On Nov 25, 2019, at 4:22 PM, Rui Chen <rchen6@ualberta.ca> wrote:

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

<rep0_chianA_6058_pose1.pdb><rep0_dimer_prepared.pdb><rep0_6058_pose1_dimer.pdb>_______________________________________________
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