Hi Ahmad, The Change Chain IDs tool (in menu under Tools… Structure Editing) or “changechains” command changes the chain ID of all kinds of atoms, including ligand and solvent. For example, if you change the ID of chain A to chain F instead, the ligand and solvent atoms of chain A will become ligand and solvent atoms of chain F. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechains.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/changechains.html> However, if you mean you want to change ONLY the ligand chain ID without changing the ID of other atoms in the same chain (only change the ID of part of a chain), there is no tool do that in Chimera. You could just text-edit the ligand atom lines in the PDB file using your favorite text editor. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 17, 2018, at 6:50 PM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Is there a way to do it in chimera?
Regards.
Thanks, but I have ligands under a certain chain that I want to change to the other chain. In other words, I want to switch ligand chain ID to another chain ID. How can I do that? On Mon, Aug 20, 2018 at 2:07 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ahmad, The Change Chain IDs tool (in menu under Tools… Structure Editing) or “changechains” command changes the chain ID of all kinds of atoms, including ligand and solvent. For example, if you change the ID of chain A to chain F instead, the ligand and solvent atoms of chain A will become ligand and solvent atoms of chain F.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/ changechains.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/changechains.html>
However, if you mean you want to change ONLY the ligand chain ID without changing the ID of other atoms in the same chain (only change the ID of part of a chain), there is no tool do that in Chimera. You could just text-edit the ligand atom lines in the PDB file using your favorite text editor.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 17, 2018, at 6:50 PM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Is there a way to do it in chimera?
Regards.
If you can’t do it with the Change Chain IDs tool, then you can’t do it in Chimera. As I said before, you could just text-edit the PDB file manually. If you have a large number of PDB files to edit, you could write some kind of script to do it. Elaine
On Aug 20, 2018, at 11:55 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thanks, but I have ligands under a certain chain that I want to change to the other chain. In other words, I want to switch ligand chain ID to another chain ID. How can I do that?
On Mon, Aug 20, 2018 at 2:07 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, The Change Chain IDs tool (in menu under Tools… Structure Editing) or “changechains” command changes the chain ID of all kinds of atoms, including ligand and solvent. For example, if you change the ID of chain A to chain F instead, the ligand and solvent atoms of chain A will become ligand and solvent atoms of chain F.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechains.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/changechains.html>
However, if you mean you want to change ONLY the ligand chain ID without changing the ID of other atoms in the same chain (only change the ID of part of a chain), there is no tool do that in Chimera. You could just text-edit the ligand atom lines in the PDB file using your favorite text editor.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 17, 2018, at 6:50 PM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Is there a way to do it in chimera?
Regards.
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