User:Mglerner - Revision history

Bell at 18:57, 31 October 2015

2015-10-31T18:57:17Z

2014-03-28T01:20:07Z

21 revisions

2011-02-15T15:16:54Z

APBS Plugin FAQ

2011-01-04T16:35:56Z

My open-source toolchain

2010-03-01T22:01:59Z

2010-03-01T21:52:59Z

2010-01-28T20:36:39Z

2010-01-28T20:29:11Z

2010-01-28T20:23:43Z

2010-01-28T20:14:55Z

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 . Download and install the most recent (post Dec. 1 2009) version of APBS from [http://www.poissonboltzmann.org/apbs/downloads]. Then copy the apbs binary into the freemol directory (mv it to /Applications/PyMOLX11Hybrid.app/pymol/freemol/bin/apbs.exe, overwriting the version that comes installed with PyMOL).
-. Download [[File:Libgfortran.3.dylib.bz2]], unzip it ("bunzip2 libgfortran.3.dylib.gz2") and move it to /usr/local/lib ("mv libgfortran.3.dylib /usr/local/lib" ... on some machines, you may need "sudo mv libgfortran.3.dylib /usr/local/lib").
+. Download [[File:Libgfortran.3.dylib.zip]], unzip it ("unzip libgfortran.3.dylib.zip") and move it to /usr/local/lib ("mv libgfortran.3.dylib /usr/local/lib" ... on some machines, you may need "sudo mv libgfortran.3.dylib /usr/local/lib").
 <source lang="bash">
-bunzip2 libgfortran.3.dylib.gz2
+unzip libgfortran.3.dylib.zip
 mv libgfortran.3.dylib /usr/local/lib
 </source>

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 = APBS Plugin FAQ =
-There is an issue with the freemol version of APBS shipped with PyMOL 1.2r2 for OS X.
+== Visualizing multiple maps at once ==
-== Leopard and Snow Leopard (10.5 and 10.6) ==
+=== Method 1: all at once ===
 There are three fairly easy ways to resolve it
@@ Line 84: / Line 155: @@
 The version of libgfortran above is covered by the GNU General Public License (GPL). A copy of the GPL may be found at [http://www.gnu.org/licenses/licenses.html], and the source may be obtained from MacPorts ([http://www.macports.org/]).
-== Tiger (10.4) ==
+=== Tiger (10.4) ===
 You'll need to install APBS yourself via MacPorts or via fink. Fink instructions may be found on the [[APBS]] page. Installation via MacPorts requires first installing MacPorts from [http://www.macports.org/] and then typing

@@ Line 99: / Line 99: @@
 * numpy (efficient numerical library)
 * scipy (including traits for simple GUIs)
-* matplotlib (2D plotting)
+* matplotlib (2D and 3D plotting)
 * GROMACS (simulations)

@@ Line 10: / Line 10: @@
 == New Features ==
-I've been working with Jason Vertrees on a new version of the PyMOL-APBS plugin and it's now ready for pre-release. There are three big advantages of the new version:
+I've been working with Jason Vertrees on a new version of the PyMOL-APBS plugin and it's now ready for pre-release. There are several big advantages of the new version:
 * It's been tested modern OS X, Windows and Linux systems and fixes several long-standing bugs.

@@ Line 14: / Line 14: @@
 * It's been tested modern OS X, Windows and Linux systems and fixes several long-standing bugs.
 * It allows you to call through to PDB2PQR directly.
 * It has two visualization panels to aid in showing multiple potential surfaces at once.
 I've also upped the default maximum allowed memory since typical users have bigger and faster computers these days.
@@ Line 43: / Line 45: @@
 * The ability to call through directly to PDB2PQR
 * More modern apbs input files
 * Two visualization panels. It's often quite useful to look at two different electrostatic potentials at once. It's also quite useful to look at electrostatic potentials mapped onto two different surfaces at once. Multiple visualization panels makes this a snap: just set up one surface on panel 1 and another surface on panel 2.
 * Fixes several bugs that caused crashes on both OS X and Linux systems
 * Increased maximum allowed memory
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 * Gives better diagnostic information so that PyMOL/APBS developers can find bugs more easily
 * Lots of internal code cleanup
 = APBS Plugin FAQ =

← Older revision	Revision as of 01:20, 28 March 2014
(No difference)

@@ Line 32: / Line 32: @@
 </source>
-* You can download the it from http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py
+* You can download it from http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py
 That should give you a file called apbsplugin.py

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 I've also upped the default maximum allowed memory since typical users have bigger and faster computers these days.
 A slightly longer list of changes is included below.
@@ Line 30: / Line 32: @@
 </source>
-* You can download the zip file from http://pymolwiki.org/index.php/User:Mglerner . Upon unzipping it, you should have a file called apbsplugin.py
+* You can download the it from http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py
 Once you have the plugin, you can install it via PyMOL's plugin installer: Plugin --> Manage Plugins --> Install

@@ Line 12: / Line 12: @@
 I've been working with Jason Vertrees on a new version of the PyMOL-APBS plugin and it's now ready for pre-release. There are three big advantages of the new version:
-#. It's been tested modern OS X, Windows and Linux systems and fixes several long-standing bugs.
+* It's been tested modern OS X, Windows and Linux systems and fixes several long-standing bugs.
-#. It allows you to call through to PDB2PQR directly.
+* It allows you to call through to PDB2PQR directly.
-#. It has two visualization panels to aid in showing multiple potential surfaces at once.
+* It has two visualization panels to aid in showing multiple potential surfaces at once.
 I've also upped the default maximum allowed memory since typical users have bigger and faster computers these days.
@@ Line 24: / Line 24: @@
 There are two ways to get the new plugin
-#. If you have subversion installed,
+* If you have subversion installed,
 <source lang="bash">
@@ Line 30: / Line 30: @@
 </source>
-#. Copy the text directly from http://pymolwiki.org/index.php/User:Mglerner and put it in a file called apbsplugin.py
+* Copy the text directly from http://pymolwiki.org/index.php/User:Mglerner and put it in a file called apbsplugin.py
 Once you have the plugin, you can install it via PyMOL's plugin installer: Plugin --> Manage Plugins --> Install