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 group on axis (selection 2 atoms, mouse control) 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. Reset Structure

New Project or New File will return to the initial structure when clicked.

6.2.5. Select Element for Editing Ops

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

6.2.6. Add atom by

6.2.6.1. 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 of Toolbar.

Hint

You can also operate with F4 or from Toolbar.

6.2.6.2. 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 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.

6.2.6.3. Adding dummy atoms to the center of gravity of a group

Adds a dummy atom at the specified distance away from the atom with the marker (red bold circle). You can select the direction (axis) to add.

6.2.6.4. Dummy atoms added along selected 2 atoms

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

6.2.6.5. Adding dummy atoms to the center of gravity of a group

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

6.2.7. Delete atom

Delete the atom marked with marker.

Hint

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

6.2.8. Change attributes of atoms

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 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 for the selected atoms.

The optimization flag is a flag that specifies whether each degree of freedom should be fixed (flag is ‘0’) or variable (flag is ‘1’) in the structural optimization calculation. By default, all degrees of freedom are variable (1).

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 value of the charge (User charge) or spin density of the selected atoms. If a group is selected, all group-selected atoms will be affected. If Overwrite is checked, all values of the selected atoms will be overwritten with the input values. If Scale is checked, all values of the selected atoms will be scaled equally.

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.

6.2.8.5. Occupancy

Changes the occupancy of the site where the marked atom is located or the site where the group-selected atom is located. The total value of Occupancy must be 1.

Sites with an occupancy set other than 1 will be treated by Winmostar as if there are multiple atoms in the site. The same is the behavior when a CIF file with Occupancy set is read.

6.2.8.6. Atom Name

Changes the atomic name of the site where the highlighted atom is placed or group selected atoms, affecting read/write in PDB, mol2, and gro formats.

6.2.8.7. Residue Name

Changes the residue name of the site where the marked atom is placed or the group-selected atom, affecting read/write in PDB, mol2, and gro formats.

6.2.8.8. Residue Number

Changes the residue number of the site where the marked atom is placed or group selected atoms, affecting read/write in PDB, mol2, and gro formats.

6.2.9. Move atom

6.2.9.1. Translate

Drag and move marker atom on Viewport.

Hint

You can also operate it with F5.

6.2.9.2. Translate (with hydrogen)

Drag and move the atoms with marker and the hydrogen bonded to them on the Viewport.

Hint

You can also use Ctrl+F5 or Alt + drag.

6.2.9.3. 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.

6.2.9.4. Change Dihedral

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

6.2.9.5. Change fractional coordinates

:ref:Specifies the fractional coordinate of the atom with the marker.

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 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). If a group has been selected, each group-selected atom will be replaced.

Fragment registration and deletion is done via Save Fragment and Delete Fragment.

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 .

The order of fragments can be changed in fragment_list.txt in the user configuration folder ( UserPref ).

6.2.15.1. Save Fragment

Register the molecular structure displayed in the main window as a fragment. Atoms with markers (bold red circles) will be set as connections during the substitution.

6.2.15.2. Delete Fragment

Deletes the registration of a fragment selected by fragment in the Toolbar.

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 group on axis (selection 2 atoms, mouse control)

Rotate the group-selected structure around a vector between two atoms with two markers (red thick circle, red thin circle) as axes by mouse operation.

Hint

You can also operate with Ctrl + R.

6.2.17.2. Rotate group on axis (select 2 atoms, specify values)

Rotate the group-selected structure around a vector between two atoms with two markers (red thick circle, red thin circle), specifying a numerical value.

6.2.17.3. 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.

6.2.17.4. 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.

6.2.17.5. 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.

6.2.17.6. Rotate by Aligning Marked Atoms

Rotates the group-selected structure so that it is oriented with respect to a specific axis or plane.

Align principle axis to target direction
Rotate the inertia spindle so that its major axis points in the specified direction.

Align 2 marked atoms to target direction
Rotate so that the two atoms marked face the specified axis. The two atoms marked must be included in the group-selected structure.

Align 3 marked atoms to target plane
Rotate so that the marked 3-atom is included in the specified plane. The marked 3 atoms must be included in the group-selected structure.

6.2.17.7. Move (Direct)

Move group-selected structure in Viewport.

Hint

You can also operate with Ctrl + M.

6.2.17.8. Move (Numerical)

Translate selected group structure by slider operation or numerical input.

If Definition = Relative coordinate from original position: specify coordinates relative to the position before the move.

If Definition = Relative coordinate between marked atoms: Specifies the relative coordinate between two marked atoms. Before activating this function, you must first click (mark) an atom that is not included in the group of atoms to be moved, then click (mark) an atom whose position relative to the atom you want to specify and that is included in the group of atoms to be moved, and then select the group of atoms to be moved. The group of atoms to be moved must be selected.

If Definition = Absolute coordinate for center of mass: specifies the absolute coordinates for the center of mass of the group.

If Definition = Absolute coordinate for center of geometry: Specifies the absolute coordinates for the geometric center of the group.

6.2.17.9. Quick Optimization

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

Hint

You can also operate with Ctrl + L.

