MAC Install - Revision history

Cchem: 2 revisions

2018-11-12T04:22:58Z

2 revisions

Jaredsampson: /* Pre-compiled */ Make Homebrew the recommended package manager

2018-10-08T17:05:05Z

Pre-compiled: Make Homebrew the recommended package manager

Jaredsampson: /* Pre-compiled */ Update Homebrew info to reflect new location of PyMOL formula and no more need for flags in dependencies.

2018-10-08T17:01:48Z

Pre-compiled: Update Homebrew info to reflect new location of PyMOL formula and no more need for flags in dependencies.

Cchem: 1 revision

2018-08-20T02:21:35Z

1 revision

Speleo3: updated for PyMOL 2.x

2018-07-26T08:00:16Z

updated for PyMOL 2.x

Cchem: 1 revision

2017-08-28T01:14:33Z

1 revision

Pavel: /* X11 Hybrid */

2017-08-17T19:07:02Z

X11 Hybrid

Cchem: 7 revisions

2017-07-24T02:39:15Z

7 revisions

Tlinnet: /* Problems with precompiled brew installed */

2017-06-29T12:59:41Z

Problems with precompiled brew installed

Tlinnet: /* Problems with precompiled brew installed */

2017-06-29T12:54:53Z

Problems with precompiled brew installed

@@ Line 38: / Line 38: @@
 == Open-Source PyMOL ==
-=== Pre-compiled ===
+=== Package managers ===
-Pre-compiled Open-Source PyMOL is available [https://github.com/schrodinger/pymol-open-source/blob/master/LICENSE free of charge] with the [https://www.macports.org/ MacPorts], [http://www.finkproject.org/ Fink] and [http://brew.sh/ Homebrew] environments.
+Open-Source PyMOL is available [https://github.com/schrodinger/pymol-open-source/blob/master/LICENSE free of charge] and may be readily installed via the [http://brew.sh/ Homebrew] (recommended), [https://www.macports.org/ MacPorts], or [http://www.finkproject.org/ Fink] package managers.
 <source lang="bash">
 # Fink
 fink install pymol-py27
@@ Line 48: / Line 51: @@
 # MacPorts
 sudo port install pymol
 </source>

@@ Line 50: / Line 50: @@
 # Homebrew
-brew install homebrew/science/pymol
+brew install brewsci/bio/pymol
 </source>
-Make sure that the dependencies are installed with the required flags:
+You may need to make sure that the dependencies are installed with the required flags, e.g. for MacPorts:
 <source lang="bash">
@@ Line 59: / Line 59: @@
 sudo port install tcl -corefoundation
 sudo port install tk -quartz
 </source>

@@ Line 3: / Line 3: @@
 == Incentive PyMOL ==
-=== MacPyMOL ===
+[http://www.schrodinger.com Schrödinger] provides pre-compiled PyMOL to paying sponsors. The bundle also includes ready-to-use [[APBS]], [[morph|RigiMOL]], an MPEG encoder for movie export, and a small molecule energy minimization engine.
-MacPyMOL is available exclusively to paying sponsors. [http://www.schrodinger.com Schrödinger] provides a DMG package which also includes ready-to-use [[APBS]], [[morph|RigiMOL]], an MPEG encoder for movie export, and a small molecule energy minimization engine.
+Download: https://pymol.org/
-Download: http://pymol.org/download
+Installation: Drag '''PyMOL.app''' on the '''/Applications''' shortcut. (In principle, you could drag it into any Finder window and run it from there, it doesn’t have to live in /Applications).
-Installation: Drag '''MacPyMOL.app''' on the '''/Applications''' shortcut. (In principle, you could drag it into any Finder window and run it from there, it doesn’t have to live in /Applications).
+Uninstallation: Move '''/Applications/PyMOL.app''' to Trash
 === Launching from Command Line ===
-The unix executable resides at '''/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL'''
+The unix executable resides at '''/Applications/PyMOL.app/Contents/MacOS/PyMOL'''
 === X11 Hybrid ===
 MacPyMOL can optionally run with the same two-window GUI which PyMOL uses on Windows and Linux. This GUI has some additional features, like the [[Plugins|Plugin]] menu and the [[Builder]].
@@ Line 34: / Line 34: @@
 </source>
-'''Source:''' ''Warren DeLano; PyMOL Users Archive''
+'''Source:''' [https://sourceforge.net/p/pymol/mailman/message/11671952/ Warren DeLano; PyMOL Users Archive]
 == Open-Source PyMOL ==
@@ Line 40: / Line 40: @@
 === Pre-compiled ===
-Pre-compiled Open-Source PyMOL is available [https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/LICENSE free of charge] with the [https://www.macports.org/ MacPorts], [http://www.finkproject.org/ Fink] and [http://brew.sh/ Homebrew] environments.
+Pre-compiled Open-Source PyMOL is available [https://github.com/schrodinger/pymol-open-source/blob/master/LICENSE free of charge] with the [https://www.macports.org/ MacPorts], [http://www.finkproject.org/ Fink] and [http://brew.sh/ Homebrew] environments.
 <source lang="bash">
@@ Line 71: / Line 71: @@
 If you want the latest PyMOL code (warning: might include experimental changes), then follow the [[Linux_Install#Install_from_source|Linux installation instructions]]. You will need an environment like Fink, MacPorts or Homebrew to install the dependencies. Make sure you use the appropriate python interpreter (e.g. '''/sw/bin/python2.7''' when using Fink).
 === Install APBS with Fink ===

