6.2. Edit menu

It is a menu related to modeling function of atomic/molecular structure.

See Select menu for how to select atoms to be edited.

Automatically generated bonds are generated when the interatomic distance is less than (sum of covalently bonded radii) × (coefficient). The coefficient defaults to `` 1.15``, and this value can be changed with Tools ‣ Preferences .

Functions with mouse operations such as Add atom by, Rotate Around Axis(2 Marked Atoms) can be canceled by unchecking the Esc key or the menu of the same function.

6.2.1. Undo

Revert various editing operations. It is possible up to 50 times.

6.2.2. Redo

Redo the undone operation. It is possible up to 50 times.

6.2.3. Undo text

Restore the edited contents in keyword display area.

6.2.4. Select Element for Editing Ops

Select element to be applied in Add atom by or Element .

6.2.5. Add atom by

6.2.5.1. Specifying Position

Add atoms to the position you click in Viewport. The types of atoms to be added are selected by Select element for editing ops pull-down menu chg of Toolbar.

Hint

You can also operate with F4 or from Toolbar.

6.2.5.2. Specifying Position and Connectivity

Add atom by specifying joint relation and coordinate in Z-Matrix format at the same time. The types of atoms to be added are selected by Select element for editing ops pull-down menu chg of Toolbar. First click on the place where the atom is placed, then click on three connecting atoms (Na, Nb,Nc) in Z-Matrix notation in order.

6.2.6. Delete atom

Delete the atom marked with marker.

Hint

You can also operate it with Shift + F4 or Toolbar.

6.2.7. Move atom

6.2.7.1. Translate

Drag and move marked atom on Viewport.

Hint

You can also operate it with F5.

6.2.7.2. Translate While Keeping Z-Matrix

Drag and move the atom with marker and the atom connected with Z-Matrix on the Viewport at the same time. Suitable for movement by functional group.

6.2.7.3. Change Dihedral

Drag and move the atom with marker on the Viewport. Only the dihedral angle of Z-Matrix changes.

6.2.8. Atom Properties

6.2.8.1. Element

The element of the selected atom is changed to the element selected by the Select element for editing ops pull-down menu chg in the Toolbar. If a group is selected, all atoms selected in the group are targeted.

Hint

You can also operate with Chg button of Shift + F5 or Toolbar.

Note

Lp 0 is a Lone pair, Cb 104 is a Capped bond used to cut out a molecular structure in MOPAC, ++ 105 to -108 is a MOPAC sparkle, Tv 109 is a MOPAC translation vector , Xx 110 through Z 112 means the dummy atom of each solver.

6.2.8.2. Optimization Flags

Changes the optimization flag of the selected atom. If a group is selected, all atoms selected in the group are targeted. If General is selected in Solver, the selected flag for X, Y, and Z is set as it is. If a specific solver is selected in Solver, the corresponding flag will be set for each.

Warning

In the case of OpenMX, if 0 is displayed on the Coordinate Viewer, 1 is displayed when saving the file, and conversely 1 is displayed, the output is 0. In other words, the operation follows the `` Variable`` and `` Fixed`` notation of this function.

6.2.8.3. Charge/Spin Density

Changes the charge (User charge) or spin density value of the selected atom. If a group is selected, all the atoms selected in the group will be covered.

Note

If you want to display User Charge or Spin Density on the main window, select User Charge or Spin Density of View ‣ Labels/Charges.

6.2.8.4. Connectivity

Click on the three connecting atoms (Na, Nb, Nc) in the Z-Matrix of the atom with the marker in order to set again.

6.2.9. Add Dummy Atom

By effectively arranging dummy atoms, it is possible to increase the efficiency of structure optimization calculation and IRC calculation using Z-Matrix, or to avoid errors derived from Z-Matrix.

6.2.9.1. Along 2 marked atoms

Add a dummy atom on a straight line passing through two atoms with markers (red round, red circle).

6.2.9.2. To Center of Mass of Selected Group

Group Add dummy atoms to the position of the center of gravity of the selected structure.

