6.21. Tools ‣ Preferences menu

We make various settings of Winmostar.

Basic Tab
Select a language.
License code
Set the license code.
Internal UNIX environment
Choose whether to use cygwin for internal UNIX environment or Windows Subsystem for Linux (Bash on Ubuntu on Windows).
Use internal editor at [File]-[Open in Text Editor]
If checked, use Edit-> Direct Editor function up to V8 when you click File ‣ Open in Text Editor. If not, use the program set in Editor with Preferences ‣ Program Path.
Use old function adopted up to V8 for unzip
In the remote job, specify the code used to get and unzip the zip file of the working directory from the remote server. Old-style code generates errors when decompressing huge files (hundreds of MB or more).
Use old format adopted up to V9 when saving xyz file
When saving in xyz file format, save as xyz file without header which was the default before V9.
Edit tab
Bonding Factor
Set the threshold for judging the presence or absence of covalent bond from interatomic distance.
Keep Z-Matrix connectivity while modifying structure
If checked, make sure that the Z-Matrix join relationship does not change when editing molecular structure.
Convert aromatic ring to single + double bond for MOL file
When storing the MOL file, change the aromatic ring to a combination of single bond and double bond before outputting.
Bonding exceptions
Use this function when you do not want to create bonds between specific elements in the function to automatically generate bonds. First press the Add button. Then select the two elements you want to exclude the join in the two pull-down menus below the list and press the Apply button. After that, applying Regenerate All Bonds etc will break the bond between the specified elements. To restore, select the line you want to unset from the list andpress the Delete button.
Move markers to pasted atoms.
If checked, move the marker to the pasted atom when using Paste.
Max # of atoms to show atom list
Set the maximum number of atoms to display coordinates in Coordinate Viewer.
Max # of atoms to generate Z-Matrix
Set the maximum number of atoms to automatically generate Z-Matrix.
Max # of atoms to generate bonds
Set the maximum number of atoms to automatically generate Z-Matrix.
Calculation tab
Run MOPAC using Job Manager

When checked, use Winmostar Job Manager when executing MOPAC. If it is not entered, Winmostar will be in a wait state until calculation by MOPAC is completed, and the output result of MOPAC will be automatically loaded into the main window.

It can also be set from Use Job Manager.

Run the other solvers using Job Manager
Specify whether to use Winmostar Job Manager to execute programs other than MOPAC.
Set the time-out period of time-consuming processing.
Default extensions
Set the extension set by default when creating input files for each solver.
Use Gnuplot as default plotting tool
If you check, use Gnuplot for some graph drawing functions. Otherwise, use Grace. From V9, the graph drawing function using Grace or Gnuplot will gradually replace the graph drawing function of Winmostar native. The Gnuplot file can be saved from the Export button of the Winmostar native graph drawing function.
Confirm before starting calculation
If checked, a confirmation dialog will be displayed when executing each solver.
Use old format adopted up to V9 when saving xyz file
If checked, use the directory name with “wm_” appended to the user name for the work directory for Remote Job Submission.
Forcibly sleep after GAMESS run
If this is checked, GAMESS will be forced to sleep for the specified number of seconds after executing GAMESS on the local machine. This function is useful when you want to check the contents of a log immediately after calculation.
View Tab
Color set
Select the color set from Winmostar, GaussView, Jmol, Rasmol, and Old Winmostar.
Selected atom
Change the color of the atom type of the selected particle.
Change the color of the bond.
Change the color of the background.
Background (Viewer)
Change the background color of Winmostar Viewer.
Change the color of the character on the molecule display window.
VDW radius of selected atom
Change the VDW radius for the element of the atom with marker in Viewport.
Scaling factor of charge

Adjust the size of the charge display when displaying charges in Label/Charge.

You can also be set from View ‣ Items.

Font size on Keyword Editor
Specify the font size of the Keyword Editor.
Scrolling speed
Adjust the speed of zoom in/out by the mouse wheel in Viewport.
Depth cue

Adjusts the fog density used for depth expression.

Depth cue density
Adjusts the fog density used for depth expression.
Maximum # of atoms for depth cue
Enable depth cue if the number of atoms is greater than the specified value.
Items to be drawn

Check the items to be displayed in Viewport.

You can also be set from View ‣ Items.

View center after opening file
Check View Marked Atom autoatically when opening a file.
For patent application
Display in black and white and no gradation, which can be used when applying for a patent.
Program Path Tab
Specify the install path of various programs.