I'm amazed at the pedestal people put their precious coordinates on --
isn't the first thing you learn about MX that our models are rubbish
parametrizations of the actual content of the crystal? And thus they
will remain as long as we have the R-factor gap, and no amount of
coordinate-sigmas or dark-density will change that.
What we *are* trying to do is communicate something, and the bedrock of
communication is /convention/ - also known as "standardization". What
is science other than one large standardization exercise? So yes,
standardization is *exactly* what is needed: when the same phenomenon
is described in so many different ways by different people, what that
indicates is not that they have different opinions, it indicates only
that everybody has to second-guess what their audience will understand.
But once we've laid down a convention, the guessing stops and both
speaker and listener know what the hell is being said.
phx.
On 30/03/2011 19:04, James Holton wrote:
I'm afraid this is not a problem that can be solved by "standardization".
Fundamentally, if you are a scientist who has collected some data (be
it diffraction spot intensities, cell counts, or substrate
concentration vs time), and you have built a "model" to explain that
data (be it a constellation of atoms in a unit cell, exponential
population growth, or a microscopic reaction mechanism), I think it is
generally expected that your model explain the data "to within
experimental error". Unfortunately, this is never the case in
macromolecular crystallography, where the model-data disagreement
(Fobs-Fcalc) is ~4-5x bigger than the "error bars" (sigma(F)).
Now, there is nothing shameful about an incomplete model, especially
when thousands of very intelligent people working over half a century
have not been able to come up with a better way to build one. In
fact, perhaps a better name for the "disordered side chain problem"
would be "dark density"? This name would place it properly amongst
"dark matter", "dark energy" and other fudge factors introduced to try
and explain why our "standard model" is not consistent with
observation? That is, "dark density" is the stuff we can't see, but
nonetheless must be there somewhere.
Whatever it is, I personally do hold a vain belief that perhaps
someday soon the problem of "dark density" will be solved, and that
presently instituting a "policy" requiring that all macromolecular
models from this day forward remain at least as incomplete as
yesterday's models is not a very good idea. I say: if you think there
is "something there" then you should build it in, especially if it is
important to the conclusions you are trying to make. You can defend
your model the same way you would defend any other scientific model:
by using established statistics to show that it agrees with the data
better than an "alternative model" (like leaving it out). It is YOUR
model, after all! Only you are responsible for how "right" it is.
I do appreciate that students and other novices may have a harder time
defining "surfaces" and measuring hydrogen bond lengths in these pesky
"floppy regions", but perhaps their education would be served better
by learning the truth sooner than later?
-James Holton
MAD Scientist
On 3/30/2011 9:26 AM, Filip Van Petegem wrote:
Hello Mark,
I absolutely agree with this. The worst thing is when everybody is
following their own personal rules, and there are no major guidelines
for end-users to figure out how to interpret those parts. I assume
there are no absolute guidelines simply because there isn't any
consensus among crystallographers... (from what we can gather from
this set of emails...). On the other hand, this discussion has flared
up many times in the past, and maybe it's time for a powerful
dictator at the PDB to create the law...
Filip Van Petegem
On Wed, Mar 30, 2011 at 8:37 AM, Mark J van Raaij
<[email protected] <mailto:[email protected]>> wrote:
perhaps the IUCr and/or PDB (Gerard K?) should issue some
guidelines along these lines?
And oblige us all to follow them?
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3, Campus Cantoblanco
E-28049 Madrid, Spain
tel. (+34) 91 585 4616 <tel:%28%2B34%29%2091%20585%204616>
http://www.cnb.csic.es/content/research/macromolecular/mvraaij/index.php?l=1
On 30 Mar 2011, at 17:29, Phoebe Rice wrote:
> I've now polled 4 fairly savvy "end users" of crystal
structures and there seems to be a consensus:
>
> - they all know what B is and how to look for regions of high B
(with, say, pymol) and they know not to make firm conclusions
about H-bonds to flaming red side chains.
> - None of them would ever think to look at occupancy and they
don't know how anyway.
> - they expect that loops with disordered backbones would not be
included in the models, and can figure out truncated or fake-ala
side chains with some additioanl effort, but that option makes
viewing surfaces and e-stats more of a pain.
>
> Phoebe
>
> =====================================
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723 <tel:773%20834%201723>
>
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
> http://www.rsc.org/shop/books/2008/9780854042722.asp
>
>
> ---- Original message ----
>> Date: Tue, 29 Mar 2011 17:43:49 -0400
>> From: CCP4 bulletin board <[email protected]
<mailto:[email protected]>> (on behalf of Ed Pozharski
<[email protected] <mailto:[email protected]>>)
>> Subject: [ccp4bb] what to do with disordered side chains
>> To: [email protected] <mailto:[email protected]>
>>
>> The results of the online survey on what to do with disordered
side
>> chains (from total of 240 responses):
>>
>> Delete the atoms 43%
>> Let refinement take care of it by inflating B-factors 41%
>> Set occupancy to zero 12%
>> Other 4%
>>
>> "Other" suggestions were:
>>
>> - Place atoms in most likely spot based on rotomer and
contacts and
>> indicate high positional sigmas on ATMSIG records
>> - To invent refinement that will spread this residues over
many rotamers
>> as this is what actually happened
>> - Delet the atoms but retain the original amino acid name
>> - choose the most common rotamer (B-factors don't "inflate",
they just
>> rise slightly)
>> - Depends. if the disordered region is unteresting, delete atoms.
>> Otherwise, try to model it in one or more disordered model
(and then
>> state it clearly in the pdb file)
>> - In case that no density is in the map, model several
conformations of
>> the missing segment and insert it into the PDB file with zero
>> occupancies. It is equivalent what the NMR people do.
>> - Model it in and compare the MD simulations with SAXS
>> - I would assumne Dale Tronrod suggestion the best. Sigatm labels.
>> - Let the refinement inflate B-factors, then set occupancy to
zero in
>> the last round.
>>
>> Thanks to all for participation,
>>
>> Ed.
>>
>> --
>> "I'd jump in myself, if I weren't so good at whistling."
>> Julian, King of Lemurs
--
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3
phone: +1 604 827 4267
email: [email protected] <mailto:[email protected]>
http://crg.ubc.ca/VanPetegem/
