Naail Kashif-Khan

icon location London, United Kingdom icon location I make proteins in the lab and with AI 🔬💻 I wield the pipette and the keyboard 🧫⌨️

Results 3 comments of Naail Kashif-Khan

The shape of contact map is not consistent with residue length

It looks like T1042 does indeed have a length of 73 residues, but from the PDB text you post @zhenyuhe00 the crystal structure only models residues 3-73. This would mean...

Torch module no longer supported

On DeepSpeed compatibility: this is actually an issue with OpenFold - see here [https://github.com/aqlaboratory/openfold/issues/276](https://github.com/aqlaboratory/openfold/issues/276). Replacing all occurrences of `deepspeed.utils.is_initialized()` with `deepspeed.comm.comm.is_initialized()` in `openfold/model/primitives.py` fixes the issue and allows you to...

Upgrade DeepSpeed version?

I had a similar issue when trying to use Openfold as part of ESMFold, with DeepSpeed version `0.9.2` I get the error that `deepspeed.utils.is_initialized()` doesn't exist anymore. But replacing all...