Farzaneh Parizi

You can use the following PDB files for this issue for PDB ID: 5KSA (change the extension from _txt_ to _pdb_) [BL00060001_decoy.txt](https://github.com/DeepRank/pdb2sql/files/9674788/BL00060001_decoy.txt) [BL00060001_ref.txt](https://github.com/DeepRank/pdb2sql/files/9674789/BL00060001_ref.txt)

The previous case had an alternative location in the Receptor region. The following case has an alternative location in the Ligand region. PDB ID: 6DFS [6DFS_6BLX_BL00140001_decoy.txt](https://github.com/DeepRank/pdb2sql/files/9706885/6DFS_6BLX_BL00140001_decoy.txt) [6DFS_6BLX_BL00140001_ref.txt](https://github.com/DeepRank/pdb2sql/files/9706888/6DFS_6BLX_BL00140001_ref.txt)

Thanks @NicoRenaud for the check . With this new fix this new error message is then printed: > rmsd = sim.compute_lrmsd_pdb2sql(exportpath=None, method='svd') > File "..../pdb2sql/pdb2sql/StructureSimilarity.py", line 597, in compute_lrmsd_pdb2sql >...

I am puzzled, should not pdbsql ignore missing residues/atoms? So if there is a missing atom in one PDB ignore that also for the other PDB? Maybe I am wrong...

So then it should give an RMSD value for this case, not an error. Even if I use only 'CA' LRMSD, it still leads to error (the difference in two...