6.2.10. Add/Change Bond

A bond is created between two atoms with markers (red round, red circle). If it has already been created, the type of join is changed. As types of bonds, single, double, triple, aromatic ring (1.5-fold), red are defined as 5. Please use red coupling for presentation and other purposes.

Hint

you can also operate with F7 or Toolbar.

6.2.11. Delete Bond

Delete the bond between 2 atoms with markers (red round, red circle).

Hint

You can also operate with F8 or Delete bond button of Edit button area.

6.2.12. Add Hydrogens

Make up for missing hydrogen atoms. If you import a file whose bond distance is extremely different from the original equilibrium length (such as ChemDraw or PubChem mol format), you may not be able to add hydrogen normally. In that case, please use Edit ‣ Automatically Adjust Atoms/Bonds –> Adjust All Bond Lengths.

6.2.12.1. To all atoms

Automatically adds hydrogen to all atoms. If atoms are group selected, hydrogens are added only to the atoms.

Hint

You can also operate with Ctrl + H.

6.2.12.2. To marked atoms (Auto)

Add hydrogens to the markered atom. If atoms are group selected, hydrogens are added to the atoms.

Hint

You can also operate with + H button of Toolbar.

6.2.12.3. To marked atoms (Single), (Double), (Triple)

Add one to three hydrogens with markers to the atoms. If atoms are group selected, hydrogens are added to the atoms.

6.2.12.4. Using pdb2gmx

Use the Gromacs gmx pdb2gmx command to automatically add hydrogen to proteins read from pdb or gro files. If the original pdb or gro file contains atoms that do not have amino residue information, the process will fail. An intermediate file is created in a working folder called * _protonate_tmp.

Note

If the structure displayed in the main window contains molecules other than proteins such as ligands and solvents, delete them with Select ‣ Select by Molecular Species and Edit ‣ Modify Selected Group ‣ Delete in advance.

Warning

To use this function, CygwinWM setup is required.

6.2.12.5. Using OpenBabel

We will automatically add hydrogen using OpenBabel. It is mainly used for ligand molecules cut out from pdb file. An intermediate file is created in the working folder named * _protonate_tmp.

Note

If the structure displayed in the main window contains molecules other than proteins such as ligands and solvents, delete them with Select ‣ Select by Molecular Species and Edit ‣ Modify Selected Group ‣ Delete in advance.

Warning

To use this function, CygwinWM setup is required.

6.2.13. Delete All Hydrogens

Delete all hydrogen atoms.

6.2.14. Replace with Fragment

Replaces Marked atoms (thick red circles) with the parts (substituents) selected with the Fragment to be replaced with pull-down menu repl on the Toolbar. In the pull down menu, - CHCH - and - CH - are parts for making a polycyclic structure, which are generated to point in the direction of the atom with the second marker (thin red circle).

Hint

You can also operate with F6, Replace button, or by right-clicking an atom.

6.2.15. Select Fragment

Select the fragment to be replaced with Replace with Fragment .

6.2.16. Build Ring

When selecting the same function with markers (thick red circle, fine red circle) attached to 2 atoms at both ends of the connected 4 atoms, it generates aromatic rings containing the 4 atoms in the skeleton.

Hint

You can also operate it with F9.

Hint

For example, if you move a marker to H on both ends of the HCCH portion of a benzene molecule and call this function, a naphthalene molecule will be created.

6.2.17. Modify Selected Group

Do the operation on the atom for which group selection (blue circle) was performed.

6.2.17.1. Rotate Around Axis(2 Marked Atoms)

Rotate a group-selected structure around a vector between two atoms with two markers (red circle, red circle)

Hint

You can also operate with Ctrl + R.

6.2.17.2. Rotate Around Axis(3 Marked Atoms)

Rotate the group selected structure around the normal vector of the plane defined by three atoms with a marker (These can be confirmed by top left Marked Order on Viewport).

Hint

You can also operate with Ctrl + A.

6.2.17.3. Rotate Group Around Marked Atom

Rotate group-selected structure around the atom with marker (thick red circle).

Hint

You can also operate with Ctrl + F.

