History ModeHunter was initially developed in 2009 by Joseph Stember and Willy Wriggers at Weill Cornell Medical College, with later contributions by Sebastian Stolzenberg added to version 1.3. Updated information on our research can be found at the URL biomachina.org. The program history below describes changes that were implemented over the years after version 1.0. Changes in Version 1.3 vs. Version 1.2: Normal modes and frequencies in the work flow were combined into one single pickle file, so MH 1.3 is no longer compatible with older pickle files and they have to be newly generated. New tool eldecoy.py added for normal mode-based decoy generation. New tool traject.py added for simulating trajectories based on mode superposition. Network tuning capability (perturbations) added to enmhunt.py. An option to scale mode amplitudes by inverse frequency was added to various tools using negative amplitude argument. extract.py was renamed augment.py to better reflect its interpolation purpose. Output of needles.py now written as .vmd files to be recognized in recent VMD versions. All tools were significantly revised / rewritten to be compatible with both Python 2.7 and Python 3.9. Changes in Version 1.2 vs. Version 1.1: Using cosine instead of sine in animate.py to support single-frame output of modes for subsequent analysis with structural bioinformatics programs. Minor change in the output of animation frames: now using input file template for output PDB (animate.py and m_inout.py). Type selection parameter added for "arrows" or "needles" display in needles.py. Bug fix: Amplitude of modes in animate.py and needles.py adjusted based on RMSD.  Changes in Version 1.1 vs. Version 1.0: Output of modes in NOMAD-Ref format was added to the log files generated by btshunt.py, enmhunt.py, and extract.py (via m_inout.py). Default number of frames of animate.py was changed to 50. Also, a PDB formatting bug affecting files > 1000 pseudo-atoms was fixed. Return to the front page .