IndexError: too many indices for array Prepare_Input_Single.py

[jiyanbio]

Using TensorFlow backend. /home/ft_local/ppi_structData/684/bm5_pydock/1JTD/pdb/1JTD_1114_conv888 existed REMARK total,bonds,angles,improper,dihe,vdw,elec,noe,cdih,coup,sani,vean,dani

[error] encountered blank atom name REMARK bonds,angles,impropers,dihe,noe,cdih,coup,sani,vean,dani

[error] encountered blank atom name REMARK noe,cdih,coup,sani,vean,dani

[error] encountered blank atom name REMARK >0.3,>5,>1,>0,>5,>0.2

[error] encountered blank atom name REMARK CVpartition#,violations,rms

[error] encountered blank atom name END

[error] encountered blank atom name waiting dealing1 in total, we have 486 residues in receptor, 0 residues in ligand in the interface 10A cut off, we have 0 residue, 0 atoms in the receptor in the interface 10A cut off, we have 0 residue, 0 atoms in the ligand Traceback (most recent call last): File "main.py", line 67, in record,input_path=run_pred_single(file_path,random_id,gpu_id) File "main.py", line 16, in run_pred_single input_path=Prepare_Input_Singe(file_path,random_id) File "/home/ft_local/PycharmProjects/DOVE/Input_Preparing/Prepare_Input_Single.py", line 45, in Prepare_Input_Singe tempload, rlength, llength = reform_input(rlist, llist, 1) File "/home/ft_local/PycharmProjects/DOVE/data_processing/prepare_input.py", line 286, in reform_input xmean=np.mean(coordinate[:,0]) IndexError: too many indices for array Using TensorFlow backend.

[jiyanbio]

pdb file location: https://www.dropbox.com/s/tpyguaa2mgxng0w/1JTD_1114_conv.pdb?dl=0

[wang3702]

Sorry for the late response. I think the error comes from the receptor and ligand recognition. To fix this bug, personally I think you should change your pdb format. Please first put receptor with chain "A" in pdb, then put the ligand with chain "B" in pdb.