Instructions for Operating DirAx on the VAX ============================================= Installation -------------- The stand-alone DirAx VAX version is suited both for input from a CAD4 CrystFile as for input from a manually edited file. The distributed DIRAX-SET includes: README.TXT - this file DIRAX.EXE - the executable program DIRAX.OBJ LIBRARY_CAD4.OBJ LIBRARY_RTL.OBJ - object files LINK.COM - to create your DIRAX.EXE from .OBJ files DIRAX.HLP - the DIRAX HELP facility DIRAX.HLB - the DIRAX HELP facility in binary format DIRAX.INIT - file with defaults and macros EX**.DRX files - input files for demonstration and exercise EX_SOLUTIONS.COM - job to run the examples EX_SOLUTIONS.INP - input to run the examples EX_SOLUTIONS.OUT - output for the examples Include in your LOGIN.COM file something like: $ DIRAX == "$device:[root.sub.dirax]DIRAX" General --------- The program differs slightly from the description in the DirAx paper (see Final Notes) but the essentials are still the same. Main differences concern the parameters LevelFit and IndexFit (see below). Unlike the PC version the VAX version cannot be interrupted during the t-vector generating process, there is no need for this as the VAX is much faster. For the same reason the random selection of triplets is only applied with more than 25 reflections. In most cases DirAx will run automatically with the default parameters. To unravel obstinate problems some familiarity with the method is desirable. We therefore recommend to practice with the example .DRX files first. If these problems cannot be solved properly (even after you have read the DIRAX HELP facility) there may somezing be wronk with your copy of DirAx, or you are doing something we did not anticipate. The parameter Dmax -------------------- Dmax should exceed amply the maximum expected axis length in order not to miss this axis, but it should not be very much larger than twice this length to avoid unnecessary calculations and erroneous results. The default value is set to 80 Angstrom which proved adequate for most of our problems. (For the example EX02.DRX use Dmax=120.) The parameters IndexFit and LevelFit -------------------------------------- In the paper LevelFit and IndexFit are defined as RELATIVE criteria (p 96, last line 1st column and 1st line 2nd column). Now both parameters are used in the ABSOLUTE sence. They refer to distances in reciprocal space (reciprocal Angstroms) and not any more to fractions of level spacings or to fractions of indices respectively. IndexFit is a factor: IndexFit*LevelFit is used as the criterion for fitting the indices. If LevelFit corresponds to realistic errors (see below) IndexFit should not differ too much from 2. A) Actually, for LevelFit the precision of the setting angles ('delta_angle') should be taken into account. DTheta, DOmega and DChiB, the absolute errors in reciprocal space in reciprocal Angstroms, are given by: DT = (2/lambda)*delta_theta, DO = (2/lambda)*sin(theta)*delta_omega, DC = (2/lambda)*sin(theta)*delta_chiB, with all delta's in radians and delta_omega = delta_phiB*cos(chiB) (Capital B for 'Bisecting'). The corresponding vectors, DT>, DO> and DC>, form a "monoclinic cell" with unique angle (90+theta) between DT> and DO>. The maximal combined error D is given by: D = sqrt(DT*DT + DO*DO + DC*DC + 2*DO*DT*sin(theta)), from D> = DT> - DO> + DC>, the longest body diagonal of the "cell". Example: for Mo-radiation (lambda = 0.71), theta = 15 degrees and errors of 0.01 degree in theta and omega, and 0.03 in chiB we have (if we are not mistaken): DT = 1/2034, DO = 1/7859, DC = 1/2620 and therefore D = 1/1514 reciprocal Angstrom, so 1/1000 is a good choice here. (We prefer writing 1/1514 to 0.000660501 because this is easier to visualize, and to emphasise the reciprocal nature of the magnitudes.) B) But in general it is unnecessary to go through these calculations: simply start with the default value of 1/1000 and if this does not work try 1/500, or 1/2000; all this is not very critical. Too large a LevelFit is worse than a too small one, i.e.: 1/1000 is better than 1/500, mostly. NOTE: only the denominator of LevelFit is to be put in, not the symbols '1/'. Selection of Acceptance Level (ACL) ------------------------------------- The program selects ACL for the geometrical correct solution with the maximum number of fitting reflections. Usually this is crystallographically correct too, but sometimes a lower solution is better, as may occur with twin lattices or an incommensurate structure, where a super lattice may accomodate more or even all reflections. Therefore