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[ccp4bb]: MOSFLM and CCD images
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Using MOSFLM to process data from ADSC Quantum4 and Mar CCD detectors
I believe that there may be "example scripts" for processing data
from CCD detectors that use the generic form for the DETECTOR or
SCANNER keyword, and which therefore are not optimal for processing
these type of images. For example, data from the Mar CCD detectors may
be processed with the keywords:
SIZE 2048 2048 HEADER 1
SCANNER ROTATION HORIZ ANTI FAST HORIZ ORIGIN UR CIRCULAR
LIMITS XMAX 82.5 YMAX 82.5 RMAX 82.5 RSCAN 82.5
All of these keywords can be replace with the single keyword:
The problem with using the generic form of the DETECTOR keyword is
that the information in the file header (wavelength, crystal to
detector distance, two-theta value and oscillation angles) is ignored
by the program, so all of these parameters have to be input
explicitly by the user.
In addition, when using DETECTOR MARCCD keywords the program will
determine from the image if this is a small or large MarCCD detector,
and automatically assign the correct pixel size (which can vary
slightly from detector to detector) and the value assigned to pixels
outside the active area of the detector.
The same comments apply to images from the ADSC quantum 4 detector,
which should be processed using the keywords:
The BIAS keyword
Some of the example scripts also contain a BIAS keyword. THIS SHOULD
NOT BE USED !!! The BIAS keyword was introduced in order to process
images that were so weak that there were pixels with a value of zero
in the active region of the detector (not a common situation with data
collected at a synchrotron).
If the BIAS keyword is used, then spots which lie at the very edges of
the detector, so that part of the measurement box (and quite possibly
the spot) actually lies outside the active area, may not be flagged
to be rejected. This will probably result in a large number of
"badspots" and warning messages, and quite possibly systematic errors
in the intensities of some reflections that still pass the "badspot"
checks. In addition, the active area of the detector is automatically
reduced by about 2mm from its correct value, so that you may loose
spots that are, in fact, fully present.
It should not be necessary to use the BIAS keyword.
Autoindexing using the ADSC interface
Autoindexing using the ADSC GUI uses the DPS autoindexing algorithm
from Michael Rossmann's laboratory. The same algorithm (and code) is
used in MOSFLM, but there is an important additional step in the
MOSFLM implementation that refines the cell parameters that come from
the DPS indexing. The refinement step makes the autoindexing
significantly more robust. If the autoindexing using the ADSC GUI
fails, it is worth trying to autoindex using MOSFLM.