As a relatively inexperienced scientist, I find this discussion
fascinating.
I wonder if NMR and EM people are also worried about depositing enough
"modeled info" to allow back calculation of data.
Regarding the original discussion of whether to deposit riding
hydrogens used in the refinement, 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.
I wonder if it would help to deposit two different models; one
precisely reflects the model used in refinement and the other an
energy minimized model with predicted hydrogens and alternative
conformations removed?
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]
On Sep 17, 2010, at 8:28 AM, Ian Tickle wrote:
Oh, goodness, I see: even here, we would need clear rules what the
calculated structure factors are, which weights are were, which
bulk solvent
correction was applied ... a maze, too!
Fortunately the X-ray & restraint weights/target values are not an
issue here: varying them changes the refined model parameters of
course, but they do not appear in the structure factor formula, so
don't need to be specified in the mathematical model to obtain the
Fcalcs. You would of course need to know all the weights & target
values (as well as the SF formula) to reproduce the refinement to get
the deposited model.
But could future programs really re-calculate the same structure
factors
from the deposited model? Because of the expected development of more
advanced methods and algorithms, I have my doubts ... *sigh*
Yes, if the deposited mathematical model is completely specified in
terms of the SF formula used and the values of *all* the parameters
that go into it, then in principle future versions of software using
more advanced models will be able to reproduce the exact Fcalcs. This
assumes that the advanced models will use the same 'core' formula but
with additional terms and adjustable parameters, so that the simple
model can be obtained from the advanced one by constraining the extra
parameters to fixed values. However if the simple model is not
'nested' inside the more advanced model in this way, then no it will
not be possible to reproduce the Fcalcs.
However as I implied, the main issue is that we're rather lax at fully
specifying our models (both formulae & parameters): obviously if in
future you don't have all the information you need to reproduce the
calculation then you have no hope of getting the same Fcalcs!
Cheers
-- Ian
