Gaussian mixture model based atomic model refinement (2024)
Refine atomic models to better fit into a given map, and get better PDB validation score.
Compile model parameters
First we compute some parameters from the input model that will be used in the following refinement.
e2gmm_model_compile.py --model model_input.pdb
Some non-protein structures are not supported at the moment. It is recommended to remove them from input and add them back after refinement.
Fit to density map
e2gmm_model_fit.py --path gmm_model_00 --map map_input.hdf --resolution 3
Here gmm_model_00 is the folder generated by the e2gmm_model_comple.py command. This step can be skipped if there is no input map.
Full model refinement
e2gmm_model_refine.py --path gmm_model_00 --model gmm_model_00/fit_03.pdb
gmm_model_00/fit_03.pdb is produced by e2gmm_model_fit.py. If the fitting step is skipped, simply remove the --model option.