[Chimera-users] Save pdb problem

[Rui Chen]

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 at 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
>
>
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