[Chimera-users] Save pdb problem

Rui Chen rchen6 at ualberta.ca
Mon Nov 25 16:18:16 PST 2019


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
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,
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