These options are designed to change a number of settings in order to achieve specific behaviors

• -A1 or -a1 → launch as a molecular viewer window with no user interface visible.

  pymol -a1 1tii.pdb -d 'as cartoon'

• -A3 or -a3 → launch as a molecular viewer window with only the internal user interface visible.

• -A5 or -a5 → launch as a molecular viewer window configured for use as a helper application (with output suppressed, interrupts disabled, etc.).

• -A6 or -a6 → launch in full-screen presentation mode with no external GUI present.

• -h → launch using the old helper application settings (these days, use -A5 instead).

• -c → launch in command-line only mode for batch processing.

• -f number → show number lines of text input and output in the display window (default: 1).

• -F → do not show any text input or output lines in the display window.

• -i → turn off the internal GUI.

• -N external-gui-name → use the named external GUI module (default: pmg_tk).

• -P → handle scenes as if the session were opened in presentation mode.

• -T skin-name → launch external GUI using the indicated skin (default: normal).

Launching | Alphabetical