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RE: [ccp4bb]: Improving data processing with Gaussian blur
Title: Message
It is
also known that Photoshop is the most
effective density modification program
available....
It is
believed that together with combinatorial
data
generation and phases from predicion models it
will
replace CCP4 with the next few years.
Adobe
Xtallator...
br
PS:
dibbs on that patent.
Hi y'all,
We have been looking for a program
to print diffraction images and found
Photoshop to be very useful for a
variety of CCD formats. When playing
around with some options, we stumbled
upon an interesting effect with
images from the SBC2 CCD detecor (APS
beamline ID19): When using a
Gaussian blur with a radius of 2.3, data
processing and structure
refinement improved significantly. R syms for
typical datasets get better
by about 2-3% overall, but the I/sigma(I)
decreases somewhat. Refinement
with CNS yielded R factors between 1-4%
better (0.5-2% in Rfree).
The filter has to applied in CMYK space, gray
scale and RGB don't
work. Heated discussions are going on here why this
might be.
The effect is similar to binning followed by lossy
compression and
uncompression. The procedure seems to even out spot
background.
An alternative explanation is that the Gaussian blur acts like
data
sharpening by applying a B factor. Interestingly, the radius for
the
Gaussian blur needs to be between 2.1 and 2.5, otherwise data
processing
gets really bad.
A similar effect can be achieved by the
"Pointillize" command in the
"Pixelate" submenu. Here, the cell size should
be between 7 and 13% for
the procedure to work, but the chi^2 values in
Denzo will be artificially
lowered while the B factors of refined models in
CNS will be too high by a
constant factor (compared to non-treated data).
However, the electron
density looks qualitatively better than the one
obtained with the Gaussian
blur and significantly better than without
blurring the images.
>From now on, we will routinely do a
pre-processing of our images with
Photoshop. However, it doesn't work in
all cases: image plate data did not
improve, whereas CCD data from
beamlines with beams that are not entirelyhomogeneous did benefit a
lot.
Our results strongly suggest to include Gaussian blur and
pixelating
protocols in current data processing software, although going
through
Photoshop is not such a big deal, because it can be
automated.
Any thoughts?
Mischa
--------------------------------------------------------------------------------
Mischa
Machius, PhD
Assistant Professor
UT Southwestern Medical Center at
Dallas
5323 Harry Hines Blvd.; Y4.330A
Dallas, TX 75390-9038;
U.S.A.
Tel: +1 214 648 9760
Fax: +1 214 648
8954