I just ran Alphafold3 predictions on our dinoflagellate pks proteins. Will chimerax read the models which are .cif files? I want to highlight the various domains in the 3D models. I am running on OSx. Al Allen R. Place(he/him/his) Professor, Associate Director of Research, Director of BASLab, Director of HAB-CTI Institute of Marine and Environmental Technology University of Maryland Center for Environmental Sciences The Rita Rossi Colwell Center 701 East Pratt Street Baltimore, MD 21202 410-234-8828 place@umces.edu ALAN, ALLAN, ALLEN From the Gaelic word for “cheerful” He is smart, makes friends easily, and never loses his sense of humour. He thrives on a challenge  Sign up to receive our quarterly newsletter, Inside IMET!
Hi Allen, You could have just tried opening them! Yes, ChimeraX reads mmCIF format. Here is a big list of the formats it knows: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats> You can also open the PAE data for that model from Alphafold 3 *if* you download a new daily build of ChimeraX ... older versions like the ChimeraX 1.7 release will only read PAE data from earlier versions of Alphafold. For example, ChimeraX commands: open test_7bbv_model_4.cif alphafold pae #1 file test_7bbv_full_data_4.json 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 May 15, 2024, at 6:44 AM, Allen Place via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I just ran Alphafold3 predictions on our dinoflagellate pks proteins. Will chimerax read the models which are .cif files? I want to highlight the various domains in the 3D models. I am running on OSx. Al
Hi Allen, ChimeraX will read the AlphaFold 3 mmCIF files -- this is a standard atomic structure file. To read the the AlphaFold PAE json files (the ones with "full_data" in the name e.g. fold_2024_05_08_18_58_full_data_0.json) first open the .cif file then use ChimeraX menu Tools / Structure Prediction / AlphaFold Error Plot. That needs the current ChimeraX daily build since I just enhanced the ChimeraX PAE code to handle the new AlphaFold 3 PAE format which includes ligand atoms. Tom
On May 15, 2024, at 8:46 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Allen, You could have just tried opening them! Yes, ChimeraX reads mmCIF format. Here is a big list of the formats it knows:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats>
You can also open the PAE data for that model from Alphafold 3 *if* you download a new daily build of ChimeraX ... older versions like the ChimeraX 1.7 release will only read PAE data from earlier versions of Alphafold.
For example, ChimeraX commands:
open test_7bbv_model_4.cif alphafold pae #1 file test_7bbv_full_data_4.json
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 May 15, 2024, at 6:44 AM, Allen Place via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I just ran Alphafold3 predictions on our dinoflagellate pks proteins. Will chimerax read the models which are .cif files? I want to highlight the various domains in the 3D models. I am running on OSx. Al
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
-
Allen Place -
Elaine Meng -
Tom Goddard