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An example of what I'm talking about is this animation from Wikipedia. I am running 32 bit 12.10 if it is relevant. Please describe step-by-step, with pictures (screenshots with the appropriate areas (that are mentioned in the text) highlighted) how I am to create these gif files with the software you name.

Methadone [wikipedia

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Just to point out that this is not a tutorial site but a Q&A site. Asking for a step by step guide to create something as simple as one of the spheres in the animation would take several pages. Answers will generally cover "which" (As you state in your title) apps in 32 Bit can help you do the animation. Not a full guide on how to do it from scratch. So you will get a software recommendation. The answer provided by maggotbrain covers this. –  Luis Apr 4 '13 at 12:04
    
Have you tried asking in chemistry.se or biology.se? –  Glutanimate Apr 4 '13 at 14:44
    
No because software recommendation is off topic there. –  Brenton Horne Apr 4 '13 at 21:20

2 Answers 2

up vote 7 down vote accepted

QuteMol


Overview

QuteMol produces some of the most beautiful molecular visualizations I have ever seen. The software is FLOSS and available from the official repositories.

Description

QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilites through OpenGL shaders to offers an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins.

  • Real Time Ambient Occlusion

  • Depth Aware Silhouette Enhancement

  • Ball and Sticks, Space-Fill and Liquorice visualization modes

  • High resolution antialiased snapshots for creating publication quality renderings

  • Automatic generation of animated gifs of rotating molecules for web pages animations

  • Real-time rendering of large molecules and protein (>100k atoms)

  • Standard PDB input

  • Support as a plugins of the NanoEngineer-1 the modeling and simulation program for nano-composites (new!)

QuteMol was developed by Marco Tarini and Paolo Cignoni of the Visual Computing Lab at ISTI - CNR.

Screenshot

enter image description here

Installation

QuteMol is available from the Ubuntu Software Centre:

Foo

If you prefer the CLI you can install QuteMol with:

sudo apt-get install qutemol

Note: The Ubuntu build appears to have a number of bugs. Some minor UI elements don't work correctly and the rendering will produce dysmorphed structures at times. The last point seems to happen mostly when working with small molecules. All of these issues can be remedied by running QuteMol under WINE or PlayOnLinux.

I tried to build QuteMol from source to see whether the issues are restricted to the version in the repositories but it turned out to be a ridiculously hard task and didn't quite work.

Usage

Basic Usage

QuteMol is very easy to use. Open a PDB file of your choice, adjust the view and hit the export button:

enter image description here

Make sure to choose the GIF format:

enter image description here

Select the rendering mode of your choice. You can set the FPS count by adjusting the rotation time of the animation and the number of frames:

enter image description here

Rendering Modes

Full rotation mode:

enter image description here

Inspection Mode:

enter image description here

Six-Sides Mode:

enter image description here

Methadone (as depicted in the question):

enter image description here

(Orientation and shader settings vary a bit but could be made to look identical with a little bit of tweaking here and there)

Finding structural data

PDB databases

QuteMol takes standard .pdb files as its input. This format is most commonly used for proteins and other macro-molecules but can be used with small molecules as well. You can find a large selection of macro-molecular .pdb files at the Protein Data Bank.

Similarly rich structural libraries for small molecules that come with .pdb downloads are hard to find, but you can try your luck on one of these:

Other databases that might or might not offer PDB files can be found here.

Just to get you started I have uploaded the PDB file I used for Methadone here. This one might work better on the WINE/PoL version.

Other ways to get PDB files

You can also attain .pdb files by converting them from other, more ubiquitous formats such as MDF .mol files. You can do so with babel, a powerful command-line tool that converts between a multitude of different chemical structural formats. Install it with

sudo apt-get install babel

babel is very straightforward to use. Simply specify the file input and desired output and let it do its magic:

babel methadone.mol methadone.pdb

Or if you want babel to add implicit hydrogens:

babel -h methadone.mol methadone.pdb

You can also change the protonation state by defining the pH:

babel -h -p 6 methadone.mol methadone.pdb

Just make sure to use files with three-dimensional structural information, otherwise your .pdb output will be nonsensical.

