Help file for running XPREP and/or SADABS
(Ver. 1.2 - 18 January, 2000)
Once the data has been integrated by SAINT, there will be a series of data files in the smartuser/mydir subdirectory in which you are operating. These need to be further converted before you can use them with either TEXSAN or SHELXTL. In the process we will also apply corrections for crystal decay (which is very rare in the way that we usually take data) and for absorption (which is common, even on weakly absorbing crystals, due to the diffraction geometry which we use). We also want to get some information about our data set and crystal; space group, density, statistics, etc. There are two programs which we use for this purpose, XPREP and SADABS. For the purposes of this exercise the raw filenames are filname0.raw, filname1.raw, filname2.raw, filname3.raw, and filnamem.raw.
Normally we will run XPREP to determine space group, density and absorption coefficient and to test the effects of absorption. The output from XPREP is reliable. If the material absorbs strongly, or if we feel like it, we can then use SADABS on the data set to do a different type of absorption correction and also to allow it to do the other things that it does to the data. (Some of these are mysterious even now.) SADABS is a release version of the program, but much of what it does is mysterious. It is significantly better than XPREP in cases of high absorption or other problems, but not much different in well-behaved cases.
XPREP is a part of the Bruker implementation of the SHELXTL 5.0 package. There is a section in the SHELXTL 5.0 documentation on XPREP, including descriptions of all of the screens and of the output results and meanings thereof. It reads either raw data files from SAINT or hkl files from other programs such as SADABS. It also reads P4P files to get information about the crystal. It writes a file with extension PRP, which is a printable output file, and optionally writes other hkl files. What follows here is an abbreviated description. We start the program as follows.
<...smartuser/mydir> % xprep filenamem.raw <cr>
If you forget to give the filename, and just type xprep, XPREP will ask for a filename. You have to specify the extension. Type: filnamem.raw
The program will read the raw data file, and also the file filnamem.p4p to get information about the cell. In the interaction which follows, there will always be a default value for a response which will be shown by the program in square brackets, [xx] To select the default response, just hit <CR>. However, you do not always want the default response. Be sure to read what the display says and react accordingly.
XPREP then will show you displays which are designed to allow you and it to choose the space group. You should be aware that XPREP is very conservative about choosing a space group, and that it misses even P21/c on a regular basis. You may very well need to force it to take the correct space group.
WARNING: In order to do an absorption correction correctly, the cell must not be transformed before the correction is applied. Frequently the correct choice of space group will result in an un-announced transformation of the unit cell. Check the Matrix section of the output periodically to make sure that you haven't been transformed without your consent. It may be necessary to lie to the program about your space group, at least initially, to get it to leave your cell alone. (Note that this lie does absolutely no damage to your data, since TeXsan will re-determine your space group and appropriate cell transformation when it processes the data.)
Input of the cell contents will allow XPREP to show you an estimate of the value of Z, and will calculate the absorption coefficient. You need to read the absorption coefficient and note its value somewhere so that you can calculate mu*R or mu*t for the absorption corrections.
After you have entered the cell contents, the next step is to check absorption using the A option at the main menu. The official "type" of absorption correction is Psi Scan. Using the default values for errors and the like is fine, but you should change the I/sigma cutoff to 10.0. You can either change the psi-scan file name to filenamem.raw, or you can leave it at the default of filenamem.psi and the program will compensate.
The usual empirical correction type is Ellipsoid, and you will have to input a value for mu*R, the absorption coefficient times the mean radius of your crystal. It is an observed fact for this kind of correction that the radius should be weighted towards the smaller half-dimensions of the crystal. You should also calculate the value of e-mu*t for your minimum crystal thickness. Compare this result to the value of Tmax which is given by the calculation. They should be about the same (i.e. 0.95 is about the same as 0.90). If they are, then the correction should be a reasonable one, and should be applied. Please do not select "print the reflections", as this makes the output file very long.
Once you have applied the absorption correction, or decided that one is not appropriate, return to the main menu and write the hkl file. Note that the default answer is not to write the file. You must answer Yes to the question about the file in order to get your results written out.
Print the results of your analysis by typing
<...smartuser/mydir> %print filenamem.prp<cr>
SADABS requires the files filname0.raw, filname1.raw, filname2.raw, and filname3.raw. I believe, but am not certain, that it also uses the corresponding *.p4p files. It is started by typing the name of the program.
In the following example, everything except the bold/underlined words are printed by the program. (Bold-face parenthetical remarks to clarify what is going on are not part of the computer output.) The numbers are taken from an actual example, but the filenames have been changed to protect the guilty. Your numbers will be different.
<...smartuser/mydir> % sadabs<CR>
SADABS - Bruker area detector absorption (and other) corrections
Enter listing filename [sad.abs]: filnames.out<CR>
(Note that the use of the substitution of "s" for "m" in the file names. This is conventional but not necessary. Just don't use the identical name to what you have been using before.)
