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- DYNMAP
- Dash Gap
- Dash Length
- Dash Radius
- Dash Round Ends
- Dash color
- Dash gap
- Dash length
- Dash radius
- Dash round ends
- Dash width
- Defer builds mode
- Dehydron
- Delete
- Delete states
- Deprotect
- Depth cue
- Deselect
- Disable
- Discrete objects
- DisplacementMap
- Displacementmap
- Display CCP4 Maps
- Display SiteMap Maps
- Display scale factor
- Displaying Biochemical Properties
- Distance
- DistancesRH
- Distancetoatom
- DivScore
- Dockingpie
- Dot radius
- Dot width
- Dots
- Draw
- DrawBoundingBox
- DrawGridBox
- DrawMinBoundingBox
- Draw Protein Dimensions
- Dss
- Dssp
- Dssp stride
- Dssr block
- Dump
- Dump2CGO
- Dunbrack Rotamers
- Dynamic mesh
- DynoPlot
- Dynoplot
- EMovie
- EZ-Viz
- Edit
- Edit Keys
- Editing atoms
- Editing set dihedral
- Elbow angle
- Ellipsoid
- Ellipsoid color
- Ellipsoid quality
- Ellipsoid scale
- Ellipsoid transparency
- Ellipsoids
- Emovie
- Enable
- Ending
- Ex
- Example Scripts
- Examples of cartoon ring and cartoon ladder settings
- Examples of nucleic acid cartoons
- Expand To Surface
- Extend
- Extend (selection operator)
- Extensions
- Extra fit
- Extract
- Fab
- Feedback
- Fetch
- FetchLocal
- Fetch Host
- Fetch Path
- Fetch type default
- Fetching scripts
- Field Of View
- FilterByMol
- FindObjectsNearby
- FindSeq
- FindSurfaceCharge
- FindSurfaceResidues
- FindSurfaceResiduesListCharged
- Find buried waters
- Find pairs
- Find symbol
- Findseq
- Findsurfaceresidueslistcharged
- Fit
- Flag
- Flatten obj
- Fnab
- FocalBlur
- Focus alignment
- Fog
- Fog start
- Fork
- Format bonds
- Forster-distance-calculator
- Forster distance calculator
- Forward
- Frag
- Fragment
- Frame
- Frame slider
- Full Screen
- Full screen
- Fuse
- GLSL Shaders
- GROMACS Plugin
- Gallery
- Geo Measures Plugin
- Geometry export mode
- Get
- GetNamesInSel
- GetRotationMatrix
- Get Angle
- Get Area
- Get Color Indices
- Get Color Tuples
- Get Coordinates I
- Get Coordinates II
- Get Dihedral
- Get Distance
- Get Extent
- Get Frame
- Get Model
- Get Names
- Get Names of Type
- Get Pdbstr
- Get Position
- Get State
- Get Symmetry
- Get Title
- Get Type
- Get Version
- Get View
- Get area
- Get chains
- Get color index
- Get color tuple
- Get colors
- Get coords
- Get coordset
- Get extent
- Get fastastr
- Get legal name
- Get names
- Get names of type
- Get object list
- Get object matrix
- Get position
- Get raw alignment
- Get raw distances
- Get sasa relative
- Get session
- Get state
- Get symmetry
- Get type
- Get unused name
- Get view
- Git
- Git admin
- Git authors
- Git include
- Git install
- Git install scripts
- Git intro
- Git script guidelines
- GoogleSearch
- GoogleSearchResults
- Gradient
- Grepsel
- Grepset
- Grid max
- Grid mode
- Grid slot
- Group
- Gsoc2008
- Gyration tensor
- H Add
- H Fill
- H add
- Half bonds
- Hardware Options
- Hash max
- Hbplus
- Helicity check
- Hide
- Hide underscore names
- HighlightAlignedSS
- Homology Modeling
- Huge surfaces
- Id Atom
- Ideas
- Identify
- Ignore case
- Ignore case chain
- ImmersiveViz
- Inchoates pymolrc
- Index
- Indicate
- Inertia tensor
- InterfaceResidues
- Internal Gui
- Internal feedback
- Internal gui
- Internal gui control size
- Internal gui mode
- Internal gui width
- Internal prompt
- Intra Fit
- Intra Rms
- Intra Rms Cur
- Intra fit
- Intra rms
- Intra rms cur
- Intra xfit
- Invert
- Isodot
- Isolevel
- Isomesh
- Isoslider
- Isosurface
- Iterate
- Iterate State
- Iterate sses
- Iterate state
- Join states
- Jump
- Jupyter
- Kabsch
- Key Wait
- Keyboard Shortcut Menu
- Label
- Label anchor
- Label angle digits
- Label color
- Label dihedral digits
- Label distance digits
- Label font id
- Label outline color
- Label position
- Label shadow mode
- Label size
- LatticeGenerator
- Launching From a Script
- Launching PyMOL
- Leap Motion
- LigAlign
- Light
- Light2
- Light3
- Light4
- Light5
- Light6
- Light7
- Light8
- Light9
- Light count
- Line color
- Line smooth
- Line width
- Lines
- Linux Install
- Linux XFree86 Configuration
- Lisica
- ListSelection2
- List Colors
- List Secondary Structures
- List Selection
- List dist
- Load
- LoadAll
- LoadDir
- Load CGO
- Load Model
- Load Traj
- Load aln
- Load brick
- Load coords
- Load img stack
- Load model
- Load new B-factors
- Load traj
- Loadall
- Ls
- MAC Install
- MOLE 2.0: advanced approach for analysis of biomacromolecular channels
- MSMS
- MacOSX-specific .pymolrc file
- Madd
- Main Page
- MakeVinaCommand
- Make Figures
- Making Movies
- ManualSymExp
- Map Double
- Map Set Border
- Map Trim
- Map auto expand sym
- Map double
- Map new
- Map set
- Mappend
- Mark center
- Mask
- Matrix Copy
- Matrix copy
- Matrix mode
- Matrix reset
- Max ups
- Mclear
- Mcsalign
- Mdo
- Mdump
- Measure Distance
- Mem
- Mesh
- Mesh color
- Mesh lighting
- Mesh mode
- Mesh negative color
- Mesh negative visible
- Mesh quality
- Mesh type
- Mesh width
- Meter Reset
- Middle
- Min mesh spacing
- Minimize ob
- Mmatrix
- Mobile
- Model Space and Camera Space
- Modeling and Editing Structures
- Modevectors
- Mole
- Mole2