Difference between revisions of "Apbsplugin"

From PyMOLWiki
Jump to: navigation, search
(pdb2pqr)
m (move Infobox)
 
(19 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 +
<div style="background-color: #9f9; padding: 10px 20px; margin-bottom: 20px">
 +
This page describes the "APBS Tools2.1" plugin, based on the
 +
[https://sourceforge.net/projects/pymolapbsplugin/ original version]
 +
by [[User:Mglerner|Michael G. Lerner]].
 +
 +
For the new plugin in Incentive PyMOL 2.0, see [[APBS Electrostatics Plugin]].
 +
</div>
 +
 +
{{Infobox script-repo
 +
|type      = plugin
 +
|filename  = plugins/apbsplugin.py
 +
|author    = [[User:Mglerner|Michael G. Lerner]]
 +
|license  = BSD
 +
}}
 +
 +
The [[apbsplugin|APBS Tool2.1]] plugin integrates the
 +
[http://www.poissonboltzmann.org APBS]
 +
software package into PyMOL.
 +
Its primary purpose is electrostatic surface visualization.
 +
 
== Software requirements ==
 
== Software requirements ==
Register use of the software. This will the authors able to require funding for further development.<br>
 
Register here, it takes 1 minutes: http://www.poissonboltzmann.org/apbs/downloads <br>
 
=== Windows ===
 
Download '''APBS.msi''' from: http://sourceforge.net/projects/apbs/files/apbs/ <br>
 
MALOC?
 
  
=== Ubuntu ===
+
* [https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/plugins/apbsplugin.py apbsplugin.py] (Install via PyMOL's plugin manager)
APBS are in the repository: http://packages.ubuntu.com/search?keywords=apbs <br>
+
* [https://github.com/Electrostatics/apbs-pdb2pqr/releases APBS] (Ubuntu users: <code>apt-get install apbs</code>)
MALOC are in the repository: http://packages.ubuntu.com/search?keywords=libmaloc1
+
* [https://github.com/Electrostatics/apbs-pdb2pqr/releases pdb2pqr] (Ubuntu users: <code>apt-get install pdb2pqr</code>)
  
=== Compile yourself ===
+
Please register at http://www.poissonboltzmann.org/ to ensure continued support for the APBS-PDB2PQR software.
If you really want, then see this section: [[APBS]]
 
  
== Example ==
+
== Examples ==
There is a nice tutorial on the APBS homepage: [http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol] <br>
 
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]
 
  
=== Example 1 - Rename of funny atom names ===
+
There is a nice tutorial on the APBS homepage:
Read about the protein here: http://www.proteopedia.org/wiki/index.php/3ig7 <br>
+
http://apbs-pdb2pqr.readthedocs.io/en/latest/examples/using-pymol.html
  
<syntaxhighlight lang="python">
+
For further help, there is a [https://sourceforge.net/projects/apbs/lists/apbs-users mailing list].
reinitialize
 
fetch 3IG7, async=0
 
#load 3ig7.pdb, 3IG7
 
create cdk2, 3IG7 and polymer
 
create EFP, 3IG7 and organic and not resn ACE
 
delete 3IG7
 
  
hide everything, all
+
=== Example 1 ===
#h_add cdk2
+
Read about the protein here: http://www.proteopedia.org/wiki/index.php/3ig7 <br>
#h_add EFP
 
show_as cartoon, cdk2
 
show_as sticks, EFP
 
util.cbay EFP
 
  
### If modules does not like funny names of atoms, we can rename them. Uncomment these lines, if it is a problem
+
{{Template:PymolScriptRepoDownload|examples/apbsplugin_1.pml}}
#python
+
<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/apbsplugin_1.pml" highlight="python" />
#Ligand_prop = []
 
#cmd.iterate("EFP", "Ligand_prop.append((resi, resn, name, elem, ID))")
 
#for resi, resn, name, elem, ID in Ligand_prop:
 
#    print("resi %s, resn %s, name %s, elem %s, ID %s"%(resi, resn, name, elem, ID))
 
#    cmd.alter('%s and id %s'%(resn,ID),'name=%s%s%s'%('"',elem,'"'))
 
## To see the change, we rewrite the list.
 
#Ligand_prop = []
 
#cmd.iterate("EFP", "Ligand_prop.append((resi, resn, name, elem, ID))")
 
#for resi, resn, name, elem, ID in Ligand_prop:
 
#    print("resi %s, resn %s, name %s, elem %s, ID %s"%(resi, resn, name, elem, ID))
 
#python end
 
  
select flexible, byres cdk2 within 3.5 of EFP
 
show sticks, flexible
 
util.cbag flexible
 
disable flexible
 
zoom cdk2
 
</syntaxhighlight>
 
 
Open the '''APBS Tool2.1...''' plugin. The executable should be found for itself:
 
Open the '''APBS Tool2.1...''' plugin. The executable should be found for itself:
  
 
Click in '''Selection to use''', and write '''cdk2'''. <br>
 
Click in '''Selection to use''', and write '''cdk2'''. <br>
Click '''Set grid'''. <br>
+
Click '''Set grid''' <br>
 +
Click '''Run APBS''' <br>
 +
To the left in '''Molecular Surface''', click '''Show'''. <br>
 +
Tadaaa!
 +
Hide it again, now show both ''Positive'' and ''Negative'' Isosurface
 +
 
