PyMOL Wiki - User contributions [en]

Talk:APBS

2010-11-04T23:13:24Z

Rendereason:

I've added some details about where and how to download and install apbs and its dependencies. I have cross-referenced a description of how this can be done on OS X.

I've put a few very tentative lines in about linux.

== Well done! ==

Hey, thanks for this plugin. It worked on an SMP 64-bit Linux machine with little effort. Still crashes a bit, but the effort is worth it.
[[User:Inchoate|Tree]] 18:21, 21 February 2008 (CST)

== Question/Crash ==

I ran APBS on 2ILK. When I try to show the solv. acc. map, it computes something for a sec, then crashes taking PyMOL with it. Is this common? Any ideas on fixing it? It's probably my lack of understanding on how APBS works.
[[User:Inchoate|Tree]] 07:40, 22 February 2008 (CST)

For me it doesn't crash, but asks me to calculate the pqr file myself. Than it calculates the map fine.
[[User:Desastre|Desastre]] 27 April 2008

== Making the default paths to work? ==

I saw a discussion in the Pymolbb dated April 15, 2010 [http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07858.html] about the default paths for binaries, psize.py, and temp files not loading automatically or even saving the paths.

I am wondering if anyone has solved this issue.

After installing pymol through fink, none of the binaries show up. After installing pdb2pqr through fink, the apbs plugin (Apbs Tools 2) does load /sw/share/pdb2pqr/pdb2pqr.py automatically. However, after installing apbs-mpi-openmpi through fink, neither APBS binary nor APBS psize.py load.

I have tried modifying apbs_tools.py (/sw/lib/pymol-py26/modules/pmg_tk/startup/apbs_tools.py) in lines 112 through 115 to:
APBS_BINARY_LOCATION = '/sw/bin/apbs-mpi-openmpi'
APBS_PSIZE_LOCATION = '/sw/share/apbs-mpi-openmpi/tools/manip/psize.py'
APBS_PDB2PQR_LOCATION = None
TEMPORARY_FILE_DIR = None

My $APBS_PSIZE returns /sw/share/apbs-mpi-openmpi/tools/manip by default, as installed through fink. I use 64-bit fink, pymol 1.3, and Snow Leopard OSX.

The default temporary file locations also do not work. I have also tried to make apbs plugin save these these to no avail.

I hope a solution to this issue can be posted in the wiki.

PS.: I have looked at the output from X11 when pymol loads, and it seems it tries to load
trying /sw/bin/apbs-mpi-openmpi/psize.py
trying '''/sw/share/apbs-mpi-openmpi/tools/manip/psize.py'''/psize.py
trying /sw/share/pdb2pqr/psize.py

and
trying '''/sw/bin/apbs-mpi-openmpi'''/apbs.exe
trying /sw/share/apbs-mpi-openmpi/tools/manip/psize.py/apbs.exe
trying /sw/share/pdb2pqr/apbs.exe
trying /sw/share/apbs/tools/manip/apbs.exe
trying /sw/bin/apbs.exe

Which are obviously wrong. The correct paths should be '''/sw/share/apbs-mpi-openmpi/tools/manip/psize.py''' and '''/sw/bin/apbs-mpi-openmpi'''.
--[[User:Rendereason|Rendereason]] 22:40, 20 July 2010 (UTC)

'''Fixed''' in the current version of the plugin, which you can download from [http://pymolwiki.org/index.php/User:Mglerner my user page]. The issue was that the plugin just didn't know about MPI-enabled versions. --[[User:Mglerner|michael]] 23:48, 22 July 2010 (UTC)

==Running with APBS 1.3 not working==
Well, I tried making the plugin run with APBS 1.3 and this is what I got:
Running:
prog=/usr/local/apbs-1.3-mac-univ/bin/apbs
args=('/usr/local/apbs-1.3-mac-univ/bin/apbs', '--version')
Results were:
Return value: -5
Output:
dyld: Library not loaded: /usr/local/lib/x86_64/libgomp.1.dylib
Referenced from: /usr/local/apbs-1.3-mac-univ/bin/apbs
Reason: image not found
Skipping /usr/local/apbs-1.3-mac-univ/bin/apbs because it appears to be broken (dyld)

Just wondering if you get the same. --[[User:Rendereason|Rendereason]] 16:36, 29 October 2010 (UTC)

I think I see why it's doing that. My folder structure is not right. APBS needs to update its install instructions/README. I'll try moving the folders to /sw64/bin/apbs, /sw64/share/apbs, etc.--[[User:Rendereason|Rendereason]] 16:49, 29 October 2010 (UTC)

The installation guide says:
"The APBS binaries do not contain dependencies on special data files, etc. and can be moved out of this directory structure without causing any problems for APBS execution." [http://www.poissonboltzmann.org/apbs/user-guide/installation-and-avil From APBS webpage.]
I have tried setting the variable ${APBS_PREFIX} to /usr/local/apbs-.13-mac-univ.
I've added these to my .zshrc but none of it works
APBS_PREFIX=/usr/local/apbs-1.3-mac-univ/
APBS_BINARY_DIR=/usr/local/apbs-1.3-mac-univ/bin/
APBS_PSIZE_DIR=/usr/local/apbs-1.3-mac-univ/share/tools/manip/
export APBS_PREFIX
export APBS_BINARY_DIR
export APBS_PSIZE_DIR
None of this had any effect on the unmodified apbsplugin.py. (When parameters set to ''None'')
Changing the parameters within apbsplugin.py to their desired folders gives the error above.
--[[User:Rendereason|Rendereason]] 16:57, 29 October 2010 (UTC)

Have you tried the pre-release version available on my page? I fixed some things recently, and this bug doesn't happen for me any more. --[[User:Mglerner|michael]] 19:40, 29 October 2010 (UTC)

Yes. Those errors happen with the pre-release version you posted. It also ignores the binary I have configured it to use in /usr/local/apbs/bin/ for the fink one in /sw64/bin/.
Also, I get this problem when running the plugin:
GENERATING PQR FILE via PDB2PQR
Erasing contents of /tmp/pymol-generated.pdb in order to generate new PDB file
Erasing contents of /tmp/pymol-generated.pdb in order to clean it up
TESTING
DONE TESTING
Appended /sw64
Unexpected error encountered while trying to import pdb2pqr: (<type 'exceptions.ImportError'>, ImportError('No module named pdb2pqr.pdb2pqr',), <traceback object at 0x116714908>)
In show error 2
Could not generate PDB2PQR file. _generatePdb2pqrPqrFile failed.
Could not generate PQR file!
--[[User:Rendereason|Rendereason]] 22:48, 4 November 2010 (UTC)

Talk:APBS

2010-11-04T22:48:17Z

Rendereason:

I've added some details about where and how to download and install apbs and its dependencies. I have cross-referenced a description of how this can be done on OS X.

I've put a few very tentative lines in about linux.

== Well done! ==

Hey, thanks for this plugin. It worked on an SMP 64-bit Linux machine with little effort. Still crashes a bit, but the effort is worth it.
[[User:Inchoate|Tree]] 18:21, 21 February 2008 (CST)

== Question/Crash ==

I ran APBS on 2ILK. When I try to show the solv. acc. map, it computes something for a sec, then crashes taking PyMOL with it. Is this common? Any ideas on fixing it? It's probably my lack of understanding on how APBS works.
[[User:Inchoate|Tree]] 07:40, 22 February 2008 (CST)

For me it doesn't crash, but asks me to calculate the pqr file myself. Than it calculates the map fine.
[[User:Desastre|Desastre]] 27 April 2008

== Making the default paths to work? ==

I saw a discussion in the Pymolbb dated April 15, 2010 [http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07858.html] about the default paths for binaries, psize.py, and temp files not loading automatically or even saving the paths.

I am wondering if anyone has solved this issue.

After installing pymol through fink, none of the binaries show up. After installing pdb2pqr through fink, the apbs plugin (Apbs Tools 2) does load /sw/share/pdb2pqr/pdb2pqr.py automatically. However, after installing apbs-mpi-openmpi through fink, neither APBS binary nor APBS psize.py load.

I have tried modifying apbs_tools.py (/sw/lib/pymol-py26/modules/pmg_tk/startup/apbs_tools.py) in lines 112 through 115 to:
APBS_BINARY_LOCATION = '/sw/bin/apbs-mpi-openmpi'
APBS_PSIZE_LOCATION = '/sw/share/apbs-mpi-openmpi/tools/manip/psize.py'
APBS_PDB2PQR_LOCATION = None
TEMPORARY_FILE_DIR = None

My $APBS_PSIZE returns /sw/share/apbs-mpi-openmpi/tools/manip by default, as installed through fink. I use 64-bit fink, pymol 1.3, and Snow Leopard OSX.

The default temporary file locations also do not work. I have also tried to make apbs plugin save these these to no avail.

I hope a solution to this issue can be posted in the wiki.

PS.: I have looked at the output from X11 when pymol loads, and it seems it tries to load
trying /sw/bin/apbs-mpi-openmpi/psize.py
trying '''/sw/share/apbs-mpi-openmpi/tools/manip/psize.py'''/psize.py
trying /sw/share/pdb2pqr/psize.py

and
trying '''/sw/bin/apbs-mpi-openmpi'''/apbs.exe
trying /sw/share/apbs-mpi-openmpi/tools/manip/psize.py/apbs.exe
trying /sw/share/pdb2pqr/apbs.exe
trying /sw/share/apbs/tools/manip/apbs.exe
trying /sw/bin/apbs.exe

Which are obviously wrong. The correct paths should be '''/sw/share/apbs-mpi-openmpi/tools/manip/psize.py''' and '''/sw/bin/apbs-mpi-openmpi'''.
--[[User:Rendereason|Rendereason]] 22:40, 20 July 2010 (UTC)

'''Fixed''' in the current version of the plugin, which you can download from [http://pymolwiki.org/index.php/User:Mglerner my user page]. The issue was that the plugin just didn't know about MPI-enabled versions. --[[User:Mglerner|michael]] 23:48, 22 July 2010 (UTC)

==Running with APBS 1.3 not working==
Well, I tried making the plugin run with APBS 1.3 and this is what I got:
Running:
prog=/usr/local/apbs-1.3-mac-univ/bin/apbs
args=('/usr/local/apbs-1.3-mac-univ/bin/apbs', '--version')
Results were:
Return value: -5
Output:
dyld: Library not loaded: /usr/local/lib/x86_64/libgomp.1.dylib
Referenced from: /usr/local/apbs-1.3-mac-univ/bin/apbs
Reason: image not found
Skipping /usr/local/apbs-1.3-mac-univ/bin/apbs because it appears to be broken (dyld)

Just wondering if you get the same. --[[User:Rendereason|Rendereason]] 16:36, 29 October 2010 (UTC)

I think I see why it's doing that. My folder structure is not right. APBS needs to update its install instructions/README. I'll try moving the folders to /sw64/bin/apbs, /sw64/share/apbs, etc.--[[User:Rendereason|Rendereason]] 16:49, 29 October 2010 (UTC)

The installation guide says:
"The APBS binaries do not contain dependencies on special data files, etc. and can be moved out of this directory structure without causing any problems for APBS execution." [http://www.poissonboltzmann.org/apbs/user-guide/installation-and-avil From APBS webpage.]
I have tried setting the variable ${APBS_PREFIX} to /usr/local/apbs-.13-mac-univ.
I've added these to my .zshrc but none of it works
APBS_PREFIX=/usr/local/apbs-1.3-mac-univ/
APBS_BINARY_DIR=/usr/local/apbs-1.3-mac-univ/bin/
APBS_PSIZE_DIR=/usr/local/apbs-1.3-mac-univ/share/tools/manip/
export APBS_PREFIX
export APBS_BINARY_DIR
export APBS_PSIZE_DIR
None of this had any effect on the unmodified apbsplugin.py. (When parameters set to ''None'')
Changing the parameters within apbsplugin.py to their desired folders gives the error above.
--[[User:Rendereason|Rendereason]] 16:57, 29 October 2010 (UTC)

Have you tried the pre-release version available on my page? I fixed some things recently, and this bug doesn't happen for me any more. --[[User:Mglerner|michael]] 19:40, 29 October 2010 (UTC)

Yes. I have. Also, I get this problem:
GENERATING PQR FILE via PDB2PQR
Erasing contents of /tmp/pymol-generated.pdb in order to generate new PDB file
Erasing contents of /tmp/pymol-generated.pdb in order to clean it up
TESTING
DONE TESTING
Appended /sw64
Unexpected error encountered while trying to import pdb2pqr: (<type 'exceptions.ImportError'>, ImportError('No module named pdb2pqr.pdb2pqr',), <traceback object at 0x116714908>)
In show error 2
Could not generate PDB2PQR file. _generatePdb2pqrPqrFile failed.
Could not generate PQR file!
--[[User:Rendereason|Rendereason]] 22:48, 4 November 2010 (UTC)

Talk:APBS

2010-11-04T22:47:07Z

Rendereason:

I've added some details about where and how to download and install apbs and its dependencies. I have cross-referenced a description of how this can be done on OS X.

