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
Although this is not a very important issue..., I am a bit surprised by
Gerard's insistance for a 'stop calling rmsd rms deviation'. Isn'it a
general term in statistical studies, valid for distances separating
homologous atoms as well as for any other factor (B factors for example) ?
Philippe
Dear all,
once again this bulletin board proved to be a great ressouce. I obtained
15 emails since I posted - thanks to everybody!
I composed a summary for the CCP4 wiki, which can be found at:
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
Here's an example (although not Fe):
Futterer, K., Ravelli, R. B. G., White, S. A., Nicoll, A. J.
Allemann, R. K. (2008). Acta Cryst. D64, 264-272.
On 8 Apr 2008, at 9:02 AM, Florian Schmitzberger wrote:
Dear All,
Are there prominent examples of ordering of an alpha-helix within a
Here is another example of ordering of alpha helix upon metal (nickel)
binding.
Nature Structural Biology 10, 794 - 799 (2003)
Crystal structure of the nickel-responsive transcription factor NikR
Eric R Schreiter, Michael D Sintchak, Yayi Guo, Peter T Chivers, Robert T
Sauer Catherine L
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
Apparently I had missed some subtle considerations...
Yet, I confess am not fully convinced: is it so wrong to speak of how much
different structures DEVIATE from each other ? I do not see what prevents
you from defining the correct underlying probability distribution. That
interatomic distances
