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
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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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