Dear all,
I'm dealing with anisotropic diffraction of a membrane protein.
I've read from previous threads that it is better to not cut off any
data, and that aimless doesn't anisotropically scale the data any way.
So my question is: given my anisotropic diffraction, what resolution
cutoff do i give aimless for scaling, and what statistics can i report?
(log bellow)
- Do I scale at 2.85A knowing that there is at least data in one
direction to this resolution? (The different Rs are all over the place,
but i can site the Karplus Science paper for the use of CC for
resolution cutoff)
- Do I scale at 3.47A as it is "the best overall estimate" (with decent
R statistics).
##### Aimless log #####
Estimates of resolution limits: overall
from half-dataset correlation CC(1/2) > 0.50: limit = 3.47A
from Mn(I/sd) > 2.00: limit = 3.83A
Estimates of resolution limits in reciprocal lattice directions:
Along 0.98 h + 0.18 l
from half-dataset correlation CC(1/2) > 0.50: limit = 3.97A
from Mn(I/sd) > 2.00: limit = 3.65A
Along k axis
from half-dataset correlation CC(1/2) > 0.50: limit = 5.12A
from Mn(I/sd) > 2.00: limit = 5.23A
Along -0.25 h + 0.97 l
from half-dataset correlation CC(1/2) > 0.50: limit = 2.85A
from Mn(I/sd) > 2.00: limit = 3.17A
################
Thank you for your input.
vincent
Le 4/25/12 5:40 PM, George Sheldrick a écrit :
I think that anything that irrevocably modifies the experimental data
should be avoided whenever possible. Since anisotropic scaling is a
relatively fast calculation and there are several ways of doing it, it
is better to apply it locally when it is needed, e.g. in phasing
(where it is applied by phaser and shelxe etc.) and refinement (with
refmac or phenix_refine etc.). Provided that the standard deviations
of the observed intensities are properly taken into account,
anisotropic data truncation is not so important (i.e. as usual I agree
with Garib and Phil).
George
On 04/25/2012 06:19 PM, Phil Evans wrote:
You can get the aimless documentation from
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/aimless.html
pending its official release through CCP4
No it does not do anisotropic scaling as such. That needs some sort
of model of the "ideal" intensity, probably best calculated from a model
I'm not sure that anisotropic cutoffs are a good idea. I believe
Garib thinks they are not and I generally defer to him
Phil
On 25 Apr 2012, at 17:00, Bryan Lepore wrote:
wondering if aimless performs anisotropic scaling or "elliptical"
rejections lately.
I ask because:
[1] last I knew, scala did not
[2] I can't seem to google up the aimless manual as readily as scala
... also, what consesquence would mosflm anisotropic resolution limits
have on scaling (if aimless anisoscaling were true).
-Bryan
--
Vincent Chaptal, PhD
Institut de Biologie et Chimie des Protéines
Drug-resistance modulation and mechanism Laboratory
7 passage du Vercors
69007 LYON
FRANCE
+33 4 37 65 29 01
http://www.ibcp.fr
