Open chenwei-zhang opened 8 months ago
Hi!
crop
can be found in model_angelo/c_alpha/inference.py
. Basically, since we are doing inference on boxes of 64 voxels across, the voxels near the edge of each box do not have information about the biological context around them. So, you would expect results of these voxels for segmentation to be worse. The crop
argument controls how many voxels from each side to ignore during inference for each box.crop_length
in the GNN is different. Since there are GPU memory constraints for the majority of our users, ModelAngelo will only look at groups of residues of length crop_length
that are close together.aggressive_pruning
is an algorithm that prunes residues that are not found in the sequence file.Could you clarify what you mean about pruning the short chains? Would you like to prune all chains shorted than N
residues from the output CIF
file? I don't believe there is such an option but it would be simple for me to write a quick python script for that if you like.
Best, Kiarash
Hi Kiarash, Thanks for your rapid reply.
pruned
and unpruned
predictions, I am wondering how do you do this pruning? I found a sentence in the paper saying "chains shorter than 4 residues are pruned and the resulting coordinates are used as the input". May I ask if this is corresponding to the pruned prediction? Is there any way I could customize thecutting threshold 4 residues
? And if I directly use the latest version of ModelAngelo without changing any configuration, will this generate the pruned or unpruned structures?Sorry for so many questions, but ModelAngelo is an awesome work and I really appreciate. Thank you in advance for your answers.
Best, Chenwei
Hi @chenwei-zhang ,
pruned
and unpruned
refers to the output files. The pruned file is output.cif
and the unpruned file is output_raw.cif
. It is not quite clean if you want to change the cutting threshold, although I can point you to where in the code you would have to change if you like? Specifically, if you go to the class MatchToSequence, you will find the bulk of the pruning code. I'm sorry it is not very clean :disappointed:
Hi, in config.json file, I don't quite understand the meaning of
"crop": 6
in dict("ca_infer_args") and"crop_length": 200, "aggressive_pruning": false,
in dict("gnn_infer_args":). Could you please give me some hints? Also, if I would like to prune some short chains. how can I set up the threshold?Thank you!