Tutorial: Cryo_fit2: Fit Biomolecules into Cryo-EM Maps using dynamics (commandline)

Contents

Overview

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

<initial_model> and <target_map>

The <initial_model> is a guide or template structure (.cif/mmCIF/.pdb) that is close to a <target_map> (.ccp4/.map) structurally.

You can use either map_to_model or UCSF chimera (Tools->Volume Data->Fit in Map).

phenix.cryo_fit2 can be executed via the GUI, or the command line:

% phenix.cryo_fit2 <initial_model> <target_map>

Tutorial/example command:

% Go to <user phenix>/modules/cryo_fit2/tutorial

% Run run_cryo_fit2_tutorial.sh by "source run_cryo_fit2_tutoria.sh"

% run_cryo_fit2_tutorial.sh is

% phenix.cryo_fit2 input/tst_00_poor.pdb input/tst_00_answer.ccp4

A final cryo_fitted structure: output/refined.pdb

Structures of intermediate steps that can be animated with pymol play button: output/all_states.pdb

In pymol commandline,

load ./tst_00_answer.ccp4, map1, 1 , ccp4

isomesh mesh1, map1, 1.5, (all), 0, 1, 3.0

cmd.color("blue","mesh1")

will show map contour as mesh.

All options will be used as default if unspecified. e.g. secondary_structure_enabled =True