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 it is better to err in the direction of having too many cycles than too few, especially in your 'final' refinement. This is also the logic applied to pdb-redo, it does 20 cycles by default (more than the typical number for Refmac) and then extends the number of cycles when it uses options that slow down convergence (jelly body, anisotropic B-factors, new data from paired refinement). This (almost) always leads to something that we can call "convergence", at least for models that were at the final stages of model building.
That said, I have only really achieved convergence in Refmac (i.e. gradients are '0') once in twenty years and that was after more than 500 cycles of jelly body refinement.* Apparently, there is a large step between "things don't change a lot anymore" and real convergence. Cheers, Robbie * Refmac crashed at that point. A division by zero if I remembered correctly. > -----Original Message----- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Robert > Oeffner > Sent: Thursday, January 18, 2024 12:05 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Automated refinement convergence > > 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/
