Code for generating movies of the most relevant movement modes of proteins from their PDB files, using rigidity clustering analysis
PyMOL
FreeMOL mpeg_encode component
Python libraries: argparse
Recompiling FIRST and diagstd is necessary!
- Go to FIRST-190916-SAW/src and run 'make'.
- You should be ready to go!
(Note that if your C++/Fortran compilers are not the ones I use, you might need to edit some Makefiles.)
python pdb2movie.py FILE [options]
FILE is your desired PDB file
--keep MOLECULE LIST - Stops the cleaning routine from removing the listed molecules from the PDB file
--output PATH - Sets the output location for the simulations and videos
--waters - Keeps water molecules in the PDB file (equivalent to --keep HOH)
--confs CONFS - Total number of configurations to be calculated
--freq FREQ - Frequency of saving intermediate configurations
--step STEP - Size of random step
--dstep DSTEP - Size of directed step
--res WID HEI - Resolution of generated videos (width, height)
--modes MODE LIST - Movement modes to be investigated
--ecuts ECUTS LIST - Energy cutoff values
--video FILE - Python file with PyMOL commands to be run before generating video
--threed - Generates anaglyph stereo videos
--combi - Creates videos combining positive and negative directions for each mode/cutoff energy
--multiple - Keeps multiple chains from the original PDB file (default: uses only chain A)
See also the web-server-based implementation at https://pdb2movie.warwick.ac.uk.