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.
- Be in the desired directory where you want to install the 3DFSC Program Suite.
- Type
git clone https://github.com/nysbc/Anisotropy.gitto get a copy of the program. Make sure you have the git package installed in your Linux machine else this would not work. - Type
cd Anisotropyto enter the directory. - Type
conda env create -f environment.ymlto 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. - Edit the file
run3DFSC.cshwith a text editor to reflect your 3DFSC directory (which containsThreeDFSC_Start.py). You can copy this file anywhere to start the 3DFSC program. It might be a good idea to make an alias to thisrun3DFSC.cshfile.
-
Be in the directory containing your maps. Relative paths are okay for the program.
-
Execute the
run3DFSC.cshscript. If no options are given, it will print out the help menu for you. -
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.
-
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.
- Go the Example directory
- Type
../run3DFSC.csh --halfmap1=T40_map1_Masked_144.mrc --halfmap2=T40_map2_Masked_144.mrc --fullmap=130K-T40.mrc --apix=1.31 --ThreeDFSC=T40-3DFSCto run the Example. It should take no longer than 2 minutes. - 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.