Scalepack8m can handle 8 x106 observations, 60,000 hkl pairs, 2000 frames and 50,000 rejections. For scalepack16m, the corresponding numbers are: 16 x106, 60,000 pairs, 2000 frames and 100,000 rejections. For scalepackmanyframes the relevant numbers are: 2 x106, 100,000 pairs, 4000 frames and 50,000 rejections.
Version 1.6.0 and upward require only one display program called ‘xdisp’. Xdisp executable along with a modifier can read various formats. Given below are the various modifiers needed to read home and synchrotron data. Add the relevant modifier to ‘xdisp’ to read a specific format, e.g., ‘xdisp raxis myxtal001.osc’ for R-axis 105 µm data collected at home.
xdisp
b raxis b myxtal001.osc |Regular r-axis data
xdisp
b raxis b 210 b
myxtal001.osc |Small r-axis format
xdisp b raxis2n b
myxtal001.osc |New r-axis
data (note
2n)
xdisp b raxis2n b 210 b
myxtal001.osc |New small r-axis format (note 2n)
xdisp
b ccd b unsupported-m165 b
xtal01.001 |MarCCD165 format
xdisp
b ccd b adsc b
unsupported-q4 b xtal01.001 |Quantum 4 format
b : indicates a required empty
space.
The same modifiers are required while processing the data using Denzo with the keyword ‘format’. In the following section, some tips for processing data sets collected specifically at synchrotron are discussed.
Synchrotron data
As mentioned in the Introduction, synchrotron data sets
are usually collected in Quantum 4 CCD or MariCCD225 formats which are
different from Image Plate detector format.
Since only Denzo and XdisplayF deal with the different formats, most
attention should be given to auto.dat,
site.dat, and expr.dat (or the equivalent of these
files). There are several important differences
in the data set collected at synchrotrons.
The first one is the wavelength of x-rays. This value can be anywhere between 0.9 to
1.5Å depending upon the experimental station.
The second major difference is that the phi axis or spindle axis is usually
horizontal (in R-Axis it is vertical and in Mar it is horizontal). The third difference is rotation of spindle
can be clockwise or anti-clockwise. The
fourth difference is ‘
Wavelength
Home sources (rotating anodes) are limited to a few distinct wavelengths depending upon the target used (copper, molybdenum, gold, or iron). In macromolecular crystallographic facilities, it is usually a copper target and therefore the wavelength lambda (l) is 1.541Å.
However, in synchrotron it is possible to get wavelengths in the range from 0.9 to 1.5Å and the user has to modify the Denzo keyword ‘wavelength’ appropriately. Given below is an illustration where a data set collected at 0.948Å is processed with wrong wavelength of 1.541Å. For comparison, data processed with the correct wavelength of 0.948Å is also shown. Note that in the wrong processing the predictions (overlaps) are much closer compared to the correct processing. The log file will also show that crystal cell dimensions are about 1.6 times (1.541/0.948=1.62) larger for the wrong one compared to the correct one.
|
|
|
|
|
Denzo
predictions on data. Wrong wavelength (1.541Å) instead of 0.948Å. Note heavy
overlaps. Cell: 180.37, 180.68, 255.94; 90.81, 90.81, 91.15. |
Data
only (Frame 2) |
Denzo
predictions on data. Correct wavelength of 0.948Å used. Cell: 110.05, 111.49,
153.12; 90.76, 90.26, 90.74 |
Figure 1. Incorrect & correct wavelength usage during synchrotron data processing
Keyword ‘step’
Synchrotron phi axis rotation can be different from that we usually see at home. One such example is at F1 Station at CHESS where they use anti-clockwise rotation to achieve the movement of phi axis. To distinguish this we have to add a special Denzo keyword ‘