EMAN2
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Welcome to VERSION 2 of EMAN, a open-source Software for Single Particle Analysis and Electron Micrograph Analysis. EMAN2 is designed to handle both small, low-symmetry single particles and large, high symmetry viruses. It uses more object-oriented technologies for better modular design, has convenient and flexible interfaces to promote extendibility, emphases easy and efficient use in Python, and many new capabilities.
Here are the Installation Instruction.