6.20. Tool menu

6.20.1. Preferences

Open the Preferences window. For details, see Tools ‣ Preferences menu.

6.20.2. Save/Delete Fragment

6.20.2.1. Save Fragment

Register the molecular structure displayed in the main window as a part. Atom replaced with marker (heavy red circle) is set as the connection part when replacing.

6.20.2.2. Delete Fragment

Delete the registation of the parts selected by select a fragment by pull down menu | repl | of toolbar.

6.20.3. Enter a structural formula

Create a molecule by entering a structural formula. JSME is used internally.

6.20.4. Conformation Search (Balloon)

We will search for conformation using Balloon. Click Search button to start processing.An intermediate file is created in the working folder *_balloon_tmp.

This feature works as follows

  1. Conformation search without GA for the initial structure

    Ballon options: -v 1 -c 10 –noGA -i 300 –randomSeed 51277

  2. For the lowest energy structure of 1, a conformation search using GA

    Ballon options: -v 1 -b -k -c 400 –full -R 0.25 –nGene 20 –random 51277

  3. Conformation search without GA for 4 structures with low energy of 2

    Ballon options: -v 1 -c 25 –noGA -i 300 –randomSeed 51277

  4. Select 100 from the low energy structures of 3

  5. If Cluster similar structures is checked, cluster 100 structures and aggregate similar structures below RMSD tolerance and display them in Winmostar (However, due to the simplicity of clustering, the candidates may not be reduced efficiently)

Warning

This function is affected by the join order.

6.20.5. Point Group Analysis

Determine point group symmetry of modeled molecules.

This function is mainly used for the following purposes.

  1. Perform point cloud analysis of modeled molecules.
  2. Based on the determined point cloud information, distortion of the molecular structure is resolved. (Symmetrization)
  3. Conversion of symmetric unit <=> asymmetric unit can be performed.

For organic molecules that do not contain metals, it is easier for point cloud analysis to succeed if cleaned structures are used.

We analyze and visualize point cloud analysis using the following functions.

Analyze
Start point cloud analysis.
Accuracy
Specify analysis accuracy of point cloud analysis. Increasing the accuracy will make the judgment of symmetry severe, and lowering will make the judgment sweeter.
Shoenflies

The symmetry of the molecule is indicated by the Shoenflies symbol.

i
Point symmetry elements are listed.
On the Axis
The rotationally symmetric elements are listed.
Sn Axis
Recurrence symmetry elements are listed.
Mirror
Mirror symmetry elements are listed.
Select
All symmetric elements listed are selected and displayed on the graphic screen.
Deselect
All symmetric elements listed will be deselected and will be hidden on the graphic screen.
Select All
All symmetric elements are selected and displayed on the graphic screen.
Deselect All
All symmetric elements are deselected and hidden on the graphic screen.

After completing point group analysis, symmetrization of molecular structure and switching between asymmetric unit and symmetric unit becomes possible by the following operation. However, it is limited only to point group symmetry other than C1.

Symmetrize
Based on the predicted point cloud information, we eliminate the distortion of the structure (deviation from perfect symmetric structure).
Show
When Symmetric Unit is checked, symmetric unit is displayed. When Asymmetric Unit is checked, only asymmetric unit is displayed. (If you go to the GAMESS Configure with only the asymmetric unit displayed, you can inherit the point cloud information and create the input.)
Text area in the lower right
Displays the coordinate information of the molecule in XYZ format.

6.20.6. Molecular Surface Area & Volume

Calculate the molecular surface area, volume and oval shape.

We use the program of Mr. Nagao of Hakodate National College of Technology to calculate the surface area and volume of the molecule. (Teruo Nagao, Improvement of molecular surface area and volume calculation program, bulletin of Hakodate National College of Technology, No. 27, p 111 - 120, 1993.)

