Superposing protein structures
We have experimental protein structures in PDB, and Alpha Fold predicted structures. Which is the best software to superpose these structures using a MAC computer. - Two different predicted proteins (predicted 1 to predicted 2) and - Same protein predicted and experimental (predicted 1 to experimental 1) Thank you and best wishes. Alicia Gardiol, PhD
Hello Alicia, You can try using the Matchmaker tool. ChimeraX menu: Tools... Structure Analysis... Matchmaker. To see the help page, you can click the Help button on the tool, or you view the copy at our website: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 31, 2022, at 12:48 PM, Alicia Gardiol via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
We have experimental protein structures in PDB, and Alpha Fold predicted structures. Which is the best software to superpose these structures using a MAC computer.
- Two different predicted proteins (predicted 1 to predicted 2) and - Same protein predicted and experimental (predicted 1 to experimental 1)
Thank you and best wishes.
Alicia Gardiol, PhD
Thank you so much. I will keep you posted about my progress. Alicia gardiol On Mon, Aug 1, 2022 at 12:45 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Alicia, You can try using the Matchmaker tool. ChimeraX menu: Tools... Structure Analysis... Matchmaker. To see the help page, you can click the Help button on the tool, or you view the copy at our website:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 31, 2022, at 12:48 PM, Alicia Gardiol via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
We have experimental protein structures in PDB, and Alpha Fold predicted structures. Which is the best software to superpose these structures using a MAC computer.
- Two different predicted proteins (predicted 1 to predicted 2) and - Same protein predicted and experimental (predicted 1 to experimental 1)
Thank you and best wishes.
Alicia Gardiol, PhD
participants (2)
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Alicia Gardiol -
Elaine Meng