Hi Edward,
But if [AMBER11] gives me de facto corrupted files I maybe just should use
the
attach_protons function of relax!
Note these are not equivalent. The relax attach_protons function does
not create atomic coordinates for the new protons whereas AMBER's
does. This means that you cannot use it for the spheroidal or
ellipsoidal diffusion tensors in a model-free analysis.
Oh, I didn't realize that. I just used the (corrupted) AMBER-generated PDB
files which worked fine with relax 2.
You should
understand how AMBER places these protons and how other programs do
this too. I hope that one day relax will be able to do this, but that
will require a volunteer to add the algorithm.
In case someone stumbles upon this thread in the future, there is
documentation for the reduce function
(http://kinemage.biochem.duke.edu/software/readme.reduce.html) which refers
to the following publication:
Word JM, Lovell SC, Richardson JS, Richardson DC (1999) Asparagine and
glutamine: using hydrogen atom contacts in the choice of side-chain amide
orientation. J Mol Biol 285: 1735–1747.
http://www.pibs.duke.edu/downloads/PDFs/1999WordJMB285b.pdf
Probably the conformational differences are too small to make a real
difference in the subsequent MF analysis, given how large the actual
errors of
my rates etc actually are. I will look into this and if there's any
difference, report back here.
I unfortunately don't understand what this means. But if you mean
bond vector orientations, the relaxation rates are highly sensitive to
these even with low levels of anisotropy.
To be honest, even I'm not understanding it. This was just a unqualified
comment to reassure myself that something that looks so bad in the first
place (a rather simplistic model of the spectral density function, a reduced
set of parameters with huge errors, imperfect pulse programs, uncertainties
in the X-ray structures and also the artificial addition of protons, and many
variables I can't perfectly control) can yield interesting and reproducable
data. You know, it's just the hope I will get some results I can work with.
Cheers,
Martin
Re: [bug #21187] "NoneType" error message while loading side chain amide protons