Element not found while I run the command "pocket_block, _ = SplitPocket._split_pocket_with_surface_atoms(pro, lig, dist_cutoff)" - Githubissues

Saoge123 / PocketFlow

an autoregressive flow model incorporated with chemical acknowledge for generating drug-like molecules inside protein pockets

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Element not found while I run the command "pocket_block, _ = SplitPocket._split_pocket_with_surface_atoms(pro, lig, dist_cutoff)" #9

Open CADDfarmer opened 3 months ago

CADDfarmer commented 3 months ago

Hello, I got an ERROR when I run "pocketblock, = SplitPocket._split_pocket_with_surface_atoms(pro, lig, dist_cutoff)" to split the pocket.

And I check the file XXXX-surface.pdb. I found some lines are wrong formatted, as follows:

Can someone help me with this?

Thanks

Saoge123 commented 3 months ago

Hi, the temperature factor seens abnormal in your pdb, it should be at colunm [61-66] in each line. (https://cupnet.net/pdb-format/).

CADDfarmer commented 3 months ago

this pdb file " XXXX-surface.pdb" was generated by the command "pocketblock, = SplitPocket._split_pocket_with_surface_atoms(pro, lig, dist_cutoff)", my input are correct.