Re: [modeller_usage] Missing residues in PDB file

On 07/11/2017 02:26 AM, Szymon Żaczek wrote: > I would like to perform a research on 4za7 protein. As long as using > Modeller to insert missing residues is rather straightforward, the > issue I have encountered is more related to PDB file itself. In the > remark 465 section in the original pdb file, there are listed several > missing residues: ... > The problem is that I lack the knowledge on how to deal with those > residues: 499A, 499B, 499C.

What's the complication? Modeller doesn't care how the PDB residues are numbered - just treat these in exactly the same way as any other missing residue. The output model is always numbered sequentially starting at 1.

Ben Webb, Modeller Caretaker