solutions from lower ACL's are presented too and you may prefer one of those although (or just because!) it produces more aliens. Obstinate Data ---------------- With poor setting angles use a less strict LevelFit (1/500). Start with a higher IndexFit and decrease it later, but be careful with a too lenient IndexFit, especially with twins, because an apparently correct but actually false (super) lattice may be found. On the other hand, with multiple lattices narrower criteria for LevelFit and IndexFit may be required to discriminate reflections almost on regular lattice points. A good procedure here is to start with LevelFit 1/3000 (if your setting angles permit this! - with a CAD4 use SET4), and then to lower the IndexFit gradually until a satisfactory solution appears. Whether a solution is crystallographically acceptable or not can NOT be decided by DirAx: it gives only geometrically possible solutions. The suggested values for the parameters in this instruction are in no way sacrosanct and seldom very critical, fortunately: try others to become experienced with the method. Input file for DirAx ---------------------- For MANUAL preparation of an input file (see Example below): First a line with the wavelength in Angstrom. Then you provide up to 50 lines, ALL with either bisecting angles (degrees) or with C-vectors (Angstrom), optionally followed by the intensity. I.e.: theta phi(Bisecting) chi(Bisecting) [intensity] NOTE: do not change the sequence of phiB and chiB. or: C(x) C(y) C(z) [intensity] You choose your own righthanded Cartesian XYZ system (origin always on the crystal, and, for instance, Z vertical, X to source), the results are expressed in your system. DirAx recognizes automatically whether bisecting angles or C-vectors are put in. NOTE: no empty lines before, between or after the input. NOTE: bisecting angles and C-vectors may not occur within one list. FORTRAN free format, neat columns as in the example are not necessary. Any sensible number of decimals. The "intensity" is just for the record and is not used as such, you may give it a different meaning or set it to 0. Example of a *.DRX input file (this is the supplied file EX01.DRX): 1.54056 16.05 118.42 30.40 471.2 14.06 -177.41 33.99 1819.7 15.58 -101.99 24.06 14093.5 16.05 116.80 25.73 6468.4 17.30 147.79 21.32 3638.7 10.37 140.39 55.14 2599.9 16.38 -173.91 54.41 1072.7 22.32 11.97 50.49 819.5 15.60 -142.60 15.09 3904.5 9.37 -78.08 9.79 442.6 17.27 58.49 58.52 1432.2 21.09 140.40 55.15 2151.4 24.20 -157.93 49.38 11920.9 23.94 -122.19 49.20 300.2 23.96 22.55 31.30 13966.5 24.40 129.37 27.68 198.5 24.40 127.77 24.92 3312.0 18.17 -51.75 12.45 1452.5 16.05 120.88 9.40 492.7 16.41 -1.54 10.47 1018.5 25.62 -21.63 47.89 2855.0 25.52 -135.42 34.69 699.1 25.68 -75.50 27.95 601.4 18.00 95.29 7.12 6772.5 16.70 31.45 4.71 21815.0 DirAx input files should have extension .drx. If a different directory and/or extension is used the complete path and name must be given at the input. Acknowledgements ------------------ The original version of DirAx (also available) was written in Borland Turbo Pascal 5.5 for PC and compatibles operating under DOS. It was translated into FORTRAN by dr A.M.M. Schreurs of our laboratory. The cell reduction in DirAx is based upon Krivy, I. & Gruber, B. (1976). Acta Cryst. A32, 297-298, but simplified (written in vector form) and demanding less steps. We adopted the sorting algorithm HeapSort from the recommendable book: William H. Press, Brian P. Flannery, Saul A. Teukolsky, William T. Vetterling: Numerical Recipes, Cambridge University Press; 1986. QuickSort was extracted from: Robert Sedgewick: Algorithms, Addison-Wesley Publishing Company; 1983. Final Notes ------------- Disclaimer: you use and distribute DIRAX.EXE (and the *.DRX files) freely, but at your own responsibility completely. Guarantee: Please do report failures, give comments and ask questions, preferable via e-mail, we will help you as much as possible. Address: a.j.m.duisenberg@chem.ruu.nl or a.m.m.schreurs@chem.ruu.nl Postal address: Laboratory for Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Padualaan 8, NL-3584 CH Utrecht, The Netherlands. Updates of DirAx and the Instructions will be announced and distributed by MAIL, so keep us informed about your actual MAIL address. If you feel DirAx was essential for solving your (indexing) problems you might refer to: Duisenberg, A.J.M.(1992). J. Appl. Cryst. 25, 92-96. (*) Read (C) and (R) wherever you miss it. --------------------------------------------------------------------------- Instructions, version June MCMCXVI (AMMS-AJMD)