Command line interface

This application features a Command Line Interface (CLI) towards the bottom of the GUI controls. Its commands are directly based on PyMol's, with the intent on easing the user experience for people used to those. A brief overview of those commands is described below:

General

• help: Lists commands
• pwd
• ls
• cd
• set seq_view

File IO

• fetch: Loads a protein from the RCSB PDB. e.g. fetch 1C8K
• save: Save the opened protein or small molecule to disk. e.g. save molecules/1htm.cif
• load: Load a protein or small molecule from disk. e.g. load ../1htm.cif

View and edit

• show: Set the view mode. e.g. show sticks
• view: Save and load scenes. e.g. view v1, view v1 store, view v2 recall
• hide: Limited options available, e.g. resn HOH, hydro, chain, hetatm etc.
• remove: Limited options available, e.g. resn HOH, hydro, chain, hetatm etc.

Selections

• select resn: Select a residue by 3-letter amino acid identifier
• select resi: Select a residue by index
• select elem: Select an atom by element abbreviation

(sele works too)

Camera controls

• turn
• move
• orient
• reset