Greetings Bethel, These all sound like the same question: yes, you can model a protein structure from input of the full sequence only, without any 3D structure. There are two tools in ChimeraX that can do this if the sequence is not too long, ESMFold and AlphaFold (both in the ChimeraX menu under Tools... Structure Prediction). In each of those you use the "Predict" function where you can input just the sequence as plain text. So first you would need to generate the whole amino acid sequence as plain text, so that you can paste it into either tool. You would do this in your favorite text-editing application (not in ChimeraX). You could probably start with a FASTA format sequence file of the wild-type protein and then manually edit it to add the insertion and/or other mutations. See the help pages please. For the AlphaFold tool: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#dialog> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict> slower for longer sequences For the ESMFold tool: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html#dialog> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html#predict> maximum sequence length 400 residues I hope this helps, 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 Apr 9, 2025, at 7:49 AM, Ogbuehi, Ulochukwu via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Greetings, I had a couple questions about the usability of ChimeraX.
• Is there a way I can insert a variant sequence, and it produce the structure that I would like modelled. Or would I have to strictly use a generated PDB file of my variant for ChimeraX to model the structure.
• I was able to upload and model my WT protein structure in ChimeraX from the AlphaFold WT PDB file I downloaded; however, I am not able to generate a PDB file for my variants and would like to know if there is a feature that allows me to insert my aa sequence into ChimeraX to model the variant structure? Or maybe even a feature that allows you to generate a PDB file using an aa sequence.
• Would I need the WT PDB file to be uploaded and modelled in ChimeraX first prior to adding in my aa sequence, granted that I am even able to insert an aa sequence directly into ChimeraX? Kindest Regards, Bethel Ogbuehi