Code used to detect possible dimers in our cryoEM data
- OS: Windows 10
- Visual Studio (tested with VS2017)
- .NET Framework 2.7
There are precompiled binaries in the bin/Release folder alongside neccessary .dll files for running the tool. If you want to compile the code yourself, open the .sln file in VisualStudio and build the solution
There is a file with example Data in the Data folder. After cloning the git repository, simply extract the .tar.gz This is the .star file of all Warp picked particles for our described data set, already merged with orientations from a 3D refinement of monomeric RdRp. You can run the following tools:
.\bin\Release\NearestNeighbor.exe: calculates for all particles in a .star file the NN distances and relative orientations. Output is a tab-seperated file with all info (to be read by pandas,excel,...) and one .star file that contains rot and tilt angles between NN monomers.\bin\Release\PredictMonomers.exe: based on monomer positions, predicts for all monomers that are not part of a dimer, the position on the micrograph where a second monomer would have to be.\bin\Release\PickDimers.exe: Calculates all NNs and then writes coordinate files (compatible with relion extraction) of all potential dimers
A simple script runTools.batch is also included that contains example commands for all three tools
#Code
The main data reading code is the same in all three main modules. Particle poses are read from a .star file and NN distances and rel. orientations are calculated for each particle.