A long time ago, I wrote a little program for turning spot picks into a
PDB file that you could load up and rotate around in a graphics program
(such as O, at the time):
http://bl831.als.lbl.gov/~jamesh/pickup/spt2xyz.com
this one works on the *.spt files that comes out of MOSFLM. You can
concatenate *.spt files for each of your images to get the full data set
represented.
I also wrote one that works on ADSC images if you have the DPS program
installed:
http://bl831.als.lbl.gov/~jamesh/pickup/adsc2pdb.com
but it only works for the "common" coordinate system convention we use
at ALS and SSRL. Not sure about other beamlines.
The algorithm for converting spot positions into reciprocal space is
not exactly new, as it is at the core of any and every autoindexing
program. All you do is figure out the take-off angle of the diffracted
ray from the crystal and then calculate the coordinate where this line
intersects the Ewald sphere. Specifically, the "distortion" is:
distortion = lambda*sqrt((Xdet)^2+(Ydet)^2+(dist)^2)
where:
lambda - the x-ray wavelength in A
Xdet - X coordinate of the spot relative to the beam center (in mm)
Ydet - Y coordinate of the spot relative to the beam center (in mm)
dist - the crystal-to-film distance (from crystal to direct-beam
spot, in mm)
You then use this "distortion" to compute the x-y-z coordinate of the
reciprocal-lattice point in reciprocal space:
x' = Xdet/distortion
y' = Ydet/distortion
z' = dist/distortion - 1/lambda
Yes, there are x-y-z coordinates in reciprocal space. They all have
units of inverse Angstroms. Of course, these x',y',z' coordinates are
at the phi value of the image you picked spots on. To get the
coordinates at phi=0, you need to "un-roate" them:
x = x'*cos(phi)-z'*sin(phi)
y = y'
z = x'*sin(phi)+z'*cos(phi)
where some people can probably tell that in this convention the phi axis
is right-handed and parallel to the "Ydet" axis of the detector.
The last step is to multiply these x,y,z coordinates by some reasonable
scale factor and put them into a PDB file. Maybe put the intensity in
the B-factor column, so that you can color it. Then you need to find a
display program that can handle a million-atom PDB. Does anyone have
one of those?
Ideally, what one would like to do is make an electron density map with
pixel-to-pixel correspondence to the image. All you do is apply the
above formulas to each pixel, do a Lorentz-Polarization correction, and
then just render the data set as a map.
Sounds like there are a couple of commercial programs that do this in 2
dimensions. Problem with doing it in 3D is there are no programs that
can display an electron density map this big. In fact, I can't even get
CCP4 to write out map or mtz files bigger than 2 GB. I get "filesize
limit exceeded" errors (even though the filesystem can handle large
files). Is this a limitation of the 32-bit binaries? Can anyone help
me confirm that re-compiling CCP4 as 64-bit will fix this? This error
can be reproduced by trying to make a 2 A data set for the largest unit
cell in the PDB:
unique hklout test.mtz << EOF
RESO 2
SYMM 1
CELL 687.900 687.900 1933.300 90 90 90
DEFAULT 1
LABOUT F=F
END
EOF
Thanks!
-James Holton
MAD Scientist
Ian Tickle wrote:
But I thought what you wanted was to reconstruct the diffraction pattern
(i.e. streaks, TDS, ice rings, zingers, warts & all) as a
pseudo-precession image, not just display a representation of the
integrated intensities. That surely would be much more useful, then one
could see whether the apparent systematic absence violations were just
streaks from adjacent spots, TDS, ice spots etc that have fooled the
integration algorithm. That would be much more useful! In the days
when we had real precession cameras this was how you assigned the space
group.
Cheers
-- Ian
-----Original Message-----
From: [email protected] [mailto:[email protected]]
On
Behalf Of Francis E Reyes
Sent: 25 June 2009 17:32
To: [email protected]
Subject: Re: [ccp4bb] From oscillation photographs to seeing specific
sections of reciprocal lattice.
Thanks all who replied.
Looks like HKLView is it..
Oddly I couldnt find it anywhere in the ccp4i interface (shouldn't it
at least appear under Program List)?
FR
On Jun 25, 2009, at 10:24 AM, Francis E Reyes wrote:
Hi all
Is there software that will take oscillation photographs and
construct a precession-like photo of specific layers of the
reciprocal lattice (say h0l), for inspection of the systematic
absences, etc?
Thanks
FR
---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
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---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
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