- Open up Chimera and launch
Tools> InsiliChem> GaudiView. Select a YAML-formatted
*.gaudi.outputfile, as generated by GaudiMM. It will also display GOLD results if you choose the corresponding
- Click on the solutions you want to view.
shiftclick will handle multiple selections. You can also navigate with up and down arrows.
- The list can be multisorted and filtered. Feel free to experiment.
- Double-click updates rotamers and mutamers in the protein, if available.
- If you want to perform some actions on every pose, write a Chimera command and it will be executed every time the selection changes.
- There's also a simple clustering algorithm!
There's a short tutorial written in the GaudiMM docs. Feel free to check it!
UCSF Chimera. Main framework.
PyYaml package. GaudiMM file parsing.
tkintertable package. Sortable and filterable table.
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
git clone https://github.com/insilichem/gaudiview.git
5 - Install the dependencies in-place with any Python 2
pip install -t . tkintertable pyyaml https://github.com/insilichem/libtangram/archive/master.zip
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"
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