GaudiView

Light interface to explore, view and analyze solutions from GaudiMM and GOLD, inside UCSF Chimera.

Usage

1. Open up Chimera and launch Tools> InsiliChem> GaudiView. Select a YAML-formatted *.gaudi.output file, as generated by GaudiMM. It will also display GOLD results if you choose the corresponding gold.conf file.
2. Click on the solutions you want to view. Ctrl and shift click will handle multiple selections. You can also navigate with up and down arrows.
3. The list can be multisorted and filtered. Feel free to experiment.
4. Double-click updates rotamers and mutamers in the protein, if available.
5. If you want to perform some actions on every pose, write a Chimera command and it will be executed every time the selection changes.
6. There's also a simple clustering algorithm!

There's a short tutorial written in the GaudiMM docs. Feel free to check it!

Requirements

• UCSF Chimera. Main framework.

• PyYaml package. GaudiMM file parsing.

• tkintertable package. Sortable and filterable table.

Installation

1 - If you don't have Chimera installed, download the latest stable copy and install it with:

chmod +x chimera-*.bin && ./chimera-*.bin

2 - Create a new directory anywhere to host the GaudiView installation files. For example:

mkdir -p ~/insilichem  # any name is OK

3 - Open a new Chimera instance and click on Favorites> Add to Favorites/Toolbar. In this dialog, add the path of the directory you created in step 2 and click save.

4 - Download the latest version of GaudiView and place it inside that directory.

cd ~/insilichem
wget https://github.com/insilichem/gaudiview/archive/master.zip
unzip master.zip
mv gaudiview-master gaudiview

You can also use git clone inside ~/insilichem:

git clone https://github.com/insilichem/gaudiview.git

5 - Install the dependencies in-place with any Python 2 pip:

pip install -t . tkintertable pyyaml https://github.com/insilichem/libtangram/archive/master.zip

Alternative A

If pip is not available in your system, you can install it with Chimera's own Python:

wget https://bootstrap.pypa.io/get-pip.py
chimera --nogui --script get-pip.py # run it twice if it segfaults
chimera --nogui --script `chimera --root`"/bin/pip install -t . tkintertable pyyaml https://github.com/insilichem/libtangram/archive/master.zip"

Alternative B

Download tkintertable source package and extract the *tar.gz file. Open Chimera display and click on Favorites> Command Line. This will bring in an input field at the bottom of the GUI, in which you need to type the following commands. Press Enter after each line.

cd /path/to/where/tkintertable/was/extracted/
runscript setup.py install

Repeat with PyYaml source package and libtangram.