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when I upload my pdb file the ligand is missing, I have checked and it is present in the original file but when loaded it is not present and is not registered in the output.
To fully diagnose some more information will be required, but it could be an issue with the PDB cleaning process done on inputs to the web server.
It would be helpful to see the input file if it can be shared: or if not, some more information about the ligand (residue name if shareable, if it consists of ATOM or HETATM records, if it is a small molecule, peptide, sugar, etc.
https://bitbucket.org/harryjubb/arpeggioweb/issues/21/incorrect-pdb-loading
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