Difference between revisions of "Autodock plugin"

	Download: examples/autodock_plugin_2.pml
	This code has been put under version control in the project Pymol-script-repo

	Download: examples/autodock_plugin_1.pml
	This code has been put under version control in the project Pymol-script-repo

Type	PyMOL Plugin
Download	plugins/autodock_plugin.py
Author(s)	Daniel Seeliger
License	-
	This code has been put under version control in the project Pymol-script-repo

Latest revision as of 01:48, 28 March 2014

Description

This plugin should help to set up docking runs with Autodock and view docking results. It has two features:

Setup of a docking grid for Autodock with PyMOL.
View the docking results.

Installation

Linux

This plugin is ready "out-of-box" for Linux users through the project Pymol-script-repo

Windows

This plugin is ready "out-of-box" for win users through the project Pymol-script-repo

You can download it manually

Download plugin
PyMOL > Plugin > Install Plugin
MGLTools/AutoDockTools
AutoDock4.2
AutoDock Vina

Tutorial Video

Watch Dan Seeliger's autodock plugin tutorial.

Important

The Autodock tools, does not like funny atoms names like "C1, N13, O28" and so on. Rename them! See example 1.
Ligands can not be in alternative configuration. Create by: create ROC_A, 1HXB and resn ROC and alt a . See example 2.

Example 1 - Rename of funny atom names

Read about the protein here: http://www.proteopedia.org/wiki/index.php/3ig7
The example of video http://wwwuser.gwdg.de/~dseelig/plugin_tutorial.html
Note, that the module "prepare_ligand4.py" does not like funny names of atoms, so we have to rename them

Open the Autodock/Vina plugin. Check/set the executable to folders (they should be automatically found):

Autodock Tools:       /home/you/another/pymol/Pymol-script-repo/modules/ADT/AutoDockTools/Utilities24
autogrid4 executable: /home/you/another/pymol/Pymol-script-repo/modules/autodock_423/ia64Linux2/autogrid4                     # Platform dependent
autogrid4 executable: /home/you/another/pymol/Pymol-script-repo/modules/autodock_423/ia64Linux2/autodock4                     # Platform dependent
vina executable:      /home/you/another/pymol/Pymol-script-repo/modules/autodock_vina/autodock_vina_1_1_2_linux_x86/vina      # Platform dependent
Working Directory:    /home/you/another/pymol/workingdir

Enlarge the window and click Save Plugin Configuration file. Plugin will not work, if you do not save.

Click tab Grid settings. In Calculate Grid Center by Selection, write EFP.
Try clicking Wired Box in top right, and then Show Box, Hide Box, Cylindric Box, Show Box.
Then push Select binding site. In PyMOL, write

show sticks, binding_site
cmd.disable("binding_site")
hide sticks, binding_site

Click tab Receptor. Mark cdk, and click Generate Receptor.
Click cdk2 to the "right", and see where the files are located.
Click tab Ligands. Mark EFP, and click EFP in the Ligand list. Here is the files stored. Click Generate Ligand
Click tab Docking, and click Run Vina. Wait 3-5 minutes, until Writing output ... done.
Click tab View poses, Browse to EFP.docked.pdbqt. Click Load, Show best 10. Experiment with "Display options, and click the candidates"
Congratulations, you did it!

Example 2 - Alternative configurations of a Ligand

Read about the protein here: http://www.proteopedia.org/wiki/index.php/1hxb
Ligands can not be in alternative configuration. Create by: create ROC_A, 1HXB and resn ROC and alt a .

References and LICENSES

Vina

If you used AutoDock Vina in your work, please cite:
O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461

MGLTOOLS

LICENSE of MGLTOOLS:

This software is copyrighted by Michel F. Sanner (sanner@scripps.edu) and TSRI.
The following terms apply to all files associated with the software 
unless explicitly disclaimed in individual files.

       MGLTOOLS SOFTWARE LICENSE AGREEMENT.

  1. Grant Of Limited License; Software Use Restrictions. The programs
     received by you will be used only for NON COMMERCIAL purposes.
     This license is issued to you as an individual.

     For COMMERCIAL use done with the software please contact Michel F. 
     Sanner for details about commercial usage license agreements.
     
     For any question regarding license agreements, please contact
             Michel Sanner:
	     TSRI, Molecular Biology Department, TCP 26,
	     10550 North Torrey Pines Road, La Jolla, CA 92037
	     sanner@scripps.edu
	     tel (858) 784-7742
	     fax (858) 784-2341

  2. COMMERCIAL USAGE is defined as revenues generating activities. These
     include using this software for consulting activities and selling
     applications built on top of, or using this software. Scientific 
     research in an academic environment and teaching are considered 
     NON COMMERCIAL.

  3. Copying Restrictions. You will not sell or otherwise distribute commercially 
     these programs or derivatives to any other party, whether with or without 
     consideration.

  4. Ownership of Software. You will not obtain, and will not attempt to 
     obtain copyright coverage thereon without the express purpose written 
     consent of The Scripps Research Institute and Dr. Sanner.

  5. IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY
     FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
     ARISING OUT OF THE USE OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY
     DERIVATIVES THEREOF, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE
     POSSIBILITY OF SUCH DAMAGE.

  6. THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES,
     INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY,
     FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT.  THIS SOFTWARE
     IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE
     NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
     MODIFICATIONS.

