File Open Options

Clicking on the Options button in the Basic Open Files dialog results in the dialog below. The same panel is present in the Advanced Open Files dialog, named File Open Options.

This dialog (panel) contains items that modify the default file opening/structure reading/processing behavior for files. This dialog can be restored to its default settings by clicking on Default Settings button at the bottom right.

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File Opening Options

Two options appear in the Gaussian Log and Checkpoint Files section:

The Save Formatted Checkpoint File menu in the Gaussian Checkpoint Files area controls saving the formatted checkpoint file:

The Use Bond Table menu in the Gaussian Checkpoint Files area controls how bonding is assigned when retrieving structures from the checkpoint file. Checkpoint files contain a bond table listing the bonds within the structure. Bonding can be assigned following this table or calculated from internuclear distances and standard atomic covalent radii. By default, GaussView uses the bond table to assign bonding for all retrieved geometries from checkpoint files created by optimizations and relaxed scans. It uses the bond table to assign bonding for the first geometry only with checkpoint files created by IRC or molecular dynamics calculation, and it uses the bond table to assign bonding for the final geometry only for checkpoint files created by all other types of calculation types. This behavior corresponds to the Auto selection on this menu. The other items on the Use Bond Table menu are:

The Skip Weak Bonds checkbox controls whether bonds with an assigned/calculated order < 0.75 are included. When it is checked, such bonds are skipped. Weak bonds can also be removed from a structure using the Edit=>Remove Weak Bonds menu path. Weak bonds may be added to a structure using the Bond SmartSlide using the dashed line bond type.

The Multiple Jobs in File menu in the Gaussian Log File area controls what happens when a log file contains results from multiple calculations:

The Gaussian Input File area has two options:

The options under PDB Files apply specifically to opening PDF files:

The following option applies to Sybyl Mol2 files:

The PDB, MDL, and Sybyl Mol2 files section at the bottom of the panel has one option, Add Hydrogens, which specifies how hydrogen atoms are dealt with when opening files: