Xiaotong Xu comments

Results 4 comments of


                                            Xiaotong Xu

I have the problem when "deeprank-gnn-esm-predict 1B6C.pdb "

Hi there, It seems to be a problem with pdb2sql, no contacting atoms were found in the structure and it caused the following error. I can not reproduce this error...

I have the problem when "deeprank-gnn-esm-predict 1B6C.pdb "

Hi, Thanks for pointing it out. I apologize for mixing up the chainIDs in the example. ChainA and chainE are not interacting, which caused the error. I think it should...

Why cannot generate the CSV

Hi there, For this pdb, in the output folder, do you have the generated '/gpfs/share/home/2200012187/lightdock_workspace/DeepRank-GNN-esm/lightdock_100_82.pdb_design_cdc42_323_dldesign_2_2_af2pred_cleaned-gnn_esm_pred_A_B/GNN_esm_prediction.hdf5' file? If so, try use 'https://github.com/DeepRank/DeepRank-GNN-esm/blob/main/src/deeprank_gnn/tools/hdf5_to_csv.py' script directly to convert it into hdf5 format; If...

Enable pdb_splitmodel to handel more than 9999 models

> And to add to that, the current version, when encountering more than 9999 models will overwrite over models, e.g. model 11000 will be written as model 1000, overwriting the...