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What Free Ubuntu-Compatible Software Exists for the 3D Visualisation of Biologic Proteins and Peptides? I asked this question http://chemistry.stackexchange.com/questions/4543/what-free-linux-compatible-software-exists-for-the-3d-virtualisation-of-biologic? but it got closed because it was software recommendation which is off-topic for chemistry stackexchange but I thought it wouldn't be off-topic for here. I am running 32 bit 12.10 if it is relevant.

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2 Answers

Check out JMOL. It's open source and Java based - so it will work on Windows, Mac, and Linux. I just spent the last 20 minutes looking a superb model of ATP and a list of other molecules in crosseyed stereographic 3D!

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I Figured This Out Myself a Few Hours After Asking This Question

There are a few different softwares for this kind of modelling that will work on Ubuntu including:

  • Avogadro (Download page, Avogadro Documentation [which is in wiki form]. You can download Avogadro from the software centre but it is an outdated version.)
  • Jmol (You can download Jmol from the software centre but this is an outdated version. This software comes in the form of a zip file from the link given, unzip this file and then go into the directory created by this unzipping and right-click on the jmol.sh file and go into permissions and click (and thus tick) the box next to "Allow executing file as a program")
  • MarvinView (This link will bring you to the page to download MarvinBeans which is a package of chemical modelling softwares by ChemAxon, including MarvinView. You will need to log in to download MarvinView but you can create this account for free and download and use MarvinView and the majority of its functions for free)
  • RasMol (This software is rarely updated [the latest stable release was July 17 2009] but appears to have many basic functionalities)

My personal preference would have to be either Jmol or MarvinView.

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Er...I did provide an answer. –  Kupiakos Apr 3 '13 at 17:54
    
Yeah but you didn't provide a comprehensive and detailed or in other words "Good" answer. You did inform me about Jmol, in that it exists and does the job for at least some (namely yourself), so I've up-voted your answer. I just won't accept it with such little detail. –  Brenton Horne Apr 4 '13 at 4:59
    
To tell you the truth, I'm not into organic chemistry and I never use any of this software on a daily basis. I'm just good with Google. Also keep in mind I was the only one to post an answer. If you wanted me to add more information, you should've commented in my answer asking for more. I probably would've. –  Kupiakos Apr 11 '13 at 19:41
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