Dhiraj Srivastava

relion 5 refinement failed with memory issue

18

Hi I am trying to do the 3D auto-refine with relion 5 and having following issue. I saw a similar issue with relion 3 but I am not sure if...

cuequivariance_ops_cu12

7

Hi I tried to install boltz by git clone https://github.com/jwohlwend/boltz.git cd boltz; pip install -e . but I am getting following error. How can I fix this issue? ERROR: Could...

protein-protein interaction interface scoring

1

Hi I have a bunch of protein-protein complex of a target with binders designed using bindcraft. I want to repredict/validate them using boltz and rank them using at least some...

colabfold_search

1

Hi If I want to install and use colabfold_search, should I install localcolabfold or colabfold? Thank you Dhiraj

Project root directory not found

2

Hi I managed to install foundry using apptainer. RFD is working but RF is giving error FileNotFoundError: Project root directory not found. Indicators: ['.project-root']. is there a way to fix...

out of memory

2

I am trying to design binders (80-160 res.) against my protein (~650 AA) but often getting this error. I have 46 GB memory / gpu and sometime its happening that...

partial diffusion

6

Hi I am confused about how to specify which chain to diffuse for protein binder complex? in the input.md, there is an example json for protein ligand complex. based on...