Good sources for 3D MOL/SDF files are Pubchem and ZINC. Make sure to choose the 3D SDF option when downloading files:

enter image description here enter image description here

Additional export options

GIFs are fine for web publishing but because of their size and other issues they can be quite a chore when used in presentations. For this particular use case I have written a Nautilus script that quickly converts GIF files into MPEG4 videos:

#!/bin/bash

# NAME          gif2mp4 0.1
# AUTHOR        Glutanimate (c) 2013 (http://askubuntu.com/users/81372/glutanimate)
# LICENSE       GNU GPL v3 (http://www.gnu.org/licenses/gpl.html)
# DESCRIPTION   Converts GIF files of a specific framerate to MP4 video files.
# DEPENDENCIES  zenity,imagemagick,avconv

TMPDIR=$(mktemp -d)
FPS=$(zenity --width 200 --height 100 --entry --title "gif2mp4" --text="Please enter the frame rate.")
VIDDIR=$(dirname $1)

if [ -z "$FPS" ]
  then
      exit
fi

notify-send -i video-x-generic.png "gif2mp4" "Converting $(basename "$1") ..."

convert $1 $TMPDIR/frame%02d.png
avconv -r $FPS -i $TMPDIR/frame%02d.png -qscale 4 "$VIDDIR/$(basename "$1" .gif).mp4"

notify-send -i video-x-generic.png "gif2mp4" "$(basename "$1") converted"

rm -rf $TMPDIR

Output sample: https://www.youtube.com/watch?v=odLnUwj8r4g

Installation instructions can be found here: How can I install a Nautilus script?

PyMOL


Overview

QuteMol is a fantastic little program but quite restricted in terms of rendering modes and image manipulation. For more advanced handling of compound visualization you might want to check out PyMOL. A tutorial on how to create simple animations can be found here. I would have written up a tutorial here but I am not proficient enough with PyMOL to do so.

One last thing, though. If you want to achieve a similar graphical fidelity with PyMOL as with QuteMol you should check out these blog entries:

http://cupnet.net/ambient-occlusion-pymol/

http://lightnir.blogspot.de/2008/09/cute-molecules.html

Screenshot

enter image description here


I hope you found this small overview of rendering options useful. If there are any mistakes in this post please feel free to edit them.

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How do I get it to show implicit hydrogens? Just so you know as soon as you answer this question you will definitely get this answer accepted it is a great job! –  Brenton Horne May 9 '13 at 20:51
    
@BrentonHorne QuteMol doesn't appear to be capable of calculating implicit hydrogens. It will only render what's defined in the input file. You can use babel to automatically add hydrogen atoms though: babel -h has_no_h_molecule.pdb has_h_molecule.pdb. Similarly, for acidic and basic groups you change the protonation state by setting the -p parameter: babel -h -p 6 filename1.pdb filename2.pdb. For more information on babel's conversion parameters please consult the official wiki. It's a very powerful tool, indeed. –  Glutanimate May 9 '13 at 21:17

I would recommend looking at the UbuntuScience packages to get you started.

There are quite a number of programmatic, as well as, visualization inclined software packages that are already available in the Main repositories.

As an example, let's take a look at gdis, under the Chemistry section on the UbuntuScience page.

This particular piece of software is a "A molecular display program that supports OpenGL and POVRay rendering."

To install gdis, run the following commands from your terminal (ctrl+alt+T):

sudo apt-get install gdis

In order to install this package, it will also need to install the following dependencies:

gdis-data
openbabel

Once it is installed, open the program from your menu.

In my case, running Xfce, I would go to Applications Menu --> Education --> GDIS Data Modeler. Or alternatively you could go open terminal (ctrl+alt+T) and type gdis.

Once you open the application, go to File --> Open.

  • From there, navigate to /usr/share/gdis/models to open up a sample file:

-- For this example, open up the file /usr/share/gdis/models/arag.gin:

In order to run a rotational animation of the molecule:

  • Select the record icon on the toolbar:

  • Right click on the molecule and drag your mouse for several seconds
  • Return to the menu -- Select Tools --> Visualisation --> Animation -- Now, select the Play button to replay your manipulation of the molecule:

For a basic tour of GDIS, take a look at their tutorials.

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You did not tell me what to click after going into the visualisation submenu. Could you please specify? I assume it's animation but animation doesn't do anything for me at all. –  Brenton Horne Apr 4 '13 at 8:57

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