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
02
[EMAIL PROTECTED]
-Message d'origine-
De : Ed Pozharski [mailto:[EMAIL PROTECTED]
Envoyé : Tuesday, April 08, 2008 3:56 PM
À : Philippe DUMAS
Cc : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] Help with Superpose results
RMS deviation refers to the variance of a random
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 '
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 ?
Disclaimer: The following is just humor with the best intentions to
entertain the bb audience and not aiming to annoy anybody, but hoping
that some
: Re: [ccp4bb] Help with Superpose results
Is the rms xyz displacement equivalent to an rmsd??
yes. it is in fact a better name than rms deviation, although i think
'root-mean-square distance' is even better, as it says exactly what you
calculate.
think of it like this, the formula for rmsd
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
Sorry for this 'joke-like' question which was not intend to be a joke
There was a misunderstanding about my question
It is not null or not null which worry me, but it is the fact there is a
value for
glycine 'side chains that I know for sure having no side chains.
From my point of view, it
an interesting way to compare structures from the same protein sequence is
reported here :
acta cryst D56 714-721, 2000 objective comparison of protein structures :
error-scaled difference distance matrice
acta cryst D60 2269-2275, 2004 domain identification by iterative
analysis of
, April 08, 2008 3:56 PM
À : Philippe DUMAS
Cc : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] Help with Superpose results
RMS deviation refers to the variance of a random variable - it is a
characteristic of the underlying probability distribution. When you
superpose two different structures, you
