Dan
Dan
I agree with this comment. I read the paper from dec 2019 and would like to try the badger architecture, but need an intro tutorial or some framework to get...
This did not work for me, as the ligand was offset far from the protein. Also, the only output I see are a set of .sdf files. How do we...
Here is an example of two ligands from the results along with the protein in pyMol. One ligand is on the far left, the other on the far right, lower...
Oh, I see the rank and confidence score is included in the sdf filename. Still have the issue of the ligands being far apart from the protein.
I enabled --save_visualizations and got both sdf and pdb files in the output. In this case, the pdb files are offset from the protein but the corresponding sdf files are...
Same problem; have not found a solution yet. There is a pip package `scripts` but it does not have .utils
Looking at the source code, scripts.utils is [here](https://github.com/aqlaboratory/openfold/blob/main/scripts/utils.py) and does have a method get_vidia_cc The problem must be with the specific pip install version-- I'll look into it later today.
Maybe it doesn't matter but in your mapper_params_localization.yaml, you have `mode: "localization"` while the example files do not have quotes. Actually, the mapper_params_localization.yaml file in this repo uses `mode: mapper`...
same thing with VG4