Yes, unfortunately an "orientation matrix" is completely useless without
a frame of reference. All it does is tell you where the cell axes lie
relative to "X", "Y" and "Z", but "X" may be the x-ray beam, or
sometimes that is "Z" and "X" is the spindle axis. Different people have
different and strongly-held opinions about this. The "fast" and "slow"
axes on the detector are also a matter of widely-varying convention.
The origin of the detector could be the first pixel in the image file,
the upper-left corner, or it could be in "cameraman view" vs "sample
view" and the beam center is also only meaningful relative to whatever
the "origin" is. Also, if you are at one of the four beamlines in the
world that rotates their spindle the opposite direction of everyone
else, then you may have to reverse the sign of one axis as well, usually
"Y", or there may be an option such as "REVERSEPHI". XDS lets you
define all these things manually and there are formally no "default"
settings.
To be fair, it is difficult for developers to keep track of what all
~150 beamlines around the world, plus commercial "home lab" equipment
manufacturers are doing. I've been trying to some time to assemble a
"library" of recent lysozyme datasets from as many beamlines as
possible, but my collection is still far from complete:
http://bl831.als.lbl.gov/example_data_sets/
That said, I have written a few jiffies for inter-converting XDS and
mosflm conventions, and posted them here:
http://bl831.als.lbl.gov/~jamesh/orientation_matrix/
Instructions are at the top of each awk script. For example,
mosflm2xds.awk takes the first three lines to be the *.mat file from
mosflm, but also needs the mosflm input script after that to figure out
how to convert it into XDS conventions. Use it like this:
cat auto.mat mosflm.inp | ./mosflm2xds.awk >> XDS.INP
You can convert the resulting XDS keywords into an XPARM.XDS file using
xds2xparm.awk, which can be useful for feeding into some pipelines. If
you already have an XPARM.XDS, you can convert it back into XDS keywords
using xparm2xds.awk, and these keywords can, in turn, be fed into
xds2mosflm.awk to get a mosflm *.mat file again. Note, however, that
there can be some information loss here. The *.mat file does NOT
contain the full description of the detector and spindle geometry that
XDS may be using. I make some guesses in these scripts if not all the
relevant XDS keywords are provided. It works with my setup at ALS
8.3.1, but I have not tested it thoroughly with other cameras. I would
be interested if you find any bugs!
As for what you're missing, could it perhaps be a reversed phi
direction? That might look like a 180-degree rotation.
Good luck!
-James Holton
MAD Scientist
On 12/28/2014 3:12 PM, Igor Petrik wrote:
Takanori and Pierre,
Thank you for your quick responses. If you read my post you will see
that I used the xds2mos.py script to convert the xds orientation to
Mosflm format, but this gives me a result that is inconsistent with
the matrix calculated directly by moslfm or DENZO. For orthorombic
space group P222 there are only a hand full of equivalent matrices
related by changing sign of one of the vectors. The matrices generated
by XDS and Mosflm do not seem equivalent. Or maybe I'm missing something.
Thanks,
- Igor
