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
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