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- 0.99beta11
- 2. Translucent Surfaces
- 2to3
- 3DNA
- 3Dstrut
- 3d pdf
- AAindex
- AKMT Lys pred
- APBS
- APBS Electrostatics Plugin
- APBS Plugin
- APBS plugin
- Aa codes
- Aaindex
- Abort
- About
- Advanced Coloring
- Advanced Scripting
- Alias
- Align
- All states
- AlphaToAll
- Alter
- Alter State
- Ambient
- AngleBetweenHelices
- Angle between domains
- Anglebetweenhelices
- Annocryst
- Annotate v
- Annotation wizard
- Antialias
- Apbs
- Apbsplugin
- Apropos
- Arrows
- As
- Assembly
- Async builds
- Atom name wildcard
- Attach
- AutoMultiFit
- Auto arg
- Auto show classified
- Auto zoom
- Autodock Plugin
- Autodock plugin
- Average b
- Axes
- Axpymol
- Azahar
- B2transparency
- Backface cull
- Backward
- Ball and Stick
- BbPlane
- Bg Color
- Bg gradient
- Bg rgb
- Bg rgb bottom
- Bg rgb top
- Biochemistry student intro
- BiologicalAssembly
- BiologicalUnit
- BiologicalUnit/Quat
- Blender
- Bnitools
- Bond
- Bondpack
- Bounding Box
- Builder
- Button
- Button mode name
- CASTp
- CAVER 2.0
- CBC
- CCTBX
- CCTBX-fedora32
- CGOCylinder
- CGO Text
- CMPyMOL
- CMYK
- COLLADA
- COM
- Cache
- CalcArea
- Capture
- Cart to frac
- Cartoon
- Cartoon Helix Settings
- Cartoon all alt
- Cartoon color
- Cartoon cylindrical helices
- Cartoon discrete colors
- Cartoon dumbbell length
- Cartoon dumbbell radius
- Cartoon dumbbell width
- Cartoon fancy helices
- Cartoon fancy sheets
- Cartoon flat cycles
- Cartoon flat sheets
- Cartoon gap cutoff
- Cartoon helix radius
- Cartoon highlight color
- Cartoon nucleic acid color
- Cartoon nucleic acid mode
- Cartoon oval length
- Cartoon oval quality
- Cartoon oval width
- Cartoon putty radius
- Cartoon putty scale max
- Cartoon putty scale min
- Cartoon putty transform
- Cartoon rect length
- Cartoon rect width
- Cartoon ring mode
- Cartoon ring transparency
- Cartoon round helices
- Cartoon sampling
- Cartoon side chain helper
- Cartoon smooth loops
- Cartoon transparency
- Castp
- Caver
- Caver2
- Caver2 1 2
- Caver3
- Cavity cull
- Ccp4 contact
- Ccp4 ncont
- Ccp4 pisa
- Cd
- Cealign
- Cealign plugin
- Cell
- Center
- Center Of Mass
- Center of mass
- Centerofmass
- Centroid
- CgoCircle
- Cgo arrow
- Cgo grid
- CheatSheet
- Check Key
- Check key
- Chem comp cartn use
- Chempy
- Cheshift
- Chromadepth
- Ciewport
- Cif keepinmemory
- Cif use auth
- CircleSelection
- Clip
- Cls
- Cluster Count
- Cluster mols
- Cmd.center
- CmdScript copy
- Cmd abort
- Cmd alias
- Cmd alter
- Cmd alter state
- Cmd attach
- Cmd backward
- Cmd bg color
- Cmd bond
- Cmd button
- Cmd center
- Cmd clip
- Cmd cls
- Cmd copy
- Cmd count atoms
- Cmd count frames
- Cmd count states
- Cmd cycle valence
- Cmd delete
- Cmd deprotect
- Cmd deselect
- Cmd disable
- Cmd distance
- Cmd dss
- Cmd edit
- Cmd edit keys
- Cmd enable
- Cmd ending
- Cmd extend
- Cmd fit
- Cmd fork
- Cmd forward
- Cmd fragment
- Cmd frame
- Cmd full screen
- Cmd fuse
- Cmd get angle
- Cmd get dihedral
- Cmd get distance
- Cmd get extent
- Cmd get names
- Cmd get pdbstr
- Cmd get symmetry
- Cmd get title
- Cmd get type
- Cmd get view
- Cmd h add
- Cmd id atom
- Cmd identify
- Cmd index
- Cmd indicate
- Cmd intra fit
- Cmd intra rms
- Cmd intra rms cur
- Cmd isodot
- Cmd isolevel
- Cmd isomesh
- Cmd isosurface
- Cmd iterate
- Cmd iterate state
- Cmd label
- Cmd load
- Cmd load model
- Cmd load traj
- Cmd ls
- Cmd map double
- Cmd map set border
- Cmd mappend
- Cmd mask
- Cmd mclear
- Cmd mdo
- Cmd mdump
- Cmd mem
- Cmd meter reset
- Cmd middle
- Cmd mmatrix
- Cmd move
- Cmd mplay
- Cmd mpng
- Cmd mset
- Cmd mstop
- Cmd order
- Cmd orient
- Cmd pair fit
- Cmd png
- Cmd protect
- Cmd push undo
- Cmd pwd
- Cmd ray
- Cmd read molstr
- Cmd read pdbstr
- Cmd rebuild
- Cmd recolor
- Cmd redo
- Cmd refresh
- Cmd reinitialize
- Cmd remove
- Cmd remove picked
- Cmd rename
- Cmd replace
- Cmd reset
- Cmd rms
- Cmd rms cur
- Cmd rock
- Cmd rotate
- Cmd run
- Cmd save
- Cmd scene
- Cmd select
- Cmd set
- Cmd set colour
- Cmd set geometry
- Cmd set key
- Cmd set name
- Cmd set symmetry
- Cmd set title
- Cmd set view
- Cmd torsion
- Cmd translate
- Cmd turn
- Cmd unbond
- Cmd undo
- Cmd unmask
- Cmd unpick
- Cmd unset
- Cmd update
- Cmd view
- Cmd viewport
- Cmd wizard
- Cmd zoom
- Cmura
- Collada geometry mode
- CollapseSel
- Color
- ColorByDisplacement
- ColorByDistance
- ColorByGroup
- ColorByRMSD
- Color By Mutations
- Color Objects
- Color Values
- Color by conservation
- Color h
- Colorama
- Colorblindfriendly
- Colorbydisplacement
- Com
- Command Line Options
- Commands
- Config Mouse
- Connect cutoff
- Connect mode
- ConnectedCloud
- Consistent
- Consistent View/ Map Inspect
- Contact Map Visualizer
- Contact Surface
- Contact map visualizer
- ContactsNCONT
- Copy
- Count Atoms
- Count Frames
- Count States
- Count molecules in selection
- Count states
- Covers
- Create
- CreateAtom
- CreateSecondaryStructure
- Cubes
- Current events
- Cycle Valence
- Cycle valence
- Cylinder shader ff workaround
- Cyspka
- DSSP
- DSSP Stride
- DYNMAP
- Dash Gap
- Dash Length
- Dash Radius
- Dash Round Ends
- Dash Width
- Dash color
- Dash gap
- Dash length