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The Ramachandran plots you used to define outliers, do they predate the
Richardson-Richardson ones? Because, invoking WWW: without the resolution,
how can you justify Ramachandran outliers? (The old procheck Rama plot
hasn't been updated since 1991, I gather...)
yes, they do - our definition was derived more than 10 years ago (using
resolution and B-factor cut-offs - see the original paper, Structure 1996).
some time ago it was argued on ccp4bb that any ramachandran definition that
didn't include the gamma-turn region was not worth it's money. however, this
is nonsense. for model-validation purposes there is no harm in that - we use
the ramachandran plot to identify outliers that are potential errors in the
model. therefore, having 'allowed regions' that are (too) small is not a
problem - you will get a few false positives (residues flagged as outliers
which are really okay) but no false negatives (compared to programs with more
permissive allowed regions). the problem with procheck's definitions is that
they are too 'nice' - you can easily have residues that are in error but not
flagged as outliers by procheck.
also, once again - ramachandran outliers can be one of two things: an error in
the model (that needs to be corrected if possible), or a genuine (albeit
unusual) feature of the structure (that suggests there is local strain, so the
residue may be of functional or structural significance). therefore, it is
silly to attempt to get a model with no outliers at all - these are indeed
very rare. all the more so at low resolution. and all the more-more so if the
outliers are 'fixed' by twiddling phi/psi. if there is something fishy about a
residue's phi/psi (not supported by rock-solid density), this is an indication
that you may need to do some local rebuilding (e.g., flip a peptide, or
rebuild a mobile loop). you may also need to look at other quality indicators
to be able to diagnose the problem (a program like OOPS helps you do that in a
systematic fashion).
here endeth today's reading from the gospel of ramachandran.
--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:[EMAIL PROTECTED]
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