AFDB README

README.md

@@ -27,7 +27,7 @@ Run:
 **For EModelX**:   
 `python run.py --protocol=temp_free --EM_map=data/inputs/maps/emd_32336.map.gz --fasta=data/inputs/fastas/7w72 --output_dir=data/outputs --run_pulchra --pulchra_path modules/pulchra304/src/pulchra` 
 
-**For EModelX(+AF)**, now we support automatically download most similar alphafold structure from alphafoldDB within a certain similarity cutoff:   
+**For EModelX(+AF)**, now we support automatically download the most similar alphafold structure from alphafoldDB within a certain similarity cutoff:   
 `python run.py --protocol=temp_flex --EM_map=data/inputs/maps/emd_32336.map.gz --fasta=data/inputs/fastas/7w72 --template_dir=data/inputs/templates --download_afdb --afdb_allow_seq_id 0.95 --output_dir=data/outputs --run_pulchra --pulchra_path=modules/pulchra304/src/pulchra`   
 , where you can replace `--EM_map` with your target EM map   
 , and `--fasta` with your target fasta   
@@ -36,7 +36,7 @@ Run:
 
 **Notice:** If you want to run **EModelX(+AF)**, please either use `--download_afdb` or prepare the `--template_dir` by yourself. To prepare the `--template_dir` by yourself, please follow our example in `./inputs/templates`. More detailedly, you need to prepare a directory with a consistent name matching the header lines in the fasta file, and the PDB file needed to be renamed as ranked_0.pdb.   
 
-## Postprocess by phenix.real_space_refinement
+## To enable postprocessing by phenix.real_space_refinement
 ### Environment
 Install phenix following <https://phenix-online.org/> into a directory, e.g. `modules/phenix-1.20.1-4487`