From 1a0a6c0b1966cc2025e983a8f92de54af2f90636 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 15 Feb 2022 16:44:40 +0000 Subject: [PATCH] JAL-3551 pymol documentation --- help/help/html/features/pymol.html | 118 +++++++++++++++++++----------------- 1 file changed, 62 insertions(+), 56 deletions(-) diff --git a/help/help/html/features/pymol.html b/help/help/html/features/pymol.html index 061434f..573310a 100644 --- a/help/help/html/features/pymol.html +++ b/help/help/html/features/pymol.html @@ -27,45 +27,47 @@ 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. + In Jalview 2.11.2, support was added for viewing structures opened + via the "View + Structure Data.." dialog with Pymol (https://pymol.org/2/). Like + with Chimera and ChimeraX, Pymol views + can be saved and restored from Jalview Project files on any machine + with it installed, and structures can be coloured and superimposed + according to the alignment.

- 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. - -

+ Configuring Jalview to use Pymol
You can configure + Pymol as your preferred structure viewer in Preferences. Jalview will + look for an existing installation, and will ask you to specify the + installation's path if it cannot be found. You can also optionally + specify the path to the Pymol program here if you want Jalview to + use a specific installation. +

+

+ Jalview requires Pymol V 2.5.0 (community edition) + or later
Jalview requires Pymol's RPC interface, which is + not available in older versions of the Pymol community edition. +

- 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: -

- + Known Limitations
+

+

Basic screen operations (see Pymol Wiki at - https://pymol.org/dokuwiki/doku.php?id=mouse - for full details). + href="https://pymol.org/dokuwiki/doku.php?id=mouse">Pymol Wiki + at https://pymol.org/dokuwiki/doku.php?id=mouse for full details). @@ -177,51 +179,55 @@ colourschemes.
The remaining entries apply the colourschemes available from the standard and user defined amino acid - colours. + href="../colourSchemes/index.html">amino acid colours.
  • Pymol
    -     This pulldown menu provides access to Pymol's capabilities from Jalview. + 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 + structure in the alignment via the pair_fit command. The regions used to calculate the superposition will be highlighted using the 'Cartoon' rendering style, and the remaining data shown as a chain - trace.
      -
      + trace. RMSD values are output in the Pymol log.

    • 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. -
        • -
      -
      • + 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.
      • + Access the Pymol Help documentation in a new browser + window. window.

    • Pymol and Windows Firewall

    - Jalview and Pymol communicate using the Pymol's XML-RPC over HTTP interface(https://pymolwiki.org/index.php/RPC). - -
    Technically this requires both Pymol and Jalview to open + Jalview and Pymol communicate using the + Pymol's XML-RPC over + HTTP interface(https://pymolwiki.org/index.php/RPC). + +
    Technically this requires both Pymol and Jalview to open ports on the local network, and this may be blocked by Windows Firewall with a warning message such as
    "Windows Firewall has blocked some features of this program" -- 1.7.10.2
    Action