On Tue, 24 Jun 2025 22:54:28 +0100 Martin Malý <[email protected]> wrote:
> Actually I would be quite interested what is your best practise when > you want to reset a structure model to not be biased towards any test > reflection set. Dear Martin, according to Ian Tickle, the idea or 'resetting' the structure is the wrong understanding, and if you notice model bias, there was a mistake in the approach. You can safely build your model and refine against all data all the way to the end. When you are interested in Rfree, you pick any random set and refine to convergence, i.e. until the target function does not drop any further. Refinement removes bias. (see Ian's emails on this topic, quite some years back) 'shaking' the model coordinates and/or adps is no good. I remember in one case when I worked on Rcomplete, there was a side chain the flipped into a different rotamer from shaking. This is a different model, and you cannot average R-values from different models (see sections "Effect of Parameter Perturbation." and "Influence of Parameter Perturbation on Convergence Rate" and Figures S4 /S5 in https://doi.org/10.1073/pnas.1502136112 / https://www.pnas.org/doi/suppl/10.1073/pnas.1502136112/suppl_file/pnas.1502136112.sapp.pdf Best, Tim -- -- Tim Gruene Head of the Core Facility Crystal Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 https://ccsa.univie.ac.at GPG Key ID = A46BEE1A ######################################################################## 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/
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