You are quite right - LSQKAB must be wrong to report a RMS
Distance?/deviation? for a GLY side chain - will look into it and
correct I hope.. Thanks for noticing it and pointing the bug out
Eleanor
Nathalie Colloc'h wrote:
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
