PDB Test Suite

Pablo has a (developing) PDB test suite.

File name

Coverage

5ap1_prepared.pdb

ACE/NME caps, unique_molecules

193L_prepared.pdb

disulfides, all 20 canonical amino acids, charged terminii, charged canonical AA side chains

2hi7_prepared.pdb

disulfide bond between two different protein chains

1p3q_noter.pdb

missing ter record between protein chains with same chain id but incompatible terminii, missing ter record between protein chains with different chain id

1hje_samechain.pdb

Disulfide bonds within chain, missing ter record between polymer and non-polymer chains with same chain id, NH2 cap, strained conformation

1hje_diffchain.pdb

Disulfide bonds within chain, missing ter record between polymer and non-polymer chains with same different id, NH2 cap, strained conformation

1A4T.pdb/.cif

NMR model direct from PDB, multi-model file, RNA and protein in same file

1a45_samechain.pdb

RNA and protein in same file, missing TER record between incompatible polymers with same chain ID

5eil_fixed.pdb

Non-canonical amino acid from CCD, iron ion

3ip9_dye_solvated.pdb

Large system with water and NaCl, non-canonical amino acid not in CCD

big_bilayer.pdb

Very large system, 4 character residue names, hexadecimal atom and residue numbers

capped_arg_altresonance.pdb

Formal charge on incorrect resonance-equivalent atom in arginine

capped_arg_altresonance_conect.pdb

Formal charge on incorrect resonance-equivalent atom in arginine with CONECT records

capped_ser_extrater

erroneous mid-chain TER record (should raise error)

e2_7nel

unique_molecules

microviridin_edited.pdb

Extensive nonstandard cross-links with CONECT records and custom residue names

prepared_pdbs/2MUM_neutralized.pdb

all 20 canonical amino acids, neutral terminii, neutral canonical AA side chains

prepared_pdbs/2MUM_blowup.pdb

Strained conformation, all 20 canonical amino acids, neutral terminii, neutral canonical AA side chains

prepared_pdbs/2MUM_composed_function.pdb

discontiguous residue numbers, discontiguous atom serials, insertion codes, hexadecimal residue numbers, hexadecimal atom serials, re-used residue numbers, re-used atom serials, all 20 canonical amino acids

prepared_pdbs/2MUM_icode.pdb

insertion codes, all 20 canonical amino acids

prepared_pdbs/2MUM_letters_in_resseq.pdb

hexadecimal residue numbers, all 20 canonical amino acids

prepared_pdbs/2MUM_letters_in_serial.pdb

hexadecimal atom serials, all 20 canonical amino acids

prepared_pdbs/2MUM_reuse_resseq.pdb

re-used residue numbers, all 20 canonical amino acids

prepared_pdbs/2MUM_reuse_serial.pdb

re-used atom serials, all 20 canonical amino acids

prepared_pdbs/2zuq_prepared.pdb

disulfide bond between two different protein chains, with additional chains between and after the crosslinked chains

prepared_pdbs/3h34_prepared.pdb

correctly named ligand in CCD with CONECT records

prepared_pdbs/ions.pdb

All Sage monatomic ions (correctly named)

prepared_pdbs/polyglycines.pdb

Stress-test chain termination