Change Atom Properties Panel

Change atom and residue properties. The changes are applied to the selected atoms, in most cases, but some changes are applied to the entire Workspace.

To open this panel, do one of the following:

  • right-click in the selection and choose Additional Edits → Change Atom Properties
  • click Other Edits in the 3D Builder panel and choose Change Atom Properties from the menu
  • click the Tasks button and browse to Workspace Operations → Change Atom Properties
  • Using
  • Features
  • Additional Resources

Using the Change Atom Properties Panel

This panel allows you to choose an atom or a residue property and change the values of that property for the atoms that are selected in the Workspace. The basic procedure is:

  1. Select the atoms in the Workspace.
  2. Choose the property from the Property option menu.
  3. Make the appropriate changes or selections with the tools that are displayed.
  4. Click Apply.

You can choose several properties and make settings for each before clicking Apply, thus making multiple changes to a single selection. Whenever you change a setting, the Apply button is activated.

You can change the selection in the Workspace while this panel is open. The Apply button is reactivated when the selection changes. This allows you to change properties for multiple atom selections. Once you close the panel the settings are cleared, so you should apply them to all desired atoms while the panel is open.

If you make settings for multiple properties, there is a risk of inadvertently make changes you did not intend. For example, you could change your structure if you have an atom type selected for the Atom Type (MacroModel) property and do not clear it before making settings for other properties or applying the settings to other atom selections. The settings are all cleared when you close the dialog box, and can be cleared manually with the Reset All button.

If you do make a mistake, you can undo the changes with Ctrl+Z (⌘Z) or Edit → Undo.

 

Change Atom Properties Panel Features

Property option menu

The Property menu lists specific properties that can be changed, and provides a general editing mechanism for any atom property. Each choice displays a set of tools in the lower part of the tab.

Property-dependent tools

The tools for changing properties depend on the property chosen. They are listed below for each property.

Residue / Chain Name

These tools allow you to set a few residue and chain properties.

Residue name option and text box

Select this option to change the residue name, and enter the new name in the text box. The name is applied to the selected atoms.

Chain name option and text box

Select this option to change the chain name, and enter the new name in the text box. The name is applied to the selected atoms.

Residue numbers option

Select this option to change residue numbers. There are two choices:

  • Renumber selected residues—Renumber the residues in the selection sequentially, starting from the lowest residue number found in the selection. Enter the starting residue number for the renumbering in the Starting number text box. This number is applied to the lowest-numbered residue in the selection, and is incremented by 1 for the next lowest, and so on. Any residue that has one or more atoms in the selection is renumbered, and the renumbering is applied to the entire residue (not just the selected atoms in the residue).

  • Apply residue number—Apply the specified residue number to all atoms in the selection. The renumbering does not apply to atoms in the same residues that are not selected. Enter the number in the New number text box.

Partial Occupancy

These tools allow you to set the occupancy for parts of the structure that occur in different conformations in the crystal structure. You can set partial occupancies for more than one set of atoms in the structure, but for each set of atoms, only two states are allowed, labeled A and B. Once you have set the partial occupancies for a set of atoms, Maestro creates a duplicate set of coordinates for the B state for these atoms. Initially, these coordinates are the same as for the A state.

Occupancy table

Lists all atoms that have been selected for assignment of partial occupancy, along with the occupancy of the B (alternate) state. You can edit the table cells to change the B occupancy. You can select multiple table rows to clear the occupancy or to expand the atom list.

Expand selection to buttons

Expand the atom list to complete the residues or side chains.

  • Residue—Include all atoms in residues to which the selected atoms belong.
  • Side chain—Include all atom in side chains to which the selected atoms belong.
Clear and Clear All buttons

Clear the partial occupancy data for the atoms selected in the table, or for all atoms in the table. When you click OK, the occupancy data is removed, and these atoms no longer have partial occupancy.

Set all B occupancies to text box and Set button

Enter the occupancy value for the B state in this text box, and click Set to apply the value. All atoms in the B state for this atom set must have the same occupancy. If any atoms had a previously assigned occupancy, this value is assigned to the other atoms when the dialog box is opened.

Atom Type (MacroModel)

MacroModel atom type symbols describe the bonding, hydrogen atom and lone electron pair configuration around an atom. Each type of atom is appropriate only for certain force fields. When you choose Atom Type (MacroModel) from the Property menu, a list of MacroModel atom types with their descriptions is displayed. To retype the selected atoms, select an atom type from the list, then click Apply to apply the changes. The atom types are listed in MacroModel Atom and Bond Types.

