Eleanor,
Do you have a rationale for assuming a lower uncertainty on the
surface than in the core? I ask this because I did once look at the
variation of the local RMSD of a difference Fourier, i.e. w(mFo-DFc)
with w=2 for acentrics, w=1 for centrics, and I didn't find any
obvious correlation wit
I am a bit out of touch with the discussion, and this may have been
mentioned already.
It is important to remember that Sigma is an OVERALL value for the whole
map, whereas one is looking for local solutions when fitting any
density. Stuff on the surface of the molecule ought to be contoured a
Yes, there has been a conflation of the standard deviation and the
r.m.s. of the distribution when it comes to "sigmas". The mathematical
formulas look similar (for a Normal distribution) so some people have
sloppily transferred the meanings of the mathematical symbols from one
concept to the o
On Wed, 2010-04-21 at 17:21 -0700, James Holton wrote:
> The "0.3% chance" of a peak being above 3
> "sigmas" assumes that the histogram of electron density values is
> Gaussian. It is not! In fact, it is a funny-looking bimodal
> distribution (the peaks are protein and solvent regions).
Ind
Like so many rules of thumb, the 3-sigma fofc and 1-sigma 2fofc is a
reasonable guideline that works very well in most cases despite being
based on a flawed assumption. The "0.3% chance" of a peak being above 3
"sigmas" assumes that the histogram of electron density values is
Gaussian. It is
Dear Tassos,
Am 19.04.10 17:31, schrieb Anastassis Perrakis:
The sigma issue a bit more complicated.
What we call usually sigma is the root mean square deviation (rmsd) of
the map.
Lets first recall, that the variation within the protein region is
quite large, while the solvent is rather f
Hi Pavel
AFAIK it's not in the literature, in fact I wasn't even aware it was
in phenix, but that's probably only because we don't use phenix
(sorry! - being commercial we would have to pay for it!). The problem
is always where you put little tidbits like this, unless it's part of
a much bigger p
Hi Ian,
... or you could just use the RMSD of the difference map (i.e. that
using 2(mFo-DFc) coefficients for acentric reflns), which is a
reasonable approximation of the uncertainty provided most of the
structure is accounted for, as the uncertainty of the Fourier map
(i.e. that using 2mFo-DFc
... or you could just use the RMSD of the difference map (i.e. that
using 2(mFo-DFc) coefficients for acentric reflns), which is a
reasonable approximation of the uncertainty provided most of the
structure is accounted for, as the uncertainty of the Fourier map
(i.e. that using 2mFo-DFc for acentri
Has anybody ever explored contouring maps using a "sigma" (i.e. rmsd)
derived only from what is clearly the solvent region?
Obviously that's not relevant during early phasing, but in the later
stages of refinement, that would be relatively clear. And it would be
fairly comparable from map to
Hello -
The sigma issue a bit more complicated.
What we call usually sigma is the root mean square deviation (rmsd) of
the map.
Lets first recall, that the variation within the protein region is
quite large, while the solvent is rather flat.
Now, lets take an 'extreme' example, of a prot
I second Tim's opinion. In the days of CNS/O, there was a popular rule
to place waters in 3 sigma peaks that make chemical sense, then
re-refine and keep those waters that produce more than 1 sigma in 2fo-fc
map. (With Coot the default cutoff is 5).
There could be a bizarre probabilistic argumen
Hello Sudhir Kumar,
most of all the waters in your structure should make chemical sense. When the
density around the water is weak it may just mean that the water is not fully
occupied.
Tim
On Sat, Apr 17, 2010 at 09:47:35PM +0900, Sudhir Kumar wrote:
> hi all
> sorry for such a basic query, i'l
hi all
sorry for such a basic query, i'ld like to know what is the acceptable sigma
cut off for waters to be kept in a model if data is of about 1.6 A.
thanks in advance
Sudhir Kumar
Research Scholar
Structural Biology Laboratory
SLS, JNU,
New Delhi-110067
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