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readme.md

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 # Topas_tools
 
+These are set of small scripts and tools that were developed to help with structure refinement (of zeolites in particular) using the program TOPAS (http://topas-academic.net/).
+
+## topasdiff
+
+Topasdiff is a tool to generate nice looking difference maps. First, output the observed structure factors, and structure in cif format from Topas:
+
+    Out_fobs(fobs.hkl)
+    Out_CIF_STR(structure.cif)
+
+Observed structure factors can be generated using this macro (add this to C:/topas5/local.inc):
+
+    macro Out_fobs(file)
+    {
+       phase_out file load out_record out_fmt out_eqn
+       {
+           "%4.0f" = H;
+           "%4.0f" = K;
+           "%4.0f" = L;
+           '"%4.0f" = M;
+           "%12.4f\n" = (Iobs_no_scale_pks / M)^(0.5);
+       }
+    }
+
+Then to calculate the difference map, run the command:
+
+    topasdiff structure.cif --diff fobs.hkl
+
+or use the GUI, accessible available via topasdiff.bat (Windows). The program will ask for the scale factor provided by TOPAS, and generates an input file for the program superflip (http://superflip.fzu.cz/). Superflip is then used to perform the fourier transform, and generates an XPLOR file that can be visualized using Chimera or VESTA.
+
+Note: There is a bug in Topas where the cif files it outputs cannot be read using CCTBX, because they lack the data header. A work-around is to open C:/topas5/topas.inc and modify all instances of:
+
+    Out_String("\ndata_")
+
+by:
+
+    Out_String("\ndata_topas_cif_out")
+
+![topasdiff gui](https://cloud.githubusercontent.com/assets/873520/14959028/c68ba2e4-108d-11e6-9942-f8e6acc1559f.png)
+
+## cif2topas
+
+cif2topas transforms a crystal structure into cif format into the corresponding TOPAS code.
+
+Usage:
+
+    cif2topas structure.cif
+
+
+## fh2topas
+
+fh2topas is a script that converts from Fenske-Hall z-matrix to TOPAS code
+
+Usage:
+
+    fh2topas.py zmatrix.fh [n]
+
+Here, is an optional parameter to give the number of molecules to generate. fh2topas will automatically number them to avoid naming conflicts.
+
+
+## topasrestraints
+
+topasrestraints is a tool that can help with the generation of bond and angle restraints for structure refinement of zeolites with TOPAS. First, generate all bonds by using the TOPAS instruction:
+
+    append_bond_lengths
+
+to generate all bonds and angles, including their symmetry codes for the current structure. Copy everything between the curly brackets to a new file called bonds.txt, and run:
+
+    topasrestraints bonds.txt
+
+This generates a file called restraints.out that contains the restraints that can be added to TOPAS. The script checks for all distances of 1.61 +- 0.4 Angstrom to identify T-O bonds. The program checks the connectivity for every atom, and reports if there is a problem (too many / not enough distances per T-atom). There is no check for symmetrically equivalent connections, so some restraints may be redundant.
+
+
 ## Requirements
 
 - Python2.7
 - numpy
 - matplotlib
 - pandas
 - CCTBX
+- superflip (http://superflip.fzu.cz/)
+
 
 ## Installation