DeepMainmast is a de novo modeling protocol to build an entire protein 3D model directly from a near-atomic resolution EM map.

If encounter problems, please contact Daisuke Kihara ( or Xiao Wang ( or Genki Terashi (

Example EMD-2513 three chains
Input Map file: emd_2513.mrc

Input Sequence file: emd_2513.fasta

Input AF2 template file: emd_2513_af2.pdb

Contour level: 0.01

Result Example:Result Example with full-atom model building and refinement by Rosetta
Tutorial PPT Tutorial Web Workshop Video

Please simply click "Schedule Job" when you filled all input fields.

Limited by the memory constraint of DM computation, please try to use DiffModeler(seq) if your structure is more than 10k residues.

Please make sure your contour level is lower than your focused region. This is absolute density threshold, not standard deviation.

If you are not sure, just use threshold 0, our model can automatically detect the structure regions.

Please use a sequence file with fasta format. If the target protein has multiple chains, please put all sequences. Each chain must have a ID line (begin with a carat (">")) and a SEQUENCE line.

AlphaFold2 modeled structure in pdb format. Please combine all single-chain structures in one PDB file, separated by "TER" for different chains' records. The chain ID does not matter, for identical chains, you only need to provide the chain records once in the pdb format.

Please simply ignore this field if you do not plan to use AlphaFold2 structure.

Plase select Yes if you have any two or more chains are identical. That is important of correct chain assignment for identical chains.

rosetta refinement to build full-atom structure, that will take very long time (5 hour/1000 residues). If you really want to build full atom structure, you can select yes but wait patiently.