The Pymol Viewer

In Jalview 2.11.2, support was added for Pymol (https://pymol.org/2/) to be used for viewing structures opened via the "View Structure Data.." dialog.

You can configure Pymol as your preferred structure viewer in Preferences. You can also optionally specify the path to the Pymol program here (if it differs from the standard paths searched by Jalview).
Jalview requires Pymol's RPC interface, which is not available in older versions of the Pymol community edition.
Please make sure your version of Pymol is up to date.

If you save your Jalview session as a project file, the state of any open Pymol windows will also be saved, and can be reopened by loading the project file on any machine with Pymol installed.

Known Limitations
Jalview provides an easy way to employ Pymol for linked analysis of sequences and structures in the same way as Chimera and ChimeraX. There are some limitations, however:

• Pymol does not support some forms of legacy structural data (e.g. the 1A70 C-alpha only PDB file included in the Jalview example project).
• Pymol to Jalview communication does not support transfer of properties or highlighting sequence regions corresponding to structure selections or mouse-overs in Pymol.

Basic screen operations (see Pymol Wiki at https://pymol.org/dokuwiki/doku.php?id=mouse for full details).

Action	Windows	Unix	Mac/OSX
Rotate View	Left Click and Drag	Left Click and Drag	Left Click and Drag
Zoom	Right Click drag mouse up or down	Right Click drag mouse up or down	cmd or Right + Click and drag mouse up or down, or use mouse scroll button
Move Origin	Middle Button + Drag	Middle Button and drag	alt + Click and drag
Select Residues	Ctrl + Click (and drag to select a region)	Ctrl + Click (and drag)	Ctrl + Click (and drag)

Jalview Controls

The Jalview Pymol View window has up to five menus:

• File
  
  • View Mapping
    Opens a text window showing the alignment between the residues corresponding to alpha-carbon atoms in the PDB structure and the residues in the associated sequence.
• View
  • Show Chains
    Select which of the PDB file's chains (if more than one) are to be displayed.
  • Colour by ..
    Submenu allowing specific alignment views to be selected for colouring associated chains in the structure display. This menu contains all the alignment views associated with the structure view, with those used to colour the view indicated by ticks. Addditionally, it contains the following menu entries:
    • Select many views
      When this option is enabled, selecting an alignment view adds it to the set used to colour the structures. Use this when colouring structures related to a number of alignments involving different domains or chains which are shown in the same structure view.
    • Select all views
      This is only enabled when Select many views is also enabled, and will add all associated views to the set used to colour the structure display.
    • Invert selection
      This is only enabled when Select many views is also enabled, and will replace the current set of views with any remaining views not currently used to colour the structure display.
• Colours
  
  • By Sequence
    Colours each residue in the structure with the colour of its corresponding residue in the associated sequence as rendered in the associated alignment views, including any UniProt sequence features or region colourings.
    Pick which of the associated alignment views are used to colour the structures using the View→Colour by .. sub menu.
    Residues which only exist in the PDB structure are coloured white if they are insertions (relative to the associated sequence in the alignment) and grey if they are N or C terminal flanks outside the region mapped to the alignment window's sequence.
  • By Chain
    Uses Pymol's 'spectrum(chain)' command to apply a different colour to each chain.
  • Charge & Cysteine
    Highlights cysteines in yellow, anionic (Aspartic Acid or Glutamic Acid) residues in red, and cationic (Lysine or Arginine) residues in blue.
  • Colour with Pymol
    Defers any colouring operations to Pymol. Select this if you want to use the Pymol scripting interface or menu to modify the view directly.
  • Standard and User Defined Jalview colourschemes.
    The remaining entries apply the colourschemes available from the standard and user defined amino acid colours.
• Pymol
  This pulldown menu provides access to Pymol's capabilities from Jalview.
  • Align
    When selected, the associated alignment will be used to superimpose all the structures in the view onto the first structure in the alignment. The regions used to calculate the superposition will be highlighted using the 'Cartoon' rendering style, and the remaining data shown as a chain trace.
    
    
  • Write Jalview features
    Selecting this option will create new atom properties for any features currently visible in the associated alignment views. This allows those atoms to be selected and analysed in Pymol directly.
    
    • Feature transfer in Pymol is experimental.
    • To select by a particular feature use the string matching syntax:
      select foo,p.jv_helix in helix
    • To view transferred properties use Pymol's Properties Inspector
    • For more information see Property based selection in Pymol's Documentation.
• Help
  
  • Pymol Help
    Access the Pymol Help documentation in a new browser window. window.

Pymol and Windows Firewall