Job tools menu (left-bottom)

  This menu appears after clicking the "Tools" button at the bottom of the left panel, which becomes visible when an output file is opened, and when the tree node corresponding do individual job step is chosen.

Save scan animation                        This item is used to create animated gif files from a scan job or a trajectory file. If the job node is not visible for your file, you should choose "Tools/Create animation/Scan animation" item from the main menu;  

Save scan steps as multiple xyz files    For scan jobs, each scan step can be saved as an individual section in .xyz file with multiple structures;

Clear all bonds extracted from the file    When an output file (e.g. Gamess) is read, it can contain bond computed by e.g. mulliken population analysis. Sometimes these bonds are quite improper, and to get rid of them, this menu item can be chosen;

Show scanned parameter on image      If you have a relaxed PES scan, you can visualize the scanned parameter (distance, angle or dihedral) with this option;

Show internal parameters used in optimization     When Gaussian performs a geometry optimization and the molecular geometry is specified in Cartesian coordinates, Gaussian chooses its own set of internal parameters which are optimized (unless you choose # OPT(CART)). You can use this option to check, whether these parameters have been chosen by Gaussian correctly (if not, probably you should use your own set of internal parameters to speed up the optimization);

Find frequencies in which the selected atoms are mostly involved         Here you can check in which frequencies the motion of selected atoms appears mostly;

Compute entropy and Gibbs energy without low frequencies                With this option you can compute entropy setting some threshold of small frequencies (to minimize the error cases by the anharmonicities of small frequencies). You can read more information about this feature at this webpage;

Calculate frequencies by Hessian       If you have opened a file with Hessian (Gaussian .fch or Orca .hess file), with this option you can compute the frequencies (this feature can mostly useful for computing the isotopic substitution effects). More information about this feature can be read at this webpage;

Trajectory analysis tools                    These subitems can be useful for processing and visualizing trajectories (e.g. of geometry optimization):

  Export all atomic coordinates...     Shows a table with the coordinates of all atoms in all trajectory steps, so you can copy it and paste e.g. into Excel for your use;

  Make modifications of all geometries...    With these subitems, each trajectory step will be edited and some changes in the atomic coordinates in it will be made:

     Set common orientations for all geometries    This menu item can be useful, if your molecule often turns over while you brose the optimization steps:

       Insert dummy atoms into centers of selected   For each trajectory step, an X atom will be added with the coordinates averaged by the coordinates of all selected atoms;

       Add vector by 2 or more...       For each step, a vector will be added along the line connecting 2 or more selected atoms;

        Add plane comprising 3 or more...     For each step, a plane will be added containing 3 or more selected atoms;

        Add vector perpendicular to last plane and passing through selected atom

        Add plane perpendicular to last vector and passing through selected atom

        Add 2 dummy atom by last vector        Adds two X atom for each step, with the coordinates equal to the starting and final positions of the vectors added previously via the menu items above;

        Add 4 dummy atom by last plane    The same for plane;

        Project selected atom on last vector    If you have added a vector to each step via menu items above, and selected an atom, an X atom will be added on the vector (with coordinates projected by selected atom);

        Project selected atom on last vector   The same for plane;

        Clear vectors/planes      Clears all vectors and planes in the trajectory (added via previous menu items);

     Compute velocities and forces...    For all trajectory steps, Chemcraft will compute the velocities as the difference between the atomic coordinates in adjacent steps, and the forces as the difference between corresponding velocities;

      Show graph "Property vs Step N"     These menu items allow you to draw graphs for your trajectory:

         Energy                         Step vs Energy

          Geometrical parameter specified..            Distance, angle or dihedral of 2-4 selected atoms;

           Angle between two vectors                     If you have added two vectors two each step of the trajectory with the menu items above, you can see the angle between them at each step;

           Angle between two planes                      Same for two previously added planes;

           Angle between the plane and the vector   

           Distance between the vector and selected atom    Before using this menu item, you must add one vector via the menu items above, and select 1 atom;

            Distance between the plane and selected atom      The same for plane;

            First geometrical parameter vs second geometrical parameter     With this menu item, a window will be opened where you can type the numbers of atoms specifying first and second geometrical parameter (distance/angle/dihedral), and the graph of the correlation between them will be shown;

              Numbers of monomers, dimers, trimers...     For each trajectory step, the program will compute the number of dimers, trimers, etc. of residues (molecules) connected via H-bonds.

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