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- Spec reflect
- Spectrum
- Spectrum states
- Spectrumany
- Spectrumbar
- Specular
- Specular intensity
- Speleo3/test1
- Speleo3/test2
- Speleo3/test3
- Sphere color
- Sphere mode
- Sphere point max size
- Sphere point size
- Sphere quality
- Sphere scale
- Sphere solvent
- Sphere transparency
- Spheres
- Splash
- Split Movement
- Split Object Along Axis
- Split States
- Split chains
- Split object
- Split selection
- Split states
- Ss
- Sst
- State
- State counter mode
- States
- Static singletons
- Stereo
- Stereo 3D Display Options
- Stereo Figures
- Stereo Mode
- Stereo Ray
- Stereo angle
- Stereo mode
- Stereo ray
- Stick ball
- Stick ball ratio
- Stick color
- Stick h scale
- Stick nub
- Stick radius
- Stick transparency
- Sticks
- Stride
- Super
- SuperSym
- SuperSymSource
- Supercell
- Surface
- Surface carve cutoff
- Surface carve normal cutoff
- Surface carve selection
- Surface cavity mode
- Surface color
- Surface edge smoothing
- Surface mode
- Surface negative color
- Surface negative visible
- Surface proximity
- Surface quality
- Surface ramp above mode
- Surface smooth edges
- Surface solvent
- Surface type
- Surfaces and Voids
- Suspend updates
- Symexp
- Symmetry
- Symmetry Axis
- Sync
- System
- TCONCOORD
- TMalign
- TODO
- TOPTOC
- Texture fonts
- Thank You
- Theseus
- Three Button Motions
- Tiff2ccp4
- Timeline
- Timeline Custom Programs
- Timeline Python API
- Tmalign
- ToGroup
- Torsion
- TransformSelectionByCameraView
- Transform object
- Transform odb
- Transform odb.py
- Transform selection
- Transformations
- Translate
- Translate And Measure
- Transparency
- Transparency mode
- Turn
- Two sided lighting
- Unbond
- Undo
- Uniprot features
- Unmask
- Unpick
- Unset
- Unset deep
- Update
- Util.cbc
- Util.mroll
- VASCo
- Valence
- Vdw
- View
- Viewport
- Views
- Virtual trackball
- VisLoad
- Visualizing a computed structure - a commented example
- Volume
- Volume color
- Voronoia
- Vrml
- WFMesh
- Warren
- Wfmesh
- Window
- Windows Install
- Wizard
- Wrap output
- WriteSS
- XFree86 Configuration
- XML-RPC server
- Xfit
- Xpyder
- Zero residues
- Zoom