The information contained in the electron density maps provided by Direct Methods has been combined with the Simulated Annealing technique in order to solve organic crystal structures from powder diffraction data. In this procedure each peak of the Fourier map is in turn associated to all the atoms of the imported model (Altomare et al., 2008). For each association (the atom of the structural model is moved on the peak) the position of the model is fixed, while its orientation and internal conformation have to be found by SA runs.
Run of Direct Methods combined with Simulated Annealing
Graphic Interface of Direct Methods combined with Simulated Annealing
Output of Direct Methods combined with Simulated Annealing
The Directives in Direct Methods combined with Simulated Annealing
About the construction of the models
Contact and References
After a run of EXPO2014, the procedure can be graphically activated by 'Simulated Annealing+Direct Methods' option of 'Solve' button in the upper menu of the EXPO2014 window.
The dialog window of Direct Methods combined with Simulated Annealing procedure in EXPO2014 is composed by 3 pages containing the general settings of the procedure.
The first page 'SA conditions' contains the general settings of the algorithm:
External model filename: the name of the imported starting structural model must be specified. Some file types can be imported: C.I.F. file (*.cif), Expo fragment or Free Fractional Format (*.fra), XYZ format (*.xyz), MOPAC file (*.mop), MDL MolFile (*.mol), Protein Data Bank file (*.pdb), Tripos SYBYL (*.mol2, *.ml2), Fenske-Hall Z-Matrix (*.zmt) and Shelx File (*.ins).
Refer to openbabel wiki or http://www.ch.ic.ac.uk/chemime for informations about common molecular file formats.
Refer to http://en.wikipedia.org/wiki/Molecule_editor and http://www.ccp14.ac.uk/solution/2d_3d_model_builders/index.html for an exhaustive list of programs for building 3D starting models. Suggested free available programs for building 3D models are ACD/ChemSketch (Windows), Avogadro (all platforms), Marvin (all platforms), Ghemical (Linux). NIST Chemistry WebBook and Drugbank are useful links to look up fragments.
Resolution: defines the maximum resolution used by Simulated Annealing + Direct Methods procedure.
The second page 'Fourier map condition' contains the information about the Fourier map at which the imported starting model will be associated:
Use Direct Methods map: if selected, the program will use the atomic positions of the Fourier map obtained at the end of the current run of EXPO2014.
Map filename: it is activated only if 'Use Direct Methods map' is de-selected. The filename of the external Fourier map (in term of atomic positions) must be supply. Some file types can be imported: C.I.F. file (*.cif), Expo fragment or Free Fractional Format (*.fra), etc.
Number of peaks of Fourier Map: the number of atomic positions selected from the map. If 'automatic' is selected, the program will use the 40% of the electron density peaks (those with the largest intensity) to associate in turn to each model atom. This number can be reduced by the user if 'automatic' is de-selected.
The third page 'Internal DOF' contains the information about the internal degrees of freedom (DOFs):
Torsion: List of torsions associated to each refinable internal DOF. The order number of each atom involved in the torsion angle to vary are also shown. The internal DOFs can be or not refined (check Refine).
Lower-Upper: range of variation of the torsion angle. 180 means that the allowed range is (x-180, x+180), where x is the value of the torsion angle in the initial model.
A visual match between the observed and calculated powder diffraction pattern is plotted when the procedure is running. When Direct Methods combined with Simulated Annealing procedure are running the progress of structure solution is monitored and the user can examine:
1) the graph of the minimum value of the cost function (CF) vs. the number of moves;
2) the match between the observed and calculated pattern.
Use the buttons to zoom on graph.
During the Direct Methods combined with Simulated Annealing procedure runs two buttons on the toolbar are activated:
opens the JAV viewer for crystal structure visualization.
stops the procedure.
Press the button to run the Simulated Annealing+Direct Methods procedure.
The output file contains information on:
1) the selected peaks of the Fourier Map imported or obtained at the end of a run of EXPO2014;
2) the imported starting structural model;
3) the table of connectivity;
4) the list of internal degree of freedoms (DOFs) to be varied;
6) the information about each association: peak of the map-atom of the model;
7) the summary of the ten best associations which are refined in sequence;
8) the selected best final structure.
Refer to openbabel wiki or http://www.ch.ic.ac.uk/chemime for information about common molecular file formats.
Refer to http://en.wikipedia.org/wiki/Molecule_editor and http://www.ccp14.ac.uk/solution/2d_3d_model_builders/index.html for an exhaustive list of programs for building 3d molecules. Suggested free available programs for building 3D molecules are ACD/ChemSketch (windows), Avogadro (linux), Marvin (all platforms), Ghemical (linux) NIST Chemisty webbook and Drugbank.
For suggestions and bugs please contact rosanna.rizzi@ic.cnr.it.
A. Altomare, R. Caliandro, C. Cuocci, C. Giacovazzo, A. G. G. Moliterni, R. Rizzi and C. Platteau. 'Direct methods and simulated annealing: a hybrid approach for powder diffraction data'. J. Appl. Cryst. (2008). 41, 56-61.
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