Like on the rcsb website it says that chain B is the protein and chain A C D are nucleic acids/hybrids. And the description says to model residues 1-85 of the PROTEIN, so I just assumed that we restrict it to B. I may be wrong because it's my first time doing protein modeling.
This would be correct; the required segment of protein should only be one chain.
Except the problem is that when I restrict to chain B, the chain starts at residue 4 not 1..... so I’m sort of confused. I don’t know enough about JMOL to know why that’s happening
The PDB file is a bit wonky. If you compare the beginning of FASTA sequences found on PDB versus Uniprot you find:
>sp|Q99ZW2|CAS9_STRP1 CRISPR-associated endonuclease
Is the first residue that is showing up the "K" immediately before the "Y"? That is what is showing up even in PyMol. I am not convinced that the first three residues are included in the PDB file that can be downloaded.