Data acquisition on each of the IMCA-CAT beamlines is accomplished with a Mar 165mm Charge-coupled Device system with one crystal-rotation axis (phi) and a computer-controllable sample-to-detector distance. This system, known as "Mar base", is found on almost all Mar installations worldwide, both at storage rings and in home labs. It has built into it a pair of slit assemblies and ion chambers, enabling users to adjust the base to maximize intensity through the chambers for a given opening size of the Mar slits. The phi axis can be manually spun and then operated from the computer, provided the user remembers to re-set the motor angle to zero (the fiducial position) after manual adjustment. The Mar phi axis has a generous z-translation capability, so you are not severely restricted in the position of the sample relative to the base of the goniometer head. Any distance between about 60 and 75 mm can be accommodated, but 70 is probably optimal. We have several spacers that replace the normal goniometer-head magnets, each providing a different height adjustment. This provides additional flexibility in the mounting.
The data acquisition is done by marccd, which runs on the Linux computer closest to the hutch ("charybdis" on the ID-line, "europa" on the BM-line). marccd is responsible for crystal manipulation, image viewing, and acquisition of data sets. It's also used to characterize the diffraction patterns: it has graphing facilities to let you overlay resolution circles and the like over the diffraction patterns. There is sketchy documentation available online on charybdis at ~marccd/documentation. Christine Muchmore has recently improved that documentation substantially, and a copy of the new version is at the beamline.
There is no data strategy software built into the Mar code, but HKL2000 and D*Trek provide this capability, and at least the HKL2000 version works well with Mar data.
Each Mar image file consists of a TIFF header, a crystallographic header, and the 16-bit image data. The files are not by default compacted in any way, but it is easy to use a standard compression program like "compress" or "gzip" to squeeze the files down. The contents of the crystallographic header are documented. By default the images are dark-current subtracted, spatially corrected, and sensitivity-corrected before being written to disk. Under special circumstances some of these corrections can be disabled; check with the staff for details.Typical exposure times on the insertion-device line with no attenuation, are: for good diffractors, 0.5 - 2 sec is sufficient. Mediocre diffractors require 2 - 8 sec; weak diffractors require 8 - 30 sec per image. On the bending-magnet beamline you should probably quadruple these numbers.
It's useful to decide in advance how far back to set the detector to collect diffraction data. For 1 Å radiation a good rule of thumb is about 0.95mm * a, where a is the longest effective cell edge in Ångstroms. Thus for a 100 Å unit cell you should set the detector at 95 mm. For longer wavelengths the reflections are spread out more, and you can reduce this linearly by the wavelength. Thus for 1.5 Å radiation you can collect data on a 150 Å unit cell at 95mm.
Last updated by Andy Howard on 25 April 2001.
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