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Hi Nick,
> i would like to get opinions on whether or not one removes side-chain
> atoms where there is no density. for example, if one can only observe
> density up to the beta-carbon for lysine (say at > 0.5 sigma), does one
> leave the lysine side chain intact, knowing it must be disordered, or
> does one terminate at the beta-carbon, making the coordinates reflect
> what is actually observed in the density.
As you said, different people treat the problem differently. It seems to
me that depositing single-conformation coordinates for a disordered
side-chain can mislead the general users of your PDB file to think that
you have actually obtained experimental evidence for the deposited
coordinates [crystallographers will probably take a good look at the
corresponding atomic temperature factors and will realise what is
happening (assuming that you have not constrained max(B) during
refinement ;-)].
If you have data to sufficiently high resolution it may worth the effort
of examining the density in the vicinity of the missing side chain for
evidence of discrete disorder. Submitting coordinates for two or three
conformations of a missing lysine will definitely pass the message across.
Nicholas
--
Dr Nicholas M. Glykos, Department of Molecular
Biology and Genetics, Democritus University of Thrace,
Dimitras 19, 68100 Alexandroupolis, Greece, Fax ++302551030613
Tel ++302551030620 (77620), http://www.mbg.duth.gr/~glykos/
