PyMol Command Line Interface

This section provides a quick introduction on the command line interface on PyMol. 'help' command lists all available commands.

If you get frustrated with using mouse buttons to control the molecule structures on MyPol, you can start to use the command line interface.

Type in "help" in the command input area, you will see a list available PyMol commands:

PyMOL>help

COMMANDS

    INPUT/OUTPUT  load      save      delete    quit
    VIEW          turn      move      clip      rock
                  show      hide      enable    disable
                  reset     refresh   rebuild
                  zoom      origin    orient
                  view      get_view  set_view
    MOVIES        mplay     mstop     mset      mdo
                  mpng      mmatrix   frame
                  rewind    middle    ending
                  forward   backward
    IMAGING       png       mpng
    RAY TRACING   ray
    MAPS          isomesh   isodot
    DISPLAY       cls       viewport  splash
    SELECTIONS    select    mask
    SETTINGS      set       button
    ATOMS         alter     alter_state
    EDITING       create    replace   remove    h_fill   remove_picked
                  edit      bond      unbond    h_add    fuse
                  undo      redo      protect   cycle_valence  attach
    FITTING       fit       rms       rms_cur   pair_fit
                  intra_fit intra_rms intra_rms_cur
    COLORS        color     set_color
    HELP          help      commands
    DISTANCES     dist
    STEREO        stereo
    SYMMETRY      symexp
    SCRIPTS       @         run
    LANGUAGE      alias     extend

Try "help <command-name>".  Also see the following extra topics:

    "api", "editing", "edit_keys", "examples", "faster", "keyboard",
    "launching", "mouse", "movies", "python", "povray", "release",
    "selections", "skip", "sync", "stereochemistry", "text_type",
    "transparency", "@".

You can also read PyMol command reference on line at pymol.org/pymol-command-ref.html.

Table of Contents

 About This Book

 Introduction of Molecules

 Molecule Names and Identifications

 Protein and Amino Acid

 Nucleobase, Nucleoside, Nucleotide, DNA and RNA

 Gene and Chromosome

 Protein Kinase (PK)

 SDF (Structure Data File)

 RDKit: Open-Source Cheminformatics Software

 PyMol Installation

PyMol GUI and CLI

 PyMol Screen Layout

 Load Molecule from File into PyMol

 Virtual Trackball Rotation on PyMol

 Zoom In and Out on PyMol

PyMol Command Line Interface

 "load" and "delete" Commands on PyMol

 "log_open" and "log_close" Commands on PyMol

 Model Space and Camera Space on PyMol

 "get_view" and "set_view" on PyMol

 View Parameters Auto Adjusted on PyMol

 Zoom In/Out by Moving Camera

 Rotation with Transformation Matrix

 Rotation with "turn" Command

 Difference of "turn" and "rotate" Commands

 Difference of "move" and "translate" Commands

 "center", "zoom" and "reset" Commands

 Model-to-Camera Space Coordinates Mapping

 Camera-to-Model Space Coordinates Mapping

 Turn Structure around Camera

 "show lines" Presentation Command

 "show sticks" Presentation Command

 "show spheres" Presentation Command

 "show surface" Presentation Command

 "show mesh" Presentation Command

 PyMol Selections

 PyMol Editing Functions

 PyMol Measurement Functions

 PyMol Movie Functions

 PyMol Python Integration

 PyMol Object Functions

 ChEMBL Database - European Molecular Biology Laboratory

 PubChem Database - National Library of Medicine

 PDB (Protein Data Bank)

 INSDC (International Nucleotide Sequence Database Collaboration)

 Resources and Tools

 Molecule Related Terminologies

 References

 Full Version in PDF/EPUB