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LPDI-EPFL / masif

MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.
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Troubleshooting MaSIF-site errors with "./data_prepare_one.sh" for multiple PDBs of my protein complex #56

Open Vmoller9 opened 1 year ago

Vmoller9 commented 1 year ago

Hello, I'm having troubles trying to run the "./data_prepare_one.sh" script for my protein complex of interest (NALCN) using MaSIF-site through Docker. I have no problem running the script for 4ZQK_A as shown in the Docker tutorial for MaSIF-site. However, when I tried to run the script for the 4 different pdb-files for my protein complex of interest (7W7G, 7SX3, 7SX4, and 7WJI). I encountered the following errors: For 7W7G_A, 7SX3_X, 7SX4_X, and 7WJI_X (by X, I mean any chain):

err1

When running the ./data_prepare_one.sh for 7W7G_B, get this error: err2

I'm able to successfully run the script for 7W7G_C and 7W7G_D. I suspect that the errors are due to the size or complexity of the protein chains, as A and B are substantially larger than C and D. However, since the small chains cannot be run on the other PDBs, and the error is different for 7W7G_A and 7W7G_B, I believe other factors might also be involved in these errors.

Cheers

TobiasPol commented 9 months ago

I had the same error before. It occurs if you take ./data_prepare_one.sh with only one chain as input. You need to comment out this line: python -W ignore $masif_source/data_preparation/01-pdb_extract_and_triangulate.py $PDB_ID\_$CHAIN2.

jche801 commented 3 months ago

Hello, I'm having troubles trying to run the "./data_prepare_one.sh" script for my protein complex of interest (NALCN) using MaSIF-site through Docker. I have no problem running the script for 4ZQK_A as shown in the Docker tutorial for MaSIF-site. However, when I tried to run the script for the 4 different pdb-files for my protein complex of interest (7W7G, 7SX3, 7SX4, and 7WJI). I encountered the following errors: For 7W7G_A, 7SX3_X, 7SX4_X, and 7WJI_X (by X, I mean any chain):

err1

When running the ./data_prepare_one.sh for 7W7G_B, get this error: err2

I'm able to successfully run the script for 7W7G_C and 7W7G_D. I suspect that the errors are due to the size or complexity of the protein chains, as A and B are substantially larger than C and D. However, since the small chains cannot be run on the other PDBs, and the error is different for 7W7G_A and 7W7G_B, I believe other factors might also be involved in these errors.

Cheers

Hi! can you give me a hint on how you can analyse local PDB files?