I have a 1vfl macro molecule with 3000 atoms in it. When i open it in DC accelrys visualizer. It has much bonds. but when i open the pdb file it just have 8 connections. You can download the pdb here(I'm linking because the pdb is much) : https://www.rcsb.org/structure/1VFL
I'm using this pdb for my program so i need to know all the connections between atoms.

Any help would be good; I'm a complete beginner at using PDB.


1 Answer 1


The CONECT entries specify the bonding of the ligands (HETATM), not your polymeric residues (ATOM). By residue I mean a collection of atoms that forms a unit, not only your standard amino acid definition.

You can export in PyMOL all connections if you wanted, but the connectivity of the polymeric residues is standardised and does not need to be specified as they ought to obey the definitions (the 'chemical component' dataset), for example https://www.rcsb.org/ligand/ILE. If I were to have a ligand, LIG, it would be HETATM entered and with CONECT entries as most likely it is not the RCSB's https://www.rcsb.org/ligand/LIG.

Crosslinks between certain residues ought to be entered via the LINK record, not CONECT so they will not feature.

Some programs connect atoms by proximity regardless of stated connectivity —spiderwebs in PyMOL.

An odd corner case are non-standard amino acids, such as phosphorylations (e.g. https://www.rcsb.org/ligand/SEP) which are ATOM not HETATM, which are not meant to have CONECT entries, but some were deposited with them. Water (HOH) (from neutron diffraction structures) does not need connections.


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