HermiteFit

About

HermiteFit is a new docking algorithm for rapid fitting atomic structures into cryo-EM density maps using 3D orthogonal Hermite functions. HermiteFit uses the cross-correlation or the Laplacian-filtered cross-correlation as the fitting criterion. HermiteFit exhaustively rotates the protein density in the Hermite space and then converts the expansion coefficients into the Fourier space for the subsequent fast FFT-based correlation computations.

Authors

Georgy Derevyanko and Sergei Grudinin,

Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, Jülich, Germany.

CEA, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France.

CNRS, UMR 5075, IBS, Grenoble, France.

Université Joseph Fourier – Grenoble 1, IBS, Grenoble, France.

NANO-D, INRIA Grenoble — Rhone-Alpes, 38334 Saint Ismier Cedex, Montbonnot, France.

Laboratoire Jean Kuntzmann, B.P. 53, 38041 Grenoble Cedex 9, France.

E-mail: Sergei.Grudinin @ inria.fr

Download

Linux executables verified on Fedora, x86-64 architecture, multi-threaded and single-threaded versions. An updated version under BSD-compatible license without dependences and a GUI SAMSON module are in preparation.

Linux: coming soon.
MacOS: coming soon.

Examples

GroEL example (input PDB files + cryo-EM map) GroEL data

A standard fitting example with automatically chosen parameters:

./HermiteFit edmName GROELdat/EMD-2001.ccp4 protName GROELdat/1AON_AcR.pdb numOutputs 14

Another fitting example with automatically chosen parameters, the protein is rotated and translated to exclude the rotational bias:

./HermiteFit edmName GROELdat/EMD-2001.ccp4 protName GROELdat/1AON_shift.pdb numOutputs 14

A rapid coarse fitting:

./HermiteFit edmName GROELdat/EMD-2001.ccp4 protName GROELdat/1AON_shift.pdb numOutputs 14 R 20 N 10 dAngle 36

Results can be visualised using PyMol:

pymol tmpOutputDir/HermiteFit_unified.pdb GROELdat/EMD-2001.ccp4

To see all models in PyMol do:

Movie -> Show All States

To split the first 14 models in PyMol type (in the command prompt):

split_states HermiteFit_unified, 1,14

License

Currently the license is being changed to a BSD-compatible one.

Reference

G. Derevyanko, and S. Grudinin. “HermiteFit: Fast fitting atomic structures into cryo-EM density maps using 3D orthogonal Hermite functions“. Acta Crystallographica Section D70: 2069-84, 2014. DOI :10.1107/S1399004714011493.Download PDF.

Comments are closed