@@ Line 24: / Line 24: @@
 There are two ways to launch the X11 interface:
-# rename '''/Applications/MacPyMOL.app''' to '''/Applications/MacPyMOLX11Hybrid.app'''
+# Rename or copy/duplicate '''/Applications/MacPyMOL.app''' to '''/Applications/MacPyMOLX11Hybrid.app''' or to '''/Applications/PyMOLX11Hybrid.app'''
-# launch the unix executable with the '''-m''' flag: '''/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -m'''
+# Launch the unix executable with the '''-m''' flag: '''/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -m'''
 === Stereo on Second Monitor ===

← Older revision		Revision as of 12:59, 29 June 2017
Line 67:		Line 67:

	If PyMOL complains that it wasn't able to find X11, try starting xquartz first, then run pymol from the console.		If PyMOL complains that it wasn't able to find X11, try starting xquartz first, then run pymol from the console.
−
−	~~=== Problems with precompiled brew installed ===~~
−	~~This was experienced on date: 2017/06/29, on macOS Sierra 10.12.5.~~
−
−	~~There was a problem with '''tcl-tk''' from brew, which gave an error '''Abort trap: 6” error'''. <br>~~
−
−	~~This can be confirmed with running the brew installed python:~~
−	~~<source lang="bash">~~
−	~~/usr/local/bin/python~~
−	~~</source>~~
−	~~<source lang="python">~~
−	~~>>> import Tkinter~~
−	~~>>> Tkinter.__file__~~
−	~~>>> Tkinter._test()~~
−	~~</source>~~
−
−	~~To fix, first un-install~~
−	~~<source lang="bash">~~
−	~~brew uninstall pymol~~
−	~~brew uninstall --ignore-dependencies python~~
−	~~brew uninstall tcl-tk~~
−	~~</source>~~
−
−	~~Then modify the brew formula~~
−	~~<source lang="bash">~~
−	~~brew edit python~~
−	~~</source>~~
−
−	~~Un-commenting the Patch fix at:~~
−	~~<source lang="bash">~~
−	~~# Patch to disable the search for Tk.framework, since Homebrew's Tk is~~
−	~~# a plain unix build. Remove `-lX11`, too because our Tk is "AquaTk".~~
−	~~#if build.with? "tcl-tk"~~
−	~~#patch do~~
−	~~#url "https://raw.githubusercontent.com/Homebrew/patches/42fcf22/python/brewed-tk-patch.diff"~~
−	~~#sha256 "15c153bdfe51a98efe48f8e8379f5d9b5c6c4015e53d3f9364d23c8689857f09"~~
−	~~#end~~
−	~~#end~~
−	~~</source>~~
−
−	~~Then install~~
−	~~<source lang="bash">~~
−	~~brew install pymol~~
−	~~</source>~~
−
−	~~Then test Tkinter~~
−	~~<source lang="bash">~~
−	~~/usr/local/bin/python~~
−	~~</source>~~
−	~~<source lang="python">~~
−	~~>>> import Tkinter~~
−	~~>>> Tkinter.__file__~~
−	~~>>> Tkinter._test()~~
−	~~</source>~~
−
−	~~Then test pymol~~
−	~~<source lang="bash">~~
−	~~brew install pymol~~
−	~~pymol~~
−	~~</source>~~

	=== Install from Source ===		=== Install from Source ===

← Older revision	Revision as of 04:22, 12 November 2018
(No difference)

← Older revision	Revision as of 02:21, 20 August 2018
(No difference)

← Older revision	Revision as of 01:14, 28 August 2017
(No difference)

← Older revision	Revision as of 02:39, 24 July 2017
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@@ Line 70: / Line 70: @@
 === Problems with precompiled brew installed ===
 This was experienced on date: 2017/06/29, on macOS Sierra 10.12.5.
 There was a problem with '''tcl-tk''' from brew, which gave an error '''Abort trap: 6” error'''. <br>