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 map.
(I think...)
phx.
On 19/04/2010 16:31, Anastassis Perrakis wrote:
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 protein with 80% solvent.
The rmsd for that will be quite low,
since most of the AU is flat. Thus, I would argue that you might want
to consider waters in relatively 'low sigma'levels.
Of course 80% solvent will also mean that most likely this protein
will only diffract to low resolution,
so you should maybe not be putting any waters.
The inverse case argument also applies.
Similar issues, maybe more severe, come up for atom removal.
Admittedly, we had this discussion with Victor back at the
EMBL-Hamburg library, back to what will soon
be two decades ago, and I do not think we have good answers, although
we try new things every couple of years.
A.
If anyone is interested thats the ARP/wARP code for removal atom
sigma, I am not sure when we came up with that, but it did make some
sense at the time.
Cant even recall if its my or Victor or both putting that in ...
basically it leaves waters in if they are above 1.0 rmsd (if
resolution is better than 2.0 A), or above 0.6 rmsd if resolution is
less than 2.8 A (I can hear the screams already ...), and uses a value
in between for resolutions between 0.6-1.0 A.
The rmsd for adding atoms is 3.4, since it does not really matter
what to add, if you remove what should not be there ...
(what a silly assumption ...? It looked logical at the time though)
On Apr 19, 2010, at 16:38, Ed Pozharski wrote:
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 argument for a particular choice
of sigma cutoff - with 3 sigmas you have ~0.3% chance of a particular
peak to be simply a random spike. Which means that if the map is on,
say, 0.5A grid, there is a decent chance to have one such peak per
3.5x3.5x3.5A volume. With 5 sigmas the size of the cube goes up to
~60x60x60A, so 5 sigma peaks are almost guaranteed not to be flukes.
On Sat, 2010-04-17 at 22:46 +0200, Tim Gruene wrote:
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'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
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /
*P** **please don't print this e-mail unless you really need to*
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