Warning: Setting the atom type also sets the atomic number and formal charge. If you apply an atom type to an atom of a different element, it is changed to the new element. It is strongly recommended that you clear the selected atom type (use control-click or use Reset All to clear all settings) before making other property changes or changing the atom selection, as clicking Apply applies all settings to the selection.

Partial Charge

These tools allow you to set both the partial charge and the solvation charge. The partial atomic charge is used in the electrostatic part of molecular mechanics calculations, and the solvation charge is used by MacroModel in GB/SA solvation calculations. In most circumstances, these should be the same value. To set the charges for the selected atoms, enter values in the text boxes, then click Apply to apply the changes.

PDB Atom Name

These tools allow you to set PDB atom names and assign unique PDB atom names within residues. Only the first four characters of the atom name are used when you set the name. To set the name for the selected atoms, select Apply PDB atom name, enter a name in the text box, then click Apply to apply the changes.

According to the PDB standard, the first two characters should contain the element symbol, right-justified; the third character is a remoteness indicator (A=alpha, B=beta, G=gamma, etc.), and the fourth is a numeric branch designator, if applicable. So, a generic carbon atom should be _C__ with the _ characters indicating spaces. A peptide alpha carbon should be _CA_, and not CA__ which is interpreted as a calcium atom.

To apply unique PDB atom names within selected residues, select Set unique PDB atom names within residues, then click Apply to apply the changes. The unique names are composed of the element symbol, right justified in the first two characters, followed by a numeric index for that element. The names are only unique within each residue.

Grow Name

Grow names are used when defining new fragments for the builder. Only the first four characters of the grow name are used. To set the grow name, enter the name in the Grow name text box and click Apply to apply the changes.

Atom Name

You can use the tools in this section to set atom names, to define and assign canonical names, and to assign unique atom names. Canonical names and unique names are applied to all atoms in the Workspace, and cannot be applied to selected atoms.

Atom name text box

To apply a specific name to selected atoms, enter the name in the text box, then click Apply to apply the changes. The name can be of any length. It cannot contain a ~ (tilde) character, as this character is used to make unique names.

Canonical names section

Assign canonical names based on a predefined composition. This action is applied to all atoms in the Workspace structure, not just to the selection.

Composition option menu

Choose the composition of the canonical name from this option menu.

Separator text box

Enter a separator of up to 4 characters in the text box (if you want to change it from the default of a space). The separator must not contain a ~ (tilde) character.

Apply to All Atoms button

Assign canonical names to all atoms in the Workspace.

Modify existing names section

Modify the atom names of all atoms in the Workspace as necessary to make them unique.

Make Unique button

Ensure that all atoms in the Workspace have unique names. If an atom has no name, the default canonical name consisting of the element and atom number is used; if two or more atoms have the same name, a numeric suffix followed by a tilde '~' character is used to distinguish them from each other.

Isotope number

These tools allow you to set the isotope number (mass number) for one or more atoms. You can specify the isotope in the text box, then click Apply to apply the changes. The isotope number is used in calculations of molecular weight.

The isotope can be displayed in an atom label in two ways. If you choose the Isotope number property to include in the atom label, it is displayed as atom-isotope, e.g. C-13. If you choose the mass number property, only the mass number is displayed. For hydrogen, you can set a preference to display the element label as H, D, or T, depending on the isotope number, under Atom Labels in the Preferences panel.

Other

When you choose Other, the tools that are displayed allow you to change the values for any of the properties that do not have special editing tools. To edit one or more properties, select them in the Properties list. These properties are added as columns to the Atoms table. The selected atoms are listed in the Atoms table by atom number, and the property columns are populated with the values. To change a property for an atom, you can edit the table cell. To set the value for multiple atoms, select the atom rows in the table, edit one of the table cells, and press Ctrl+ENTER (⌘ENTER) to apply the change to the selected rows.

If you want to delete property values for all atoms in the Workspace, choose the properties from the Property list and click Delete. The property values are removed from all atoms in the Workspace (not just those in the table), and the property is removed from the Atoms table.

If you want to add an atom-level property to the selected atoms, click Add. The Add Property dialog box opens, in which you can select the type, name the property, and provide an initial value. The property is added to the Properties list and as a column to the Atoms table, and the values are added to the selected atoms.

Reset All button

Reset all settings for all properties to their defaults, i.e. no changes to the property values.

Apply button

Apply the changes to the atoms or residues that are selected in the Workspace. You can change the atom selection and click Apply again to apply the changes to a new selection. The button is disabled after clicking, and the Cancel button changes to Close. It is enabled again (and the Close button reverts) when you change the atom selection or make another property setting. Clicking Apply does not change any of the panel settings.

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