  1. van der Waals Moleuclar Surface (VMS): Surface when atoms are replaced by spheres of van der Waals radius
  2. Accessible Molecular Surface: Surface of the solvent molecule when traced with a solvent molecule around the VMS surface
  3. Molecular Surface: Contact surface and reentrant surface traced by solvent molecules around VMS surface (also called Solvent-excluded surface or Connolly surface)

Ovality (Ovality) is calculated by the following formula.

Molecule surface/Minimum surface area = S/4π(3V/4π)**(2/3) Minimum surface area = 4π(3V/4π)**(2/3) (surface area of a true sphere having the same molecular volume)

6.20.7. Aspect Ratio

Calculate the aspect ratio of the molecule. The aspect ratio is defined as the ratio L/D of the length L and the diameter D of the cylinder of the smallest diameter inscribed by the molecule.

6.20.8. Radius of Gyration

Calculate the inertial radius of the molecule.

6.20.9. Sterimol Parameters

Calculate the Sterimol parameter for the substructure selected for the group on the main window.Click Calculate button to start the calculation.

6.20.10. Unit Normal Vector of Ring Structure

This function displays unit normal vectors of ring structures, which are necessary for NICS calculations, etc. Please group-select a target ring structure then call this function.

For example, in the case of a benzene ring, the six carbons that make up the benzene ring are group-selected.

The output vector is calculated as follows

  1. Creates a list of two atoms with covalent bond among the grouped atoms.
  2. For each two atoms in the list created in 1, compute a vector perpendicular to the plane stretched by those two atoms and the three points of the geometric center of the group selection.
  3. The average of the vectors calculated in 2 is finally displayed in this function.

6.20.11. Project Browser

Opens a window for managing files in the project.

6.20.12. Job Manager

Start Winmostar Job Manager that manages local jobs.

6.20.13. Submit Remote Job

Opens a window for executing and managing remote jobs. For details, see Each function of the Submit Job window.

6.20.14. Cygwin

Start the terminal window (terminal) of CygwinWM.

6.20.15. Unit Converter

Opens a unit conversion tool specialized for atomic and molecular systems.

6.20.16. Search String

It searches character strings in various log files and outputs the hit line to Excel or text file.

6.20.17. Batch Queue

We run Gaussian and GAMESS bat files in succession.

  1. First, run Gaussian or GAMESS using normal operation method. Confirm that there is no error on the console window (DOS window) during execution, and then press the X button on the console window to forcibly terminate processing.
  2. Next, activate this function. The bat file of the job executed in 1. is displayed in the list on the left side of the window.
  3. Select the bat file and press the => button to add it to the list on the right side of the window.
  4. When you press the Run button, continuous execution of jobs registered in the list on the right starts. When you press the Run at button, continuous execution starts at the specified time. Continuous execution jobs are saved in winmos_batjob*.bat. Save and :guilabel:` Load` button to save and load settings.

6.20.18. Superimpose Molecules

Multiple molecules are superimposed and displayed.

  1. First, select the file with the Add button and select the molecule to be superimposed. File types are various input files that can be read with Winmostar and output files of MOPAC, GAMESS, NWChem, and Gaussian. You can select multiple files simultaneously. You can also load files by drag & drop. Import From Main Window button allows you to capture molecules displayed in the main window.
  2. Selecting the filename displayed in the list will highlight that molecule blue.
  3. Delete selected molecule with Delete button, Clear button to delete all molecules.
  4. You can align the orientation of each molecule with Align All button. Clicking on 3 atoms for each molecule specifies the first point as the origin, the second point on the X axis, and the third point on the xy plane.
  5. If the structure of the molecule is close, press X,:guilabel:Y, Z button to shift the surface to be superimposed.
  6. You can display it with Winmostar Viewer by pressing Open Viewer button.

6.20.19. Aggregate multiple files into SDF format

Aggregate and save multiple files into a single SDF file. Aggregate all files contained within the selected folder. Only files that can be opened with Open are read. (Judged by the extension.)