EModelX is a method for automatic cryo-EM protein complex structure modeling.
conda env create -f EModelX.yml
For EModelX(+AF), you may need to run AlphaFold following https://github.com/deepmind/alphafold or get AlphaFold-predicted single-chain structures from AlphaFoldDB (https://alphafold.ebi.ac.uk/).
For EModelX:
python run_com_modeling.py --protocol=temp_free --EM_map=./inputs/emd_32336.map.gz --fasta=./inputs/7w72.fasta --output_dir=./outputs
For EModelX(+AF):
python run_com_modeling.py --protocol=temp_flex --EM_map=./inputs/emd_32336.map.gz --fasta=./inputs/7w72.fasta --template_dir=./inputs/templates --output_dir=./outputs
, where you can replace --EM_map with your target EM map
, and --fasta with your target fasta
, and --template_dir: directory of the template folder, only needed when --protocol == temp_flex
, and --output_dir: the output directory for modeling results
Notice: If you want to run EModelX(+AF), please place your AlphaFold-predicted single-chain structures in your --template_dir， the format should follow our example in ./inputs/templates.
EModelX's web server is accessible at https://bio-web1.nscc-gz.cn/app/EModelX