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.
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. 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. 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.
Derived quantities should be calculated as and when you need them.
---------------------------------------------------------------------------------------------------------------------------
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
