Contents
- For example, phenix.cryo_fit2 <user.pdb> <user.map> resolution=<reso> secondary_structure.protein.distance_cut_n_o=4.5
- For example, phenix.cryo_fit2 <user.pdb> <user.map> resolution=<x> map_weight_multiply=0.2.
- When he enforced stronger map_weight_multiply, he could fit the molecule.
- For example, phenix.cryo_fit2 <user.pdb> <user.map> resolution=<x> map_weight_multiply=15
- At this high map_weight_multiply, the secondary structure (helix) looked broken right after cryo_fit2 running.
- However, phenix.model_idealization which is followed by phenix.real_space_refine perfectly restored ideal secondary structures and fitted very well.
- It appears as if the molecule needs to pass through a local minimum energetically for a perferct fit.
- Therefore, he solved this problem by running phenix.dock_in_map which is followed by cryo_fit2.
- For example, flexibly fit with a 4 angstrom filtered map.
- Then with the resultant atomic model and a 2 angstrom filtered map, do flexible fitting.
- Then with the resultant atomic model and a non-filtered map, do final flexible fitting.
- Tools -> Volume Data -> Volume Viewer -> Tools -> Volume Filter -> (Set Width, e.g. 4,2) -> Filter
- File -> Save map as -> (name a filtered map) -> Save
- For example, phenix.cryo_fit2 <user.pdb> <user.map> resolution=<reso> secondary_structure.protein.distance_cut_n_o=4.5
- For more detail, see secondary_structure_restraints
- For example, phenix.cryo_fit2 nproc=40 model.pdb model.map resolution=3
Although pdb text files show similar SCALES, input (before cryo_fit2) and output (after cryo_fit2) pdb files may show different molecule sizes in Pymol when Doo Nam used map that was made from phenix.map_box
Troubleshooting is ongoing.
In the meantime, please use UCSF Chimera to visualize bio-molecules instead.
- For example, Doo Nam uses either EMDB reported resolution or phenix.mtriage derived resolution to properly run cryo_fit2.
"Sorry: Crystal symmetry mismatch between different files.
(378, 378, 378, 90, 90, 90) P 1
(103.95, 91.35, 89.25, 90, 90, 90) P 1"
The first line (378, ...) shows unit cell parameters from model.
The second line (103.95, ...) shows unit cell parameters from map.
- Just erase CRYST1 header information from an input pdb file. Then, provide that input file into cryo_fit2.
- Cryo_fit2 will automatically extract CRYST1 header from map (both from original map and phenix.map_box derived map), and prepend (write at the first line) to the pdb file.
- (Alternatively) Just leave correct CRYST1 header only in an input pdb file.
- For example, when a wrong CRYST1 header exists above a correct CRYST1 header, above error message appeared.