6.1. File menu

6.1.1. New Project

Create a new project.

The file structure of the created project is as follows. Renaming of each file/folder is not supported.

  • .wmpjdata folder: a folder containing all the files in the project. Drag and drop this folder into Winmostar to open the project.

  • .wmpj file: A file containing information about the project. Drag and drop this file into Winmostar to open the project.

  • temp.wmm : This file contains information on the molecular structure being edited.

  • index.ndx: the file where information on groups registered with select ‣ register group is stored.

  • .wmps* file: the workflow configuration file used for this project.

  • work* folder: working folder

  • Exec* folder: contains the files that control the jobs in each working folder.

6.1.2. New project with current structure

Create a new project using the structure currently displayed in the molecule display area.

6.1.3. Open Project

Open an existing project.

6.1.4. Open Recent Project

Open a recently opened project file.

6.1.4.1. Clear History

Empty the history of recently opened project files.

6.1.5. Project

6.1.5.1. Get Info

View information about the open project. Some information can be edited here.

6.1.5.2. Open Temporary File

Open a temporary file of the opened project.

6.1.5.3. Show in Explorer

Open the wmpjdata folder of the opened project.

6.1.5.4. Parameter/structure scan result display

You must purchase an add-on to use this feature. After a parameter scan or structural scan calculation, the results of each calculation can be tabulated.

Working Folders

Check the working folder that contains the calculation results you want to visualize.

Property

Select the type of calculation results you want to visualize.

X Axis

Selects the value of the X axis for visualization.

Export Animation

Create a wmm file with the values selected in End Structure and Property. For example, if you want to create a Volume-Total Energy graph, create an animation with this feature and then use the Custom Plot feature to select Volume for the X axis.

Draw

Create a graph with the conditions you set.

6.1.6. New File

Create a new file.

Hint

The shortcut is Ctrl+N .

6.1.7. Open File

Read the molecular structure from file into the main window. It corresponds to the format of various software.

Use Import File if you want to load the structure without switching the current mode file.

Hint

The shortcut is Ctrl+O .

6.1.8. Open Recent File

Open a recently opened file.

6.1.8.1. Clear History

Empty the history of recently opened files.

6.1.9. Reload

Re-load the file opened in the main window.

6.1.10. Save

Overwrites the currently open file or project.

For details, see Save As .

Hint

The shortcut is Ctrl+S .

6.1.11. Save As

Save the molecular structure displayed in the main window as a different name.

After saving, the saved file will be reopened. If you simply want to output the structure in the specified format without reopening it, use Export File.

It is recommended that you enter the file name and the folder name including all files (all upper layers) with one-byte alphanumeric characters only.

  • If multi-byte characters such as double-byte alphanumeric characters or Japanese characters or spaces are included, some processing may cause problems.

  • Underscores can be used.

When saving an input file of various solvers, a file is created based on the contents of Keyword Editor and Coordinate Viewer.

If the keyword of the solver you want to save is not displayed in Keyword Editor, Configuration window will open automatically. For MOPAC, GAMESS, Gaussian, NWChem, the coordinates are output in the format selected in File ‣ Coordinate Format.

Hint

The shortcut is Shift+Ctrl+S

6.1.12. Close

Closes the currently open project or file and returns to the startup screen.

6.1.13. Import File

Loads an existing molecular structure file. You can either discard the current structure and load it, or append it to the current structure and load it.

Open File opens the file in file mode when it is read in, but this function overwrites the structure of the molecular display area with the structure of the imported file without switching modes or files.

6.1.14. Import Recent File

Import recently used files.

6.1.15. Import

It reads a specific type of molecular structure.

6.1.15.1. SMILES

Molecular structure is generated from SMILES format string and read into the main window. When Import SMILES window opens, enter the SMILES format string in the text box and press Import button. Internally, conformational search by Bolloon or OpenBabel is also executed at the same time. A working folder named *_smiles_tmp will be created as an intermediate file.

6.1.15.2. Structural Formula

Create a molecule by entering a structural formula. Internally, JSME draws the structural formula, and Balloon or OpenBabel generates the 3D structure by generating SMILES from JSME.

6.1.15.3. Sample File

Load the files in the Samples folder.

6.1.16. Export File

Outputs the current molecular structure in any file format.

6.1.17. Export

Outputs the contents displayed in the main window in the selected format.

6.1.17.1. SMILES

Outputs the molecular structure displayed in the main window as a string in SMILES format. Not available when multiple molecules are displayed in the main window. Use OpenBabel on Cygwin. “Do you want to generate SMILES after completing the hydrogen atoms?” dialog, if “yes”, OpenBabel is executed via mol2 format with the -b option, if “no”, OpenBabel is executed via xyz format.

Warning

To use this function, CygwinWM setup is required.

6.1.17.2. Structural Formula

The image of the structural formula of the molecular structure displayed in the main window is output in SVG format. It can not be used when multiple molecules are displayed in the main window. I use OpenBabel on Cygwin.

Warning

To use this function, CygwinWM setup is required.

6.1.17.3. Image

Outputs the contents displayed in the main window in BMP or JPG format.

6.1.17.4. CHARMM crd File

Outputs the molecular structure displayed in the main window in CHARMM crd format.

6.1.17.5. SDF File

Outputs the molecular structure displayed in the main window in SDF format.

6.1.18. Get Info

Displays detailed information about the molecular structure displayed in the main window.

6.1.19. Open in Text Editor

Open the file displayed in the title of the main window with the text editor selected in the configuration window.

Note

After editing with the text editor, selecting Reload , you can reflect the change on the main window.

6.1.20. Show in Explorer

Open the directory one level higher than the file displayed in the title of the main window.

6.1.21. Exit

Quit Winmostar.