Abstract from: 2-intro.txt [dirdif manual chapter 2] 22 March 2008 Introduction to DIRDIF-2008 When to use DIRDIF : Main options & programs ------------------------------------------------------------------------ DIRDIF is a program for solving crystal structures. Major features are ---> powerful Patterson methods for use of your chemical knowledge, both fot heavy atoms structures and equal atoms structures, and ---> direct methods applied to difference structure factors, with special techniques for solving symmetry problems, all followed by ---> automated R2-driven dual-space structure expanding procedures. The program is designed to operate under a wide variety of circumstances using fully automated as well as interactive routines. All programs are written in standard FORTRAN-77 and are fully computer-independent. Using DIRDIF : enter " DIRDIF CCODE PROGNM " ----------------> PROGNM - For structures with heavy atoms, including P and S, call: PATTY - For structures of molecules with (partly) known geometry ...: ORIENT - When ab-initio direct methods gave a misplaced fragment ....: TRACOR - For expansion of a small fragment to the complete structure : PHASEX - For an enantiomorph, or a super- or pseudo-symmetry problem : PHASEX - For Fourier refinement of a partly completed structure ....: FOUR - For finding the absolute structure [when noncentrosymmetric] :BIJVOET - For generating search models for a flexible mol. fragment ...: ORFLEX Two main options in using Patterson methods ------------------------------------------- 1. To solve a heavy atom structure (including S or P in a light atom structure) use the program PATTY. Input: crystal data and reflection data. No input atoms or control data needed. After locating the heavy atoms the structure is automatically expanded until completeness. 2. To solve a structure with a partly known model (molecular fragment, often a rigid part of the molecule) use Vector Search methods. The search model (file with atomic coordinates) must be prepared in advance. To retrieve a model from the ORBASE fragment database and/or to modify the model and/or verify the format of your prefab file (all inter- actively), use the option ATMOD . To solve the structure with this search model, use the program ORIENT. After orientation, the model is automatically positioned and further expanded to the complete structure. The main individual routines ( denoted 'programs') ; a short write-up: ---------------------------- PATTY, ORIENT, TRACOR, PHASEX and FOUR are the main structure-solving programs. When the programs are called, the system will automatically perform all calculations necessary for the completion of the structure. PATTY is a program for the interpretation of a sharpened Patterson. It uses Buerger's implication theory (i.e. the so called symmetry map) and checks all cross vectors using the minimum- function value as a selection criterion. - The program is used for heavy atom structures with unknown heavy atom positions (including not-so-heavy-atoms like S or P in a light atom structure). ORIENT is a program to find the orientation of a molecular fragment (model) by means of Vector Search methods (Nordman). The input model is used for the calculation of interatomic vectors. The shape function of a single interatomic vector peak is approximated from the shape of the origin peak of the Patterson function, and it is used for the calculation of the overlap inbetween neighbouring vectors of the model. Vectors to be used the search are selected on weight (including overlap), length, and mutual separation. A fast cyclic search system in angular space (Eulerian angles denoted A, B, C), employing increasing resolution per cycle, leads to the best fitting orientation of the model. The fitting criterion is the Nordman 'minimum average' function value. - The program is used for structures with known geometry for a (relatively small) part of the molecule. Note that often such a molecular fragment (model) is available from the users own collection of related structures. TRACOR is a program to find the position of a molecular fragment (with known correct orientation) by means of reciprocal space correlation functions. The input fragment (the ATOMS file) is used for the calculation of partial structure factors for all reflections (for the entire expanded data set). The partial structure factor (which is the sum of partial structure factors of symmetry related fragments) depends on the vector t used for shifting the input fragment to another position. The correlation between calculated and observed structure factors (intensities) determines the best value for the shift vector t. The calculations are done by the Fast-Fourier-Transform method employing all symmetry elements simultaneously. - The program is used for positioning a structural fragment with correct orientation but unknown position. The program is automatically executed in the procedure initiated by calling ORIENT (see above). TRAVEC is a program which is automatically executed after the execution of TRACOR: it is based on vector search methods. It is used to test the ( maybe many ) results from ORIENT and and TRACOR, and it decides which partial structure is promising enough to warrant further structure expansion by PHASEX. PHASEX is a program to EXpand and refine the PHASes of the difference structure factors by direct methods. The input fragment (a correct but incomplete set of atomic parameters, for instance known heavy atoms or an oriented and positioned molecular model) is used to calculate normalized difference structure factors (Wilson-Parthasarathy) giving 'E1' values. Weights are calculated (Woolfson or Sim) and the E1 values with the most reliable phases are input to a modified tangent formula to refine the input phases and to calculate phases for hitherto unphased reflections. The application of DIRect methods to the DIFference structure factors is particularly powerful: . when the known part of the structure is only marginally sufficient to solve the structure, . when the model has higher translation symmetry than the space group (superstructure), . when the centrosymmetric input model comprizes an enantiomorph problem, . when the known atoms comprise another pseudosymmetry problem such as a 'chicken wire' fragment. The program recognizes the symmetry problem and uses a special symbolic addition procedure to solve the enantiomorph and/or origin ambiguity problem. - The program is used for expanding a partial structure. The program is automatically executed in the procedures initiated by calling PATTY, ORIENT or TRACOR. FOUR is a program for the calculation of Fourier and Patterson maps. It implies calculation of distances and angles, assignment and shuffling of new peaks into connected atoms. The program also arranges for further expansion and improvement of the structure via cyclic reactivation of PHASEX or FOUR. Note that the program's decision of how to assign peaks and which atoms to use is based on peak heights, partly peak - integral values and geometrical considerations, but not on valid chemical arguments: the user should apply his chemical knowledge and make the appropriate modifications in the final output atomic parameters. - The program uses input files generated by other programs. It is automatically executed after PATTY, ORIENT, or PHASEX. Some additional options, parameters and programs, which are important tools in using the DIRDIF program. ATMOD is a special option which can be used to prepare a suitable model for input to the Vector Search program ORIENT. A model can be selected interactively from the ORBASE or ORUSER database of molecular fragments. (See ORBASE-GALLERY.) Some facilities are available for modifying the model. Note: this option generates one model, although many models may be (manually) stored in the atmod file. ORFLEX is an intractive program to generate multiple search fragments for a flexible molecular fragment, in case the flexibility can be described by rotations around atom bonds. Input atoms from file ATOMS, the resulting many models are stored in file atmod. NORECY is an additional calling parameter which is used to suppress the automatic recycling procedure. The keyword NORECY is added to the calling parameters. The recycling should be bypassed only when the automatic procedure failed to solve the complete structure. BIJVOET is a program to find the absolute structure by calculating the Bijvoet-coefficient from differences in observed intensities of Friedel-related reflections. The ideal result would be either +1 for the correct structure or -1 for the inverted structure. The result is also given in Flack notation. (Input file: CCODE.ins [priority] or atoms.) AT2X conversion of file atoms to xyzn and other formats X2AT conversion of CCODE.ins ( SHELX ) to atoms ( DIRDIF format ) ------------------------------------------------------------------------