<p>The <code>CONECT</code> entries specify the bonding of the ligands (<code>HETATM</code>), not your polymeric residues (<code>ATOM</code>). By residue I mean a collection of atoms that forms a unit, not only your standard amino acid definition.</p>
<p>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 <a href="https://www.rcsb.org/ligand/ILE" rel="noreferrer">https://www.rcsb.org/ligand/ILE</a>.
If I were to have a ligand, <code>LIG</code>, it would be <code>HETATM</code> entered and with <code>CONECT</code> entries as most likely it is not the RCSB's <a href="https://www.rcsb.org/ligand/LIG" rel="noreferrer">https://www.rcsb.org/ligand/LIG</a>.</p>
<p>Crosslinks between certain residues ought to be entered via the <code>LINK</code> record, not <code>CONECT</code> so they will not feature.</p>
<p>Some programs connect atoms by proximity regardless of stated connectivity —spiderwebs in PyMOL.</p>
<p>An odd corner case are non-standard amino acids, such as phosphorylations (e.g. <a href="https://www.rcsb.org/ligand/SEP" rel="noreferrer">https://www.rcsb.org/ligand/SEP</a>) which are <code>ATOM</code> not <code>HETATM</code>, which are not meant to have <code>CONECT</code> entries, but some were deposited with them.
Water (<code>HOH</code>) (from neutron diffraction structures) does not need connections.</p>

CC BY-SA 4.0
2023-01-01T19:06:38.763Z
2023-01-01T19:06:38.763Z
Matteo Ferla
<p>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) : <a href="https://www.rcsb.org/structure/1VFL" rel="nofollow noreferrer">https://www.rcsb.org/structure/1VFL</a><br>
I'm using this pdb for my program so i need to know all the connections between atoms.</p>
<p>Any help would be good; I'm a complete beginner at using PDB.</p>

<pdb>
CONECT doesnt include all the connections the 1vfl macro molecule have in a pdb file
# CONECT doesnt include all the connections the 1vfl macro molecule have in a pdb file

(Asked by: username_0 on 2023-01-01)

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.

**Tags:** pdb

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## 1 answers

### Answer by username_1 on 2023-01-01. Score: 5

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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