I've put a few very tentative lines in about linux.

== Well done! ==

Hey, thanks for this plugin. It worked on an SMP 64-bit Linux machine with little effort. Still crashes a bit, but the effort is worth it.
[[User:Inchoate|Tree]] 18:21, 21 February 2008 (CST)

== Question/Crash ==

I ran APBS on 2ILK. When I try to show the solv. acc. map, it computes something for a sec, then crashes taking PyMOL with it. Is this common? Any ideas on fixing it? It's probably my lack of understanding on how APBS works.
[[User:Inchoate|Tree]] 07:40, 22 February 2008 (CST)

For me it doesn't crash, but asks me to calculate the pqr file myself. Than it calculates the map fine.
[[User:Desastre|Desastre]] 27 April 2008

== Making the default paths to work? ==

I saw a discussion in the Pymolbb dated April 15, 2010 [http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07858.html] about the default paths for binaries, psize.py, and temp files not loading automatically or even saving the paths.

I am wondering if anyone has solved this issue.

After installing pymol through fink, none of the binaries show up. After installing pdb2pqr through fink, the apbs plugin (Apbs Tools 2) does load /sw/share/pdb2pqr/pdb2pqr.py automatically. However, after installing apbs-mpi-openmpi through fink, neither APBS binary nor APBS psize.py load.

I have tried modifying apbs_tools.py (/sw/lib/pymol-py26/modules/pmg_tk/startup/apbs_tools.py) in lines 112 through 115 to:
APBS_BINARY_LOCATION = '/sw/bin/apbs-mpi-openmpi'
APBS_PSIZE_LOCATION = '/sw/share/apbs-mpi-openmpi/tools/manip/psize.py'
APBS_PDB2PQR_LOCATION = None
TEMPORARY_FILE_DIR = None

My $APBS_PSIZE returns /sw/share/apbs-mpi-openmpi/tools/manip by default, as installed through fink. I use 64-bit fink, pymol 1.3, and Snow Leopard OSX.

The default temporary file locations also do not work. I have also tried to make apbs plugin save these these to no avail.

I hope a solution to this issue can be posted in the wiki.

PS.: I have looked at the output from X11 when pymol loads, and it seems it tries to load
trying /sw/bin/apbs-mpi-openmpi/psize.py
trying '''/sw/share/apbs-mpi-openmpi/tools/manip/psize.py'''/psize.py
trying /sw/share/pdb2pqr/psize.py

and
trying '''/sw/bin/apbs-mpi-openmpi'''/apbs.exe
trying /sw/share/apbs-mpi-openmpi/tools/manip/psize.py/apbs.exe
trying /sw/share/pdb2pqr/apbs.exe
trying /sw/share/apbs/tools/manip/apbs.exe
trying /sw/bin/apbs.exe

Which are obviously wrong. The correct paths should be '''/sw/share/apbs-mpi-openmpi/tools/manip/psize.py''' and '''/sw/bin/apbs-mpi-openmpi'''.
--[[User:Rendereason|Rendereason]] 22:40, 20 July 2010 (UTC)

'''Fixed''' in the current version of the plugin, which you can download from [http://pymolwiki.org/index.php/User:Mglerner my user page]. The issue was that the plugin just didn't know about MPI-enabled versions. --[[User:Mglerner|michael]] 23:48, 22 July 2010 (UTC)

==Running with APBS 1.3 not working==
Well, I tried making the plugin run with APBS 1.3 and this is what I got:
Running:
prog=/usr/local/apbs-1.3-mac-univ/bin/apbs
args=('/usr/local/apbs-1.3-mac-univ/bin/apbs', '--version')
Results were:
Return value: -5
Output:
dyld: Library not loaded: /usr/local/lib/x86_64/libgomp.1.dylib
Referenced from: /usr/local/apbs-1.3-mac-univ/bin/apbs
Reason: image not found
Skipping /usr/local/apbs-1.3-mac-univ/bin/apbs because it appears to be broken (dyld)

Just wondering if you get the same. --[[User:Rendereason|Rendereason]] 16:36, 29 October 2010 (UTC)

I think I see why it's doing that. My folder structure is not right. APBS needs to update its install instructions/README. I'll try moving the folders to /sw64/bin/apbs, /sw64/share/apbs, etc.--[[User:Rendereason|Rendereason]] 16:49, 29 October 2010 (UTC)

The installation guide says:
"The APBS binaries do not contain dependencies on special data files, etc. and can be moved out of this directory structure without causing any problems for APBS execution." [http://www.poissonboltzmann.org/apbs/user-guide/installation-and-avil From APBS webpage.]
I have tried setting the variable ${APBS_PREFIX} to /usr/local/apbs-.13-mac-univ.
I've added these to my .zshrc but none of it works
APBS_PREFIX=/usr/local/apbs-1.3-mac-univ/
APBS_BINARY_DIR=/usr/local/apbs-1.3-mac-univ/bin/
APBS_PSIZE_DIR=/usr/local/apbs-1.3-mac-univ/share/tools/manip/
export APBS_PREFIX
export APBS_BINARY_DIR
export APBS_PSIZE_DIR
None of this had any effect on the unmodified apbsplugin.py. (When parameters set to ''None'')
Changing the parameters within apbsplugin.py to their desired folders gives the error above.
--[[User:Rendereason|Rendereason]] 16:57, 29 October 2010 (UTC)

Have you tried the pre-release version available on my page? I fixed some things recently, and this bug doesn't happen for me any more. --[[User:Mglerner|michael]] 19:40, 29 October 2010 (UTC)
Yes. I have. Also, I get this problem:
GENERATING PQR FILE via PDB2PQR
Erasing contents of /tmp/pymol-generated.pdb in order to generate new PDB file
Erasing contents of /tmp/pymol-generated.pdb in order to clean it up
TESTING
DONE TESTING
Appended /sw64
Unexpected error encountered while trying to import pdb2pqr: (<type 'exceptions.ImportError'>, ImportError('No module named pdb2pqr.pdb2pqr',), <traceback object at 0x116714908>)
In show error 2
Could not generate PDB2PQR file. _generatePdb2pqrPqrFile failed.
Could not generate PQR file!

APBS

2010-11-03T19:30:45Z

Rendereason: moved Michael's note under apbs plugin

== Introduction ==
[[Image:Rna_surface_apbs.png|thumb|APBS-generated electrostatic surface displayed in PyMOL]]
[http://apbs.sourceforge.net APBS], the Adaptive Poisson-Boltzmann Solver, is a [http://www.oreilly.com/openbook/freedom/ freely] available macromolecular electrostatics calculation program released under the [http://www.gnu.org/copyleft/gpl.html GPL]. It is a cost-effective but uncompromised alternative to [http://trantor.bioc.columbia.edu/grasp/ GRASP], and it can be used within PyMOL. PyMOL can display the results of the calculations as an electrostatic potential molecular surface.

== APBS Plugin with New Features ==
=== Pre-release version ===

There is often a more current pre-release version available on my user page. If you're experiencing bugs, please test the pre-release version to see if they've already been fixed. Thanks! --[[User:Mglerner|michael]] 19:43, 29 October 2010 (UTC)
----
PyMol currently supports the '''APBS plugin''' written by [http://pymolwiki.org/index.php/User:Mglerner Michael Lerner]. This plugin makes it possible to run APBS from within PyMOL, and then display the results as a color-coded electrostatic surface (units <math>K_bT/e_c</math>) in the molecular display window (as with the image to the right). This wiki page has updated instructions on how to download, install and use the plugin.

'''Nucleic acids may prove problematic for the apbs plugin.''' If so, use the [http://pdb2pqr.sourceforge.net/ pdb2pqr] command-line tool to create a pqr file manually, instead of using the plugin to generate it. Then direct the APBS GUI on the [http://www-personal.umich.edu/~mlerner/PyMOL/images/main.png main menu] to read the pqr file you '''externally generated.'''

There is 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.
* It allows you to call through to PDB2PQR directly.
* It allows you to show the electric field lines.
* It has two visualization panels to aid in showing multiple potential surfaces at once.
* It defaults to using PDB2PQR for PQR generation and APBS's psize.py for grid sizing/spacing.
* It has also an increased default maximum allowed memory since typical users have bigger and faster computers these days.
* It calls on the correct paths and binaries for multi-threaded APBS (apbs-mpi-openmpi).

The main reason it is not included in the latest PyMOL release is to receive bug reports. Once it's shown to be stable, it'll be included in the next PyMOL release. See [http://pymolwiki.org/index.php/User:Mglerner Michael Lerner]'s page.

==== How to get it ====

There are two ways to get the new plugin

* If you have subversion installed, you can always get the latest version via

<source lang="bash">
svn co http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py
</source>

* 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

Once you have the plugin, you can install it via PyMOL's plugin installer: Plugin --> Manage Plugins --> Install

You may have to run PyMOL with sudo privileges.

Note that the plugin will be installed as "APBS Tools2.1" so that you can continue to use your old version.

Further details, as well as screen shots, are given [http://www.pymolwiki.org/index.php/MAC_Install#Install_APBS_and_friends_with_fink elsewhere in this wiki].

==Required Dependencies==
[http://apbs.sourceforge.net APBS] and its dependencies like [http://pdb2pqr.sourceforge.net pdb2pqr] and [http://scicomp.ucsd.edu/~mholst/codes/maloc/ maloc] are [http://www.oreilly.com/openbook/freedom/ freely] available under the [http://www.gnu.org/copyleft/gpl.html GPL]. The author of the software however [http://agave.wustl.edu/apbs/download/ asks that users register] with him to aid him in obtaining grant funding.

----
===Installing the Dependencies on OS X===
#First, [http://agave.wustl.edu/apbs/download/ register] your use of the software. This will keep everyone happy.
#Second, if you don't already have the [http://fink.sourceforge.net fink package management system], now is a good time to get it. Here is a [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start quick-start set of instructions] for getting X-windows, compilers, and fink all installed.
#Once you are up and going, [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch in fink], and then issue the commands
<source lang="bash">
fink self-update
fink install apbs
</source>
or if you want to use the multi-processor version, issue
<source lang="bash">
fink self-update
fink install apbs-mpi-openmpi
</source>
Then install the X-windows based version of pymol using the command
<source lang="bash">
fink install pymol-py25
</source>
It is recommended to install the latest pdb2pqr as well as the APBS plugin makes use of it
<source lang="bash">
fink install pdb2pqr
</source>
Note that the fink version of PyMOL as of 1.3-4 does not have the latest version of the APBS plugin. Make sure you get the new version!

