![]() ![]() cif - this is important as it means the Z-matrices contain the same torsion angles found in the solution. inp file has been created and has been run successfully, use DASH, which is now available for free, to create Z-matrices from the solution. The easiest way to do this is to use the Durham TOPAS jEdit tools to set up the. Perform a scale-factor-only Rietveld refinement to ensure everything has worked correctly. cif and create a TOPAS Rietveld refinement input file. Once the crystal structure has been solved as normal, save the solution as a. For more detailed information, see the TOPAS manual and excellent tutorials by John Evans. The following instructions assume a basic familiarity with TOPAS used via launch mode. By default, the filename is "map_ZMs.inp". The script writes out a file with the ".inp" extension, into the working directory. Print( "Success: map_ZMs.inp written") Output file inp to disk with open( "map_ZMs.inp", "w", encoding = "utf-8") as f: ![]() # Now we need to write the last few keywords needed, like only_penalties etc # so we call the final_ZM_output() method inp += zm. write_distance_restraints( header = i = 0) # Now loop over the ZMs again, this time outputting the distance restraints to # map the rigid bodies onto the CIF atom sites for i, zm in enumerate( ZMs): # If it is the first ZM, we will want to output a bit of extra information for # the CIF, hence the call to the zm.first_ZM_output() method for i, zm in enumerate( ZMs): # Now loop over each ZM and write out the new sites and rigid bodies. With open( file, "r", encoding = "utf-8") as f: # First read in the Z-matrices, and create Zmatrix objects for each one for file in files: It will write out a file called "map_ZMs.inp" which can then be used as described in the instructions for use with TOPAS below.Īlternatively, start a python interpreter or write a simple script and write something like the following:įrom zmatrixtoinp import Zmatrix files = Python zm-to-inp.py test_1.zmatrix test_2.zmatrix To convert the Z-matrices "test_1.zmatrix" and "test_2.zmatrix" you would run the following command: If you accept the default settings for all settings described above, call the script from the directory containing the Z-matrices you wish to convert, and supply the filenames as command line arguments. This should also be supplied to the Zmatrix class during initialisation as the keyword argument useH. Toggles the inclusion of hydrogen atoms when mapping the rigid bodies onto the DASH solution. This should also be supplied to the Zmatrix class during initialisation as the keyword argument refinement_macro. This will automatically be placed adjacent to freely rotating torsion angles, and the macro will be defined at the start of the output of the script/web app. Prm bH = bnonH * 1.2 refinement_macro = "R"Īllows the user to define their own macro name for torsion angle refinement. This can be an independent parameter, or set in relation to the bnonH parameter, e.g.: Remember to include the parameter definition in the inp. Otherwise, it can be set to a numerical value of your choice. When refining a single global B iso value for hydrogens, set to bH or your preferred variable name. When using the global B-iso value, you also need to remember to include the parameter definition in the inp. You may also prefer to set it to a numerical value of your choice (e.g. If running the code locally, supply the keyword argument bnonH to the Zmatrix class during initialisation of the object. ![]() When refining a single global B-iso value for non-hydrogen atoms, set to "bnonH" by default, or your preferred variable name if you want to change this. The output file is for use with TOPAS which is also available with an academic license Settings: B for non H atoms = "bnonH" It can be accessed here:Ĭontact markspillman at for queries. The code in this repository has been completely rewritten, and I have also written a convenient web app to save you from having to download the script and run it locally. ![]()
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