Command: i -- Type the filename of the first frame of each sequence of frames. This will be the same as what you told SMART to write out, plus the sequence numbers and the frame numbers. In the standard mode you will start with the .001 frame of each series, so you only have to specify it once; the program will assume that each sequence starts with the same number. Example: filename0.001,filename1,filename2,filename3<cr>. The line will wrap at some point during your typing. Don't worry about it. Note that the filenames appear in the display as soon as you finish the entry. If you made an error, type i again and re-enter.
Command: r -- Enter the filenames which will accept the raw output data from integration. It is recommended, for the sake of memory, that you use the same name as your frame files. An exception would be if you were doing a second integration with different parameters. Then you will want to choose a different name. The extension "raw" seems to be required for proper processing. Again, you only need to enter the extension once and ignore the wraparound of the line, . Example: filename0.raw,filename1,filename2,filename3<cr>.
Command: p -- Enter the point
group/Laue group symbol and the Lattice-type
which corresponds to your data. See Appendix
to
this help file. Don't worry about it over much if it turns out to be
wrong. The only thing this information is used for is to
generate
statistics on averaging of data. There is no need to re-run SAINT just
because the point group was incorrect.
If you have a centered cell, and specify the centering it means that
SAINT does not try to integrate the systematic absences due to the
cell-centering. This improves things like spot-shape statistics and
reduces the size of the raw files by at least a factor of two. You
should do this if you know you have a centered cell. If you discover
that you have a centered cell, SAINT should be re-run with the lattice
type correctly input.
The lattice type only needs to be changed if your cell is not
a primitive cell.
NO DATA ARE AVERAGED IN SAINT. Each reflection
found is separately written to the filename#.raw
and filenamem.raw data
files.
Command: s -- Normally you will not change the box size
parameters unless you know that your spots were large, or if you have a
large unit cell and want to reduce the size of the integration box.
Once
you have started integration you will have a chance to look at the spot
size and decide if you want to change box size. The box X, Y and Z
sizes are all preset, you can if you wish change these to smaller or
larger values. The default is a box size of 1.6 x 1.6 x 1.0
degrees.
Command: u -- This value is the highest resolution of your data set. Due to the configurations of the two detectors, the SMART has a default resolution of 0.85 A and the APEX defaults to 0.80 A. If your high angle data are a lower resolution than either of these, we recommend that you reduce the resolution limit to a more reasonable value. The final merged listing output from SAINT can help you decide if you need to reduce the resolution of your integrated data, or it can be applied in SADABS or XPREP -- we recommened a cut-off where more than 75% of the data are less than 2 sigma(I) after application of SADABS. This is strictly optional.
Command: y -- If you suspect serious
crystal motion, change this value from 0 to 200, or even 100. This will
slow down processing a little, but not that much. Not useful unless you
actually have some motion.
Command: g -- To set the
global refinement of the unit cell based on all strong data observed
within the data set. The point group type should be set to match
your crystal system. NOTE:
there are three options for a monoclinic lattice. In general you should
select 3MB, (Monoclinic, B-unique) because this
is the standard setting for a monoclinic lattice).
Command: ! -- Typing the exclamation point (or "bang") causes the program to start data processing. The output will start to scroll up your screen. At any point if you want to interrupt the scrolling and look at your output, you can type <ctrl/S>, this stops the output (and holds up processing), but allows you to scroll your window up and down to examine the results. Hitting <ctrl/Q> will unlock the terminal and allow output to continue.
After integrating the data from all frame sets the program will merge the raw data into a data file called filnamem.raw and a corresponding printable output file, filnamem._ls. Print the latter with the command print132 filenamem._ls
If you feel you have to interrupt the program before it finishes, the only way is with <ctrl/C>, which crashes it. This leaves various files in an unfinished state, specifically the *.raw files and the *._ls printable output files. If you have stopped the program, you will want to delete those files before restarting SAINT.
TIPS ON INTERPRETATION OF THE OUTPUT
Laue and point group information
(back
to integration instructions)
NAME(s) DESCRIPTION
1-, -1 ................................. Laue group 1 (bar); triclinic system
2/mC ................................... Laue group 2/m, monoclinic C-unique ....NOTE **
2/mB ................................... Laue group 2/m, monoclinic B-unique ....NOTE **
2/mA ................................... Laue group 2/m, monoclinic A-unique ....NOTE **
** NOTE--The letters A, B, and C here indicate the unique
axis (ie. the axis that is perpendicular to mirror plane).
They do not
indicate a centering condition. Centering is dealt with elsewhere.
4/m ...................................... Laue group 4/m, low-symmetry tetragonal
3-H, -3H ........................... Laue group 3(bar), low-symmetry trigonal, (hexagonal cell -- a=b≠c, gamma=120.)
3-R, -3R ............................ 3-bar, low-sym. trigonal, (rhombohedral primitive cell setting -- a=b=c.)
6/m ...................................... Laue group 6/m, low-symmetry hexagonal
m3-, m-3 ........................... Laue group m3(bar), low-symmetry cubic
mmm ................................... Laue group mmm, orthorhombic system
4/mmm ................................ Laue group 4/mmm, high-symmetry tetragonal
6/mmm ................................ Laue group 6/mmm, high-symmetry hexagonal
3-m1, -3m1, 3m1 ............... Laue group 3(bar)m1, high-symmetry trigonal
3-1m, -31m, 31m ............... Laue group 3(bar)1 m, high-symmetry trigonal
3-m, -3m,............................ Laue group 3(bar)m, high-symmetry trigonal, (rhombohedral primitive cell setting)
m3-m, m-3m, m3m ............ Laue group m3(bar)m, high-symmetry cubic
Enter the number corresponding to the lattice type to be used for exclusion of systematic absences in the output. (return to integration instructions)
0 P -- Primitive
1 A -- A-centered
2 B -- B-centered
3 C -- C-centered
4 F -- Face-centered
5 I -- Body-centered
6 RO -- Rhombohedral obverse
7 RR -- Rhombohedral reverse
At this stage, there is no reason you should need to know (and hence no need to input) more specific space-group symmetry. XPREP needs the intensities of possible space-group absences in order to determine or verify the space group. (return to integration instructions)