3DFSC Program Suite Version 2.5 (5 September 2017)

This is the most recent version of 3DFSC, by Philip Baldwin, Yong Zi Tan, and Dmitry Lyumkis. Conda environment configured by Carl Negro. 3DFSC Program Suite requires Anaconda 3 to run, and UCSF Chimera to visualize the outputs.

Installation

1. Be in the desired directory where you want to install the 3DFSC Program Suite.
2. Type git clone https://github.com/nysbc/Anisotropy.git to get a copy of the program. Make sure you have the git package installed in your Linux machine else this would not work.
3. Type cd Anisotropy to enter the directory.
4. Type conda env create -f environment.yml to create the Anaconda environment containing required packages. This would only work if Anaconda 3 is installed and used as the default Python. You do not need to activate the new environment yet.
5. Edit the file run3DFSC.csh with a text editor to reflect your 3DFSC directory (which contains ThreeDFSC_Start.py). You can copy this file anywhere to start the 3DFSC program. It might be a good idea to make an alias to this run3DFSC.csh file.

Execution

1. Be in the directory containing your maps. Relative paths are okay for the program.

2. Execute the run3DFSC.csh script. If no options are given, it will print out the help menu for you.

3. Runs usually take from minutes up to hours for extremely large box sizes (we have tested 600^3). Progress bars will help indicate the state of processing.

4. 3DFSC is also accessible programmaticaly, for example:

   import Anisotropy.ThreeDFSC.ThreeDFSC_Start as run_fsc
    run_fsc.execute(options)

   where "options" is an opt-parser object containing the parameters of the program.

Example: Haemagglutinin Trimer with Preferred Orientation Collected at Tilts

1. Go the Example directory
2. Type ../run3DFSC.csh --halfmap1=T40_map1_Masked_144.mrc --halfmap2=T40_map2_Masked_144.mrc --fullmap=130K-T40.mrc --apix=1.31 --ThreeDFSC=T40-3DFSC to run the Example. It should take no longer than 2 minutes.
3. The folder already contains pre-calculated results as well as a log of a successful run (output.log).

Questions and feedback welcomed, and should be sent to prbprb2@gmail.com, ytan@nysbc.org and dlyumkis@salk.edu.