Daq-refine would run a loop for all chains to finish the whole job. For each chain in the pdb file, it needs the cryo-em map and the fasta sequence as inputs. So deciding which sequence to run for some chain is crucial for the final results.
The alignment strategy here is how you choose to do this alignment job. If you choose the 'Mannual alignment', Daq-refine would do nothing just following the order in the input files to handle the job. If you choose 'Smith Waterman alignment',it would take the Smith Waterman algorithm to align the pdb file and the fasta file.
A simple tutorial for the mannual alignment is that if you download the sources files from the same Protein Bank, like RCSB. They usually have the key words for you to align.
For example, the protein 8g05_1 sequence in fasta file is
>8G05_1|Chain A[auth R]|G-protein coupled receptor 84|Homo sapiens (9606)
DYKDDDDHHHHHHHHGQPGNGSAFLLAPNGSHAPDHNVTQQRDEENL.............
The name for this chain is G-protein coupled receptor 84 from RCSB and it will be also marked in the PDB file, using this key,you can easily finish the mannual alignment thing.