===Installing the Dependencies on Linux===

====From Scratch====
Note that this tutorial assumes you're using the bash shell and have root privileges
<OL><LI>
Obtain APBS and MALOC from... 
APBS = http://apbs.sourceforge.net (currently 0.4) 
MALOC = http://www.fetk.org/codes/maloc/index.html#download (currently 0.1-2) 
<LI>Set up some environment variables & directories (temporary for building)
<source lang="bash">
$ export FETK_SRC=/<building directory>/temp_apbs
$ export FETK_PREFIX=/usr/local/apbs-0.4.0 (or wherever you want it to live)
$ export FETK_INCLUDE=${FETK_PREFIX}/include
$ export FETK_LIBRARY=${FETK_PREFIX}/lib
$ mkdir -p ${FETK_SRC} ${FETK_INCLUDE} ${FETK_LIBRARY}
</source></LI>
<LI>Unpack the source packages
<source lang="bash">
$ cd ${FETK_SRC}
$ gzip -dc maloc-0.1-2.tar.gz | tar xvf -
$ gzip -dc apbs-0.4.0.tar.gz | tar xvf -
</source>
</LI>
<LI>Compile MALOC
<source lang="bash">
$ cd ${FETK_SRC}/maloc
$ ./configure --prefix=${FETK_PREFIX}</source>
If everything went well, then
<source lang="bash">
$ make; make install</source></LI>
<LI>Go get a coffee. Compilation/installation takes about 15 minutes on a 3GHz computer with 1GB of RAM.</LI>
<LI>Now on to compiling APBS itself
<source lang="bash">
$ cd ${FETK_SRC}/apbs-0.4.0
$ ./configure --prefix=${FETK_PREFIX}</source>
If all goes well:
<source lang="bash">
$ make all; make install</source></LI>
<LI>No time for coffee. Takes about 5 minutes on that fast computer.</LI>
<LI> There will now be an APBS binary at
<source lang="bash">/usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs</source></LI>
<LI> Make appropriate links
<source lang="bash">
$ ln -s /usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs /usr/local/bin/apbs
</source></LI>
<LI> Get rid of /<building directory dir>/temp_apbs
<LI> Open PyMOL and make sure that the APBS plugin points to /usr/local/bin/apbs
<LI> Rock and or Roll.
</OL>

====Pre-Packaged====
=====RPMs=====

A variety of RPMs are available from the [http://sourceforge.net/project/showfiles.php?group_id=148472&package_id=163734&release_id=378273 APBS downloads website]. Again, please [http://agave.wustl.edu/apbs/download/ register] your use of the software if you have not yet done so.

=====Debian packages=====

For ubuntu and other debian linux distributions, probably the simplest thing is to download a promising looking rpm, convert it with the program [http://kitenet.net/programs/alien/ alien], and then install the [http://xanana.ucsc.edu/linux newly generated debian package] with the command
<source lang="bash">
sudo dpkg -i apbs*.deb
</source>

=====Gentoo=====

You have to install apbs and pdb2pqr. Both are masked via keywords atm. Type as root:
<source lang="bash">
echo sci-chemistry/pdb2pqr >> /etc/portage/package.keywords
echo sci-chemistry/apbs >> /etc/portage/package.keywords
emerge -av sci-chemistry/apbs sci-chemistry/pdb2pqr
</source>

== Troubleshooting ==
* If the B-factor is <math>\geq 100,</math> then APBS doesn't properly read in the PDB file and thus outputs garbage (or dies). To fix this, set all b factors to be less than 100. <source lang="python">alter all, b=min(b,99.9)</source> The problem stems from how to parse a PDB file. The PDB file originally was written when most people used FORTRAN programs, and so the file format was specified by columns, not by the more modern comma separated value format we tend to prefer today. For the latest on the PDB format see the [http://www.wwpdb.org/docs.html new PDB format docs].
* APBS has problems, sometimes, in reading atoms with alternate conformations. You can remove the alternate locations with a simple script [[removeAlt]].
* ObjectMapLoadDXFile-Error: as of this writing (9-23-2008) a known problem exists, and the Baker lab is working on it. It is typically caused by the use of directories with spaces in their names under Windows.

== Problems with the bundled version of APBS ==
There is an issue with the freemol version of APBS shipped with PyMOL 1.2r2 for OS X.

=== Leopard and Snow Leopard (10.5 and 10.6) ===
There are three fairly easy ways to resolve it

1. 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).

2. 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").

<source lang="bash">
bunzip2 libgfortran.3.dylib.gz2
mv libgfortran.3.dylib /usr/local/lib
</source>

3. Use macports to install gcc 4.4.2 and link the appropriate library ("ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib" ... on some machines, you may need "sudo ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib").

<source lang="bash">
ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib
sudo ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib
</source>

If you're curious, the problem is that APBS is dynamically linked, but Apple does not provide FORTRAN libraries.

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) ===
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

<source lang="bash">
sudo port install apbs
</source>

from the command line. This process could easily take several hours on an older machine, as MacPorts will recompile gcc, gfortran, and several other packages along the way.

==Using APBS==
There is a nice tutorial on the APBS homepage: [http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol] For further help, there is a mailing list [https://lists.sourceforge.net/lists/listinfo/apbs-users] with the corresponding archive [http://sourceforge.net/mailarchive/forum.php?forum_name=apbs-users]

==Further contributions and edits are needed.==

[[Category:Electrostatics]]
[[Category:Biochemical_Properties]]
[[Category:Plugins]]

APBS

2010-11-03T19:21:27Z

Rendereason: Updated the link for svn.

== Pre-release version ==

There is often a more current pre-release version available on my user page. If you're experiencing bugs, please test the pre-release version to see if they've already been fixed. Thanks! --[[User:Mglerner|michael]] 19:43, 29 October 2010 (UTC)

== Introduction ==
[[Image:Rna_surface_apbs.png|thumb|APBS-generated electrostatic surface displayed in PyMOL]]
[http://apbs.sourceforge.net APBS], the Adaptive Poisson-Boltzmann Solver, is a [http://www.oreilly.com/openbook/freedom/ freely] available macromolecular electrostatics calculation program released under the [http://www.gnu.org/copyleft/gpl.html GPL]. It is a cost-effective but uncompromised alternative to [http://trantor.bioc.columbia.edu/grasp/ GRASP], and it can be used within PyMOL. PyMOL can display the results of the calculations as an electrostatic potential molecular surface.

=== APBS Plugin with New Features ===
PyMol currently supports the '''APBS plugin''' written by [http://pymolwiki.org/index.php/User:Mglerner Michael Lerner]. This plugin makes it possible to run APBS from within PyMOL, and then display the results as a color-coded electrostatic surface (units <math>K_bT/e_c</math>) in the molecular display window (as with the image to the right). This wiki page has updated instructions on how to download, install and use the plugin.

'''Nucleic acids may prove problematic for the apbs plugin.''' If so, use the [http://pdb2pqr.sourceforge.net/ pdb2pqr] command-line tool to create a pqr file manually, instead of using the plugin to generate it. Then direct the APBS GUI on the [http://www-personal.umich.edu/~mlerner/PyMOL/images/main.png main menu] to read the pqr file you '''externally generated.'''

There is 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.
* It allows you to call through to PDB2PQR directly.
* It allows you to show the electric field lines.
* It has two visualization panels to aid in showing multiple potential surfaces at once.
* It defaults to using PDB2PQR for PQR generation and APBS's psize.py for grid sizing/spacing.
* It has also an increased default maximum allowed memory since typical users have bigger and faster computers these days.
* It calls on the correct paths and binaries for multi-threaded APBS (apbs-mpi-openmpi).

The main reason it is not included in the latest PyMOL release is to receive bug reports. Once it's shown to be stable, it'll be included in the next PyMOL release. See [http://pymolwiki.org/index.php/User:Mglerner Michael Lerner]'s page.

==== How to get it ====

There are two ways to get the new plugin

* If you have subversion installed, you can always get the latest version via

<source lang="bash">
svn co http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py
</source>

* 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

Once you have the plugin, you can install it via PyMOL's plugin installer: Plugin --> Manage Plugins --> Install

You may have to run PyMOL with sudo privileges.

Note that the plugin will be installed as "APBS Tools2.1" so that you can continue to use your old version.

Further details, as well as screen shots, are given [http://www.pymolwiki.org/index.php/MAC_Install#Install_APBS_and_friends_with_fink elsewhere in this wiki].

==Required Dependencies==
[http://apbs.sourceforge.net APBS] and its dependencies like [http://pdb2pqr.sourceforge.net pdb2pqr] and [http://scicomp.ucsd.edu/~mholst/codes/maloc/ maloc] are [http://www.oreilly.com/openbook/freedom/ freely] available under the [http://www.gnu.org/copyleft/gpl.html GPL]. The author of the software however [http://agave.wustl.edu/apbs/download/ asks that users register] with him to aid him in obtaining grant funding.

----
===Installing the Dependencies on OS X===
#First, [http://agave.wustl.edu/apbs/download/ register] your use of the software. This will keep everyone happy.
#Second, if you don't already have the [http://fink.sourceforge.net fink package management system], now is a good time to get it. Here is a [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start quick-start set of instructions] for getting X-windows, compilers, and fink all installed.
#Once you are up and going, [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch in fink], and then issue the commands
<source lang="bash">
fink self-update
fink install apbs
</source>
or if you want to use the multi-processor version, issue
<source lang="bash">
fink self-update
fink install apbs-mpi-openmpi
</source>
Then install the X-windows based version of pymol using the command
<source lang="bash">
fink install pymol-py25
</source>
It is recommended to install the latest pdb2pqr as well as the APBS plugin makes use of it
<source lang="bash">
fink install pdb2pqr
</source>
Note that the fink version of PyMOL as of 1.3-4 does not have the latest version of the APBS plugin. Make sure you get the new version!

===Installing the Dependencies on Linux===

====From Scratch====
Note that this tutorial assumes you're using the bash shell and have root privileges
<OL><LI>
Obtain APBS and MALOC from... 
APBS = http://apbs.sourceforge.net (currently 0.4) 
MALOC = http://www.fetk.org/codes/maloc/index.html#download (currently 0.1-2) 
<LI>Set up some environment variables & directories (temporary for building)
<source lang="bash">
$ export FETK_SRC=/<building directory>/temp_apbs
$ export FETK_PREFIX=/usr/local/apbs-0.4.0 (or wherever you want it to live)
$ export FETK_INCLUDE=${FETK_PREFIX}/include
$ export FETK_LIBRARY=${FETK_PREFIX}/lib
$ mkdir -p ${FETK_SRC} ${FETK_INCLUDE} ${FETK_LIBRARY}
</source></LI>
<LI>Unpack the source packages
<source lang="bash">
$ cd ${FETK_SRC}
$ gzip -dc maloc-0.1-2.tar.gz | tar xvf -
$ gzip -dc apbs-0.4.0.tar.gz | tar xvf -
</source>
</LI>
<LI>Compile MALOC
<source lang="bash">
$ cd ${FETK_SRC}/maloc
$ ./configure --prefix=${FETK_PREFIX}</source>
If everything went well, then
<source lang="bash">
$ make; make install</source></LI>
<LI>Go get a coffee. Compilation/installation takes about 15 minutes on a 3GHz computer with 1GB of RAM.</LI>
<LI>Now on to compiling APBS itself
<source lang="bash">
$ cd ${FETK_SRC}/apbs-0.4.0
$ ./configure --prefix=${FETK_PREFIX}</source>
If all goes well:
<source lang="bash">
$ make all; make install</source></LI>
<LI>No time for coffee. Takes about 5 minutes on that fast computer.</LI>
<LI> There will now be an APBS binary at
<source lang="bash">/usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs</source></LI>
<LI> Make appropriate links
<source lang="bash">
$ ln -s /usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs /usr/local/bin/apbs
</source></LI>
<LI> Get rid of /<building directory dir>/temp_apbs
<LI> Open PyMOL and make sure that the APBS plugin points to /usr/local/bin/apbs
<LI> Rock and or Roll.
</OL>

====Pre-Packaged====
=====RPMs=====

A variety of RPMs are available from the [http://sourceforge.net/project/showfiles.php?group_id=148472&package_id=163734&release_id=378273 APBS downloads website]. Again, please [http://agave.wustl.edu/apbs/download/ register] your use of the software if you have not yet done so.