6.2.17.4. Rotate (Numerical)

The structure group selected is rotated around the atom or geometric center marked with marker (red circle) by slider operation or numerical input. Specify the Euler angles.

Hint

You can also operate with Ctrl + F.

6.2.17.5. Rotate by Aligning Marked Atoms

Rotates group selected structures to orient to a specific axis or plane. 2 atoms with markers, if oriented in a specific axis, or 3 atoms. if oriented in a specific plane, must be included in the group selected structure (It can be confirmed by Marked Order: in the upper left of Viewport).

6.2.17.6. Move (Direct)

Move group-selected structure in Viewport.

Hint

You can also operate with Ctrl + M.

6.2.17.7. Move (Numerical)

Translate selected group structure by slider operation or numerical input.

6.2.17.8. Quick Optimization

We will optimize structure using molecular force field for group selected structure.

Hint

You can also operate with Ctrl + L.

6.2.17.9. Cut

Cut the group-selected structure to the clipboard.

Hint

You can also operate with Ctrl + X.

6.2.17.10. Copy

Copy the group-selected structure to the clipboard.

Hint

You can also operate with Ctrl + C.

6.2.17.11. Paste

Paste the group-selected structure from the clipboard. After pasting, drag to determine the position.

Hint

You can also operate with Ctrl + V.

6.2.17.12. Replicate Group

Duplicate and arrange the group-selected structures at regular intervals. Specify the arrangement interval and number of copies in each direction in the subwindow.

6.2.17.13. Delete

Delete the group-selected structure or any other structure. When a part of the structure in the molecule is deleted, hydrogen atoms are automatically supplemented to the disconnected part.

Hint

You can also operate with Ctrl + D.

6.2.17.14. Change Optimization Flags of Group

Set the optimization flag of all components of the group-selected structure to `` 0`` (fix) or `` 1`` (free). If you want to control more finely, select Edit ‣ Change Atom Property ‣ Optimization Flags.

Hint

You can also operate with Ctrl + I.

6.2.17.15. Shift Charges of Group

The total point charge of the group-selected structure is uniformly shifted to the specified value. This function is useful when you want to reduce the total system charge to 0, such as when performing MD calculations.

6.2.18. Automatically Adjust Atoms/Bonds

6.2.18.1. Quick Optimization

We will perform structure optimization using molecular force field.

Hint

You can also operate with Ctrl + G.

6.2.18.2. Regenerate All Bonds

Determine the presence and type of bonds from interatomic distances and reassign the bonds.

6.2.18.3. Adjust All Bond Lengths

Adjust the coupling length to a reasonable value to some extent.

Hint

Please use this function with Quick Optimization, if necessary.

6.2.18.4. Regenerate Z-Matrix

Automatically regenerate Z-Matrix. Connection atom is also set automatically.

6.2.18.5. Convert Aromatic Rings to Single and Double Bonds

Change the aromatic ring bond to a combination of a single bond and a double bond.

6.2.18.6. Change unknown elements to hydrogen.

Change the atoms recognized as Lp or dummy atoms to hydrogen.

Hint

This is useful, for example, for converting deuterium to hydrogen in a CIF file.

6.2.19. Change Distance/Angle Between Marked Atoms

Enter and change the distance, angle, or dihedral angle between 2 and 4 atoms with markers (red circles) (you can check with the Marked Order: at the top left of Viewport).

6.2.20. Renumber/Sort

6.2.20.1. Exchange Between 2 Marked Atoms

Exchange the numbers of the two atoms with the marker. It is mainly used when editing Z-Matrix.

6.2.20.2. Sort by H atoms and Others

Arrange the atom numbers so that they are in the order of atoms other than hydrogen, hydrogen atoms.

6.2.20.3. Sort by Molecular Species

We will rearrange the order of the atoms so that molecules of the same kind are continuous.

6.2.21. Adjust Axes

6.2.21.1. Set to Camera Coordinate

Redefine the molecule by redefining the current direction of the camera's line of sight as Z axis, the camera upward direction as Y axis, and the camera right direction as X axis.

