Hi Jim, We (ChimeraX developers) are not the AlphaFold developers and I personally haven't looked at the details of any of its output files, nor am I an expert on your particular protein of interest. So although your inference sounds reasonable, I can't say anything authoritative about it. ....except that you should say that the calculation is actually done with ColabFold, as mentioned in the documentation: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html> Maybe a careful reading of the AlphaFold and ColabFold papers would help to confirm the rest of your description. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 9, 2023, at 1:38 PM, James Raymond via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, I am writing up some results. Would you please see if I am describing our method correctly? Our protein has 2 domains, one whose structure is well known and for which many PDBs are available, and another that is novel. The PDB IDs below came from your file entitled af512_template_domain_names.json
"Protein structure was predicted with AlphaFold2 (Jumper et al., 2021) as implemented by UCSF ChimeraX v. 1.6rc (Pettersen et al., 2021) with the option to use PDB templates. In practice, this meant that the N-terminal DUF3494 domain of the protein was predicted based on several existing PDB structures (7bwy_A, 7bwx_A, 3uyu_A, 6a8k_A, 3wp9_A, 4nu3_A, 4nu3_B, 6bg8_B, 4nu2_A, 3vn3_A, 6eio_A, 4nuh_A, 7dc5_B, 5uyt_A, 5uyt_B, 5uyt_A, 5uyt_B) and the C-terminal domain was predicted de novo by AlphaFold."
Is it OK?
thank you Jim