The dialog window of Simulated Annealing+Direct Methods procedure in EXPO 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 is 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 EXPO.
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 the torsions associated to each refinable internal DOF. The order numbers of the four atoms that identify the torsion angle to be varied 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 observed and calculated powder diffraction pattern is plotted when the procedure is running. When the Simulated Annealing + Direct Methods procedure is running the progress of structure solution is monitored and the user can examine:
1) the graph of minimum value of the cost function (CF) vs. the number of moves;
2) the match between observed and calculated pattern;
Use the buttons to zoom on graph.
During Simulated Annealing + Direct Methods runs two buttons on the toolbar are activated:
open the JAV viewer for crystal structure visualization
stop the procedure.
Press the button to run the Simulated Annealing+Direct Methods procedure.
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