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). In particular, the menu subitem "Set common orientation for all geometries" can be useful, if your molecule often turns over while you brose the optimization steps:

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