=====Debian packages=====

For ubuntu and other debian linux distributions, probably the simplest thing is to download a promising looking rpm, convert it with the program [http://kitenet.net/programs/alien/ alien], and then install the [http://xanana.ucsc.edu/linux newly generated debian package] with the command
<source lang="bash">
sudo dpkg -i apbs*.deb
</source>

=====Gentoo=====

You have to install apbs and pdb2pqr. Both are masked via keywords atm. Type as root:
<source lang="bash">
echo sci-chemistry/pdb2pqr >> /etc/portage/package.keywords
echo sci-chemistry/apbs >> /etc/portage/package.keywords
emerge -av sci-chemistry/apbs sci-chemistry/pdb2pqr
</source>

== Troubleshooting ==
* If the B-factor is <math>\geq 100,</math> then APBS doesn't properly read in the PDB file and thus outputs garbage (or dies). To fix this, set all b factors to be less than 100. <source lang="python">alter all, b=min(b,99.9)</source> The problem stems from how to parse a PDB file. The PDB file originally was written when most people used FORTRAN programs, and so the file format was specified by columns, not by the more modern comma separated value format we tend to prefer today. For the latest on the PDB format see the [http://www.wwpdb.org/docs.html new PDB format docs].
* APBS has problems, sometimes, in reading atoms with alternate conformations. You can remove the alternate locations with a simple script [[removeAlt]].
* ObjectMapLoadDXFile-Error: as of this writing (9-23-2008) a known problem exists, and the Baker lab is working on it. It is typically caused by the use of directories with spaces in their names under Windows.

== Problems with the bundled version of APBS ==
There is an issue with the freemol version of APBS shipped with PyMOL 1.2r2 for OS X.

=== Leopard and Snow Leopard (10.5 and 10.6) ===
There are three fairly easy ways to resolve it

1. 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).

2. 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").

<source lang="bash">
bunzip2 libgfortran.3.dylib.gz2
mv libgfortran.3.dylib /usr/local/lib
</source>

3. Use macports to install gcc 4.4.2 and link the appropriate library ("ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib" ... on some machines, you may need "sudo ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib").

<source lang="bash">
ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib
sudo ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib
</source>

If you're curious, the problem is that APBS is dynamically linked, but Apple does not provide FORTRAN libraries.

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) ===
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

<source lang="bash">
sudo port install apbs
</source>

from the command line. This process could easily take several hours on an older machine, as MacPorts will recompile gcc, gfortran, and several other packages along the way.

==Using APBS==
There is a nice tutorial on the APBS homepage: [http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol] For further help, there is a mailing list [https://lists.sourceforge.net/lists/listinfo/apbs-users] with the corresponding archive [http://sourceforge.net/mailarchive/forum.php?forum_name=apbs-users]

==Further contributions and edits are needed.==

[[Category:Electrostatics]]
[[Category:Biochemical_Properties]]
[[Category:Plugins]]

Talk:APBS

2010-10-29T19:29:43Z

Rendereason:

Talk:APBS

2010-10-29T19:27:58Z

Rendereason:

I've added some details about where and how to download and install apbs and its dependencies. I have cross-referenced a description of how this can be done on OS X.

I've put a few very tentative lines in about linux.

== Well done! ==

Hey, thanks for this plugin. It worked on an SMP 64-bit Linux machine with little effort. Still crashes a bit, but the effort is worth it.
[[User:Inchoate|Tree]] 18:21, 21 February 2008 (CST)

== Question/Crash ==

I ran APBS on 2ILK. When I try to show the solv. acc. map, it computes something for a sec, then crashes taking PyMOL with it. Is this common? Any ideas on fixing it? It's probably my lack of understanding on how APBS works.
[[User:Inchoate|Tree]] 07:40, 22 February 2008 (CST)

For me it doesn't crash, but asks me to calculate the pqr file myself. Than it calculates the map fine.
[[User:Desastre|Desastre]] 27 April 2008

== Making the default paths to work? ==

I saw a discussion in the Pymolbb dated April 15, 2010 [http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07858.html] about the default paths for binaries, psize.py, and temp files not loading automatically or even saving the paths.

I am wondering if anyone has solved this issue.

After installing pymol through fink, none of the binaries show up. After installing pdb2pqr through fink, the apbs plugin (Apbs Tools 2) does load /sw/share/pdb2pqr/pdb2pqr.py automatically. However, after installing apbs-mpi-openmpi through fink, neither APBS binary nor APBS psize.py load.

I have tried modifying apbs_tools.py (/sw/lib/pymol-py26/modules/pmg_tk/startup/apbs_tools.py) in lines 112 through 115 to:
APBS_BINARY_LOCATION = '/sw/bin/apbs-mpi-openmpi'
APBS_PSIZE_LOCATION = '/sw/share/apbs-mpi-openmpi/tools/manip/psize.py'
APBS_PDB2PQR_LOCATION = None
TEMPORARY_FILE_DIR = None

My $APBS_PSIZE returns /sw/share/apbs-mpi-openmpi/tools/manip by default, as installed through fink. I use 64-bit fink, pymol 1.3, and Snow Leopard OSX.

The default temporary file locations also do not work. I have also tried to make apbs plugin save these these to no avail.

I hope a solution to this issue can be posted in the wiki.

PS.: I have looked at the output from X11 when pymol loads, and it seems it tries to load
trying /sw/bin/apbs-mpi-openmpi/psize.py
trying '''/sw/share/apbs-mpi-openmpi/tools/manip/psize.py'''/psize.py
trying /sw/share/pdb2pqr/psize.py

and
trying '''/sw/bin/apbs-mpi-openmpi'''/apbs.exe
trying /sw/share/apbs-mpi-openmpi/tools/manip/psize.py/apbs.exe
trying /sw/share/pdb2pqr/apbs.exe
trying /sw/share/apbs/tools/manip/apbs.exe
trying /sw/bin/apbs.exe

Which are obviously wrong. The correct paths should be '''/sw/share/apbs-mpi-openmpi/tools/manip/psize.py''' and '''/sw/bin/apbs-mpi-openmpi'''.
--[[User:Rendereason|Rendereason]] 22:40, 20 July 2010 (UTC)

'''Fixed''' in the current version of the plugin, which you can download from [http://pymolwiki.org/index.php/User:Mglerner my user page]. The issue was that the plugin just didn't know about MPI-enabled versions. --[[User:Mglerner|michael]] 23:48, 22 July 2010 (UTC)

==Running with APBS 1.3 not working==
Well, I tried making the plugin run with APBS 1.3 and this is what I got:
Running:
prog=/usr/local/apbs-1.3-mac-univ/bin/apbs
args=('/usr/local/apbs-1.3-mac-univ/bin/apbs', '--version')
Results were:
Return value: -5
Output:
dyld: Library not loaded: /usr/local/lib/x86_64/libgomp.1.dylib
Referenced from: /usr/local/apbs-1.3-mac-univ/bin/apbs
Reason: image not found
Skipping /usr/local/apbs-1.3-mac-univ/bin/apbs because it appears to be broken (dyld)

Just wondering if you get the same. --[[User:Rendereason|Rendereason]] 16:36, 29 October 2010 (UTC)

I think I see why it's doing that. My folder structure is not right. APBS needs to update its install instructions/README. I'll try moving the folders to /sw64/bin/apbs, /sw64/share/apbs, etc.--[[User:Rendereason|Rendereason]] 16:49, 29 October 2010 (UTC)

I found out:
"The APBS binaries do not contain dependencies on special data files, etc. and can be moved out of this directory structure without causing any problems for APBS execution." [http://www.poissonboltzmann.org/apbs/user-guide/installation-and-avil From APBS webpage.]
I have tried setting the variable ${APBS_PREFIX} to /usr/local/apbs-.13-mac-univ.
I've added these to my .zshrc but none of it works
APBS_PREFIX=/usr/local/apbs-1.3-mac-univ/
APBS_BINARY_DIR=/usr/local/apbs-1.3-mac-univ/bin/
APBS_PSIZE_DIR=/usr/local/apbs-1.3-mac-univ/share/tools/manip/
export APBS_PREFIX
export APBS_BINARY_DIR
export APBS_PSIZE_DIR
None of this works.
--[[User:Rendereason|Rendereason]] 16:57, 29 October 2010 (UTC)

Talk:APBS

2010-10-29T16:58:27Z

Rendereason:

I've added some details about where and how to download and install apbs and its dependencies. I have cross-referenced a description of how this can be done on OS X.

I've put a few very tentative lines in about linux.

== Well done! ==

Hey, thanks for this plugin. It worked on an SMP 64-bit Linux machine with little effort. Still crashes a bit, but the effort is worth it.
[[User:Inchoate|Tree]] 18:21, 21 February 2008 (CST)

== Question/Crash ==

I ran APBS on 2ILK. When I try to show the solv. acc. map, it computes something for a sec, then crashes taking PyMOL with it. Is this common? Any ideas on fixing it? It's probably my lack of understanding on how APBS works.
[[User:Inchoate|Tree]] 07:40, 22 February 2008 (CST)

For me it doesn't crash, but asks me to calculate the pqr file myself. Than it calculates the map fine.
[[User:Desastre|Desastre]] 27 April 2008

== Making the default paths to work? ==

I saw a discussion in the Pymolbb dated April 15, 2010 [http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07858.html] about the default paths for binaries, psize.py, and temp files not loading automatically or even saving the paths.

I am wondering if anyone has solved this issue.

After installing pymol through fink, none of the binaries show up. After installing pdb2pqr through fink, the apbs plugin (Apbs Tools 2) does load /sw/share/pdb2pqr/pdb2pqr.py automatically. However, after installing apbs-mpi-openmpi through fink, neither APBS binary nor APBS psize.py load.

I have tried modifying apbs_tools.py (/sw/lib/pymol-py26/modules/pmg_tk/startup/apbs_tools.py) in lines 112 through 115 to:
APBS_BINARY_LOCATION = '/sw/bin/apbs-mpi-openmpi'
APBS_PSIZE_LOCATION = '/sw/share/apbs-mpi-openmpi/tools/manip/psize.py'
APBS_PDB2PQR_LOCATION = None
TEMPORARY_FILE_DIR = None

My $APBS_PSIZE returns /sw/share/apbs-mpi-openmpi/tools/manip by default, as installed through fink. I use 64-bit fink, pymol 1.3, and Snow Leopard OSX.

The default temporary file locations also do not work. I have also tried to make apbs plugin save these these to no avail.

I hope a solution to this issue can be posted in the wiki.

