> issue. Could I just confirm whether or not you think its necessary to
> transfer initial free R assignment to any new data sets or to isomorphous
> data sets such as substrate complexes.
well, i would always do a slow-cool at the start so then it would not be
necessary to transfer them
ian says:
> Slow cooling or pseudo-MD such as randomly shifting co-ordinates
> actually moves you away from convergence, and as I said convergence is
but at the stage of the refinement we're talking about (you have just placed
the model in the asu, and no refinement has taken place against the new data
yet) you are far away from convergence anyway. a slow-cool then does several
beneficial things: it "decouples" r and rfree, reduces "memory"/model bias,
and refines your starting model with a larger radius of convergence than
minimisation
see some of axel brunger's papers, reviews and book chapters from the mid
1990s onward - he has done a lot of tests involving SA, rfree, etc.
by the way - if you *do* want to transfer test flags, or extend a test set to
higher resolution, etc. - dataman has a fair number of options for doing so;
see http://xray.bmc.uu.se/usf/dataman_man.html#H9
--dvd
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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]
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