 +
== Saving default locations ==
 +
=== Via environment variables ===
 +
 
 +
Set the environment variables APBS_BINARY_DIR, APBS_WEB_DIR, APBS_PSIZE_DIR, APBS_PDB2PQR_DIR, and/or TEMP, and things should work properly as long as you're using the most recent version of the plugin.
 +
 
 +
=== Via editing the plugin ===
 +
 
 +
Open up the python file associated with the plugin (typically apbsplugin.py), look for the section near the top labeled "Global config variables" and change the values from None to a string.
 +
 
  
 
== Troubleshooting ==
 
== Troubleshooting ==
Line 103: Line 102:
 
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 
</syntaxhighlight>
 
</syntaxhighlight>
 +
 +
[[Category:Pymol-script-repo]]

Latest revision as of 13:11, 26 July 2018

This page describes the "APBS Tools2.1" plugin, based on the original version by Michael G. Lerner.

For the new plugin in Incentive PyMOL 2.0, see APBS Electrostatics Plugin.

Type PyMOL Plugin
Download plugins/apbsplugin.py
Author(s) Michael G. Lerner
License BSD
This code has been put under version control in the project Pymol-script-repo

The APBS Tool2.1 plugin integrates the APBS software package into PyMOL. Its primary purpose is electrostatic surface visualization.

Software requirements

  • apbsplugin.py (Install via PyMOL's plugin manager)
  • APBS (Ubuntu users: apt-get install apbs)
  • pdb2pqr (Ubuntu users: apt-get install pdb2pqr)

Please register at http://www.poissonboltzmann.org/ to ensure continued support for the APBS-PDB2PQR software.

Examples

There is a nice tutorial on the APBS homepage: http://apbs-pdb2pqr.readthedocs.io/en/latest/examples/using-pymol.html

For further help, there is a mailing list.

Example 1

Read about the protein here: http://www.proteopedia.org/wiki/index.php/3ig7

Download: examples/apbsplugin_1.pml
This code has been put under version control in the project Pymol-script-repo
reinitialize 
fetch 3IG7, async=0
#load 3ig7.pdb, 3IG7
create cdk2, 3IG7 and polymer
create EFP, 3IG7 and organic and not resn ACE
delete 3IG7
 
hide everything, all
#h_add cdk2
#h_add EFP
show_as cartoon, cdk2
show_as sticks, EFP
util.cbay EFP
 
select flexible, byres cdk2 within 3.5 of EFP
show sticks, flexible
util.cbag flexible
disable flexible
zoom cdk2

Open the APBS Tool2.1... plugin. The executable should be found for itself:

Click in Selection to use, and write cdk2.
Click Set grid
Click Run APBS
To the left in Molecular Surface, click Show.
Tadaaa! Hide it again, now show both Positive and Negative Isosurface

Saving default locations

Via environment variables

Set the environment variables APBS_BINARY_DIR, APBS_WEB_DIR, APBS_PSIZE_DIR, APBS_PDB2PQR_DIR, and/or TEMP, and things should work properly as long as you're using the most recent version of the plugin.

Via editing the plugin

Open up the python file associated with the plugin (typically apbsplugin.py), look for the section near the top labeled "Global config variables" and change the values from None to a string.


Troubleshooting

See: APBS#Troubleshooting

References and LICENSES

APBS

When using the APBS, you are "obligated" to register your use of the software. This will the authors able to require funding for further development.
Register here, it takes 1 minutes: http://www.poissonboltzmann.org/apbs/downloads

Please acknowledge your use of APBS by citing:
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. doi:10.1073/pnas.181342398

Please acknowledge your use of the Holst group software by citing:
M. Holst and F. Saied, Multigrid solution of the Poisson-Boltzmann equation. J. Comput. Chem. 14, 105-113, 1993.
M. Holst and F. Saied, Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods. J. Comput. Chem. 16, 337-364, 1995.
For PMG (the multigrid solver):
M. Holst, Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics 15, 139-191, 2001. doi:10.1023/A:1014246117321
For FEtk (the finite element solver):
R. Bank and M. Holst, A New Paradigm for Parallel Adaptive Meshing Algorithms. SIAM Review 45, 291-323, 2003. doi:10.1137/S003614450342061

pdb2pqr

When using the pdb2pqr, you are "strongly encourage" to register your use of the software. This will the authors able to require funding for further development.
Register here, it takes 1 minutes: http://www.poissonboltzmann.org/pdb2pqr/d/downloads

MALOC

Please acknowledge the use of MALOC and FETK by citing:
M. Holst, Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics, 15 (2001), pp. 139-191.

Copyright and Terms of Use:
GNU General Public License: http://www.gnu.org/copyleft/gpl.html

This version of MALOC is distributed under the following guidelines:
MALOC (Minimal Abstraction Layer for Object-oriented C) 
Copyright (C) 1994-2010 Michael Holst 

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. 

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. 

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.