a program for fitting subunits into density map of complex using GMM (Gaussian Mixture Model)
LastModified: 2021/05/27
[GMM for atoms] [GMM for map] [Download source code] [MANUAL(gmconvert)] [MANUAL(gmfit)]


The program gmfit is developed to superimpose several subunit atomic models determined by X-ray crystallograph or NMR into the low resolution 3D density map detemined by electron microscopy. This superimposition generally requires large computatinal costs, because the atomic models often contains 103--104 atoms, and 3D density map contains 105--106 grids. We employed Gaussian Mixture Model (GMM) to approximate shapes of atomic models and 3D density map. GMM is a distribution function consisting of linear combinations of several Gaussian functions. The GMM enables us to quickly calculate the fitness of the density map and subunit models, because the overlap of the product of two Gaussian functions can be analyticaly obtained.

We prepare two programs for fitting. The program gmconvert converts various models of molecules (atomic model, 3D density map) into GMM. The program gmfit superimposes GMM subunits into the GMM density map of the complex.

Download the source codes

Source codes of gmfit and gmconvert programs are freely downloadable from the download page. They are mainly written in C language, supposed to be executed in the Linux environment.

Manuals of the programs

Future plan

The current version of gmfit program can only handle a rigid-body fitting of molecule represented by GMM. We know including interaction of subunit atomic models, and flexible transformation of subunits are necessary for more accurate modeling. We are now planning to develop the refinement of GMM models by atomic model, and flexible transformation of subunit models. If you have a question and a suggestion about gmfit, please contact to Takeshi Kawabata.

Example of GMM (Gaussian Mixture Model)

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