Hello all,
I have still a question about LSQKAB
Why LSQKAB gives a rmsd (or a rms xyz I don't mind) non null for glycine
side chains ?
thanks a lot
nathalie
Eleanor Dodson a écrit :
Q1) Rms xyz and rmsd mean exactly the same . And as for what you
should report - that depends on the problem. As long as you state
clearly what has been fitted ( all atoms, CAs, loops excluded etc etc )
Q2) The algorithms for SSM and LSQKAB are different - SSM fits
secondary structure elements only, then checks the rmsd of all CAs.
This is particularly useful for fitting homolous proteins.
LSQKAB requires a list of all the atoms to be matched and that "rms
xyz" considers all those atoms and only those.
If you want a report of all differences you must click for that on the
GUI.
And as you say this is helpful for finding differences in different
copies of the same molecule.
Eleanor
--
Dr. Nathalie Colloc'h, PhD
CI-NAPS, UMR 6232 - UCBN - CNRS
GIP Cyceron
Bd Becquerel, BP5229
14074 Caen cedex
FRANCE
Tel. 33.2.31.47.01.32
Fax. 33.2.31.47.02.22
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