UCSF Chimera and Firefox

I’ve been doing some protein structure modelling using the amazing PHYRE2. Viewing the results summary in Firefox shows a list of models with thumbnails. Clicking on a thumbnail links to the corresponding PDB file and by default the browser will display it either as text or will ask you to download the PDB file. I, however, have the Gnome Chemistry Utils (installed from SBo) which provides a browser plugin.

The plug in is fine for simple molecules, but when dealing with a domain structure or more, it becomes quite difficult to interpret the data. A great program for 3D structure viewing, presenting and much more is UCSF Chimera. That’s why I wanted to make Firefox open Chimera directly.

After Googling around I found some tips of what to do. So, long story short, that’s what I did:

  1. In Firefox, I had to disable the Gnome Chemistry Utils plugin. This is done from Tools > Add-ons > Plugins
  2. Open UCSF Chimera and go to Tools > Utilities > Browser Configuration
  3. Following the wizard I selected filetypes Chimera web data, PDB and Mol2
  4. Now, clicking on a link to a PDB file brings up a menu asking if I want this file opened by the chimera_send script from the directory where the executables are. I actually do not want this, because it just fires up Chimera without opening the file. In stead, I chose Other from the menu and selected the shortcut to chimera, that I have installed in /usr/local/bin
  5. Check Do this automatically for files like this from now on and and select OK

That’s it!

Now a few words about the program. It’s great. It’s installation is a breeze. The version I have at the moment is chimera-1.8-linux_x86_64, I installed it to /opt/UCSF/Chimera64-1.8 and I have created symlinks in /usr/local/bin.


One Comment on “UCSF Chimera and Firefox”

  1. […] out, I have had the answer all the time: UCSF Chimera. I have mentioned this powerful program before. It can open a protein MSA (let’s say in FASTA format) in it’s own window. You simply […]


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