>> - they all know what B is and how to look for regions of high B >> (with, say, pymol) and they know not to make firm conclusions about H-bonds >> to flaming red side chains. > >But this "knowledge" may be quite wrong. If the flaming red really indicates >large vibrational motion then yes, one whould not bet on stable H-bonds. >But if the flaming red indicates that a well-ordered sidechain was incorrectly >modeled at full occupancy when in fact it is only present at half-occupancy >then no, the H-bond could be strong but only present in that half-occupancy >conformation. One presumes that the other half-occupancy location (perhaps >missing from the model) would have its own H-bonding network. >
I beg to differ. If a side chain has 2 or more positions, one should be a bit careful about making firm conclusions based on only one of those, even if it isn't clear exactly why one should use caution. Also, isn't the isotropic B we fit at "medium" resolution more of a "spherical cow" approximation to physical reality anyway? Phoebe
