Abstract from: 3-options.txt [dirdif manual chapter 3] 22 March 2008 How to run the various options of DIRDIF ------------------------------------------------------------------------ Preliminary comments on input/output files (for details see section 4). Most programs need a reflection data file and a crystal data file. For the application of vector search methods (ORIENT), the user has to prepare the atmod file (with the a-priori known molecular geometry) before the automatic execution of ORIENT. For some programs (in cases with problem structures) the user has to prepare an ATOMS file. No control data is needed at the outset of a job. At the end of a DIRDIF run results and comments are given on file lis1 and the output atomic parameters on the atoms file as well as on a SHELX type CCODE.res file and on some other files (to be listed is section 4). Instruction syntax: DIRDIF [CCODE] [PROGRAM [PARAMETER(S)]] CCODE: compound code, name of the structure, working directory PROGRAM: program name or option, ====> means : enter the instruction ( being in directory CCODE ) Major program calls are: Patterson option 1: ------------------ run PATTY for Heavy Atom Patterson interpretation. When the structure contains Heavy Atoms (including S or P in a light atom structure): =====> DIRDIF CCODE PATTY No input atoms needed. The system automatically arranges for the following procedure: first calculate the Patterson function (program FOUR), then locates the heavy atom(s) (program PATTY), expand the partial structure (program PHASEX, followed by FOUR), and recycle several times (programs DDMAIN, PHASEX and FOUR) for complete elucidation of the structure. Output: structural parameters in the atoms file. Note : all acceptable PATTY solutions will be tested, and sorted on a FOM (figure of merit) based on the Patterson fit and the R2 value; the most probable solutions are partly expanded, and the result with the lowest R2 value is fully expanded to find the complete structure. Patterson option 2: ------------------- run ORIENT for application of Vector Search methods. Vector Search methods are used when a (relatively small) part of a structure has known geometry. The known part usually (but not necessarily) is a rigid molecular fragment. The search model (ATMOD file, fractional or Cartesian coordinates) must be prepared before executing ORIENT (see Section 4 for the write-up of the atmod file): =====> DIRDIF CCODE ATMOD Procedures: -: When the user has prepared an atmod file in advance (from literature data, molecular modelling or his own archieves): checking the format of the file. -: Else: interactive retrieval of a model from the database ORBASE and/or ORUSER (see the fragments listed in the ORBASE-GALLERY). -: In either case: interactive fragment modification (add atoms, delete or rename atoms, etcetera). Output: an (updated) atmod file with Cartesian coordinates. Note : the user may manually store more then one atoms sets in the atmod file (must be in Cartesian coordinates). =====> DIRDIF CCODE ORFLEX When a flexible molecular fragment is available (stored in file atoms), and in case the flexibility can be described by rotations around atom bonds, the user is asked to supply these bonds, and the program ORFLEX generates multiple search fragments Output: many search models, stored in the atmod file. =====> DIRDIF CCODE ORIENT Input: atmod file with one or more Cartesion molecular fragments. When the user calls for ORIENT, the system automatically arranges for the following procedure: - first check and perhaps rewrite the atmod file with the atomic parameters of the model, - then calculate the Patterson function (program FOUR), - search for the orientation of the model (program ORIENT), and repeat this for all search fragments, - use translation functions to position the model according to space group symmetry (program TRACOR) and repeat this for all accepted ORIENT results, - call program TRAVEC to collect all results of TRACOR for all orientations for all input models, and to calculate a FOM based on TRACOR correlation results, TRAVEC vector fit results and R2 for all resulting trial structures. Output: selected trial structures. - expand all selected partial structures, and recycle several times (programs DDMAIN, PHASEX, FOUR) for partial structure elucidation. - select the best result, based on R2, and recycle again to achieve complete structure elucidation. Output: atoms file (and other files) with final atomic parameters. Additional options ------------------ =====> DIRDIF CCODE PHASEX Expansion and recycling of a partial structure, i.e. when some atoms are known (on correct positions). Input fractional atomic coordinates are given in the atoms file. The program is automatically executed after PATTY, ORIENT or TRACOR. The program is explicitely called by the user in a number of cases - The user should call for PHASEX when he has his own suggestions for atomic positions: for instance he may have modified the atoms in the ATOMS file available from a foregoing DIRDIF run (which, of course, is only useful if something went wrong ...). - When the user calls for PHASEX, the system automatically arranges for structure factor calculation and normalization (program DDMAIN), then executes the program PHASEX to expand and refine the phases of the difference structure factors, calculates and interprets a Fourier synthesis (program FOUR), and finally organi- zes recycling several times (programs DDMAIN, PHASEX and FOUR) for expansion of the fragment and completion of the structure. Output: atomic parameters in atoms file. =====> DIRDIF CCODE FOUR The program FOUR is automatically executed after PATTY, ORIENT, TRACOR or PHASEX The program is explicitely called by the user in a number of cases similar as for PHASEX (see above). Input: atoms file. When the user calls for FOUR, the system will automatically arrange for structure factor calculation (by program DDMAIN) and then calls program FOUR for a default Fourier synthesis. The program FOUR then arranges for recycling (programs DDMAIN and FOUR) until the structure evaluation is completed. Output: atomic parameters in the atoms file. =====> DIRDIF CCODE BIJVOET This call for the NUTS option BIJVOET is especially useful after the structure has been refined, for finding the absolute structure in case of a non-centrosymmetric space group. . Input atomic parameters: CCODE.ins [priority] or atoms . Output only when structure inversion is required: CCODE.res and atoms =====> DIRDIF CCODE AT2X =====> DIRDIF CCODE X2AT AT2X is a rogram for the conversion of the (final) atoms file into into files for other propgrams e.g. CCODE.res for SHELX . X2AT converses a SHELX CCODE.ins file into an atoms file. =====> DIRDIF CCODE NORECY Prepare one more Fourier systhesis with interpretation, which may be very usefull if just a few atoms are renamed, or the cell contents are slightly modified in crysin. -----------------------------------------------------------------------