StructureEditor
Introduction
The StructureEditor plugin shows the loaded molecules in hierarcical tree.
The window is divided to two panes: Left listing every top-level object, and
Right showing a tree for one selected top-level object. Data read from one file
forms usually a top-level object. Alignments are also top-level objects.
Basic operations
Mouse:
- Over List:
- Left Button: Select, show on tree
- Middle Button: Delete object
- Rigth Button: Show object property menu
- Over Tree:
- Left Button on branch-arrow: Expand/Close subtree
- Left Button elsewhere: Select object, removing previous selections
- Left Button dragging: Select range of objects
- Left Button + Ctrl: Select object and keep previous selections
- Left Button + Shift: Select objects in range from previous current item
- Middle Button: Delete objects (not on root item)
- Rigth Button on Object: Show object property menu
- Rigth Button on Show: Toggle Visibility (global to Graphic views)
- Rigth Button on Select: Toggle Selection of one object
- Rigth Button on Partial: Toggle Partial selection of one object
The shortcut keys:
- F: Change atoms of selected residues to use the first 'Model' of coordinates
- P: Change atoms of selected residues to use the previous 'Model' of coordinates
- N: Change atoms of selected residues to use the next 'Model' of coordinates
Menus
- File
- Select
- Clear: Remove selection in current tree.
- Invert: toggle selection for every atom in current tree.
- Full groups: Select completely each group, that has at least one selected atom.
- Within rad: Select all atoms within radius from currently selected atoms.
- All Fgroups: As Full groups, but for all trees, not just current one.
- Any w/ rad: As Within rad., but from all trees, not just current one.
- Atoms by type: Asks for atom type, and selects atoms of that type.
- Nearby Grids: Adjust shown region of each grid to enclose
only the currently selected atoms. Useful for making a
subsurface for part of a molecule from an existing grid.
- Query: Show a query definition dialog.
- Display
- Hide: selected objects (Note: hiding a Surface hides its atoms, try Render:Shape:None instead).
- Hide unselected: objects
- Hide All unsels: unselected objects also in other trees.
- Show: selected objects
- Set color: Ask the user a new color for selected objects
- Color by Temp: Color selected atoms by their temperature factor (from PDB)
- Default color: restore the default color of selected objects
- Modify
- FirstModel: change selected model in selected residues.
- Prev Model: change selected model in selected residues.
- Next Model: change selected model in selected residues.
- Colour Atoms by Residue: change color of atoms in selected residues to match
the color of the residue.
- Add
- Rotamers: Call Rotamer-plugin to add alternative
coordinates from rotamer-library to selected amino acids.
- ContourHi: Call Volume-plugin to create a contour to each
selected Grid, enclosing space with higher-than-threshold values.
- ContourLo: Call Volume-plugin to create a contour to each
selected Grid, enclosing space with lower-than-threshold values.
- ConnollySurface: Call Volume-plugin to create a Connolly
molecular surface to each selected chain.
- ElectronDensSurf: Call Volume-plugin to create a surface
to each selected chain EXPERIMENTAL.
- GaussianSurface: Call Volume-plugin to create a surface
to each selected chain EXPERIMENTAL.
- VdWaalsSurface: Call Volume-plugin to create a Van der
Waals surface to each selected chain.
- SolAccesSurface: Call Volume-plugin to create a solvent
accessible surface to each selected chain.
- SubSurface: like ContourHi, but creates a surface and maps
atoms to it.
- Set: define a named set from currently selected objects.
- Cartesian: Create three 20 Å lines representing the xyz axis of the Cartesian coordinate system.
- MapGrid2Surface: Call Potential-plugin to map values from one grid to one surface.
- Delete
- Tree: Delete currently shown tree.
- Chain: Delete currently selected chains from the shown tree.
- Group: Delete currently selected groups (residues and ligands) from the shown tree.
- Residue: Delete currently selected amino acids from the shown tree.
- Atom: Delete currently selected atoms from the shown tree.
- Bond: Delete currently selected bonds from the shown tree.
- Grid: Delete currently selected grids from the shown tree.
- Surface: Delete currently selected surfaces from the shown tree.
- All: Delete all data objects from Bodil.
- Help: Show this help
The Query dialog
The query dialog lets the user to define regular expressions for chain, residue and atom. The action buttons
will then perform such query on the current tree, selecting and deselecting atoms.
- Union: Keep current selections and select matching atoms.
- Intersection: Keep current selections if they match the criteria.
- Difference: Keep current selections if they do not match the criteria.
Note: Residues in polypeptide chains use three-letter name of the amino-acid combined with a Sequence
identifier. The sequence identifier contains a integer number and an insertion character, which is usually
a whitespace. The regular expression must take this into account.
Configuration file entries
Section Key Valuetype
Description
Contents