6.2.21.2. Set Using 3 Marked Atoms

The normal direction of the plane passing through the three atoms with the marker is taken as the Z axis, and the vector passing through the two atoms with the marker is taken as the X axis.

6.2.21.3. Set to Principal Axes

Rotate the entire system so that the principal axis of inertia matches the X, Y, Z axes. The long axis is the X axis.

6.2.21.4. Set Origin to Marked Atom

Set atoms with markers as origin.

6.2.21.5. Set Origin to Lower Bound Edge of Cell

Rewrite the coordinate system so that the cell's origin coordinates are (0, 0, 0).

6.2.21.6. Swap Axes

Swap the axes and recreate the coordinate system.

6.2.21.7. Invert X/Y/Z Axis

Inverts the specified axis and recreates the coordinate system.

6.2.22. Chirality

6.2.22.1. Invert Chirality

Convert the molecular structure displayed in the main window to an enantiomer. The sign of the x coordinate is inverted.

6.2.22.2. Generate Enantiomer

Generate an enantiomer of the molecular structure displayed in the main window adjacent to the current structure.

6.2.23. Create/Edit Cell

6.2.23.1. Create/Edit Cell

Create the simulation cell

  • Set Distance is checked, it creates cell borders at a specified distance from the minimum and maximum values for each direction of the molecular structure shown in the main window. If Use Cubic Cell is checked, a cubic cell will be created.
  • :guilabel:If Set Dimension is checked, a cell with the specified size cube will be created.

6.2.23.2. Transform Cell

1. How to transform cell specifies how to transform the cell.

  • Check the Transform only along the selected axis if you want to deform the cell only along the selected axis. Check Set incremental length for length, Set total length for size after deformation, or Set normal strain for vertical strain. or Set density to specify the deformed density.
  • If you want to transform a cell similarly, check Transform similarly. Enter the target density after the transformation in Target Density.
  • Check Transform by shear strain if you want to apply a shear strain. Specify the direction to be deformed and the strain to be applied.

2. Atomic positions specifies how to move atoms.

  • Check Do not change if you want to keep the position of the atoms and only change the cells.
  • If you want to change the position of the atoms fixed as the cell is deformed, check the Move with keeping fractional coordinates checkbox. For molecular systems, check Keep intramolecular coordinates, then intramolecular coordinates are kept fixed.

6.2.23.3. Edit Cell Manually

The Create/Edit Cell window opens, where you can create or edit simulation cells such as MD calculations and plane wave DFT calculations. If the cell does not exist, clicking the Create button creates a cell at a distance of` Distance` from the minimum and maximum values in each direction of the molecular structure displayed in the main window. Click the Expand button to expand the cell size in the specified direction. On the right side of the Create/Edit Cell window, you can edit the cell size value directly. Click Box Vecors, Lattice Constants, LAMMPS Tilt Factors to change the cell size notation.

Note

  • You can also display the lattice parameters in the Viewport by checking Preferences ‣ View ‣ Items to be drawn ‣ Lattice constant.
  • Even if you change the cell size with this function, the coordinates of the atoms do not change, so if you want to change atomic coordinates similarly to the cell size, use Change Density.
  • If you want to return atoms outside the simulation cell to the simulation cell before editing, use the Wrap Around Cell Boundary function.

6.2.24. Delete Cell

Delete Cell.

6.2.25. Wrap Around Cell Boundary

We return the coordinates of the atoms outside the simulation cell into the cell taking into account the period boundary. Mainly in molecular systems Wrap for each molecules, mainly in inorganic systems Wrap for each atoms.

Note

  • If Display-> Wrap Around Cell Boundary ‣ Do not wrap is selected, it will be easier to check the change of coordinates.
  • In tne Display ‣ Wrap Around Cell Boundary function, only the display changes and the coordinates do not change, but in this function the coordinates actually change.

6.2.26. Change Density

Specify to change the density and simulatively expand or shrink simulation cell and atomic coordinates. The coordinates of each atom are scaled with respect to the center of gravity of the molecule, and the relative position within the molecule does not change.

6.2.27. Edit Charge

Specify the type of charge and set it to user charge. You can also delete specified charges.