Use Chimera to do Cryo-Em crystal fit Here are some links of how to do this. https://www.cgl.ucsf.edu/chimera/data/tutorials/eman2011/index.html http://www.cgl.ucsf.edu/chimera/videodoc/RousSarcomaVirus/ http://www.cgl.ucsf.edu/chimera/data/cellcomplexity06/tcell-demo.html