Hi, Probably a stupid question. Could you multiply a, b and c cell dimensions by 2 or 3 (to give 8 or 27 structures) and restrain well defined parts of structure to be ‘identical’ ? To give you a more NMR like chemically sensible ensemble of structures? Ben
> On 18 Mar 2023, at 12:04, Helen Ginn <ccp...@hginn.co.uk> wrote: > > Models for crystallography have two purposes: refinement and interpretation. > Here these two purposes are in conflict. Neither case is handled well by > either trim or not trim scenario, but trimming results in a deficit for > refinement and not-trimming results in a deficit for interpretation. > > Our computational tools are not “fixed” in the same way that the standard > amino acids are “fixed” or your government’s bureaucracy pathways are > “fixed”. They are open for debate and for adjustments. This is a fine example > where it may be more productive to discuss the options for making changes to > the model itself or its representation, to better account for awkward > situations such as these. Otherwise we are left figuring out the best > imperfect way to use an imperfect tool (as all tools are, to varying > degrees!), which isn’t satisfying for enough people, enough of the time. > > I now appreciate the hypocrisy in the argument “do not trim, but also don’t > model disordered regions”, even though I’d be keen to avoid trimming. This > discussion has therefore softened my own viewpoint. > > My refinement models (as implemented in Vagabond) do away with the concept of > B factors precisely for the anguish it causes here, and refines a > distribution of protein conformations which is sampled to generate an > ensemble. By describing the conformations through the torsion angles that > comprise the protein, modelling flexibility of a disordered lysine is > comparatively trivial, and indeed modelling all possible conformations of a > disordered loop becomes feasible. Lysines end up looking like a frayed end of > a rope. Each conformation can produce its own solvent mask, which can be > summed together to produce a blurring of density that matches what you would > expect to see in the crystal. > > In my experience this doesn’t drop the R factors as much as you’d assume, > because blurred out protein density does look very much like solvent, but it > vastly improves the interpretability of the model. This also better models > the boundary between the atoms you would trim and those you’d leave > untrimmed, by avoiding such a binary distinction. No fear of trimming and > pushing those errors unseen into the rest of the structure. No fear of > leaving atoms in with an inadequate B factor model that cannot capture the > nature of the disorder. > > Vagabond is undergoing a heavy rewrite though, and is not yet ready for human > consumption. Its first iteration worked on single-dataset-single-model > refinement, which handled disordered side chains well enough, with no need to > decide to exclude atoms. The heart of the issue lies in main chain > flexibility, and this must be handled correctly, for reasons of > interpretability and elucidating the biological impact. This model isn’t > perfect either, and necessitates its own compromises - but will provide > another tool in the structural biology arsenal. > > —- > > Dr Helen Ginn > Group leader, DESY > Hamburg Advanced Research Centre for Bioorganic Chemistry (HARBOR) > Luruper Chaussee 149 > 22607 Hamburg > > ######################################################################## > > 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/
