6.19. Tool menu

6.19.1. Preferences

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

6.19.2. Save/Delete Fragment

6.19.2.1. Save Fragment

Same as Save Fragment.

6.19.2.2. Delete Fragment

Same as Delete Fragment.

6.19.3. Enter a structural formula

6.19.4. 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.

6.19.5. 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.

6.19.6. 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/4pi(3V/4pi)**(2/3) Minimum surface area = 4pi(3V/4pi)**(2/3) (surface area of a true sphere having the same molecular volume)

6.19.7. 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.

6.19.8. Radius of Gyration

Calculate the inertial radius of the molecule.

6.19.9. Sterimol Parameters

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

6.19.10. 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.

6.19.11. Job Manager

Start Winmostar Job Manager that manages local jobs.

6.19.12. Submit Remote Job

Open a window to run and manage remote jobs in file mode. See Each function of the Submit Remote Job window for details.

6.19.13. emote Server

Operate remote servers for each profile in project mode.

6.19.13.1. Configure

Configure profile settings.

6.19.14. Cygwin

Start the terminal window (terminal) of CygwinWM.

6.19.15. Log Viewer

Displays the end of a text file (such as a solver’s log file) that is updated in real time. Drag and drop text files into the window.

6.19.16. Unit Converter

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

6.19.17. Search String

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

6.19.18. Superimpose Molecules

Multiple molecules are superimposed and displayed. It is useful for checking the similarity of multiple molecular structures.

  1. Import from Main Window or Import from File button to load the molecular structure you want to display and add it to the list of Structures. You can also drag and drop to load them directly from Explorer.

  2. In the Structures list, click on the filename you want to highlight and the molecule will be highlighted in blue.

  3. Delete selected molecule with Delete button, Reset button to delete all molecules.

  4. You can align the orientation of each molecule with Rotate to align 3 atoms 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 molecular structures are close, adjust the X , Y , and Z values in the Offset to shift the overlapping plane.

  6. If there are only two molecules in the list of Structures, the RMS-Fit All button will automatically rotate the molecules so that the RMS (root mean square of the coordinates) between the two molecules is minimized. Also, the RMS will show the RMS between the two molecules.

  7. You can display it with Winmostar Viewer by pressing Open Viewer button.

6.19.19. 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 File are read. (Judged by the extension.)

6.19.20. Animation

6.19.20.1. Switch to animation

Using this function while no animation is displayed will switch to one frame of animation being displayed.

6.19.20.2. Discard animation

Using this function while animation is displayed will leave only the current frame and switch to no animation being displayed.

6.19.20.3. Add a frame

Duplicates the current frame and adds a new frame to the animation.

6.19.20.4. Delete current frame

Delete current frame for animation

6.19.20.5. Structure scan

Generate and animate a structure with slightly different coordinates and cell sizes.

Transform cell only along the selected axis

Stretch or compress the cell in the direction of the axis selected in Axis. If Variable is Length change, the value is the incremental length (in angstroms); if it is Normal strain, the value is the strain. A value of 0 in either case means that the cell size is the same as the original cell size. If Change Atomic Position with keeping fractional coordinates is checked, the coordinates of each atom will change with keeping the fractional coordinates fixed, if unchecked, the coordinates of each coordinate will remain unchanged.

Transform cell similarly

Deforms the cell in a similar manner. Specify the strain in each axis as a value (e.g., a value of 0.1 will multiply the volume by (1+0.1)^3 = 1.331, a value of -0.1 will multiply the volume by (1-0.1)^3 = 0.729). The coordinates of each atom vary while the fractional coordinates are fixed. Use this when you want to calculate volume strain.

Translate group along selected axis/vector

Translates the coordinates of the selected group in the direction of the axis selected by Axis. The value is the distance to translate (in angstroms).

Min

Specify the minimum value.

Max

The maximum value of the Max value is displayed. The Max is automatically set from Min, Interval and # of steps and cannot be specified directly.

Interval

Specifies the interval between values.

# of steps

Specifies the number of values.

Show Preview

You can see a preview of the animation with your settings.

OK

Generate animation.