Job tools menu
This menu appears on 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.
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;
Set common orientation for all geometries This menu item can be useful, if you have geometry optimization job, and while you browse the optimization steps, the molecule often turns over:
Set custom centroids for all geometries By default, when you click on each optimization step, the molecule on the main window is automatically updated from the coordinates read from the output file, so if you have added centroids previously, they disappear.. If you want to insert centroids into molecule and see it in each optimization step (or obtain an animation with them), do the following: choose a job step node, then add one or several centroids, and then choose this menu item;
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).