Table of Contents

• Copyright for the PyMOL Manual
• PyMOL License

• Why PyMOL?
• Strengths
• Weaknesses
• Future Outlook

• Windows
• Unix

• Launching
• By Mouse
• By Command
• PyMOL's Windows
• Viewer Window
• External GUI Windows
• Loading PDB Files
• Manipulating the View
• Basic Mouse Control
• Free Rotation
• Moving Clipping Planes
• Sessions and Scripts
• Atom Selections
• Origins
• Hierarchical Atom Selections
• Algebraic Atom Selections
• Named Selections
• Selection Algebra
• Actions on Objects and Selections
• Using the Internal GUI:

• Command Completion using TAB
• Filename Completion using TAB
• Automatic Inferences

• Background
• Accessibility
• Beautiful and Realistic
• Customization
• Cartoon Types
• Fancy Helices
• Secondary Structure Assignment

• Important Settings
• Saving Images
• png

• Concepts
• States and Frames
• Important Commands To Know
• load
• mset
• mdo
• mmatrix
• Simple Examples
• Complex Examples
• Previewing Ray-traced Movie Images
• cache_frames
• mclear
• Saving movies
• mpng

• Picking Atoms and Bonds
• Example Usage of the "pk" Atom Selections
• The "lb" and "rb" Selections
• Conformational Editing

• Crystal Symmetry
• load
• symexp
• Electron Density Maps
• load
• isomesh and isodot

• Under Rennovation
• set
• Reference

• Introduction
• Molscript Ribbons
• load
• Using Molscript
• Creating Compiled Graphics Objects
• CGO Reference
• load_cgo

• Introduction
• Example
• load_callback

• Electron density (density.pml)
• Crystal Packing with Ribbons (packing.pml)
• A Crystal Contact Interaction (contact.pml)

• GroEL/ES (groel_es.pml)
• Nucleic Acid in the Ribosome (ribosome.pml)
• Crystal Packing With Surfaces (packsurf.pml)

• alias
• alter
• alter_state
• api
• at_sign
• attach
• backward
• bg_color
• bond
• button
• cartoon
• cd
• clip
• cls
• color
• commands
• copy
• count_atoms
• count_states
• create
• cycle_valence
• delete
• deprotect
• disable
• distance
• do
• edit
• edit_keys
• editing
• enable
• ending
• examples
• extend
• faster
• feedback
• find_pairs
• finish_object
• fit
• flag
• forward
• fragment
• frame
• full_screen
• fuse
• get_area
• get_extent
• get_frame
• get_model
• get_names
• get_state
• get_type
• get_view
• h_add
• h_fill
• help
• hide
• id_atom
• identify
• index
• intra_fit
• intra_rms
• intra_rms_cur
• invert
• isodot
• isomesh
• iterate
• iterate_state
• keyboard
• label
• launching
• load
• load_brick
• load_callback
• load_cgo
• load_map
• load_model
• load_object
• ls
• mask
• mclear
• mdo
• mem
• meter_reset
• middle
• mmatrix
• mouse
• move
• movies
• mplay
• mpng
• mset
• mstop
• orient
• origin
• pair_fit
• png
• protect
• push_undo
• pwd
• quit
• ray
• read_mmodstr
• read_molstr
• read_pdbstr
• rebuild
• redo
• refresh
• release
• remove
• remove_picked
• rename
• replace
• reset
• rewind
• rms
• rms_cur
• rock
• run
• save
• select
• selections
• set
• set_color
• set_key
• set_title
• set_view
• show
• sort
• spawn
• splash
• stereo
• symexp
• system
• torsion
• turn
• unbond
• undo
• unmask
• unpick
• update
• view
• viewport
• wizard
• zoom

Copyright © 2001 DeLano Scientific. All rights reserved.