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Refine atomic models to better fit into a given map, and get better PDB validation score. Refine atomic models to better fit into a given map, and get better PDB validation score. Gradually updating...
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== Multi-model refinement ==

After heterogeneity analysis, we can build models for a continuous conformational change using a stack of volumes generated by `e2gmm_eval.py`.

{{{
e2gmm_model_multi.py --path gmm_model_00 --modelpdb gmm_model_00/model_02.pdb --modeltxt gmm_model_00/fit_03.txt --maps gmm_00/ptcls_cls_01.hdf --resolution 10 --ndim 2
}}}


{{attachment:model_movie.gif | movement movie |width=600}}

Gaussian mixture model based atomic model refinement (2024)

Refine atomic models to better fit into a given map, and get better PDB validation score. Gradually updating...

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.

Multi-model refinement

After heterogeneity analysis, we can build models for a continuous conformational change using a stack of volumes generated by e2gmm_eval.py.

e2gmm_model_multi.py --path gmm_model_00 --modelpdb gmm_model_00/model_02.pdb --modeltxt gmm_model_00/fit_03.txt --maps gmm_00/ptcls_cls_01.hdf --resolution 10 --ndim 2

movement movie

EMAN2/e2gmm_model (last edited 2024-10-01 19:32:51 by MuyuanChen)