Olivia Viessmann

Results 6 comments of Olivia Viessmann

Shift of UMAP points when using .transform()

Many thanks for the quick reply. Installing directly from the git repo solved the issue. Thanks for pointing me in that direction.

Openfold not compatible with newest Flash attention 2.0.4

And in addition to that: will there be version compatible with pytorch lightning 2.0? That causes a couple downstream import issues too.

Looking for CSAR dataset and test folds for pose prediction task

I have a similar question -- would it be possible for you to upload a txt with the matching of receptor_ids to cluster id for the CrossDocked data set? To...

Looking for CSAR dataset and test folds for pose prediction task

Fantastic. Thank you for the swift reply. I see "receptor_ids" in the format of "XXX/pdb_id_Y". Am I understanding correctly that the "XXX" prefix is the id of the "structural homology...

Missing the metadata_one.csv

I ran into the same issue. This is how I resolved it: 1. The code to pre-process a single or a directory of cifs/pdbs is in the FrameDiff repo here:...

Retraining OpenFold on Cath4.2

It would be wonderful if the "big models" had small scale versions of them to quantify their scaling behaviour. Ok, I just set up the openfold repo locally to retrain...