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Nick,
as you see from the responses you got, there are really three options:
1. Set the occupancies of atoms in question to 0.0
2. Remove the atoms in question
3. Let refinement take care of it by "inflating" B-factors
In terms of refinement, first two options may seem to give identical
results, but they in fact differ. Zero occupancies will give zero
contribution to Fcalc, whereas with atoms removed the corresponding
volume will be filled with bulk solvent. IMHO, the first option (zero
occupancies) thus lead to the biggest possible error introduced to your
model. The third option will contribute to Fcalc about the same way the
second option does, because the corresponding volume will be "filled"
with diffuse density resulting from high B-factor.
So, I guess the zero occupancy option should be rejected because it
introduces larger error into your model. I would also reject it on
semantic grounds. Crystallographic models with isotropic B-factors
describe every atom in your structure using 5 numbers - three
coordinates (x,y,z), occupancy (q) and B-factor. The meaning of it can
be summarized as follows:
"This atom (known from chemical information to be present in the
structure) spends the q fraction of time in the vicinity of (x,y,z),
with the probability to find the atom at a certain distance from it
falling off according to the normal distribution whose width is defined
by the B-factor"
Zero occupancy is thus complete nonsense - what it means is that the
atom is NEVER in the vicinity of (x,y,z) given in your pdb-file. It is
not even zero-information statement, it is plain wrong, given that you
choose, say, the highest probability rotamer. The atoms missing from
density in fact has some probability to be where you put them!
So what about omitting atoms from the structure? You are then just
saying that you have no idea where these atoms are, which sounds OK.
Indeed, structural models are always incomplete. If I replace
individual waters and whatever else is in my mother liquor by bulk
solvent, why should disordered sidechains be special? Here is why:
No protein structure (except for crambin, I presume) is ever determined
without prior knowledge about its chemical structure. Unless you have
strong reasons to believe that an xray fairy has cut off this lysine
sidechain with a tiny magic saw with an explicit purpose to drive you
crazy, you should leave atoms in because you know from sequence that
they are there. The B-factor of 200 corresponds to rmsd of ~1.6A, which
transforms to "atom spends 95% of time inside a sphere of 6.4A in
diameter", so you are not really narrowing down its spatial position too
much. In fact, covalent bonds will keep it in much smaller volume.
Crystallographers worry, however, that non-crystallographers may misuse
their models because non-crystallographers don't understand the basic
concepts behind B-factors. IMHO, it is crystallographer's job then to
educate non-crystallographers. But at the end of the day, it is
driver's responsibility to learn the meaning of red light, and if a
reasonable effort was made by RMV to deliver the information, that is
all what they can do.
Maybe what we need is the new graphic representation, where higher
B-factors will be shown not by red color, but by some kind of
"fuzziness". I don't think thicker tubes really deliver the message,
not to mention how ugly they look.
Ed.
Nicholas Noinaj wrote:
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Hi,
i would like to get opinions on whether or not one removes side-chain atoms where
there is no density. for example, if one can only observe density up to the
beta-carbon for lysine (say at > 0.5 sigma), does one leave the lysine side
chain intact, knowing it must be disordered, or does one terminate at the
beta-carbon, making the coordinates reflect what is actually observed in the
density.
It seems both approaches are published and people seem to have conflicting opinions on the topic. It would be nice to come to some concensus, possibly clear up the issue for us newbies.
Thanks in advance for all feedback!
Cheers,
NIck
________________________________________
Nicholas Noinaj
University of Kentucky College of Medicine
Department of Molecular and Cellular Biochemistry
The Center for Structural Biology
Biomedical Biological Sciences Research Building, Rm 236
741 S. Limestone
Lexington, Ky 40536
Lab: 859-323-8183
Cell: 859-893-4789
Home: 859-228-0978
[EMAIL PROTECTED]
noinaj.com
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way or Method ceased to be observed,
benevolence and righteousness came into vogue.
Then appeared wisdom and shrewdness,
and there ensued great hypocrisy.
------------------------------ / Lao Tse /
