This is a read-only mirror of pymolwiki.org

Difference between revisions of "Apbsplugin"

From PyMOL Wiki
Jump to navigation Jump to search
m (2 revisions)
 
(27 intermediate revisions by 5 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>)
 +
 
 +
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
  
=== Compile yourself ===
+
For further help, there is a [https://sourceforge.net/projects/apbs/lists/apbs-users mailing list].
If you really want, then see this section: [[APBS]]
 
  
== Example 1 - Rename of funny atom names ==
+
=== Example 1 ===
 
Read about the protein here: http://www.proteopedia.org/wiki/index.php/3ig7 <br>
 
Read about the protein here: http://www.proteopedia.org/wiki/index.php/3ig7 <br>
  
<syntaxhighlight lang="python">
+
{{Template:PymolScriptRepoDownload|examples/apbsplugin_1.pml}}
reinitialize
+
<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/apbsplugin_1.pml" highlight="python" />
fetch 3IG7, async=0
+
 
</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 tab '''Grid settings'''. In '''Calculate Grid Center by Selection''', write '''EFP'''. <br>
+
Click in '''Selection to use''', and write '''cdk2'''. <br>
Try clicking '''Wired Box''' in top right, and then '''Show Box''', '''Hide Box''', '''Cylindric Box''', '''Show Box'''.<br>
+
Click '''Set grid''' <br>
Then push '''Select binding site'''. In PyMOL, write
+
Click '''Run APBS''' <br>
show sticks, binding_site
+
To the left in '''Molecular Surface''', click '''Show'''. <br>
cmd.disable("binding_site")
+
Tadaaa!
hide sticks, binding_site
+
Hide it again, now show both ''Positive'' and ''Negative'' Isosurface
Click tab '''Receptor'''. Mark '''cdk''', and click '''Generate Receptor'''.<br>
+
 
Click cdk2 to the "right", and see where the files are located.<br>
+
== Saving default locations ==
Click tab '''Ligands'''. Mark '''EFP''', and click '''EFP''' in the Ligand list. Here is the files stored. Click '''Generate Ligand'''<br>
+
=== Via environment variables ===
Click tab '''Docking''', and click '''Run Vina'''. Wait 3-5 minutes, until '''Writing output ... done.'''<br>
+
 
Click tab '''View poses''', Browse to '''EFP.docked.pdbqt'''. Click '''Load''', '''Show best 10'''. Experiment with "Display options, and click the candidates"<br>
+
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.
Congratulations, you did it!
+
 
 +
=== 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 ==
* 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].
+
See: [[APBS#Troubleshooting]]
* 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.
 
  
 
== References and LICENSES ==
 
== References and LICENSES ==
Line 61: Line 83:
 
=== pdb2pqr ===
 
=== 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.<br>
 
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.<br>
Register here, it takes 1 minutes: https://spreadsheets.google.com/viewform?hl=en&formkey=dHFpa3Nvcnl0cjR1U3g3UTdSYU1pWWc6MA..
+
Register here, it takes 1 minutes: http://www.poissonboltzmann.org/pdb2pqr/d/downloads
  
 
=== MALOC ===
 
=== MALOC ===
Line 80: 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 02:21, 20 August 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

<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/apbsplugin_1.pml" highlight="python" />

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.