Fitting to a cryo-EM map



CryoFit fits biomolecule (protein and nucleic acids) to Cryo-EM map that is reconstructed by single particle analysis.

Install method, tutorial run files, troubleshooting can be found at this publicly shared dropbox.


<initial_model>.pdb and <target_map>.sit All options will be used as default. Gromacs expert users are welcome to customize those options if they wish.

Running the program can be executed via the GUI, or the command line:

% <initial_model>.pdb <target_map>.sit

example command line:

% tRNA.pdb tRNA.sit


A final cryo_fitted structure: steps/7_cryo_fit/cryo_fitted.pdb (or cryo_fitted.gro if you specified .gro for your vmd visualization)

Correlation coefficients (CC) between cryo_fitted structures and cryo-EM maps: steps/7_cryo_fit/cc_record


CryoFit example with tRNA

../images/cryo_fit_tRNA.png ../images/cryo_fit_tRNA_cc.png


S. Kirmizialtin, J. Loerke, E. Behrmann, C. MT. Spahn, K. Y Sanbonmatsu, Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions, Methods Enzymol., 558, 2015, 497-514

List of all available keywords