Tutorial: Fit Biomolecules into Cryo-EM Maps using MD Simulation (commandline)

Contents

Tutorial: Fit Biomolecules into Cryo-EM Maps using MD Simulation (commandline)
Overview
Input files
Initial Model
Target Map
Running the program
Output
Examples
Limitation
Reference
Options
List of all options

Overview

This tutorial will show you how to fit biomolecule atomic structures into cryo-EM maps using molecular dynamics simulation with PHENIX commandline

For GUI execution, please see the cryo_fit_gui_tutorial

Theoretical explanation of cryo_fit is here

For installation of cryo_fit, please see the installation notes for cryo_fit

Input files

<initial_model> and <target_map>

Initial Model

Available format: .cif and .pdb

The initial model is a guide or template structure (CIF/mmCIF/pdb) that is close to a target cryo EM map structurally.

You can use either map_to_model or UCSF chimera (Tools -> Volume Data -> Fit in Map)) to prepare the initial model.

Target Map

Available format: .ccp4 and .map (MRC style in binary file) and .sit (Situs style in text file)

Running the program

% phenix.cryo_fit <initial_model> <target_map>

example command line:

% phenix.cryo_fit tRNA.pdb tRNA.map

Output

A final cryo_fitted structure: steps/8_cryo_fit/cryo_fitted.pdb (and cryo_fitted.gro for vmd visualization)

Correlation coefficients (CC) between cryo_fitted structures and cryo-EM maps: steps/8_cryo_fit/cc_record

Examples

cryo_fit example with tRNA

Limitation

gromacs4.5.5 seems to not handle H2O (water) heteroatom. cryo_fit will remove water molecules (if any) from the input .cif/.pdb and fit to cryo electron microscopy map.

cryo_fit doesn't handle non-canonical "residue"s such as 7C4, BMA, GDP, ILX, NAG, SEP, TRX. The cryo_fit will simply erase those residues.

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

Options

All options will be used as default if unspecified. Gromacs expert users are welcome to customize those options if they wish.