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
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/
Hi Antony, Greg is correct. The current ChimeraX 1.8 release candidate and daily build will open AlphaFold 3 PAE files (e.g. fold_2024_05_08_15_09_full_data_0.json) using menu Tools / Structure Prediction / AlphaFold Error Plot. Our current production ChimeraX 1.7 does not open those files if they contain ligands, ions, or modified residues since AlphaFold 3 introduced those with PAE on a per-atom basis that was not done in AlphaFold 2. This was already discussed on the ChimeraX mailing list https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/... The ChimeraX Python code is in your ChimeraX distribution, for instance, on Mac in ChimeraX.app/Contents/lib/python3.11/site-packages/chimerax The alphafold pae code will be under that directory in alphafold/pae.py or you can see it on GitHub https://github.com/RBVI/ChimeraX/blob/c84672e41a2f89cc3ec46ecaf1efe70e04ef4c... For most ChimeraX commands the ChimeraX Programmer documentation shows the corresponding Python APIs https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/core/commands/user_comm... But the "alphafold pae" command is not in the documentation currently. I will add it. Tom
On May 24, 2024, at 10:45 AM, Antony Merlin Jose via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you very much! I will join. Antony
On Friday, May 24, 2024, Greg Couch <gregc@cgl.ucsf.edu <mailto: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/
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participants (3)
-
Antony Merlin Jose -
Greg Couch -
Tom Goddard