Please find attached the PDB files. The first one is the monomer/ligand PDB file, the second is the homodimer PDB file, the last one is the PDB file saved by chimera. Thank you. Have a good night. On Mon, Nov 25, 2019 at 5:18 PM Rui Chen <rchen6@ualberta.ca> wrote:
Hello,
I docked a ligand into a monomer, now I want to save a new pdb file. In the new pdb file, chian A will be docked monomer, chain B will be the chain B of homodimer. I already superimposed the two PDB files and deleted chain A of homodimer. I also used change chain ID to add chain IDs to the combined PDB file. However I got the following problems: 1. In my system, there are glycans (residue name: 0YB), *I cannot add chain ID to the glycans* (residue 209-216 belongs to chain A, residue 425-432 belongs to chain B) 2. In my system, I also have a small molecule docked in chain A, I realized only *the last line of the ligand was given a chain ID "h"*, is this a problem? 3. I want to *save these two PDB files as two chains, not two models* (actually it's a homodimer except for the ligand) 4. Can I manually *delete all the connections*?
Looking forward to your reply.
Best regards, Rui