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https://github.com/insilichem/gaudiview

UCSF Chimera extension to explore and analyze GaudiMM & GOLD solutions
https://github.com/insilichem/gaudiview

docking molecular-structures ucsf-chimera visualization

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UCSF Chimera extension to explore and analyze GaudiMM & GOLD solutions

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README 

        
# GaudiView #



Light interface to explore, view and analyze solutions from [GaudiMM](https://github.com/insilichem/gaudi) and [GOLD](https://www.ccdc.cam.ac.uk/solutions/csd-discovery/components/gold/), inside [UCSF Chimera](http://www.cgl.ucsf.edu/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](http://gaudi.readthedocs.io/en/latest/tutorial-visualization.html). Feel free to check it!



## Requirements



* **[UCSF Chimera](http://www.cgl.ucsf.edu/chimera/download.html)**. Main framework.



* **[PyYaml](https://pypi.python.org/pypi/PyYAML) package**. GaudiMM file parsing.



* **[tkintertable](https://pypi.python.org/pypi/tkintertable) package**. Sortable and filterable table.



## Installation



1 - If you don't have Chimera installed, download the [latest stable copy](http://www.cgl.ucsf.edu/chimera/download.html) 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](https://github.com/insilichem/gaudiview/archive/master.zip) 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](https://pypi.python.org/pypi/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](https://pypi.python.org/pypi/PyYAML) source package and [libtangram](https://github.com/insilichem/libtangram/archive/master.zip).