PS.: I have looked at the output from X11 when pymol loads, and it seems it tries to load
trying /sw/bin/apbs-mpi-openmpi/psize.py
trying '''/sw/share/apbs-mpi-openmpi/tools/manip/psize.py'''/psize.py
trying /sw/share/pdb2pqr/psize.py

and
trying '''/sw/bin/apbs-mpi-openmpi'''/apbs.exe
trying /sw/share/apbs-mpi-openmpi/tools/manip/psize.py/apbs.exe
trying /sw/share/pdb2pqr/apbs.exe
trying /sw/share/apbs/tools/manip/apbs.exe
trying /sw/bin/apbs.exe

Which are obviously wrong. The correct paths should be '''/sw/share/apbs-mpi-openmpi/tools/manip/psize.py''' and '''/sw/bin/apbs-mpi-openmpi'''.
--[[User:Rendereason|Rendereason]] 22:40, 20 July 2010 (UTC)

'''Fixed''' in the current version of the plugin, which you can download from [http://pymolwiki.org/index.php/User:Mglerner my user page]. The issue was that the plugin just didn't know about MPI-enabled versions. --[[User:Mglerner|michael]] 23:48, 22 July 2010 (UTC)

==Running with APBS 1.3==
Well, I tried making the plugin run with APBS 1.3 and this is what I got:
Running:
prog=/usr/local/apbs-1.3-mac-univ/bin/apbs
args=('/usr/local/apbs-1.3-mac-univ/bin/apbs', '--version')
Results were:
Return value: -5
Output:
dyld: Library not loaded: /usr/local/lib/x86_64/libgomp.1.dylib
Referenced from: /usr/local/apbs-1.3-mac-univ/bin/apbs
Reason: image not found
Skipping /usr/local/apbs-1.3-mac-univ/bin/apbs because it appears to be broken (dyld)

Just wondering if you get the same. --[[User:Rendereason|Rendereason]] 16:36, 29 October 2010 (UTC)

I think I see why it's doing that. My folder structure is not right. APBS needs to update its install instructions/README. I'll try moving the folders to /sw64/bin/apbs, /sw64/share/apbs, etc.--[[User:Rendereason|Rendereason]] 16:49, 29 October 2010 (UTC)

I found out:
"The APBS binaries do not contain dependencies on special data files, etc. and can be moved out of this directory structure without causing any problems for APBS execution." [http://www.poissonboltzmann.org/apbs/user-guide/installation-and-avil From APBS webpage.]
So maybe ${APBS_PREFIX} is what needs to be fixed. I'll try that.--[[User:Rendereason|Rendereason]] 16:57, 29 October 2010 (UTC)

Talk:APBS

2010-10-29T16:57:19Z

Rendereason: /* Running with APBS 1.3 */

I've added some details about where and how to download and install apbs and its dependencies. I have cross-referenced a description of how this can be done on OS X.

I've put a few very tentative lines in about linux.

== Well done! ==

Hey, thanks for this plugin. It worked on an SMP 64-bit Linux machine with little effort. Still crashes a bit, but the effort is worth it.
[[User:Inchoate|Tree]] 18:21, 21 February 2008 (CST)

== Question/Crash ==

I ran APBS on 2ILK. When I try to show the solv. acc. map, it computes something for a sec, then crashes taking PyMOL with it. Is this common? Any ideas on fixing it? It's probably my lack of understanding on how APBS works.
[[User:Inchoate|Tree]] 07:40, 22 February 2008 (CST)

For me it doesn't crash, but asks me to calculate the pqr file myself. Than it calculates the map fine.
[[User:Desastre|Desastre]] 27 April 2008

== Making the default paths to work? ==

I saw a discussion in the Pymolbb dated April 15, 2010 [http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07858.html] about the default paths for binaries, psize.py, and temp files not loading automatically or even saving the paths.

I am wondering if anyone has solved this issue.

After installing pymol through fink, none of the binaries show up. After installing pdb2pqr through fink, the apbs plugin (Apbs Tools 2) does load /sw/share/pdb2pqr/pdb2pqr.py automatically. However, after installing apbs-mpi-openmpi through fink, neither APBS binary nor APBS psize.py load.

I have tried modifying apbs_tools.py (/sw/lib/pymol-py26/modules/pmg_tk/startup/apbs_tools.py) in lines 112 through 115 to:
APBS_BINARY_LOCATION = '/sw/bin/apbs-mpi-openmpi'
APBS_PSIZE_LOCATION = '/sw/share/apbs-mpi-openmpi/tools/manip/psize.py'
APBS_PDB2PQR_LOCATION = None
TEMPORARY_FILE_DIR = None

My $APBS_PSIZE returns /sw/share/apbs-mpi-openmpi/tools/manip by default, as installed through fink. I use 64-bit fink, pymol 1.3, and Snow Leopard OSX.

The default temporary file locations also do not work. I have also tried to make apbs plugin save these these to no avail.

I hope a solution to this issue can be posted in the wiki.

PS.: I have looked at the output from X11 when pymol loads, and it seems it tries to load
trying /sw/bin/apbs-mpi-openmpi/psize.py
trying '''/sw/share/apbs-mpi-openmpi/tools/manip/psize.py'''/psize.py
trying /sw/share/pdb2pqr/psize.py

and
trying '''/sw/bin/apbs-mpi-openmpi'''/apbs.exe
trying /sw/share/apbs-mpi-openmpi/tools/manip/psize.py/apbs.exe
trying /sw/share/pdb2pqr/apbs.exe
trying /sw/share/apbs/tools/manip/apbs.exe
trying /sw/bin/apbs.exe

Which are obviously wrong. The correct paths should be '''/sw/share/apbs-mpi-openmpi/tools/manip/psize.py''' and '''/sw/bin/apbs-mpi-openmpi'''.
--[[User:Rendereason|Rendereason]] 22:40, 20 July 2010 (UTC)

'''Fixed''' in the current version of the plugin, which you can download from [http://pymolwiki.org/index.php/User:Mglerner my user page]. The issue was that the plugin just didn't know about MPI-enabled versions. --[[User:Mglerner|michael]] 23:48, 22 July 2010 (UTC)

==Running with APBS 1.3==
Well, I tried making the plugin run with APBS 1.3 and this is what I got:
Running:
prog=/usr/local/apbs-1.3-mac-univ/bin/apbs
args=('/usr/local/apbs-1.3-mac-univ/bin/apbs', '--version')
Results were:
Return value: -5
Output:
dyld: Library not loaded: /usr/local/lib/x86_64/libgomp.1.dylib
Referenced from: /usr/local/apbs-1.3-mac-univ/bin/apbs
Reason: image not found
Skipping /usr/local/apbs-1.3-mac-univ/bin/apbs because it appears to be broken (dyld)

Just wondering if you get the same. --[[User:Rendereason|Rendereason]] 16:36, 29 October 2010 (UTC)

I think I see why it's doing that. My folder structure is not right. APBS needs to update its install instructions/README. I'll try moving the folders to /sw64/bin/apbs, /sw64/share/apbs, etc.--[[User:Rendereason|Rendereason]] 16:49, 29 October 2010 (UTC)

I found out:
"The APBS binaries do not contain dependencies on special data files, etc. and can be moved out of this directory structure without causing any problems for APBS execution."
So maybe ${APBS_PREFIX} is what needs to be fixed. I'll try that.--[[User:Rendereason|Rendereason]] 16:57, 29 October 2010 (UTC)

Talk:APBS

2010-10-29T16:50:37Z

Rendereason:

Talk:APBS

2010-10-29T16:49:34Z

Rendereason: /* Running with APBS 1.3 */

Talk:APBS

2010-10-29T16:38:58Z

Rendereason:

Talk:APBS

2010-10-29T16:36:30Z

Rendereason: /* Making the default paths to work? */

User:Rendereason

2010-10-29T15:35:26Z

Rendereason:

=About Me=
My name is Daniel Ra and I'm a student at the University of Houston. I am the lab system admin for Dr. Choel Kim Lab in Baylor College of Medicine and I regularly maintain computers at or near the Texas Medical Center.
==Hardware and Software==
I am interested in computer hardware, and in all structural biology software.
Most of the work I do is on OSX, and Intel based Macs. I have built and have some interest in Hackintoshes (Xeon 8-core workstation).

User:Rendereason

2010-10-29T15:31:36Z

Rendereason: Created page with '=About Me= My name is Daniel Ra and I'm a student University of Houston. I am the lab system admin for Dr. Choel Kim Lab in Baylor College of Medicine. ==Hardware and Software== …'

=About Me=
My name is Daniel Ra and I'm a student University of Houston. I am the lab system admin for Dr. Choel Kim Lab in Baylor College of Medicine.
==Hardware and Software==
I am interested in computer hardware and in all molecular replacement software. I regularly maintain computers at or near the Texas Medical Center.
Most of the work I do is on OSX, and Intel based Macs. I have some interest in Hackintoshes.

APBS

2010-10-29T15:21:30Z

Rendereason: Finished adding APBS plugin information, cleaned and updated some info.

== Introduction ==
[[Image:Rna_surface_apbs.png|thumb|APBS-generated electrostatic surface displayed in PyMOL]]
[http://apbs.sourceforge.net APBS], the Adaptive Poisson-Boltzmann Solver, is a [http://www.oreilly.com/openbook/freedom/ freely] available macromolecular electrostatics calculation program released under the [http://www.gnu.org/copyleft/gpl.html GPL]. It is a cost-effective but uncompromised alternative to [http://trantor.bioc.columbia.edu/grasp/ GRASP], and it can be used within PyMOL. PyMOL can display the results of the calculations as an electrostatic potential molecular surface.

=== APBS Plugin with New Features ===
PyMol currently supports the '''APBS plugin''' written by [http://pymolwiki.org/index.php/User:Mglerner Michael Lerner]. This plugin makes it possible to run APBS from within PyMOL, and then display the results as a color-coded electrostatic surface (units <math>K_bT/e_c</math>) in the molecular display window (as with the image to the right). This wiki page has updated instructions on how to download, install and use the plugin.

'''Nucleic acids may prove problematic for the apbs plugin.''' If so, use the [http://pdb2pqr.sourceforge.net/ pdb2pqr] command-line tool to create a pqr file manually, instead of using the plugin to generate it. Then direct the APBS GUI on the [http://www-personal.umich.edu/~mlerner/PyMOL/images/main.png main menu] to read the pqr file you '''externally generated.'''

There is 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.
* It allows you to call through to PDB2PQR directly.
* It allows you to show the electric field lines.
* It has two visualization panels to aid in showing multiple potential surfaces at once.
* It defaults to using PDB2PQR for PQR generation and APBS's psize.py for grid sizing/spacing.
* It has also an increased default maximum allowed memory since typical users have bigger and faster computers these days.
* It calls on the correct paths and binaries for multi-threaded APBS (apbs-mpi-openmpi).

The main reason it is not included in the latest PyMOL release is to receive bug reports. Once it's shown to be stable, it'll be included in the next PyMOL release. See [http://pymolwiki.org/index.php/User:Mglerner Michael Lerner]'s page.

==== How to get it ====

There are two ways to get the new plugin

* If you have subversion installed, you can always get the latest version via

<source lang="bash">
svn co https://pymolapbsplugin.svn.sourceforge.net/svnroot/pymolapbsplugin/trunk/pymolapbsplugin
</source>
''Subversion is not up to date. Download it instead from the link below.''

* 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

Once you have the plugin, you can install it via PyMOL's plugin installer: Plugin --> Manage Plugins --> Install

You may have to run PyMOL with sudo privileges.

Note that the plugin will be installed as "APBS Tools2.1" so that you can continue to use your old version.

Further details, as well as screen shots, are given [http://www.pymolwiki.org/index.php/MAC_Install#Install_APBS_and_friends_with_fink elsewhere in this wiki].

==Required Dependencies==
[http://apbs.sourceforge.net APBS] and its dependencies like [http://pdb2pqr.sourceforge.net pdb2pqr] and [http://scicomp.ucsd.edu/~mholst/codes/maloc/ maloc] are [http://www.oreilly.com/openbook/freedom/ freely] available under the [http://www.gnu.org/copyleft/gpl.html GPL]. The author of the software however [http://agave.wustl.edu/apbs/download/ asks that users register] with him to aid him in obtaining grant funding.

----
===Installing the Dependencies on OS X===
#First, [http://agave.wustl.edu/apbs/download/ register] your use of the software. This will keep everyone happy.
#Second, if you don't already have the [http://fink.sourceforge.net fink package management system], now is a good time to get it. Here is a [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start quick-start set of instructions] for getting X-windows, compilers, and fink all installed.
#Once you are up and going, [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch in fink], and then issue the commands
<source lang="bash">
fink self-update
fink install apbs
</source>
or if you want to use the multi-processor version, issue
<source lang="bash">
fink self-update
fink install apbs-mpi-openmpi
</source>
Then install the X-windows based version of pymol using the command
<source lang="bash">
fink install pymol-py25
</source>
It is recommended to install the latest pdb2pqr as well as the APBS plugin makes use of it
<source lang="bash">
fink install pdb2pqr
</source>
Note that the fink version of PyMOL as of 1.3-4 does not have the latest version of the APBS plugin. Make sure you get the new version!

