I'm using the latest Python API.

I have a PDB file from RCSB.org (it's 3roc, taken from Ilenia's pharmacophore overlay set Q16539) which I have overlaid back onto the ligand in the Q16539 set.  If I read it in from PDB file and write the identifiers for the first 10 residues and first 30 atoms, all is ok, and specifically the residue label for the atoms corresponds to the residue identifiers printed.  However, if I write it as a MOL2 and read it back in, the residue labels that the atoms have start from number 1, not 5 as previously.  This makes matching the atom to residue by identifier a non-trivial task.  It looks like a bug in the MOL2 reader.  Can you confirm that this is  what you get, too, and suggest a remedy?

I am attempting to attach some sample Python and the input file.  It's not clear if it's going to work.




Ok, so I managed to attach the PDB file.  Now I'll try the Python script.

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