On Tue, Mar 28, 2023, James Holton wrote:
Members of an ensemble spread out over a supercell are equivalent to a conventional multi-conformer model, but only when it comes to the density derived from the coordinate atoms alone. They are not the same when it comes to bulk solvent and also not the same when it comes to clashes at crystal packing interfaces.
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You might think that with enough copies in the ensemble it should be possible to fit any density with geometrically reasonable molecules, but that is not what happens in practice. This is actually quite remarkable! So many "free parameters" and yet the tug-o-war between R factors and geometry remains. Now, of course, the real molecules in the real crystal are simultaneously obeying the laws of chemistry and generating the diffraction patterns that we see, but I have never found a way to make a macromolecular model that does both. Neither has anybody else, of course, but wouldn't it be cool if someone figured out how?
I have not "figured out how", but do see what seem to be significant improvements using supercell refinements combined with a force field to represent the "laws of chemistry". This is basically what James has described, but also setting useAmber=True in phenix; I actually use my own codes in order to get more speed and to gain better control over the sampling. Quite a number of high-resolution globular proteins refine to structures with excellent geometries and Rwork in the 5-6% range (and Rfree 1-2% higher). Peptides can be even better: 2ol9 has 4.0/4.9 for Rwork/Rfree. Please note that these are the best examples, illustrating what is possible. They are not typical, and my current method seems to require data at 1 Ang. or better. But my results suggest that there is more backbone heterogeneity than is typically accounted for in the atomic models deposited in the PDB. The examples cited above use 12 copies of each protein chain; I don't know much about the dependence on copy number. Improving the model for solvent contributions can improve things, but so far not by a lot. And the (current?) restriction to high-resolution data sets is a pretty severe limitation. But having a few people exploring the supercell idea seems worthwhile, and I'm happy to share ideas (and code) with anyone who is interested. ....dave case ######################################################################## 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/