===Installing the Dependencies on Linux===

====From Scratch====
Note that this tutorial assumes you're using the bash shell and have root privileges
<OL><LI>
Obtain APBS and MALOC from... 
APBS = http://apbs.sourceforge.net (currently 0.4) 
MALOC = http://www.fetk.org/codes/maloc/index.html#download (currently 0.1-2) 
<LI>Set up some environment variables & directories (temporary for building)
<source lang="bash">
$ export FETK_SRC=/<building directory>/temp_apbs
$ export FETK_PREFIX=/usr/local/apbs-0.4.0 (or wherever you want it to live)
$ export FETK_INCLUDE=${FETK_PREFIX}/include
$ export FETK_LIBRARY=${FETK_PREFIX}/lib
$ mkdir -p ${FETK_SRC} ${FETK_INCLUDE} ${FETK_LIBRARY}
</source></LI>
<LI>Unpack the source packages
<source lang="bash">
$ cd ${FETK_SRC}
$ gzip -dc maloc-0.1-2.tar.gz | tar xvf -
$ gzip -dc apbs-0.4.0.tar.gz | tar xvf -
</source>
</LI>
<LI>Compile MALOC
<source lang="bash">
$ cd ${FETK_SRC}/maloc
$ ./configure --prefix=${FETK_PREFIX}</source>
If everything went well, then
<source lang="bash">
$ make; make install</source></LI>
<LI>Go get a coffee. Compilation/installation takes about 15 minutes on a 3GHz computer with 1GB of RAM.</LI>
<LI>Now on to compiling APBS itself
<source lang="bash">
$ cd ${FETK_SRC}/apbs-0.4.0
$ ./configure --prefix=${FETK_PREFIX}</source>
If all goes well:
<source lang="bash">
$ make all; make install</source></LI>
<LI>No time for coffee. Takes about 5 minutes on that fast computer.</LI>
<LI> There will now be an APBS binary at
<source lang="bash">/usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs</source></LI>
<LI> Make appropriate links
<source lang="bash">
$ ln -s /usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs /usr/local/bin/apbs
</source></LI>
<LI> Get rid of /<building directory dir>/temp_apbs
<LI> Open PyMOL and make sure that the APBS plugin points to /usr/local/bin/apbs
<LI> Rock and or Roll.
</OL>

====Pre-Packaged====
=====RPMs=====

A variety of RPMs are available from the [http://sourceforge.net/project/showfiles.php?group_id=148472&package_id=163734&release_id=378273 APBS downloads website]. Again, please [http://agave.wustl.edu/apbs/download/ register] your use of the software if you have not yet done so.

=====Debian packages=====

For ubuntu and other debian linux distributions, probably the simplest thing is to download a promising looking rpm, convert it with the program [http://kitenet.net/programs/alien/ alien], and then install the [http://xanana.ucsc.edu/linux newly generated debian package] with the command
<source lang="bash">
sudo dpkg -i apbs*.deb
</source>

=====Gentoo=====

You have to install apbs and pdb2pqr. Both are masked via keywords atm. Type as root:
<source lang="bash">
echo sci-chemistry/pdb2pqr >> /etc/portage/package.keywords
echo sci-chemistry/apbs >> /etc/portage/package.keywords
emerge -av sci-chemistry/apbs sci-chemistry/pdb2pqr
</source>

== Troubleshooting ==
* If the B-factor is <math>\geq 100,</math> then APBS doesn't properly read in the PDB file and thus outputs garbage (or dies). To fix this, set all b factors to be less than 100. <source lang="python">alter all, b=min(b,99.9)</source> The problem stems from how to parse a PDB file. The PDB file originally was written when most people used FORTRAN programs, and so the file format was specified by columns, not by the more modern comma separated value format we tend to prefer today. For the latest on the PDB format see the [http://www.wwpdb.org/docs.html new PDB format docs].
* APBS has problems, sometimes, in reading atoms with alternate conformations. You can remove the alternate locations with a simple script [[removeAlt]].
* ObjectMapLoadDXFile-Error: as of this writing (9-23-2008) a known problem exists, and the Baker lab is working on it. It is typically caused by the use of directories with spaces in their names under Windows.

== Problems with the bundled version of APBS ==
There is an issue with the freemol version of APBS shipped with PyMOL 1.2r2 for OS X.

=== Leopard and Snow Leopard (10.5 and 10.6) ===
There are three fairly easy ways to resolve it

1. 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).

2. 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").

<source lang="bash">
bunzip2 libgfortran.3.dylib.gz2
mv libgfortran.3.dylib /usr/local/lib
</source>

3. Use macports to install gcc 4.4.2 and link the appropriate library ("ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib" ... on some machines, you may need "sudo ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib").

<source lang="bash">
ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib
sudo ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib
</source>

If you're curious, the problem is that APBS is dynamically linked, but Apple does not provide FORTRAN libraries.

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) ===
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

<source lang="bash">
sudo port install apbs
</source>

from the command line. This process could easily take several hours on an older machine, as MacPorts will recompile gcc, gfortran, and several other packages along the way.

==Using APBS==
There is a nice tutorial on the APBS homepage: [http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol] For further help, there is a mailing list [https://lists.sourceforge.net/lists/listinfo/apbs-users] with the corresponding archive [http://sourceforge.net/mailarchive/forum.php?forum_name=apbs-users]

==Further contributions and edits are needed.==

[[Category:Electrostatics]]
[[Category:Biochemical_Properties]]
[[Category:Plugins]]

APBS

2010-10-29T15:19:15Z

Rendereason: Undo revision 8581 by Rendereason (Talk)

== Introduction ==
[[Image:Rna_surface_apbs.png|thumb|APBS-generated electrostatic surface displayed in PyMOL]]
[http://apbs.sourceforge.net APBS], the Adaptive Poisson-Boltzmann Solver, is a [http://www.oreilly.com/openbook/freedom/ freely] available macromolecular electrostatics calculation program released under the [http://www.gnu.org/copyleft/gpl.html GPL]. It is a cost-effective but uncompromised alternative to [http://trantor.bioc.columbia.edu/grasp/ GRASP], and it can be used within pymol. Pymol can display the results of the calculations as an electrostatic potential molecular surface.

=== APBS Plugin with New Features ===
PyMol currently supports the '''APBS plugin''' written by [http://pymolwiki.org/index.php/User:Mglerner Michael Lerner]. This plugin makes it possible to run APBS from within PyMOL, and then display the results as a color-coded electrostatic surface (units <math>K_bT/e_c</math>) in the molecular display window (as with the image to the right). This wiki page has updated instructions on how to download, install and use the plugin.

'''Nucleic acids may prove problematic for the apbs plugin.''' If so, use the [http://pdb2pqr.sourceforge.net/ pdb2pqr] command-line tool to create a pqr file manually, instead of using the plugin to generate it. Then direct the APBS GUI on the [http://www-personal.umich.edu/~mlerner/PyMOL/images/main.png main menu] to read the pqr file you '''externally generated.'''

There is 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.
* It allows you to call through to PDB2PQR directly.
* It allows you to show the electric field lines.
* It has two visualization panels to aid in showing multiple potential surfaces at once.
* It defaults to using PDB2PQR for PQR generation and APBS's psize.py for grid sizing/spacing.
* It has also an increased default maximum allowed memory since typical users have bigger and faster computers these days.
* It calls on the correct paths and binaries for apbs-mpi-openmpi.

The main reason it is not included in the latest PyMOL release is to receive bug reports. Once it's shown to be stable, it'll be included in the next PyMOL release. See [http://pymolwiki.org/index.php/User:Mglerner Michael Lerner]'s page.

==== How to get it ====

There are two ways to get the new plugin

* If you have subversion installed, you can always get the latest version via

<source lang="bash">
svn co https://pymolapbsplugin.svn.sourceforge.net/svnroot/pymolapbsplugin/trunk/pymolapbsplugin
</source>
''Subversion is not up to date. Download it instead from the link below.''

* 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

Once you have the plugin, you can install it via PyMOL's plugin installer: Plugin --> Manage Plugins --> Install

You may have to run PyMOL with sudo privileges.

Note that the plugin will be installed as "APBS Tools2.1" so that you can continue to use your old version.

Further details, as well as screen shots, are given [http://www.pymolwiki.org/index.php/MAC_Install#Install_APBS_and_friends_with_fink elsewhere in this wiki].

==Required Dependencies==
[http://apbs.sourceforge.net APBS] and its dependencies like [http://pdb2pqr.sourceforge.net pdb2pqr] and [http://scicomp.ucsd.edu/~mholst/codes/maloc/ maloc] are [http://www.oreilly.com/openbook/freedom/ freely] available under the [http://www.gnu.org/copyleft/gpl.html GPL]. The author of the software however [http://agave.wustl.edu/apbs/download/ asks that users register] with him to aid him in obtaining grant funding.

----
===Installing the Dependencies on OS X===
#First, [http://agave.wustl.edu/apbs/download/ register] your use of the software. This will keep everyone happy.
#Second, if you don't already have the [http://fink.sourceforge.net fink package management system], now is a good time to get it. Here is a [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start quick-start set of instructions] for getting X-windows, compilers, and fink all installed.
#Once you are up and going, [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch in fink], and then issue the commands
<source lang="bash">
fink self-update
fink install apbs
</source>
or if you want to use the multi-processor version, issue
<source lang="bash">
fink self-update
fink install apbs-mpi-openmpi
</source>
Then install the X-windows based version of pymol using the command
<source lang="bash">
fink install pymol-py25
</source>
It is recommended to install the latest pdb2pqr as well as the APBS plugin makes use of it
<source lang="bash">
fink install pdb2pqr
</source>
Note that the fink version of PyMOL as of 1.3-4 does not have the latest version of the APBS plugin. Make sure you get the new version!

===Installing the Dependencies on Linux===

====From Scratch====
Note that this tutorial assumes you're using the bash shell and have root privileges
<OL><LI>
Obtain APBS and MALOC from... 
APBS = http://apbs.sourceforge.net (currently 0.4) 
MALOC = http://www.fetk.org/codes/maloc/index.html#download (currently 0.1-2) 
<LI>Set up some environment variables & directories (temporary for building)
<source lang="bash">
$ export FETK_SRC=/<building directory>/temp_apbs
$ export FETK_PREFIX=/usr/local/apbs-0.4.0 (or wherever you want it to live)
$ export FETK_INCLUDE=${FETK_PREFIX}/include
$ export FETK_LIBRARY=${FETK_PREFIX}/lib
$ mkdir -p ${FETK_SRC} ${FETK_INCLUDE} ${FETK_LIBRARY}
</source></LI>
<LI>Unpack the source packages
<source lang="bash">
$ cd ${FETK_SRC}
$ gzip -dc maloc-0.1-2.tar.gz | tar xvf -
$ gzip -dc apbs-0.4.0.tar.gz | tar xvf -
</source>
</LI>
<LI>Compile MALOC
<source lang="bash">
$ cd ${FETK_SRC}/maloc
$ ./configure --prefix=${FETK_PREFIX}</source>
If everything went well, then
<source lang="bash">
$ make; make install</source></LI>
<LI>Go get a coffee. Compilation/installation takes about 15 minutes on a 3GHz computer with 1GB of RAM.</LI>
<LI>Now on to compiling APBS itself
<source lang="bash">
$ cd ${FETK_SRC}/apbs-0.4.0
$ ./configure --prefix=${FETK_PREFIX}</source>
If all goes well:
<source lang="bash">
$ make all; make install</source></LI>
<LI>No time for coffee. Takes about 5 minutes on that fast computer.</LI>
<LI> There will now be an APBS binary at
<source lang="bash">/usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs</source></LI>
<LI> Make appropriate links
<source lang="bash">
$ ln -s /usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs /usr/local/bin/apbs
</source></LI>
<LI> Get rid of /<building directory dir>/temp_apbs
<LI> Open PyMOL and make sure that the APBS plugin points to /usr/local/bin/apbs
<LI> Rock and or Roll.
</OL>

====Pre-Packaged====
=====RPMs=====

A variety of RPMs are available from the [http://sourceforge.net/project/showfiles.php?group_id=148472&package_id=163734&release_id=378273 APBS downloads website]. Again, please [http://agave.wustl.edu/apbs/download/ register] your use of the software if you have not yet done so.

