UROX 1.0 : An interactive tool for fitting atomic models into Electron Microscopy reconstructions

Xavier Siebert (1) , Jorge Navaza (1)

1 LMES - Laboratoire de Microscopie Electronique Structurale

Electron microscopy of a macromolecular structure can lead to three-dimensional reconstructions whose resolution is typically in the 30-10 {Å} range. Fitting atomic models of the macromolecular structure's individual components (e.g., obtained by X-ray crystallography or nuclear magnetic resonance) into an electron microscopy map allows an interpretation of the latter at nearly atomic resolution, providing insights into the interactions between the components. We present a graphical software designed for interactive fitting and refinement of atomic models into electron microscopy reconstructions. Several characteristics make it applicable over a wide range of cases and resolutions. First, calculations are performed in reciprocal space, which results in fast algorithms. This allows big volumes of the map to be used by taking into account the symmetry of the reconstruction (both in the calculations and in the graphical display) while working only with independent variables. Second, atomic models can be placed graphically in the map while the correlation between the model-based electron density and the electron microscopy reconstruction is computed and displayed in real-time. The positions and orientations of the models are refined by a least-squares minimization. We illustrate these features on three practical cases with different symmetries and resolutions. The software as well as examples and user instructions are available free of charges at {\tt \, http://mem.ibs.fr/UROX/}.

Mots clés: electron microscopy; X-ray crystallography; graphical software; real-time fitting; reciprocal space; symmetry

Domaines: Biophysique [physics.bio-ph]

Xavier Siebert, Jorge Navaza. UROX 1.0 : An interactive tool for fitting atomic models into Electron Microscopy reconstructions. 2008. ⟨hal-00308759⟩