The problem
How to
interpret
low-resolution reconstructions of macromolecular assemblies (typically
Transmission EM reconstructions) at atomic scale ?
The problem can be solved in the particular but frequent case where subunits are known at atomic scale (typically MX or NMR molecular models).
The problem can be solved in the particular but frequent case where subunits are known at atomic scale (typically MX or NMR molecular models).
Our solution
The
main idea is to fit the available atomic models (considered as
rigid bodies) into the EM
reconstruction.
The method is to compare, the EM map with a calculated model-based electron density within a selected volume.
The numerical problem consists in determining and optimizing the variables that specify the positions of the rigid models within the macromolecular assembly.
The method is to compare, the EM map with a calculated model-based electron density within a selected volume.
The numerical problem consists in determining and optimizing the variables that specify the positions of the rigid models within the macromolecular assembly.
What is VEDA ?
VEDA is a visual environment developed to fit interactively atomic models into 3D reconstructions.
Calculations are performed in reciprocal-space and the symmetry of the reconstruction is taken into account.
The computations are fast and an entire EM reconstruction can be used.
Calculations are performed in reciprocal-space and the symmetry of the reconstruction is taken into account.
The computations are fast and an entire EM reconstruction can be used.
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VEDA working !
Download and Install VEDA
VEDA_lin_64_Linux version 22-12-2010 (compiled with gfortran)
VEDA_lin_32_Linux version 22-12-2010 (compiled with gfortran)
The OSX version and stand-alone packages are comming soon ...
Installation Guide (for Linux Ubuntu)
User Guide (Beta Version)
Examples (small tubes and dlp Rotavirus, contain density files and PDBs)
VEDA_lin_32_Linux version 22-12-2010 (compiled with gfortran)
The OSX version and stand-alone packages are comming soon ...
Installation Guide (for Linux Ubuntu)
User Guide (Beta Version)
Examples (small tubes and dlp Rotavirus, contain density files and PDBs)