Load input file

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Load input file for Simulated Annealing

       To run EXPO2011 for structure solution by Simulated Annealing you need to create an input file (*.exp).  You can create an input file accessing by graphic interface and selecting the creation of a new project by the menu "File" > "New".

You must specify the structure name, the profile counts filename and his format, the type of radiation source. It is supposed that the cell parameters and the space group have been determined before so, fill the frame 'Cell Parameters' and 'Space Group'. Activate the check buttons 'Structure Solution', select 'Simulated Annealing' in the frame 'Structure Solution' and import the starting model from 'fragment filename'. Otherwise use the button 'Open' to import an existing input exp, for example you could load the file paracetamol.exp already existing in the directory examples. The following picture is an example for the crystal structure determination of the paracetamol molecule. The profile counts file (paracetamol.pow) is in the directory 'examples'.

When you press the button 'Save' an input file paracetamol.exp (shown below) will be created and automatically loaded by the program for the structure solution process by Simulated Annealing.

%Structure paracetamol
%Initialize
%Job paracetamol
%Data
Cell  7.100  9.380  11.708  90.0  97.42  90.0
SpaceGroup p 21/n
Content    c 32  o 8 n 4 h 36
Pattern   paracetamol.pow
Wavelength 1.54056
filetype xy
%fragment paracetamol.mol
%sannel
%continue


"%sannel" is a command to access to the Simulated Annealing graphical interface.

"%fragment  paracetamol.mol"  is the command to import the starting structural model for Simulated Annealing in MDL Molfile format (*.mol). This command can be repeated several times to import more than one fragment. Some other file type can be import in the same way: MOPAC file (*.mop), Tripos Sybyl file (*.mol2,*.ml2), C.I.F. file (*.cif), Protein Data Bank file (*.pdb), EXPO fragment or Free Fractional Format (*.frac), XYZ format (*.xyz). 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.

Instead of command "%fragment name_starting_model.ext", with ext=mol,frac, cif etc, you can import the starting structural model directly from the graphic interface from menu "File">"import".

'File'>'Add fragments' to add fragment to an existing partial structural model.

 


Instead of command "%sannel", you can access directly to the graphic interface from menu "Solve" > "Simulated  Annealing".  


Press the button in the dialog window to run the Simulated Annealing procedure.

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