Hi Natasha, I don't know what you mean by "ran AlphaFold on it" -- it all depends on exactly how you told AlphaFold what sequence to use, or if you even used predict (new calculation) or fetch or match (which does not run a new calculation but gets an existing model from a database). You would need to give much more detail on what you actually did. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Jun 24, 2024, at 7:30 AM, Suwisanto, Natasha via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello,

My name is Natasha Suwisanto. I’ve been using UCSF Chimera X and AlphaFold servers for a personal research project to mutate a GPCR protein. I just had a quick question. I was mutating a structure using the Rotamer tool on ChimeraX. I mutated a single amino acid (Tyrosine) to a Proline using the Richardson Common Atom library. However, when I ran AlphaFold on it, the predicted 'best model' structure they gave me had a different amino acid (Leucine) on the position I previously mutated the Tyrosine to the Proline. I was just wondering if I did something wrong or if AlphaFold/ChimeraX works differently than I thought.

Best, Natasha Suwisanto