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.

File Opening Options
Two options appear in the Gaussian Log and
Checkpoint Files section:
- : When checked, all of the geometries in an
Optimization calculation will be loaded, instead of only the final one.
- : When checked, all of the geometries in a Scan or
IRC calculation will be loaded, instead of only the final one.
The menu
in the Gaussian Checkpoint Files area
controls saving the formatted checkpoint file:
- : When selected, the
formatted checkpoint file will not be saved.
- :
When selected, the formatted checkpoint file will be saved with the
same base name as the file being opened.
- :
When selected, a window will open when the formatted checkpoint file is
ready to be saved, allowing the user to input a name.
The menu in the 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 menu are:
- : Use the Bond Table to assign bonding for first geometry only. The bonding for any other retrieved structures is calculated.
- : Use the Bond Table to assign bonding for last geometry only. The bonding for any other retrieved structures is calculated.
- : Use the Bond Table to assign bonding for all retrieved geometries.
- : Don't use Bond Table to assign bonding for any geometries. In other words, calculate the bonding for all geometries.
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 menu path. Weak bonds may be added to a structure using the Bond SmartSlide using the dashed line bond type.
The menu in the Gaussian Log File area controls what happens
when a log file contains results from multiple calculations:
- : When selected,
GaussView will open a window to prompt the user to select what to do
with the multiple jobs contained in the file.
- : When
selected, GaussView will load the first job in the file and delete the
rest.
- : When
selected, GaussView will load the last job in the file and delete the
rest.
- : When selected,
GaussView will load all of the jobs in the file as seperate windows,
allowing each to be run.
The Gaussian Input File area has two
options:
- :
controls what happens when an input file contains more than one job.
- : When selected,
GaussView will open a window to prompt the user to select what to do
with the multiple jobs contained in the file.
- : When
selected, GaussView will load the first job in the file and delete the
rest, unless the checkbox, explain below, is checked.
- : When
selected, GaussView will load the last job in the file and delete the
rest, unless the checkbox, explain below, is checked.
- : When
selected, GaussView will load all of the jobs in the file as seperate
windows, allowing each to be run.
- : When checked, GaussView will place the input
for all jobs after the first into the Additional
Data tab in the Gaussian Calculation Setup
window.
The options under PDB Files apply
specifically to opening PDF files:
- :
Specifies handling of crystallographic structures, interpreting them as
an asymmetric unit, a unit cell, or a biological unit.
- : If unchecked, GaussView determines connectivity, using
the default distance cutoffs-based method. When checked, applies
connectivity based on the contained residue specifications.
- :
Ignore connectivity records.
- : If
checked, ignores any water molecules present in the PDB file
(specifically, HOH, WAT, and/or H2O).
The following option applies to Sybyl Mol2 files:
- :
Determines whether lone pairs are skipped or replaced with open valence
atoms.
The PDB, MDL, and Sybyl Mol2 files section at the bottom of the
panel has one option, , which
specifies how hydrogen atoms are dealt with when opening files:
- :
Prompt whether to add hydrogens when a file is opened and no hydrogens
are present.
- :
Automatically add hydrogens to the file when it is opened if it does
not already have hydrogens.
- : Ask the user
whether hydrogens should be added regardless if there are any present
in the file.
- : The file is opened,
and no attempt is made to add any missing hydrogen atoms.
- : Missing hydrogens
are always added where necessary when a file is opened.