=====Debian packages=====

For ubuntu and other debian linux distributions, probably the simplest thing is to download a promising looking rpm, convert it with the program [http://kitenet.net/programs/alien/ alien], and then install the [http://xanana.ucsc.edu/linux newly generated debian package] with the command
<source lang="bash">
sudo dpkg -i apbs*.deb
</source>

=====Gentoo=====

You have to install apbs and pdb2pqr. Both are masked via keywords atm. Type as root:
<source lang="bash">
echo sci-chemistry/pdb2pqr >> /etc/portage/package.keywords
echo sci-chemistry/apbs >> /etc/portage/package.keywords
emerge -av sci-chemistry/apbs sci-chemistry/pdb2pqr
</source>

== Troubleshooting ==
* If the B-factor is <math>\geq 100,</math> then APBS doesn't properly read in the PDB file and thus outputs garbage (or dies). To fix this, set all b factors to be less than 100. <source lang="python">alter all, b=min(b,99.9)</source> The problem stems from how to parse a PDB file. The PDB file originally was written when most people used FORTRAN programs, and so the file format was specified by columns, not by the more modern comma separated value format we tend to prefer today. For the latest on the PDB format see the [http://www.wwpdb.org/docs.html new PDB format docs].
* APBS has problems, sometimes, in reading atoms with alternate conformations. You can remove the alternate locations with a simple script [[removeAlt]].
* ObjectMapLoadDXFile-Error: as of this writing (9-23-2008) a known problem exists, and the Baker lab is working on it. It is typically caused by the use of directories with spaces in their names under Windows.

== Problems with the bundled version of APBS ==
There is an issue with the freemol version of APBS shipped with PyMOL 1.2r2 for OS X.

=== Leopard and Snow Leopard (10.5 and 10.6) ===
There are three fairly easy ways to resolve it

1. 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).

2. 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").

<source lang="bash">
bunzip2 libgfortran.3.dylib.gz2
mv libgfortran.3.dylib /usr/local/lib
</source>

3. Use macports to install gcc 4.4.2 and link the appropriate library ("ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib" ... on some machines, you may need "sudo ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib").

<source lang="bash">
ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib
sudo ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib
</source>

If you're curious, the problem is that APBS is dynamically linked, but Apple does not provide FORTRAN libraries.

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) ===
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

<source lang="bash">
sudo port install apbs
</source>

from the command line. This process could easily take several hours on an older machine, as MacPorts will recompile gcc, gfortran, and several other packages along the way.

==Using APBS==
There is a nice tutorial on the APBS homepage: [http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol] For further help, there is a mailing list [https://lists.sourceforge.net/lists/listinfo/apbs-users] with the corresponding archive [http://sourceforge.net/mailarchive/forum.php?forum_name=apbs-users]

==Further contributions and edits are needed.==

[[Category:Electrostatics]]
[[Category:Biochemical_Properties]]
[[Category:Plugins]]

APBS

2010-10-29T15:14:07Z

Rendereason:

== Introduction ==
[[Image:Rna_surface_apbs.png|thumb|APBS-generated electrostatic surface displayed in PyMOL]]
[http://apbs.sourceforge.net APBS], the Adaptive Poisson-Boltzmann Solver, is a [http://www.oreilly.com/openbook/freedom/ freely] available macromolecular electrostatics calculation program released under the [http://www.gnu.org/copyleft/gpl.html GPL]. It is a cost-effective but uncompromised alternative to [http://trantor.bioc.columbia.edu/grasp/ GRASP], and it can be used within pymol. Pymol can display the results of the calculations as an electrostatic potential molecular surface.

=== APBS Plugin with New Features ===
PyMol currently supports the '''APBS plugin''' written by [http://pymolwiki.org/index.php/User:Mglerner Michael Lerner]. This plugin makes it possible to run APBS from within PyMOL, and then display the results as a color-coded electrostatic surface (units <math>K_bT/e_c</math>) in the molecular display window (as with the image to the right). This wiki page has updated instructions on how to download, install and use the plugin.

'''Nucleic acids may prove problematic for the apbs plugin.''' If so, use the [http://pdb2pqr.sourceforge.net/ pdb2pqr] command-line tool to create a pqr file manually, instead of using the plugin to generate it. Then direct the APBS GUI on the [http://www-personal.umich.edu/~mlerner/PyMOL/images/main.png main menu] to read the pqr file you '''externally generated.'''

There is 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.
* It allows you to call through to PDB2PQR directly.
* It allows you to show the electric field lines.
* It has two visualization panels to aid in showing multiple potential surfaces at once.
* It defaults to using PDB2PQR for PQR generation and APBS's psize.py for grid sizing/spacing.
* It has also an increased default maximum allowed memory since typical users have bigger and faster computers these days.
* It calls on the correct paths and binaries for multi-threaded APBS (apbs-mpi-openmpi).

The main reason it is not included in the latest PyMOL release is to receive bug reports. Once it's shown to be stable, it'll be included in the next PyMOL release. See [http://pymolwiki.org/index.php/User:Mglerner Michael Lerner]'s page.

==== How to get it ====

There are two ways to get the new plugin

* If you have subversion installed, you can always get the latest version via

<source lang="bash">
svn co https://pymolapbsplugin.svn.sourceforge.net/svnroot/pymolapbsplugin/trunk/pymolapbsplugin
</source>
''Subversion is not up to date. Download it instead from the link below.''

* 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

Once you have the plugin, you can install it via PyMOL's plugin installer: Plugin --> Manage Plugins --> Install

You may have to run PyMOL with sudo privileges.

Note that the plugin will be installed as "APBS Tools2.1" so that you can continue to use your old version.

Further details, as well as screen shots, are given [http://www.pymolwiki.org/index.php/MAC_Install#Install_APBS_and_friends_with_fink elsewhere in this wiki].

==Required Dependencies==
[http://apbs.sourceforge.net APBS] and its dependencies like [http://pdb2pqr.sourceforge.net pdb2pqr] and [http://scicomp.ucsd.edu/~mholst/codes/maloc/ maloc] are [http://www.oreilly.com/openbook/freedom/ freely] available under the [http://www.gnu.org/copyleft/gpl.html GPL]. The author of the software however [http://agave.wustl.edu/apbs/download/ asks that users register] with him to aid him in obtaining grant funding.

----
===Installing the Dependencies on OS X===
#First, [http://agave.wustl.edu/apbs/download/ register] your use of the software. This will keep everyone happy.
#Second, if you don't already have the [http://fink.sourceforge.net fink package management system], now is a good time to get it. Here is a [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start quick-start set of instructions] for getting X-windows, compilers, and fink all installed.
#Once you are up and going, [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch in fink], and then issue the commands
<source lang="bash">
fink self-update
fink install apbs
</source>
or if you want to use the multi-processor version, issue
<source lang="bash">
fink self-update
fink install apbs-mpi-openmpi
</source>
Then install the X-windows based version of pymol using the command
<source lang="bash">
fink install pymol-py25
</source>
It is recommended to install the latest pdb2pqr as well as the APBS plugin makes use of it
<source lang="bash">
fink install pdb2pqr
</source>
Note that the fink version of PyMOL as of 1.3-4 does not have the latest version of the APBS plugin. Make sure you get the new version!

===Installing the Dependencies on Linux===

====From Scratch====
Note that this tutorial assumes you're using the bash shell and have root privileges
<OL><LI>
Obtain APBS and MALOC from... 
APBS = http://apbs.sourceforge.net (currently 0.4) 
MALOC = http://www.fetk.org/codes/maloc/index.html#download (currently 0.1-2) 
<LI>Set up some environment variables & directories (temporary for building)
<source lang="bash">
$ export FETK_SRC=/<building directory>/temp_apbs
$ export FETK_PREFIX=/usr/local/apbs-0.4.0 (or wherever you want it to live)
$ export FETK_INCLUDE=${FETK_PREFIX}/include
$ export FETK_LIBRARY=${FETK_PREFIX}/lib
$ mkdir -p ${FETK_SRC} ${FETK_INCLUDE} ${FETK_LIBRARY}
</source></LI>
<LI>Unpack the source packages
<source lang="bash">
$ cd ${FETK_SRC}
$ gzip -dc maloc-0.1-2.tar.gz | tar xvf -
$ gzip -dc apbs-0.4.0.tar.gz | tar xvf -
</source>
</LI>
<LI>Compile MALOC
<source lang="bash">
$ cd ${FETK_SRC}/maloc
$ ./configure --prefix=${FETK_PREFIX}</source>
If everything went well, then
<source lang="bash">
$ make; make install</source></LI>
<LI>Go get a coffee. Compilation/installation takes about 15 minutes on a 3GHz computer with 1GB of RAM.</LI>
<LI>Now on to compiling APBS itself
<source lang="bash">
$ cd ${FETK_SRC}/apbs-0.4.0
$ ./configure --prefix=${FETK_PREFIX}</source>
If all goes well:
<source lang="bash">
$ make all; make install</source></LI>
<LI>No time for coffee. Takes about 5 minutes on that fast computer.</LI>
<LI> There will now be an APBS binary at
<source lang="bash">/usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs</source></LI>
<LI> Make appropriate links
<source lang="bash">
$ ln -s /usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs /usr/local/bin/apbs
</source></LI>
<LI> Get rid of /<building directory dir>/temp_apbs
<LI> Open PyMOL and make sure that the APBS plugin points to /usr/local/bin/apbs
<LI> Rock and or Roll.
</OL>

====Pre-Packaged====
=====RPMs=====

A variety of RPMs are available from the [http://sourceforge.net/project/showfiles.php?group_id=148472&package_id=163734&release_id=378273 APBS downloads website]. Again, please [http://agave.wustl.edu/apbs/download/ register] your use of the software if you have not yet done so.

=====Debian packages=====

For ubuntu and other debian linux distributions, probably the simplest thing is to download a promising looking rpm, convert it with the program [http://kitenet.net/programs/alien/ alien], and then install the [http://xanana.ucsc.edu/linux newly generated debian package] with the command
<source lang="bash">
sudo dpkg -i apbs*.deb
</source>

=====Gentoo=====

You have to install apbs and pdb2pqr. Both are masked via keywords atm. Type as root:
<source lang="bash">
echo sci-chemistry/pdb2pqr >> /etc/portage/package.keywords
echo sci-chemistry/apbs >> /etc/portage/package.keywords
emerge -av sci-chemistry/apbs sci-chemistry/pdb2pqr
</source>

== Troubleshooting ==
* If the B-factor is <math>\geq 100,</math> then APBS doesn't properly read in the PDB file and thus outputs garbage (or dies). To fix this, set all b factors to be less than 100. <source lang="python">alter all, b=min(b,99.9)</source> The problem stems from how to parse a PDB file. The PDB file originally was written when most people used FORTRAN programs, and so the file format was specified by columns, not by the more modern comma separated value format we tend to prefer today. For the latest on the PDB format see the [http://www.wwpdb.org/docs.html new PDB format docs].
* APBS has problems, sometimes, in reading atoms with alternate conformations. You can remove the alternate locations with a simple script [[removeAlt]].
* ObjectMapLoadDXFile-Error: as of this writing (9-23-2008) a known problem exists, and the Baker lab is working on it. It is typically caused by the use of directories with spaces in their names under Windows.

