The Pymol PDB Viewer

From cc7e689bec78376ed404e42ec8f425496bb435c0 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 8 Dec 2021 18:53:57 +0000 Subject: [PATCH] JAL-3551 pymol docs - work in progress --- help/help/help.jhm | 1 + help/help/helpTOC.xml | 3 +- help/help/html/features/chimera.html | 5 +- help/help/html/features/pymol.html | 234 ++++++++++++++++++++++++++++++++++ 4 files changed, 240 insertions(+), 3 deletions(-) create mode 100644 help/help/html/features/pymol.html diff --git a/help/help/help.jhm b/help/help/help.jhm index 7dbb76d..449f34c 100755 --- a/help/help/help.jhm +++ b/help/help/help.jhm @@ -55,6 +55,7 @@ + diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml index 5479291..9f1942c 100755 --- a/help/help/helpTOC.xml +++ b/help/help/helpTOC.xml @@ -133,7 +133,8 @@ - + + diff --git a/help/help/html/features/chimera.html b/help/help/html/features/chimera.html index e1227de..eadfa06 100644 --- a/help/help/html/features/chimera.html +++ b/help/help/html/features/chimera.html @@ -24,13 +24,14 @@

- The Chimera Viewer + The Chimera and ChimeraX Viewers

Since Jalview 2.8.2, Chimera (http://www.cgl.ucsf.edu/chimera/) can be used for viewing structures opened via the "View - Structure Data.." dialog. + Structure Data.." dialog. In Jalview 2.11.2, support + was also added for ChimeraX.

You can set a default choice of Jmol or Chimera structure viewer in diff --git a/help/help/html/features/pymol.html b/help/help/html/features/pymol.html new file mode 100644 index 0000000..061434f --- /dev/null +++ b/help/help/html/features/pymol.html @@ -0,0 +1,234 @@ + + + +The Pymol PDB Viewer + + +

+ 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 +

+ 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" + (where the program may be java.exe or javaw.exe). +
To allow Jalview and Pymol to interact, you may need to add + permission for the program to communicate over the network. This can + be done from the warning dialogue, or in Control Panel, Firewall + settings. + + -- 1.7.10.2

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)