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This tutorial will show you how to fit biomolecule atomic structures into cryo-EM maps using dynamics simulation with PHENIX commandline
<initial_model>, <target_map> and <map resolution>
The <initial_model> is a guide or template structure (.cif/mmCIF/.pdb) that is close to a <target_map> (.ccp4/.map) structurally.
User can use map_to_model to build the atomic model.
User can use either dock_in_map or UCSF chimera (Tools->Volume Data->Fit in Map) to roughly place the model into a map.
At command line:
% phenix.cryo_fit2 <initial_model> <target_map> <map resolution in Angstrom>
Tutorial command:
% Go to <user phenix>/modules/cryo_fit2/tutorial % source run_me.sh % (run_me.sh is phenix.cryo_fit2 input/tutorial_cryo_fit2_model.pdb input/tutorial_cryo_fit2_map.ccp4 resolution=4)
A final cryo_fitted structure: output/cryo_fit2_fitted.pdb
Structures of intermediate steps that can be animated with pymol play button: output/all_states.pdb
Open this pdb file with pymol, then click play button (triangle at right bottom) plays the movie.
(below difference is observed with MacPymol ver. 2.2.2)
If a user dragged all_states.pdb into pymol after opening it, the biomolecule structure looks simplified and movie playing is fast.
If a user dragged all_states.pdb into pymol icon, pymol opens along with all_states.pdb, the biomolecule structure is more detailed, and movie playing is slow.
In pymol commandline:
% load ./user_map.ccp4, map1, 1 , ccp4
% isomesh mesh1, map1, 1.5, (all), 0, 1, 3.0
% cmd.color("blue","mesh1")
Otherwise, use pymol GUI:
% A (action) -> Mesh -> @ Level 3.0
As a user is playing a movie (by clicking a bottom right triangle movie playing button),
File -> Export Movie As -> MPEG
All options will be used as default if unspecified. e.g. secondary_structure_enabled =True
| Option | Default value | Description of inputs and uses |
| resolution | none | cryo-EM map resolution (angstrom) that needs to be specified by a user |
| start_temperature | 300 | Start temperature (Kelvin) for molecular dynamics simulation |
| final_temperature | 0 | Final temperature (Kelvin) for molecular dynamics simulation |
| cool_rate | 10 | Rate of cooling temperature (Kelvin) for MD simulation |
| number_of_steps | 1000 | Number of MD simulation steps at each temperature |
| map_weight | automatically optimized | A weight toward cryo-EM map |
| secondary_structure.en abled | True | Most MD simulations tend to break secondary structure. Therefore, turning on this option is recommended. If HELIX/SHEET records are present in supplied .pdb file, automatic search of the existing secondary structures in the given input pdb file will not be executed. |
| secondary_structure.pr otein.remove_outliers | True | False may be useful for very poor low-resolution structures by ignoring some hydrogen "bond" if it exceed certain distance threshold |
| output_dir | output | Output folder name prefix |
| keep_progress_on_screen | True | If True, temp=xx dist_moved=xx angles=xx bonds=xx is shown on screen rather than cryo_fit2.log |
| keep_origin | True | If True, write out model with origin in original location. If False, shift map origin to (0,0,0) |