model-angelo
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3dem
Automatic atomic model building program for cryo-EM maps
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,...
shell closes when running source install_script.sh any way to see what is going on?
Hello there! I was trying Model Angelo's refine module with my .mrc and pdb file. I am getting error: File "/home/******/.conda/envs/model_angelo/lib/python3.10/site-packages/model_angelo-1.0.1-py3.10.egg/model_angelo/gnn/inference.py", line 60, in infer voxel_size = args.voxel_size └ {'num_rounds':...
Dear all, I am currently attempting to execute model-angelo for a sizable system utilizing a FASTA file containing multiple sequences. However, following the initial C-alpha prediction, the program crashes and...
Hey, I have a fasta file where certain residues are unknown and therefor represented with `X` such as (1 at the start and 1 at place 105): ``` >chain 'CM'...
After installing v1.0.5, I am getting a message saying cuda is not recognized: `/opt/mamba/envs/model_angelo/lib/python3.10/site-packages/torch/amp/autocast_mode.py:204: UserWarning: User provided device_type of 'cuda', but CUDA is not available. Disabling` I am running this...
I tested model-angelo on map EMD-6149 and EMD-3133. The final modeled structure will be shifted because current pipeline did not handle the nxstart well. You can consider to use this...
Hi everyone, I installed modelangelo on our server (as described in README), and noticed that Ca building took ~5 hours, and GPU utilization was 0 at that time. After that,...
I'm trying to generate a model using a map generated in cryosparc and protein fasta file. The process runs through the Initial C-alpha prediction phase and then terminates, leaving behind...
