Hi Nicholas,
Thank you for your reply.
<snip>
it seems that we are trying to deposit one model to satisfy two
different purposes - one for model validation and the other for model
interpretation (use in docking etc), and what's good for one purpose
might not be necessarily good for the other.
</snip>
This has been discussed before on this list, but allow me to repeat
it:
You would have expected that the crystallographers' aim would be to
deposit the model that maximises the product (likelihood * prior).
Clearly, this is not what we do, mainly because (a) the calculation of
likelihood is only based on a subset of the 'data' that are obtained
from
an X-ray diffraction experiment (for example, we ignore diffuse
scattering
as Ian pointed-out), (b) we consciously avoid 'prior' because this
would
make the models 'subjective', meaning that better informed people
would
deposit (for the same data) different models than the less well
informed,
(c) the format of the PDB does not offer much room for 'creative
interpretations' of the electron density maps [for example, you
can't have
discrete disorder on the backbone (or has this changed ?)]. I sense
that
what is being deposited is not the 'best model' in any conceivable
way,
but the model that 'best' accounts for the final 2mFo-DFc map within
the
limitations of the program used for the final refinement.
I don't quite understand your point. We currently deposit electron
densities and movies, I don't see how depositing an energy minimized
structure is so difficult. It doesn't need to be on the same pdb file
as the model used in refinement nor does it need to be deposited into
the PDB server, but even if it does, is it not possible to have it as
a new "Chain" or new "atom type" in the current pdb file format?
ps. May I say parenthetically that making the deposited models
dependant
on their intended usage, would possibly qualify as 'fraud' ;-)
I don't quite understand this either. When I prepare a protein model
for simulation, I would remove all alternative conformations, add
hydrogens, and then minimize the structure. If I make such a minimized
structure available for others to use with full disclosure, how would
that constitute "fraud"? I was going to start offering minimized
models on our future structures on our lab website, but if that
constitutes fraud, then I might have to rethink.
I don't know enough to argue with anyone here and that's not the
intention of my posts - I am just trying to help figure out a way to
resolve a significant problem that will likely to resurface down the
road. It would be helpful if the more experienced people here can
start a discussion of 'how to resolve' the problems exposed by this
thread so far - assuming that you agree that it's a problem worth your
time.
Cheers,
Quyen
__________________________________
Quyen Hoang, Ph.D
Assistant Professor
Department of Biochemistry and Molecular Biology,
Stark Neurosciences Research Institute
Indiana University School of Medicine
635 Barnhill Drive, Room MS0013D
Indianapolis, Indiana 46202-5122
Phone: 317-274-4371
Fax: 317-274-4686
email: [email protected]
--
Dr Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office)
+302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
