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On Sunday 28 January 2007 09:57, Gerard DVD Kleywegt wrote: > >> in principle, you could use 'floating chirality' (i.e., unrestrained improper > >> of the chiral carbon) but this is likely to lead to distorted geometry (i.e., > >> an improper that lies somewhere in between +35 and -35 degrees). > > > > That would be true were it not for the cleverness of whoever set up > > the sugar restraint system for refmac. The syntax allows you to set the > > chirality restraint on the anomeric sugar to "both". This restrains to the > > correct absolute value of the chiral volume, thus accepting either anomer. > [...] > also, depending on the make-up of the binding site, i would suspect that quite > often two stereo-isomers are "bound" to be bound in different orientations > (since stereo-selectivity is a hallmark of many biological molecules and > processes), making the option with two different molecules a better > representation of what's in your crystal I may not have been clear enough. Yes, one would be refining two molecules, one the alpha- and one the beta- anomer, each at partial occupany, resulting in two distinct models for the molecule occupying that binding site. That was already stated in the original query. The refined model may well end up with different positions for all atoms, as you point out. My only point was that so far as refmac restraints are concerned, the same dictionary entry can handle both molecules. > finally, although admittedly a debatable issue, i consider it preferable, both > philosophically and educationally, to treat different chemicals as different > entities Sure. But the specific question was "how do you generate restraints?". The answer, at least for refmac, is that the same restraint file can be applied to both anomers so long as you insure that the anomeric restraint is marked "both". Ethan > > --dvd > > ****************************************************************** > Gerard J. Kleywegt > [Research Fellow of the Royal Swedish Academy of Sciences] > Dept. of Cell & Molecular Biology University of Uppsala > Biomedical Centre Box 596 > SE-751 24 Uppsala SWEDEN > > http://xray.bmc.uu.se/gerard/ mailto:[log in to unmask] > ****************************************************************** > The opinions in this message are fictional. Any similarity > to actual opinions, living or dead, is purely coincidental. > ****************************************************************** > > -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742