Fitting to a cryo-EM map

Contents

Overview

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.

Input

<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

cyro_fit.run can be executed via the GUI, or the command line:

% cyro_fit.run <initial_model>.pdb <target_map>.sit

example command line:

% cyro_fit.run tRNA.pdb tRNA.sit

Output

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

Examples

CryoFit example with tRNA

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

Reference

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

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