Read PDB

This Node Is Deprecated — This node is kept for backwards-compatibility, but the usage in new workflows is no longer recommended. The documentation below might contain more information.

Read molecule in pdb format file


PDB file
Select one or more pdb files
Ignore SEQRES records
If Integrate SEQRES Records is on, then all residues in the SEQRES records will be created, including those without corresponding entries in the ATOM records.
Ignore CONECT records
If Ignore CONECT Records is on, then CONECT records will not be used when creating bonds.
Enable AutoConnect
If Enable Auto-connect is on, automatic bonding of atoms [Labute 2005] is performed after CONECT records are applied. Automatic bonding is always done on atoms of amino acid residues.
Ignore Waters
If Waters is on, then all waters in the PDB file will be ignored.
Ignore Hetero
If Hetero is on, then all hetero residues in the PDB file will be ignored.
Automatic Chain tags
If Auto-tag is on, then any chain with an empty tag will receive the name of the PDB file as its tag. This ensures that chains which originate from a single file are grouped together by their tags even in the case where no tag is specified in the file.
Source File Name
If on the source file name will be written to a new column
Crystallographic will read the MTRIXn records, Biomolecule will apply the BIOMT transforms if any.
All models
Read all models if applicable
Output Format
Select the intended cell format for the output database. Mol2 is default.

Input Ports

This node has no input ports

Output Ports

Input Data


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