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- Molecular Sculpting
- Monitor file continuously
- Monitors Hardware Options
- Morph
- Morpheasy
- Morpheasy linear
- Motif
- Mouse Controls
- Mouse Settings
- Mouse modes
- Move
- Movie.produce
- Movie.roll
- MovieSchool
- MovieSchool 1
- MovieSchool 2
- MovieSchool 3
- MovieSchool 4
- MovieSchool 5
- MovieSchool 6
- Movie color fade
- Movie fade
- Movie fps
- Movie from scenes
- Movie loop
- Movie panel
- Movie pdf
- Movie school
- Movit
- Mplay
- Mpng
- Mset
- Msms
- Msms surface
- Mstop
- MtsslDock
- MtsslPlotter
- MtsslTrilaterate
- MtsslWizard
- Multifilesave
- Multisave
- Mutagenesis
- Mview
- Named Atom Selections
- Nb spheres
- Nmr cnstr
- Nonstandard Amino Acids
- Normalize ccp4 maps
- NsSNP Loader
- Nuccyl
- Nucleic Acid Sequence
- Nucleic acid cartoon settings
- O
- OLD TOPTOC
- ObjectByArrows
- ObjectFocus
- Object Matrix
- Objects and Selections
- Older News
- Opaque background
- OptAlign
- Optimize
- Order
- Orient
- Origin
- Orthoscopic
- Outline
- Overview of nucleic acid cartoons
- PDB Entry Search
- PDB Index Search
- PDB Loader Service
- PDB Web Services Script
- PDB plugin
- PDBe plugin
- PDIviz
- PDIviz plugin
- PICv
- PLoS
- PML
- PYMOL PATH
- Pair Fit
- Pair fit
- Pairwise distances
- Palette Colorbars
- Pdb Conect All
- Pdb conect all
- Pdb conect nodup
- Pdb echo tags
- Pdb reformat names mode
- Pdb retain ids
- Pdb use ter records
- Pdbsurvey
- Peptide Sequence
- Perp Maker
- Perp maker
- Pickable
- Plane Wizard
- Plot noe
- PluginArchitecture
- PluginDirectory
- Plugin Manager
- Plugin manager
- Plugin nsSNP Loader
- Plugindirectory
- Plugins
- Plugins Tutorial
- Pml
- Pml2py
- Pmlbeta
- Png
- PocketPicker
- Polarpairs
- PoseView
- Poseview
- PovRay
- Povray vs. pymol
- PowerMate Dial OS X
- Practical Pymol for Beginners
- Preset
- ProBiS H2O
- ProMOL
- Process All Files In Directory
- Properties Inspector
- Property Selectors
- Propka
- Protect
- Protein contact potential
- Proxy Config
- Pse binary dump
- Pse export version
- Pseudoatom
- Pseudorotation
- Psico
- Publication Quality Images
- Pucker
- Push Undo
- Pwd
- PyANM
- PyDet
- PyMOL
- PyMOLProbity
- PyMOL mailing list
- PyMod
- PyShifts
- Pymol-script-repo
- Pymol.stored
- Pymol2glmol
- Pymolrc
- Pymolscriptrepo
- Python
- PythonTerminal
- Python Integration
- Pytms
- Quick dist
- Quickdisplays
- Quit
- RPC
- RUCAP UM-5
- Radius of gyration
- Ramp New
- Ramp new
- Ramp update
- Rasmol
- Rasmolify
- Ray
- Ray Shadows
- Ray Trace Fog
- Ray Trace Gain
- Ray Tracing
- Ray blend blue
- Ray blend colors
- Ray blend green
- Ray blend red
- Ray direct shade
- Ray opaque background
- Ray orthoscopic
- Ray shadow
- Ray shadows
- Ray texture
- Ray texture settings
- Ray trace disco factor
- Ray trace fog
- Ray trace frames
- Ray trace gain
- Ray trace mode
- Read Molstr
- Read PDB-String
- Read Pdbstr
- Read pdbstr
- Rebuild
- Recolor
- Redo
- Reflect
- Refresh
- Reinitialize
- Remote Desktop
- Remove
- RemoveAlt
- Remove Picked
- Remove picked
- Removealt
- Rename
- Rendering Plugin
- Rendering plugin
- Rendering plugin metric
- Renumber
- Replace
- ResDe
- Reset
- Resicolor
- Resicolor plugin
- Retain order
- Rewind
- Ribbon
- Ribbon Width
- Ribbon color
- Ribbon sampling
- Ribbon side chain helper
- Ribbon smooth
- Ribbon transparency
- Ribbon width
- Ribosome PyMOL Plugin
- Rigimol.morph
- Rms
- Rms Cur
- Rms cur
- RmsdByResidue
- Rock
- Rotamer Toggle
- Rotate
- RotationAxis
- Rotkit
- Roving
- Roving byres
- Roving delay
- Roving detail
- Roving nb spheres
- Run
- Running Scripts
- S2S
- SURFNET
- San Francisco Bay Area
- Save
- Save2traj
- SaveGroup
- Save Mopac
- Save mopac
- Save pdb with anisou
- Save sep
- Save settings
- Save traj
- Scene
- Scene buttons
- Script Highlighting
- Script Tutorial
- Scripting
- Scripting FAQa
- Scripting FAQs
- Scripts
- Sculpt field mask
- Search Pymol source
- Search pymol-users mailing list
- SelInside
- Select
- SelectCONTACTContacts
- SelectClipped
- SelectNCONTContacts
- SelectPISAContacts
- Select sites
- Selection
- Selection-expressions
- Selection Algebra
- Selection Exists
- Selection Language Comparison
- Selection Macros
- Selection algebra
- Selection overlay
- Selection round points
- Selection visible only
- Selection width
- Selector
- Selectors
- 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 Colour
- Set Dihedral
- Set Geometry
- Set Key
- Set Name
- Set Symmetry
- Set Title
- Set View
- Set bond
- Set dihedral
- Set name
- Set phipsi
- Set raw alignment
- Set state order
- Set title
- Set toggle
- Set view
- Settings
- Shininess
- Show
- ShowLigandWaters
- Show NMR constrains
- Show NMR constraints
- Show aromatics
- Show as
- Show bumps
- Show charged
- Show contacts
- Show hydrophilic
- Show hydrophobics
- Sidechaincenters
- Simple Scripting
- Single-word Selectors
- Single-word selectors
- Slerpy
- Slice
- Slice new
- Smooth
- Software Codecs
- Solvent radius
- Sort
- Space
- Spaceball plugin
- Spawn
- Spec direct
- Spec direct power
- Spec power