A horrible bug -
this line was somehow lost from lsqkab in the mists of time:
Lines 1029-132 - ish
should be
IF (ATNMW(I)(1:3).EQ.'CA ' .OR. ATNMW(I)(1:3).EQ.'N ' .OR.
+ ATNMW(I)(1:3).EQ.'C ' .OR. ATNMW(I)(1:3).EQ.'O ' .OR.
+ ATNMW(I)(1:3).EQ.'P ' .OR. ATNMW(I)(1:3).EQ.'O1P' .OR.
etc
NOT
IF (ATNMW(I)(1:3).EQ.'CA ' .OR. ATNMW(I)(1:3).EQ.'N ' .OR.
+ ATNMW(I)(1:3).EQ.'P ' .OR. ATNMW(I)(1:3).EQ.'O1P' .OR.
Thank you for noticing this!
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
