Thank you very much! I will join. Antony On Friday, May 24, 2024, Greg Couch <gregc@cgl.ucsf.edu> wrote:
HI Anthony,
Please send all ChimeraX question to the chimerax-users mailing list, so the appropriate person can answer you. While in general I am not involved with the alphafold support, in this particular case, I believe the answer is to use the current ChimeraX release candidate or daily build. Alphafold 3 changed the PAE format, so new code had to be written. And that has been mentioned on the mailing list, so if you are not already a member, I recommend joining.
-- Greg
On 5/24/2024 6:24 AM, Antony Merlin Jose wrote:
Dear Greg, I have been using the alphafold contacts to parse the .pkl files to show the pseudobonds in ChimeraX (e.g., alphafold contacts #1/A to #1/B maxPae 5 distance 6). The .pkl files were generated from a locally installed Alphafold 2.3. Now that there is an AlphaFold 3 server, ( https://golgi.sandbox.google.com/) I ran some complexes on there and downloaded the results. The results include .json files that have the PAE information. Would using the same commands with this file also result in the correct parsing of the PAE values? How can I see the python code that corresponds to each command on ChimeraX? Thank you Best, Antony
-- Antony M Jose [he/him/his] Associate Professor, Department of Cell Biology & Molecular Genetics, Director, MOCB Concentration Area - Biological Sciences Graduate Program University of Maryland, Rm 2136, Bioscience Research Building, 4066 Campus Drive, College Park, MD - 20742. Website: https://science.umd.edu/cbmg/joselab/