model-angelo
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3dem
Automatic atomic model building program for cryo-EM maps
Hello, Model angelo fails when using fasta files. I also see the following user warning message: TypedStorage is deprecated. It will be removed in the future and UntypedStorage will be...
Good afternoon, Very genuine question. I would like to run ModelAngelo through SBGrid on a cluster. I use this command : salloc -p gpu -n 1 -c 1 --gres=gpu:1 srun...
Hi, If I submit a single protein sequence, I get out multiple chains despite the fact that the sequence is just a single chain. Additionally, the chain numbering doesn't make...
Great Work! It seems that ModelAngelo organizes a training set with good quality. Do you have plans to release them? I think it's a great resources for the computational CryoEM...
Dear all, I have encountered this UserWarning when running `model_angelo build_no_seq`: >~/anaconda3/envs/model-angelo_local/lib/python3.10/site-packages/torch/nn/modules/conv.py:605: UserWarning: Applied workaround for CuDNN issue, install nvrtc.so (Triggered internally at /opt/conda/conda-bld/pytorch_1711403388920/work/aten/src/ATen/native/cudnn/Conv_v8.cpp:80.) Following this StackOverflow [question](https://stackoverflow.com/questions/76216778/userwarning-applied-workaround-for-cudnn-issue-install-nvrtc-so) I have...
Hi! Due to network environment issues, I am unable to directly download the model weights through the installation script. Therefore, I used the download script mentioned in Issue #39 for...
running -c with custom config.json. Only want to change threshold but more arguments need defining
I am trying to run the following command with the standard values but just changing the threshold of the run. It has difficulties at many stages in the program mostly...
Hi Kiarash! Since 1.0.8, there are additional checks/rewrites for .fasta files (`write_fasta_only_aa` and `write_fasta_no_gaps`). Both of those checks output the reformatted file next to the input file. I propose the...
Hello, is there any way of getting ModelAngelo to work on a Mac with Apple M1 or M2 silicon, i.e. without Nvidia GPU? I cannot seem to find a definitive...
Hello, thanks for your excellent work! I have some questions about the residues you excluded and included in the protein sequence. I found this code: ```python def remove_non_residue(sequence: str) ->...
