Leginon

h1. Tilt-wrangler launcher in appion

Given ctf file with beam-image tilt X and Y values, tilt-wrangler runs "k-means clustering":https://en.wikipedia.org/wiki/K-means_clustering on X ad Y values and groups them into clusters. 

Input: 

* Relion star file

* Number of clusters for k-means

h2. Installation

If you used "auto-installation tool":https://emg.nysbc.org/projects/appion/wiki/Install_using_the_auto-installation_tool, you can skip installation procedure below since auto-installation does this for you. Otherwise, if you are doing manual installation follow the procedure below to install tilt-wrangler and its dependencies.

On a web server, download "tiltgroup_wrangler_cli.py":https://emg.nysbc.org/projects/appion/repository/revisions/trunk/raw/programs/tiltgroup_wrangler/tiltgroup_wrangler_cli.py, copy to /usr/local/bin and make it executable:

<pre>

wget https://emg.nysbc.org/projects/appion/repository/revisions/trunk/raw/programs/tiltgroup_wrangler/tiltgroup_wrangler_cli.py

cp tiltgroup_wrangler_cli.py /usr/local/bin

chmod +x /usr/local/bin/tiltgroup_wrangler_cli.py

</pre> 

Install numpy and scikit-learn:

<pre>

pip install numpy==1.13.3 scikit-learn==0.19.2

</pre>

This particular versions are needed for this to work on CentOS 7 with Python 2.7.

For CentOS 6 use:

<pre>

pip install numpy==1.13.3 scikit-learn==0.18.2 scipy=1.2.0

</pre>

h2. Usage

After you run CTF estimation, on processing/ctfreport.php page, scroll down to find Download button under @Relion star file with beam tilt group@.

!https://emg.nysbc.org/attachments/download/20931/r1.png!

Here you can set the number of tilt groups and choose from a drop down menu the output format (Relion version 3.1 or 3.0). Click on Download button to download Relion star file with beam-image tilt X and Y values grouped into clusters with tilt-wrangler.