improve the structure. The default number of macro-cycles in > programs such as Phenix-refine and Refmac are probably sensible for most > cases but in some cases it would be nice if the programs automatically > extended the number of macro-cycles as needed (or decreased the number). > > > > The user can of course examine log files from refinement themselves and > decide whether to continue refinement. But since starting a new session of > refinement appears to always create an initial fluctuation in the > refinement metrics before they align with the values of the last > macro-cycles in the previous refinement session, the user is compelled to > do at least, say 3 or more macrocycles in addition to whatever may be > needed for reaching convergence. I guess it would therefore be more > efficient if this was implemented directly in the refinement programs and > presented as an option for the user to choose. > > > > There could be cases where alternate conformations of a structure will > repeatedly be oscillating in and out of density thus causing the refinement > metrics also to oscillate. Hopefully such cases could be covered by gauging > the level of fluctuations of the refinement metrics and terminate the > refinement accordingly. > > > > Many thanks, > > > > Robert > > > > ######################################################################## > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