6.2.17.10. Creates bonds between adjacent atoms in a group

Automatically generates bonds between neighboring atoms in the group-selected structure. Adjacency is determined by Voronoi splitting.

Hint

You can also operate with Ctrl + L.

6.2.17.11. Cut

Cut the group-selected structure to the clipboard.

Hint

You can also operate with Ctrl + X.

6.2.17.12. Copy

Copy the group-selected structure to the clipboard.

Hint

You can also operate with Ctrl + C.

6.2.17.13. Paste

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

Hint

You can also operate with Ctrl + V.

6.2.17.14. 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.

6.2.17.15. 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.

6.2.17.16. Change Optimization Flags of Group

groupSet the optimization flags for all components of the XYZ coordinates of the selected structure to 0 (fix) or 1 (free). See Optimization Flags for more information on the optimization flags. For more fine-grained control, choose edit ‣ change attribute ‣ Optimization Flags.

Hint

You can also operate with Ctrl + I.

6.2.17.17. Fix/Unfix Groups (Z-Matrix)

Sets the optimization flags of all components of Z-Matrix for the group selected structure to 0 (fix) or 1 (free). See Optimization Flags for more information on the optimization flags. For more fine-grained control, choose edit ‣ change attribute ‣ Optimization Flags.

6.2.17.18. 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.

6.2.17.19. Average the group’s charge

Corrects the sum of the point charges that a group-selected structure has to their average value. This is useful if you want to average the charges of equivalent atoms (e.g. the three hydrogen atoms of a methyl group) after running Use RESP charges or RESP Charges.

6.2.18. Automatically Adjust Atoms/Bonds

6.2.18.1. Quick Optimization

We will perform structure optimization using molecular force field.

The algorithm used can be changed with Tools ‣ Preferences menu.

If the method is “Winmostar”, the algorithm used in Winmostar before V10 is used. The number of applicable atoms is limited, but the process is faster.

If the method is “OpenBabel”, the OpenBabel installed in CygwinWM is used. Although the process is slower, there is no limit to the number of atoms that can be applied, and parameters such as the type of force field can be finely tuned.

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. Delete all bonds

Delete all bonds.

6.2.18.5. Regenerate Z-Matrix

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

6.2.18.6. Convert Aromatic Rings to Single and Double Bonds

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

6.2.18.7. 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.

6.2.18.8. Assign different residue numbers to each molecule.

Assign a different residue number to each molecule. A group of atoms connected by bonds is recognized as a molecule.

6.2.18.9. Assign different residue numbers to each molecule.

Assign a different residue number to each molecule. A group of atoms connected by bonds is recognized as a molecule.

6.2.18.10. Remove all optimization flags

Set the optimization flags for all atoms to their default (variable) values.

6.2.18.11. Overwrite Bonds from File

Overwrites the bond information for the current structure with the bond information for the structure written in the specified file.

If the bond order changes from the order before force field assignment after force field assignment in MD calculations (LAMMPS, Gromacs, etc.), save a file in mol2, wmm, etc. format before force field assignment and load the file with this function after force field assignment, and the bond order will be restored to the one before force field assignment. If you save the file in mol2, wmm, etc. format before force field assignment, and then load the file with this function after force field assignment, you can restore the bond information before force field assignment. This function is useful in cases where a force field has been assigned once and an MD calculation has been performed, but the bond order has changed since the initial force field assignment and the force field cannot be assigned again.

The bond order after force field assignment is determined by Winmostar’s criterion based on the bond equilibrium length of the assigned force field, so the aforementioned phenomenon occurs for some types of force fields.

6.2.19. Renumber/Sort

6.2.19.1. Exchange Between 2 Marked Atoms

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

6.2.19.2. Sort by H atoms and Others

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

6.2.19.3. Sort by Molecular Species

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

6.2.19.4. Renumber Across Each Molecule

Number the molecules sequentially from the end within the molecule. This is useful, for example, when selecting both ends of a polymer.

6.2.20. Adjust Axes

6.2.20.1. 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.

6.2.20.2. 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.

6.2.20.3. 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.

6.2.20.4. Set Origin to Marked Atom

Set atoms with markers as origin.

6.2.20.5. Set Origin to Lower Bound Edge of Cell

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

6.2.20.6. Swap Axes

Swap the axes and recreate the coordinate system.

6.2.21. Invert Coordinates/Chirality

6.2.21.1. Invert along X/Y/Z/a/b/c Axis

Inverts the specified axis and recreates the coordinate system.

6.2.21.2. Generate Enantiomer

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

6.2.22. Create/Edit Cell

6.2.22.1. Create/Edit Cell

Create the simulation cell

Set Margin 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.

6.2.22.2. 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.

Check Transform by angle if you want to change the angle of a cell. Specify the type and value of the angle to be transformed.

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.

6.2.22.3. 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 Lattice 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 Transform Cell.

If you want to return atoms outside the simulation cell to the simulation cell before editing, use the Wrap Around Cell Boundary function.

6.2.23. Delete Cell

Delete Cell.

6.2.24. 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.

6.2.25. Edit Charge

Edit the value of the charge. Specify the type of charge and set it to user charge. You can also delete specified charges. It can be adjusted so that the total charge is at a specific value.