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:[log in to unmask]
> ******************************************************************
> The opinions in this message are fictional. Any similarity
> to actual opinions, living or dead, is purely coincidental.
> ******************************************************************
>
--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
M310
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Crawley WA 6009
Australia
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+61 8 6488 4406
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