Protein/DNA/RNA model fitting in cryoEM map



  • Hello,
    There is no really good program/server/tool which provides an interface to fit a model into the EM map interactively or statically.
    Although inspite of various good tools for particle picking and map generation, but no such program to provide a reasonably good fitting of the model in the generated map.
    Even Chimera and VMD is also not able to provide solution for this.
    (such a tool is In high demand)
    Thanks a lot



  • Hello, we're actually working on such a module ! (we had an early prototype in 2010, that we never released: https://www.youtube.com/watch?v=oDHqJjAfr_I)

    Could you please tell us what was missing in existing software?



  • Hi,
    Actually interactive fitting only VMD is providing and that is also very limited. VMD chops off your actual EM map according to the provided pdb model instead of fitting it into the density.
    So, as I want to fit multiple structures in the map, I can not do it. I was trying to fit my multi-chain PDB in the same map but it failed.

    Chimera do not provide interactive fitting and it fits the protein poorly in the map. Therefore, it is hard to get a proper knowledge of the conformation of any of these tools.

    Rest tools are more programming centric, making them hard to be used by biologists having limited programming skills like me.


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