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.