How to supply a custom pdb file (without pdb id) for protein? about protocaller HOT 2 CLOSED

Thanks for your clarification, I learned a lot from it, thank you!

from protocaller.

The issue was related to a missing FASTA file, since you neither supplied one, nor specified a valid PDB ID so that ProtoCaller could retrieve the FASTA automatically. I relaxed this condition, but it is something to bear in mind when manually feeding data into ProtoCaller, because Modeller works with FASTA files and might silently fail to add residues if there is no FASTA file.

In addition, you have a non-standard residue, which is normally converted to a standard one by ProtoCaller, but it needs to be specified in the MODRES section of the PDB. While I could relax this restriction as well and detect the non-standard residues based on their name, I am going to keep it like that to encourage the user to submit PDB files with valid headers. Many pieces of software don't output fully-functional PDB files, so I want to maximise the chance of the user spotting this if they fail to. The main reason for this is that the SSBOND directive in the PDB header is crucial for specifying disulfide bonds and if it's not specified ProtoCaller will simply not add any disulfide bonds, resulting in silent wrong behaviour.

from protocaller.