GraphicsView
Introduction
The GraphicsView plugin uses OpenGL graphics to show the molecules
in 3-D. The user may have more than one window open, thus having
simultaneously different views.
The main functions are the change of viewpoint and selection.
Thus, the user can look the molecules from different angles and select
atoms for some operation. The operations provided by the View are a
change of rendering mode, i.e. to draw the molecule in different way,
and Molecular transformation. The transformation moves and rotates selected
chains by changing the actual coordinates. Thus, one molecule can be interactively
moved relative to another, or a ligand can be moved relative to protein.
This transformation and addition of bonds are the only real data changing operation currently available.
The stereo mode uses hardware stereo, if available, and is globally
on or off for all windows.
Basic operations
Mouse has three events: Click, DoubleClick, and Drag. These are used in following manner:
- Left Button + event: Pick mode specific operation, see below.
- Middle Button + Drag (x,y): Translate along x,y.
- Rigth Button + Drag (x,y): Rotate around y,x.
- Left + Middle Button + Drag (y): Translate along z.
- Left + Rigth Button + Drag (y): Rotate around z.
- Middle + Rigth Button + Drag (y): Zoom.
- Shift + Middle + Rigth Button + Drag (x): Slab.
- Middle Button + DC: Return to original Zoom + Slab.
- Rigth Button + DC: Return to original Transform.
The Left button operations:
- PICK + Click: Toggle selection of pointed atom.
- PICK + DC (on atom): Toggle selection of whole residue with the pointed atom.
- PICK + DC (miss): Deselect all.
- PICK + Drag: Create sphere and toggle all atoms within it.
- PICK + Shift + Click: Show the property menu of pointed atom.
- CENTER + Click: Center view to pointed atom.
- CENTER + DC (miss): Center view by all atoms.
- ERASE + Click: Set pointed atom invisible.
- ERASE + Drag: Create sphere and set all included atoms invisible.
- INV_ERASE + Drag: Create sphere and set all unincluded atoms invisible.
- DISTANCE + Click: Add pointed atom to distance measurement object (2 atoms).
- ANGLE + Click: Add pointed atom to angle measurement object (3 atoms).
- TORSION + Click: Add pointed atom to torsion measurement object (4 atoms).
The shortcut keys:
- F5: Use mono graphics (default)
- F6: Use side-by-side view
- F7: Use hardware stereo, if available
- L: Change to local transform mode
- M: Change to molecular transform mode
- G: Change to global transform mode
- ArrowUp: Rotate 90 degrees aroud X ccw
- ArrowDown: Rotate 90 degrees aroud X cw
- ArrowLeft: Rotate 90 degrees aroud Y ccw
- ArrowRight: Rotate 90 degrees aroud Y cw
Menu options
- File: Misc operations.
- Print: Save framebuffer as a PNG-file
- Freeze: Add Camera transformations to all atoms and reset camera.
- Clear measures: Remove all Distance, Angle, and Torsion-angle objects
- Push: Copy current render mode of objects into main data structure.
- Exit: Close this View
- Add: Create objects.
- Bond: Create chemical bonds from existing Distance measures.
- Surface: Call plugins to compute surfaces for selected atoms.
- Mouse: Select mouse operation mode.
- Pick: Select
- Center: view to pointed point
- Hide: Hide (set invisible) every picked atom.
- Keep: Hide everything but picked atoms. (Sphere-selection recommended)
- Distance: between two points
- Angle: of three points
- Torsion: angle in four point system
- Render: Change rendering mode of selected objects.
- Atom: Change rendering mode of selected atoms and bonds.
- None
- Wireframe
- Stick
- Ball-and-Stick
- CPK
- Chain: Change rendering mode of selected chains.
- None
- Ca-trace
- Schematic secondary structure
- Opaque surface
- Transparent surface
- Shape: Change rendering mode of other selected shapes.
- None
- Dots
- Wire
- Opaque surface
- Transparent surface
- Label mode: Change labeling mode of selected residues and atoms.
- None
- Residue name
- Residue type
- Residue Id
- Atom name
- Atom type
- Atom Id (number from file)
- Atom charge
- Options: Toggle options
- Light: Open fog and light tuning menu
- Stereo: Open stereo parameters tuning menu
- AntiAlias: Toggle computation of antialiased lines
- Fast AA: If Antialias is ON and this is OFF, use more accurate (slower) antialiasing
- BackFaces: Toggle drawing of back-faces of polygons
- AlphaTest: If ON, don't draw objects with transparency over 40%
- SelectionColor: Toggle showing of selected items as green. Note, this is global to whole Bodil.
- Demo: Rotate camera continuously around the y-axis
- Transform: Change between local, global and molecular transformations.
- Local affects viewpoint of that window.
- Molecular does not change viewpoint but moves selected chains.
- Global affects viewpoint of every window.
Configuration file entries
Section Key Valuetype
Description
GV2 DefaultSizeX integer
Default screen width
GV2 DefaultSizeY integer
Default screen height
GV2 Icon filename
Icon for minimized window
GV2 BackgrndColor int int int
Banckground color as RGB of type [0 .. 255]
GV2 LabelColor int int int
Color of text labels as RGB of type [0 .. 255]
GV2 LabelFont fontname
Font for label text
GV2 LineWidth float
width of lines
GV2 MeasureColor int int int
Color of measures as RGB of type [0 .. 255]
GV2 SurfaceAlpha float
Transparently rendered surface may use this [0.0 .. 1.0] Alpha value
GV2 FogMode string
Default fog mode: NONE, LINEAR, EXP, EXP2
GV2 FogStart float
Start distance of linear for ]0.0 .. 1.0]
GV2 Light00Position float float float
Light source position xyz
GV2 EyeSeparation float
Default stereo eye separation fraction, legal range [40.0 .. 10.0]
GV2 LevelOfDetail integer
level of detail in sphers and cylinders
GV2 Demo bool
continuous rotation. (demo mode)
GV2 DemoAngle float
degrees to rotate around y every DemoTime
GV2 DemoTime msec
Demo mode rotation interval
GV2 TurnDown float
degrees to rotate on DownArrow
GV2 TurnUp float
degrees to rotate on UpArrow
GV2 TurnLeft float
degrees to rotate on LeftArrow
GV2 TurnRight float
degrees to rotate on RightArrow
GV2 BallDepth integer
number of subdivisions of 20 sided sphere
GV2 BondSides integer
Sides in cylinders
GV2 StrandThickness float
half Thickness of beta-strand
GV2 StrandWidth float
half Width of beta-strand
GV2 HelixThickness float
half Thickness of alpha-helix
GV2 HelixWidth float
half Width of alpha-helix
GV2 UseLists bool
use OpenGL displaylists
GV2 UseTexture bool
use textured cylinders
GV2 AntiAlias bool
enable antialias
GV2 FastAA bool
if antialias is on, use faster approximation
GV2 BackFaces bool
draw backfaces of polygons
GV2 AlphaTest bool
enable alpha test
GV2 NeighDistance float
Default cutoff for creating
distances to neighbours
Cursors Erase filename
Cursor pixmap
Cursors InvErase filename
Cursor pixmap
Cursors Distance filename
Cursor pixmap
Cursors Angle filename
Cursor pixmap
Cursors Torsion filename
Cursor pixmap
Directories Icons dirname
Location of all icon/button/cursor pixmaps
Stereo Enable string
Hardware specific system command to enable stereo mode
Stereo Disable string
Hardware specific system command to disable stereo mode
Known bugs
- Picking (Ca) atoms from Ca-trace succeeds only, when Ca-trace mode has been selected after
Setting atom/bond mode to None, not vice versa.
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