Hi Gerard,
Interesting - isn't it the case that for Arg, the the NH1 and NH2 atoms
are chemically distinguishable and the convention is unambiguous (NH1
cis to CD and NH2 trans, if I recall correctly).
The truly symmetric sidechains of Asp, Glu, Tyr, Phe, and the
pseudosymmetric sidechains of Asn, Gln and His are more straightforward,
but for Arg I would have thought quite a strong case would have to be
made for ignoring the convention for RMSD purposes. Put differently, I
find it hard to envision a scenario where swapping the names of NH1 and
NH2 for the purposes of an RMSD would be useful. Would one also not have
to include NE in the redundancy?
Cheers,
Charlie
Gerard DVD Kleywegt wrote:
Is there any convention to define the order of the two terminal
nitrogens (NH1 and NH2) of the arginine side chain. For example,
should the name NH1 be assigned to the nitrogen that is in trans
position with respect to the CD carbon, and NH2 to the nitrogen in cis
(or viceversa)?
Yes there is a convention. Programs such as LSQMAN
(http://xray.bmc.uu.se/usf/lsqman_man.html#S32) and WhatCheck can
detect/fix these for you. This is something you would normally do at the
end of your refinement. When you compare two models using all atoms,
it's not so important that you use the correct convention but rather the
one that gives the smallest RMSD (as the atoms are chemically
indistinguishable). See: http://xray.bmc.uu.se/usf/lsqman_man.html#S33
--dvd
******************************************************************
Gerard J. Kleywegt
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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The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
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--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
M310
35 Stirling Highway
Crawley WA 6009
Australia
[email protected]
+61 8 6488 4406
