Python Molecular Viewer (PMV) Installation

autoPACK: INSTALLATION for the Python Molecular Viewer (PMV)

autoPACK for PMV is a very early alpha version released only for MAC as of March 14, 2013. Please check back frequently for updates.

Overview

This installation uses a preview nightly build of PMV and requires the installation of two additional modules to the package.

PMV is a powerful molecular viewer that has a number of customizable features and comes with many pluggable commands ranging from displaying molecular surfaces to advanced volume rendering.

Pre-requisites

1. Windows, Mac, or Linux

2. Respect the license that you will agree to during installation.

Install the latest version of MGL Tools that includes PMV

1. Install the latest build of MGL Tools (which includes PMV) from here

2. http://mgltools.scripps.edu/downloads/latest

3. or directly for Mac OS here http://mgltools.scripps.edu/downloads/tars/releases/nightly/latest/REL/mgltools_i86Darwin9_latest.dmg

4. or directly for Windows here http://mgltools.scripps.edu/downloads/tars/releases/nightly/latest/REL/mgltools_win32_latest_Setup.exe

Install autoPACK and patch MGLTools on Windows

Download the following installer and follow the instruction. Restart PMV.

uPy-PMV installer for Windows

Install autoPACK and patch MGLTools on MAC OS

1. Download the following zipped file for Mac OS

   1. uPy-aP-eP_PMVlatest_mac32_1_1_man.zip

2. Unzip the file

3. Place the contents of the unzipped file as follow into your MGL folder location.

• 1. Move upy, ePMV, and AutoFill contents of MGLToolsPkgs goes to /Library/MGLTools/latest/MGLToolsPckgs/

• 1. Move the contents of MGLToolsPckgs/DejaVu to /Library/MGLTools/latest/MGLToolsPckgs/

• 1. Move the contents of site-package-2.7 to /Library/MGLTools/latest/lib/python2.7/site-packages

Open PMV and start autoPACK

1. Start PMV by...

   1. 1. Mac: Application/MGLTools-Latest/PMV-latest...

      2. In order to activate autoPack plugin open the python shell and paste this line :

      3. self.browseCommands('autoPackpmvCommands', package="AutoFill.plugin", commands=['autoPACK'],topCommand=0)

• 1. Start autoPACK by....

     1. Click on Compute -> autoPACK

Load the HIV model v 1.4

After Selecting the recipe HIV and the version 1.4 click "Construct" and wait while the plugin build the scene. You know it is done when the viewer Gui appears.

In the viewport you should see something similar as the imge below after recentering the scene (click on the cross or type "r","c","n")

PMV is molecular viewer as well as a 3D framework. Thus it provide two distinct outliner, one for the molecules loaded (here none), and one for the geometries. The outliner will let you hide/show and change the material. To access click on

To access the 3D outliner click on

After playing around, and activating the SSAO (type 'o' while the mouse is over the 3D viewport). At first you will not see any change, we need to change the near and far clipping plane.