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- San Francisco Bay Area
- Save
- Save2traj
- SaveGroup
- Save Mopac
- Save pdb with anisou
- Save sep
- Save settings
- Save traj
- Scene
- Scene buttons
- Script Highlighting
- Script Tutorial
- Scripting FAQs
- Sculpt field mask
- Search Pymol source
- SelInside
- Select
- SelectClipped
- Select sites
- Selection-expressions
- Selection Algebra
- Selection Exists
- Selection Language Comparison
- Selection Macros
- Selection overlay
- Selection round points
- Selection visible only
- Selection width
- Seq view
- Seq view alignment
- Seq view color
- Seq view discrete by state
- Seq view fill char
- Seq view format
- Seq view gap mode
- Seq view label color
- Seq view label mode
- Seq view label spacing
- Seq view location
- Seq view overlay
- Seq view unaligned color
- Seq view unaligned mode
- Set
- Set Color
- Set Dihedral
- Set Geometry
- Set Key
- Set Symmetry
- Set Title
- Set View
- Set bond
- Set name
- Set phipsi
- Set raw alignment
- Set state order
- Set title
- Set toggle
- Settings
- Shininess
- Show
- ShowLigandWaters
- Show aromatics
- Show as
- Show bumps
- Show charged
- Show contacts
- Show hydrophilic
- Show hydrophobics
- Sidechaincenters
- Simple Scripting
- Slerpy
- Slice
- Smooth
- Software Codecs
- Solvent radius
- Sort
- Space
- Spaceball plugin
- Spec direct
- Spec direct power
- Spec power
- 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 chains
- Split object
- Split selection
- Split states
- Ss
- Sst
- State counter mode
- States
- Static singletons
- Stereo
- Stereo 3D Display Options
- Stereo Mode
- Stereo angle
- Stereo ray
- Stick ball
- Stick ball ratio
- Stick color
- Stick h scale
- Stick nub
- Stick radius
- Stick transparency
- Sticks
- Super
- SuperSym
- SuperSymSource
- Supercell
- Surface
- Surface carve normal cutoff
- Surface carve selection
- Surface cavity mode
- Surface color
- Surface mode
- 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
- ToGroup
- Torsion
- TransformSelectionByCameraView
- Transform object
- Transform odb
- 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.mroll
- VASCo
- Valence
- Vdw
- View
- Viewport
- Views
- Virtual trackball
- VisLoad
- Visualizing a computed structure - a commented example
- Volume
- Volume color
- Voronoia
- Vrml
- Warren
- Wfmesh
- Window
- Windows Install
- Wizard
- Wrap output
- WriteSS
- XFree86 Configuration
- XML-RPC server
- Xfit
- Xpyder
- Zero residues
- Zoom