Tools menu

Apply custom geometrical parameters                               Opens the Console editor window to make complex geometry modifications;

Data Explorer                                 Shows the Data Explorer window, which represents all data read from an output file (this window is shown automatically when opening a new log file);

Build Z-matrix                                Allows one to obtain a Z-matrix for the input file by clicking atoms in the molecule and specifying some additional information (see Z-matrix builder for details);

GED tools                                      These subitems can be useful in Gas Electron Diffraction:

   Group distances in molecule:           Calculates all interatomic distances in the current structure and groups them by distance values with specified threshold convergence;

   Enumerate internal coordinates        Shows internal coordinates in the molecule, based on the atoms bonding (bond lengths, bond angles, dihedrals);

Crystallography tools/                     These subitems provide the conversion of crystallographic fractional coordinates into Cartesian, and vice versa  (see Conversion between fractional and Cartesian coordinates);

Create animation/                            These subitems allow one to create an animation and save it as animated gif file or multiple bmp/jpg files, or to build an animated gif file from several bmp/jpg files;  

Data summary                                 These subitems show a data summary from the opened file(s)

             Show parameters table                   Shows a table representing structural parameters of the current molecule and vibrational frequencies;  

             Show energy graph                  If you have opened an XYZ files containing energies (like the file /Chemcraft/samples/MultXYZ/caffeine.xyz), these energies will be shown on graph;

Create section for input file              Opens a dialog box which automatically generates sections of input file with non-standard basis sets;

Fragments Extractor                       Open the Fragments Extractor windows which can be used for extracting fragments from big molecules (e.g. duplicated crystallographic cells);

Orbitals                                          These subitems can be activated when a file with molecular orbitals is opened:

   Render molecular orbitals                Allows molecular orbitals (or natural orbitals, etc) read from the file to be visualized in the form of isosurfaces or colored figures;

   Analyze molecular orbitals               Shows a window with analysis of orbitals read from the file. At the moment this analysis is very simple and not well-elaborated. In future versions of the program the analysis will probably be improved and possibly become based on calculation of overlap integrals;

   Convert orbitals into input format    These subitems allow molecular orbitals to be saved in text format, for use in an input file as an initial guess for new computation;

   Show MO energies diagram            Shows a window with the diagram of MO energies from the file;  

Structures comparer                     These subitems allow the user to compare two or more structures:

Get RMSd of two structures...                Opens a window in which the root-mean-square displacements between the structures in two instances of Chemcraft are shown. To use this feature, you should firstly launch 2 Chemcraft applications and load a structure in each of them;

Merge structures from multiple files Before using this utility, you should open either several files or one .xyz file with multiple structures; these structures will be merged to make comparisons;  

Structures combiner

Merge two structures from two Chemcraft windows by selected subunits                  As with the previous menu item, one should firstly launch 2 Chemcraft applications, and the structures in them will be merged;

Calculate molecular mass                These subitems calculate the exact mass of current molecule, using two methods (see this help page for more information):

   By isotope redundancies              Computes the molecular mass using isotope redundancies;

   By isotope masses                       Computes the molecular mass using isotope masses;  

Calculate moments of inertia           Computes three moments of inertia of current molecule;

Calculate collisional diameter          Computes the volume occupied by current molecule. The value shown at the top is the average size of current molecule, (A*B*C)^1/3;

Simple utilities/                                This subitems provide a simple tool for calculating occupancies of states by their energies, and for calculating relative energy:

   Calculate occupancies by energies   This item opens a window where you can paste the energies of some of your molecules, and Chemcraft will compute their relative energies in kJ and the Boltzmann occupancies with these energies;

  Calculate the energy of a reaction  Here you can paste some energies of intermediate compounds to compute the energy of a reaction;

  Calculate mean absolute deviations for a linear fit   We think this utility can be useful if you have a linear fit and want to compute the mean absolute error for it;

  Table formatter                           This tool can e.g. cut some digits after the decimal point in your table;

  Create custom spectrum              Here you can paste the xy values of your spectrum and use the standard Chemcraft tools for spectrum visualization (broadening, etc);

  Create custom 3d graph              Here you can paste x1,x2,y columns and build a 3d graph;

  Utilities not related to chemistry

    Simple job scheduler                Maybe you can find this job scheduler interesting for your purposes;

Scripts                                            These subitems can be useful for automation of some jobs:

   Generate .bat script for files conversion     This tool allows one to convert e.g. multiple output files into images or .mfj files;

   Generate Gaussian batch file        Creates and runs a .bcf file with multiple Gaussian jobs;

   Generate .bat file for PCGamess/Firefly     Generates and runs a .bat file with multiple Firefly jobs;

   Generate .bat file for Wingamess  Generates a .bat file with multiple Wingamess jobs;  

   Generate .bat file for Orca         Generates and runs a .bat file with multiple Orca jobs;  

  Generate custom script file    Generates a custom batch file for other QC programs;

  Modify multiple Gaussian files      This utility can be useful if you e.g. have  performed a series of Gaussian computations of some molecules, and want to repeat these computations with another method;

  Modify multiple Orca files            Same for Orca;

  Extract energies from multiple output files   These tool allows you to get a series of energies of your computations as a column, for copying into Clipboard;

  Run currently opened file in Gaussian     If you have previously set up the "Generate Gaussian batch file" window and currently Chemcraft has opened a Gaussian input file (.gjf), after clicking on this menu item this file will run in Gaussian;

Run currently opened file in Orca   Same with Orca

Run currently opened file with custom script   Same with other QC package.

Supporting...                                   These subitems allow internal program settings to be modified:

   Edit fragments database                  Shows the Fragments Editor window to view and edit the standard set of molecular fragments (see Working with molecular fragments);  

Chemcraft incorrectly identifies....     This menu item can be used to alter the tables of standard bond lengths, used in bond identification, or alter the bond identification method;

Associate Chemcraft with files         Allows Chemcraft to be registered as a program for viewing certain types of files (.out, .xyz). When Chemcraft is registered, these files can be opened immediately in Explorer, Total Commander or another shell. Note that this tool usually works only when Chemcraft is run from Administrator;  

Utilities for working with custom graphs

  Old graphs data digitizer              If you have a graph as a picture, you can click on its ticks and peaks to compute the positions of peaks in graph values;

  Graph analyzer                           This tool can be used if you have a graph and want to compute (integrate) the area of a peak on it;

Jobs archive                                   These subitems provide working with the archive of computed jobs:

   Scan directories and show...           Scans a chosen directory and all its subdirectories and finds Gaussian output files in them, and shows found jobs in a hierarchical list. If the checkbox "Add found jobs to the archive" is checked, all found jobs will be permanently added to the archive of output files;

   View contents of the jobs archive    Shows the archive of Gaussian output files in a hierarchical list;

   Clear jobs archive                           Clears the archive;

Preferences      Allows the program settings to be changed (see Preferences window).

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