== Problems with the bundled version of APBS ==
There is an issue with the freemol version of APBS shipped with PyMOL 1.2r2 for OS X.

=== Leopard and Snow Leopard (10.5 and 10.6) ===
There are three fairly easy ways to resolve it

1. 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).

2. 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").

<source lang="bash">
bunzip2 libgfortran.3.dylib.gz2
mv libgfortran.3.dylib /usr/local/lib
</source>

3. Use macports to install gcc 4.4.2 and link the appropriate library ("ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib" ... on some machines, you may need "sudo ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib").

<source lang="bash">
ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib
sudo ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib
</source>

If you're curious, the problem is that APBS is dynamically linked, but Apple does not provide FORTRAN libraries.

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) ===
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

<source lang="bash">
sudo port install apbs
</source>

from the command line. This process could easily take several hours on an older machine, as MacPorts will recompile gcc, gfortran, and several other packages along the way.

==Using APBS==
There is a nice tutorial on the APBS homepage: [http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol] For further help, there is a mailing list [https://lists.sourceforge.net/lists/listinfo/apbs-users] with the corresponding archive [http://sourceforge.net/mailarchive/forum.php?forum_name=apbs-users]

==Further contributions and edits are needed.==

[[Category:Electrostatics]]
[[Category:Biochemical_Properties]]
[[Category:Plugins]]

APBS

2010-10-29T15:12:25Z

Rendereason:

== Introduction ==
[[Image:Rna_surface_apbs.png|thumb|APBS-generated electrostatic surface displayed in PyMOL]]
[http://apbs.sourceforge.net APBS], the Adaptive Poisson-Boltzmann Solver, is a [http://www.oreilly.com/openbook/freedom/ freely] available macromolecular electrostatics calculation program released under the [http://www.gnu.org/copyleft/gpl.html GPL]. It is a cost-effective but uncompromised alternative to [http://trantor.bioc.columbia.edu/grasp/ GRASP], and it can be used within pymol. Pymol can display the results of the calculations as an electrostatic potential molecular surface.

=== APBS Plugin with New Features ===
PyMol currently supports the '''APBS plugin''' written by [http://pymolwiki.org/index.php/User:Mglerner Michael Lerner]. This plugin makes it possible to run APBS from within PyMOL, and then display the results as a color-coded electrostatic surface (units <math>K_bT/e_c</math>) in the molecular display window (as with the image to the right). This wiki page has updated instructions on how to download, install and use the plugin.

'''Nucleic acids may prove problematic for the apbs plugin.''' If so, use the [http://pdb2pqr.sourceforge.net/ pdb2pqr] command-line tool to create a pqr file manually, instead of using the plugin to generate it. Then direct the APBS GUI on the [http://www-personal.umich.edu/~mlerner/PyMOL/images/main.png main menu] to read the pqr file you '''externally generated.'''

There is 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.
* It allows you to call through to PDB2PQR directly.
* It allows you to show the electric field lines.
* It has two visualization panels to aid in showing multiple potential surfaces at once.
* It defaults to using PDB2PQR for PQR generation and APBS's psize.py for grid sizing/spacing.
* It has also an increased default maximum allowed memory since typical users have bigger and faster computers these days.
* It calls on the correct paths and binaries for apbs-mpi-openmpi.

The main reason it is not included in the latest PyMOL release is to receive bug reports. Once it's shown to be stable, it'll be included in the next PyMOL release. See [http://pymolwiki.org/index.php/User:Mglerner Michael Lerner]'s page.

==== How to get it ====

There are two ways to get the new plugin

* If you have subversion installed, you can always get the latest version via

<source lang="bash">
svn co https://pymolapbsplugin.svn.sourceforge.net/svnroot/pymolapbsplugin/trunk/pymolapbsplugin
</source>
''Subversion is not up to date. Download it instead from the link below.''

* 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

Once you have the plugin, you can install it via PyMOL's plugin installer: Plugin --> Manage Plugins --> Install

You may have to run PyMOL with sudo privileges.

Note that the plugin will be installed as "APBS Tools2.1" so that you can continue to use your old version.

Further details, as well as screen shots, are given [http://www.pymolwiki.org/index.php/MAC_Install#Install_APBS_and_friends_with_fink elsewhere in this wiki].

==Required Dependencies==
[http://apbs.sourceforge.net APBS] and its dependencies like [http://pdb2pqr.sourceforge.net pdb2pqr] and [http://scicomp.ucsd.edu/~mholst/codes/maloc/ maloc] are [http://www.oreilly.com/openbook/freedom/ freely] available under the [http://www.gnu.org/copyleft/gpl.html GPL]. The author of the software however [http://agave.wustl.edu/apbs/download/ asks that users register] with him to aid him in obtaining grant funding.

----
===Installing the Dependencies on OS X===
#First, [http://agave.wustl.edu/apbs/download/ register] your use of the software. This will keep everyone happy.
#Second, if you don't already have the [http://fink.sourceforge.net fink package management system], now is a good time to get it. Here is a [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start quick-start set of instructions] for getting X-windows, compilers, and fink all installed.
#Once you are up and going, [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch in fink], and then issue the commands
<source lang="bash">
fink self-update
fink install apbs
</source>
or if you want to use the multi-processor version, issue
<source lang="bash">
fink self-update
fink install apbs-mpi-openmpi
</source>
Then install the X-windows based version of pymol using the command
<source lang="bash">
fink install pymol-py25
</source>
It is recommended to install the latest pdb2pqr as well as the APBS plugin makes use of it
<source lang="bash">
fink install pdb2pqr
</source>
Note that the fink version of PyMOL as of 1.3-4 does not have the latest version of the APBS plugin. Make sure you get the new version!

===Installing the Dependencies on Linux===

====From Scratch====
Note that this tutorial assumes you're using the bash shell and have root privileges
<OL><LI>
Obtain APBS and MALOC from... 
APBS = http://apbs.sourceforge.net (currently 0.4) 
MALOC = http://www.fetk.org/codes/maloc/index.html#download (currently 0.1-2) 
<LI>Set up some environment variables & directories (temporary for building)
<source lang="bash">
$ export FETK_SRC=/<building directory>/temp_apbs
$ export FETK_PREFIX=/usr/local/apbs-0.4.0 (or wherever you want it to live)
$ export FETK_INCLUDE=${FETK_PREFIX}/include
$ export FETK_LIBRARY=${FETK_PREFIX}/lib
$ mkdir -p ${FETK_SRC} ${FETK_INCLUDE} ${FETK_LIBRARY}
</source></LI>
<LI>Unpack the source packages
<source lang="bash">
$ cd ${FETK_SRC}
$ gzip -dc maloc-0.1-2.tar.gz | tar xvf -
$ gzip -dc apbs-0.4.0.tar.gz | tar xvf -
</source>
</LI>
<LI>Compile MALOC
<source lang="bash">
$ cd ${FETK_SRC}/maloc
$ ./configure --prefix=${FETK_PREFIX}</source>
If everything went well, then
<source lang="bash">
$ make; make install</source></LI>
<LI>Go get a coffee. Compilation/installation takes about 15 minutes on a 3GHz computer with 1GB of RAM.</LI>
<LI>Now on to compiling APBS itself
<source lang="bash">
$ cd ${FETK_SRC}/apbs-0.4.0
$ ./configure --prefix=${FETK_PREFIX}</source>
If all goes well:
<source lang="bash">
$ make all; make install</source></LI>
<LI>No time for coffee. Takes about 5 minutes on that fast computer.</LI>
<LI> There will now be an APBS binary at
<source lang="bash">/usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs</source></LI>
<LI> Make appropriate links
<source lang="bash">
$ ln -s /usr/local/apbs-0.4.0/bin/i686-intel-linux/apbs /usr/local/bin/apbs
</source></LI>
<LI> Get rid of /<building directory dir>/temp_apbs
<LI> Open PyMOL and make sure that the APBS plugin points to /usr/local/bin/apbs
<LI> Rock and or Roll.
</OL>

====Pre-Packaged====
=====RPMs=====

A variety of RPMs are available from the [http://sourceforge.net/project/showfiles.php?group_id=148472&package_id=163734&release_id=378273 APBS downloads website]. Again, please [http://agave.wustl.edu/apbs/download/ register] your use of the software if you have not yet done so.

=====Debian packages=====

For ubuntu and other debian linux distributions, probably the simplest thing is to download a promising looking rpm, convert it with the program [http://kitenet.net/programs/alien/ alien], and then install the [http://xanana.ucsc.edu/linux newly generated debian package] with the command
<source lang="bash">
sudo dpkg -i apbs*.deb
</source>

=====Gentoo=====

You have to install apbs and pdb2pqr. Both are masked via keywords atm. Type as root:
<source lang="bash">
echo sci-chemistry/pdb2pqr >> /etc/portage/package.keywords
echo sci-chemistry/apbs >> /etc/portage/package.keywords
emerge -av sci-chemistry/apbs sci-chemistry/pdb2pqr
</source>

== Troubleshooting ==
* If the B-factor is <math>\geq 100,</math> then APBS doesn't properly read in the PDB file and thus outputs garbage (or dies). To fix this, set all b factors to be less than 100. <source lang="python">alter all, b=min(b,99.9)</source> The problem stems from how to parse a PDB file. The PDB file originally was written when most people used FORTRAN programs, and so the file format was specified by columns, not by the more modern comma separated value format we tend to prefer today. For the latest on the PDB format see the [http://www.wwpdb.org/docs.html new PDB format docs].
* APBS has problems, sometimes, in reading atoms with alternate conformations. You can remove the alternate locations with a simple script [[removeAlt]].
* ObjectMapLoadDXFile-Error: as of this writing (9-23-2008) a known problem exists, and the Baker lab is working on it. It is typically caused by the use of directories with spaces in their names under Windows.

== Problems with the bundled version of APBS ==
There is an issue with the freemol version of APBS shipped with PyMOL 1.2r2 for OS X.

=== Leopard and Snow Leopard (10.5 and 10.6) ===
There are three fairly easy ways to resolve it

1. 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).

2. 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").

<source lang="bash">
bunzip2 libgfortran.3.dylib.gz2
mv libgfortran.3.dylib /usr/local/lib
</source>

3. Use macports to install gcc 4.4.2 and link the appropriate library ("ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib" ... on some machines, you may need "sudo ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib").

<source lang="bash">
ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib
sudo ln -s /opt/local/lib/gcc44/libgfortran.3.dylib /usr/local/lib/libgfortran.3.dylib
</source>

If you're curious, the problem is that APBS is dynamically linked, but Apple does not provide FORTRAN libraries.

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) ===
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

<source lang="bash">
sudo port install apbs
</source>

from the command line. This process could easily take several hours on an older machine, as MacPorts will recompile gcc, gfortran, and several other packages along the way.

==Using APBS==
There is a nice tutorial on the APBS homepage: [http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol] For further help, there is a mailing list [https://lists.sourceforge.net/lists/listinfo/apbs-users] with the corresponding archive [http://sourceforge.net/mailarchive/forum.php?forum_name=apbs-users]

==Further contributions and edits are needed.==

[[Category:Electrostatics]]
[[Category:Biochemical_Properties]]
[[Category:Plugins]]

Talk:APBS

2010-07-20T23:04:37Z

Rendereason: /* Making the default paths to work? */

Talk:APBS

2010-07-20T22:54:29Z

Rendereason: /* Making the default paths to work? */

Talk:APBS

2010-07-20T22:52:32Z

Rendereason: /* Making the default paths to work? */

Talk:APBS

2010-07-20T22:40:10Z

Rendereason: /* Making the default paths to work? */ new section