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 utilities for conversion of crystallographic fractional coordinates into Cartesian, and vice versa:

    Recount fractional to Cartesian    You can enter the crystal cell parameters (a, b, c, alpha, beta, gamma, or 3 lattice vectors) for recounting the fractional coordinates of atoms into Cartesian;

    Recount Cartesian to fractional    Vice versa, this tool recounts Cartesian coordinates into fractional;

    Build cells from Cartesian coordinates and a, b.. parameters    This menu item is very close to previous one, but it also creates a node in the tree nodes list at the left, with the information about crystal cell, and this allows you to build duplicated cells (e.g. 2*2*2);

    Build cells from Cartesian coordinates and 3 lattice vectors   With this menu item, you can create your custom .cif file with any positions of the A, B, C lattice vectors. Firstly you need to add 3 vectors via "Edit/Operations with vectors and planes/Add vectors or planes/Add vector...". These 3 vectors will be considered by Chemcraft as the A, B, C lattice vectors. Note that it is easy to make a mistake and specify the 3 vectors in wrong order, and this will not allow Chemcraft to build a cell, because this cell will generate enantioners; if the error message about this is shown, you can change the order of the 3 vectors via "Edit/Operations with vectors and planes/Edit vectors and planes in text format/Update from shown" (copy-paste some lines in the shown window);

Divide current structure into individual molecules   If your structure contains several fragments which are not bonded with each other, Chemcraft will enumerate and show them all;

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);

Structures combinerr                     These subitems allow the user to compare or combine 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;

Update atomic sequence...   If you have two nearly identical structures, but with different atoms ordering, you can reorder atoms in them for best match;

Show together  two structures... Chemcraft will superimpose the structure from two opened windows and show them in a single window;

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. The difference is that with this menu item, you will be manually select atoms to be excluded from the final superimposed structure:

https://youtu.be/Tz1dUoDJc2w

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;  

Mass spectrum analysis tools                These subitems calculate the exact mass of current molecule, using two methods, and enumerate possible fragment ions for interpreting the mass spectrum (see this help page for more information):

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;

Calculate molecular area               Computes the effective area of the molecule (3 or more atoms which determine the plane must be selected firstly);

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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