Laue group numbers:
 -1...................................................  -3m (rhombohedral axes)
 2/m (Y unique)..............................  -31m (Z unique)
 mmm ...........................................  -3m1 (Z unique)
 4/m (Z unique)............................  6/m (Z unique)
 4/mmm (Z unique)......................  6/mmm (Z unique)
 -3 (rhombohedral axes).............  m3
 -3 (Z unique)..............................  m3m
Enter Laue group number : nn<CR> --- (Pick the correct number and input it.)
Treat Friedel opposites as equivalent for parameter refinement (Y or N) ?
If you answer with Y, you may suppress the anomalous differences, but for N a higher redundancy is needed for a good correction. A chiral space group is assumed for the answer N [Y]: <CR>
(In fact, even if you have a chiral space group with anomalous scatterers, it is a good idea to use the default here. The changes induced by anomalous scattering do not follow the same symmetries as absorption and the other affects corrected for by SADABS.)
Read reflection files written by SAINT (.raw assumed if no extension)
Enter filename (/ if no more) [ ]: filname0<CR>
Enter filename (/ if no more) [filname1.raw]: <CR>
Enter filename (/ if no more) [filname2.raw]: <CR>
Enter filename (/ if no more) [filname3.raw]: <CR>
Enter filename (/ if no more) [filname4.raw]: /<CR> (Note the / mark before the <CR>.)
Mean and maximum errors in direction cosine check function = 0.000 0.000
The mean error should not exceed 0.005, and is usually caused by matrix changes during data processing. Maximum 2-theta = 52.27 degrees
(Note that your value may be 46.5 or 49.2 degrees, rather than 52 degrees.)
9251 Reflections of which 2353 unique; 7.01 data per frame
Redundancy: ............1.... 2 .... 3 .... 4 .... 5 .... 6 .... 7..... 8 ..... 9+
Number of groups: 146 223 . 723 446 402 . 242 . 128 .. 39 ... 4
Enter mean(I/sigma) threshold (must be positive) : <CR>
(Intensity+sigma)/(mean intensity) threshold [0.25]: <CR>
Savitsky-Golay filter (Y or N, but almost always Y) [Y]: <CR>
Highest even order for spherical harmonics (0,2,4,6 or 8) : <CR>
Highest odd order for spherical harmonics (0,1,3,5 or 7) : <CR>
Number of refinement cycles : <CR>
Suppress rescaling of sigmas (Y or N) [Y]: <CR>
6492 Reflections employed for parameter determination
Effective data to parameter ratio = 7.40
R(int) = 0.0298 before parameter refinement
R(int) = 0.0220 after parameter refinement
Batch...R(int)...Factor range...Sigma(ib)...Sigma(db)...K(sigI).......Total ....I>2sig(I)
1 ....... 0.0246 .... 0.937 - 1.111 ..... 0.0249 ..... 0.0156 ..... 1.000 ... 4294 ... 3618
2 ....... 0.0245 .... 0.902 - 1.109 ..... 0.0310 ..... 0.0097 ..... 1.000 ... 2985 ... 2539
3 ....... 0.0270 .... 0.880 - 1.044 ..... 0.0210 ..... 0.0100 ..... 1.000 ... 1574 ... 1334
4 ....... 0.0247 .... 0.955 - 1.083 ..... 0.0206 ..... 0.0110 ..... 1.000 ... 398 ...... 334
Sigma(ib) and sigma(db) are the square roots of the variances of the normalized incident and diffracted beam correction factors. K(sigI) multiplies the sigma(I) values for the batch in question.
(At this point you can either do as follows and write out the processed data, or you can test other parameters by Repeating the analysis. If your crystal shape is unusual or you just want to test the results, try increasing the number of even coefficients.)
Repeat (R), write .hkl file (W) or quit (Q) [W]: <CR>
Enter name of output .hkl file [sad.hkl]: filnameS.hkl<CR>
Effective mu*t (0 if theta-dependent absorption to be ignored) : .03<CR>
9251 Corrected reflections written to file filnames.hkl
Maximum and minimum effective transmission: 0.976562 0.907397
(If the value of Tmax is not appropriate, then you can recycle through the data correction process by picking W in the next statement, inputing the same filenameS.hkl to be overwritten and changing the value of mu*t until you like the result.)
Repeat (R), write .hkl file (W) or quit (Q) [Q]: <CR> (This returns you to the system prompt.)
Print the results of your analysis by typing
<...smartuser/mydir> %print filenames.out<cr>
Now back up your frames to DAT tape, as related in the Help File Data Backup to Tape.
Now move on to creating an account on BIGCHEX or to starting transferring your data.