@@ Line 1: / Line 1: @@
+{{Infobox script-repo
+|type      = plugin
+|filename  = plugins/autodock_plugin.py
+|author    = [[User:Dseelig|Daniel Seeliger]]
+|license   = -
+}}
 == Description ==
 This plugin should help to set up docking runs with Autodock and view docking results. It has two features:
@@ Line 6: / Line 13: @@
 == Installation ==
-you can download it manually
+=== Linux ===
+This plugin is ready "out-of-box" for Linux users through the project [[git_intro | Pymol-script-repo]]
+=== Windows ===
+This plugin is ready "out-of-box" for win users through the project [[git_intro | Pymol-script-repo]]
+You can download it manually
 # Download [http://wwwuser.gwdg.de/~dseelig/adplugin.html plugin]
 # '''PyMOL > Plugin > Install Plugin'''
@@ Line 16: / Line 29: @@
 Watch Dan Seeliger's [http://wwwuser.gwdg.de/~dseelig/plugin_tutorial.html autodock plugin tutorial].
-== Author ==
-[[User:Dseelig|Daniel Seeliger]]
 == Important ==
@@ Line 29: / Line 38: @@
 The example of video http://wwwuser.gwdg.de/~dseelig/plugin_tutorial.html <br>
 Note, that the module "prepare_ligand4.py" does not like funny names of atoms, so we have to rename them
-<syntaxhighlight lang="python">
-reinitialize
+{{Template:PymolScriptRepoDownload|examples/autodock_plugin_1.pml}}
-fetch 3IG7, async=0
+<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/autodock_plugin_1.pml" highlight="python" />
-#load 3ig7.pdb, 3IG7
-create cdk2, 3IG7 and polymer
+Open the Autodock/Vina plugin. Check/set the executable to folders (they should be automatically found):
-create EFP, 3IG7 and organic and not resn ACE
+  Autodock Tools:       /home/you/another/pymol/Pymol-script-repo/modules/ADT/AutoDockTools/Utilities24
-delete 3IG7
+  autogrid4 executable: /home/you/another/pymol/Pymol-script-repo/modules/autodock_423/ia64Linux2/autogrid4                     # Platform dependent
+  autogrid4 executable: /home/you/another/pymol/Pymol-script-repo/modules/autodock_423/ia64Linux2/autodock4                     # Platform dependent
-hide everything, all
+  vina executable:      /home/you/another/pymol/Pymol-script-repo/modules/autodock_vina/autodock_vina_1_1_2_linux_x86/vina      # Platform dependent
-#h_add cdk2
-#h_add EFP
-show_as cartoon, cdk2
-show_as sticks, EFP
-util.cbay EFP
-python
-# The module "prepare_ligand4.py" does not like funny names of atoms, so we have to rename them
-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
-</syntaxhighlight>
-Open the Autodock/Vina plugin. Set executable to folders:
-  Autodock Tools:       /home/you/another/pymol/Pymol-script-repo/modules/autodock_tools/AutoDockTools/Utilities24
-  autogrid4 executable: /home/you/another/pymol/Pymol-script-repo/modules/autodock_42/autogrid4
-  autogrid4 executable: /home/you/another/pymol/Pymol-script-repo/modules/autodock_42/autodock4
-  vina executable:      /home/you/another/pymol/Pymol-script-repo/modules/autodock_vina/vina
   Working Directory:    /home/you/another/pymol/workingdir
-Enlarge the window and click '''Save Plugin Configuration file'''.
+Enlarge the window and click '''Save Plugin Configuration file'''. Plugin will not work, if you do not save.
 Click tab '''Grid settings'''. In '''Calculate Grid Center by Selection''', write '''EFP'''. <br>
@@ Line 85: / Line 65: @@
 == Example 2 - Alternative configurations of a Ligand ==
 Read about the protein here: http://www.proteopedia.org/wiki/index.php/1hxb <br>
+Ligands can not be in alternative configuration. Create by: create ROC_A, 1HXB and resn ROC and alt a .
-<syntaxhighlight lang="python">
+{{Template:PymolScriptRepoDownload|examples/autodock_plugin_2.pml}}
-reinitialize
+<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/autodock_plugin_2.pml" highlight="python" />
-fetch 1HXB, async=0
-#load 1hxb.pdb, 1HXB
-create HIV-1_PROTEINASE, 1HXB and polymer and not resn ROC
-create ROC_A, 1HXB and resn ROC and alt a
-create ROC_B, 1HXB and resn ROC and alt b
-delete 1HXB
-hide everything, all
-#h_add cdk2
-#h_add EFP
-show_as cartoon, HIV-1_PROTEINASE
-show_as sticks, ROC_A or ROC_B
-util.cbay ROC_A
-util.cbap ROC_B
-select flexible_A, byres HIV-1_PROTEINASE within 3.5 of ROC_A
-select flexible_B, byres HIV-1_PROTEINASE within 3.5 of ROC_B
-show sticks, flexible_A or flexible_B
-util.cbag flexible_A or flexible_B
-disable flexible_A or flexible_B
-</syntaxhighlight>
-= References and LICENSES=
+== References and LICENSES ==
+=== Vina ===
 If you used AutoDock Vina in your work, [http://vina.scripps.edu/ please cite:]<br>
 O. Trott, A. J. Olson, ''AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading'', '''Journal of Computational Chemistry''' 31 (2010) 455-461
+=== MGLTOOLS ===
 LICENSE of MGLTOOLS:
 <syntaxhighlight lang="text">
@@ Line 164: / Line 126: @@
       MODIFICATIONS.
 </syntaxhighlight>
-== Python Code ==
-{{Template:PymolScriptRepoDownload|plugins/autodock_plugin.py}}
 [[Category:Plugins]]
+[[Category:Pymol-script-repo]]