Salt Dream

Thanks for the software I got the files shown in README after I finished running but when I tried to visualize the PDB using D the following error statement appears....

About dataset size

2

I look at the file for loveda data: config / base / love, which looks like a size of 512 at train, but 1024 at test and val?It is understood...

HHblits with FFindexDatabase error

7

After conda install hhsuite=3.3.0, i try to run the hhblits command: hhblits -i query.seq -o query.hhr -d ./uniclust30 ,but got these errors: - ERROR: In /opt/conda/conda-bld/hhsuite_1594935877759/work/src/ffindexdatabase.cpp:11: FFindexDatabase: - ERROR: could...

Here are some questions~ I found that the output implementation about pdb is missing in code network_2tracker?How should it be realized? It seems to be different here from the relevant...

Hello, some problem about Masif-search and Masif-site. If I want to obtain a new model which only train on some interacted single protein structure, can it be achieved? It seems...

Hello,i'm running the rgn2_predict.ipynb, and it show me that 'No such file or directory: runs/15106000/1/outputsTesting/test_26f842.tertiary', I see that 'TER_PATH = os.path.join(RUN_DIR, '1', 'outputsTesting', f'{seq_id}.tertiary')' and 'ter2pdb.run_ca_to_allatom(seq_path=SEQ_PATH, ter_path=TER_PATH,output_dir=OUTPUT_DIR, seq_id=seq_id)' here, which...

关于visualizer的嵌入问题

2

感谢您的代码，有些问题想要请教一下 目前我已经在框架下搭好了我的网络模型，所以只想要把attention可视化的这部分嵌入到网络中，看到您的文件中涉及的timm（已有）和visualizer部分，是否可以只使用您visualizer下的内容完成操作呢？ 感谢回复

convert PSSM from 3dcons to deeprank

2

Hello, I try to convert the download pssm files from 3dcons with DeepRank_GNN/deeprank_gnn/tools/pssm_3dcons_to_deeprank.py, but it seem no result files?

Hello, some problem about Masif-search and Masif-site. It seems that well-trained models for masif-search and masif-site steps have been provided,if I want to add some new interacted pairs with interaction...

I found that in Netsurfp3 it only shows the HHblits in example/netsurfp_3，but not same as netsurfp2 which also has the MMseqs? Otherwise，should I train before I predict？It seems that the...