X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fpymol.html;h=7bf565132455311237618eb848d9819b87e2a8d1;hb=00a0552110d2d6a9f4e4da584b28d53fc3bfffd0;hp=061434fb55c093bb9938949bd30ac92fb3a961d6;hpb=cc7e689bec78376ed404e42ec8f425496bb435c0;p=jalview.git
diff --git a/help/help/html/features/pymol.html b/help/help/html/features/pymol.html
index 061434f..7bf5651 100644
--- a/help/help/html/features/pymol.html
+++ b/help/help/html/features/pymol.html
@@ -27,45 +27,44 @@
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:
-
-
- - 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.
-
+ Known Limitations
+
+
+ - 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).
+ href="https://pymol.org/dokuwiki/doku.php?id=mouse">Pymol Wiki
+ at https://pymol.org/dokuwiki/doku.php?id=mouse for full details).
Action |
@@ -177,51 +176,69 @@
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.
+ Troubleshooting
+
+ Jalview will try to automatically configure itself according to the
+ configured Pymol installation (or the first one it discovers in the
+ standard installation locations). You can see which Pymol executable
+ is being used by enabling
+ DEBUG output in
+ Jalview's Java console.
+
+
If Jalview raises warning messages about Pymol not being located
+ or executed, or no structures appear when Jalview launches Pymol,
+ please ask for help on
+ Jalview's discussion forum.
+
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"