On Monday 31 March 2008 08:58, [EMAIL PROTECTED] wrote:
> In the end, we're solving all these structures because we believe (or
> at least hope) that they'll be useful for understanding
> biology. That means that biologists should be able to understand
> what we deposit.
Agreed, but...
> When I've tried to teach undergraduates "what to make of" structural
> models, I find I can give (most of) them an intuitive feel for what B
> tells or doesn't tell them.
The whole concept of a "B factor" is an artificial construct.
It is one way of modeling the inherent flexibility/uncertainty/variability
in the protein. But it is not the only way. TLS descriptions are
arguably a better model, in that they capture more information in
fewer parameters than individual Biso values (or for that matter
anisotropic Uij values). The same for ElNeMo-derived vibrational
mode models, or other explicit descriptions of concerted variation.
If the structural model was not refined using individual B factors,
then *any* value inserted in the Biso slot of a PDB file is just
an approximation to the true model.
> I don't have time to even bring up TLS parameters.
> The file that gets downloaded from the databank and displayed by
> pymol or PDBviewer needs to be as simple as possible while still
> being true.
There is no inherent "truth" to B values.
> Exactly how those Bs were derived should be included in
> the file, but in a way that the non-specialist users can get by
> without reading it all (since they most certainly won't ;-) ).
>
> Phoebe
>
> At 03:56 PM 3/29/2008, you wrote:
>
> >I believe the simplest and most honest thing to deposit are the
> >parameters of your model,
> >viz the TLS parameters and the residual B factors.
I agree with this. It is our responsibility to present the
true structural model that was refined. If end-users want to
approximate this true model with a different representation,
that's up to them. We should not be degrading or obscuring the
actual, deposited, model for the convenience of out-of-date analysis
programs.
> >Derived quantities should be calculated as and when you need them.
Exactly.
Ethan
> ---------------------------------------------------------------------------------------------------------------------------
> Phoebe A. Rice
> Assoc. Prof., Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723
> fax 773 702 0439
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
>
> RNA is really nifty
> DNA is over fifty
> We have put them
> both in one book
> Please do take a
> really good look
> http://www.rsc.org/shop/books/2008/9780854042722.asp
>
--
Ethan A Merritt Courier Deliveries: 1959 NE Pacific
Dept of Biochemistry
Health Sciences Building
University of Washington - Seattle WA 98195-7742
