The scores.rank_0.json file contains summary confidence scores (per-chain pTM, between chain ipTM, ...) and clashes on a whole model or per-chain level. ChimeraX doesn't have any tool to visualize those but you can show them in any text editor, image below.
Tom
Chai-1 predicted structure and PAE plot shown in ChimeraX 1.9 (Nipah virus G protein with Zanamivir (pink) bound, low confidence).
Chai-1 scores.rank_0.json shown in a text editor
Files returned by Chai-1 server
On Jan 25, 2025, at 3:11 PM, Artie Kushner via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:Your best bet is probably finding how the data in your files relates to chimerax' api and writing a script to connect the two.Hi Reza, if you mean Chai the machine learning model/alphafold clone then you'd have to do a bit of work in connecting their output with Chimerax..npy files are generally the format in which python's `numpy` package saves multidimensional arrays to disk. I'm not sure what their json output is._______________________________________________On Sat, Jan 25, 2025 at 4:36 PM Reza Salavati, Prof. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:_______________________________________________Hello,
I have downloaded the Chai discovery data in .npy and .json file formats.
How can I open these files in Chimera X?
Thank you
Reza
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/
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/