Read PDB

Read molecule in pdb format file

Options

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

Symmetries

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.

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Links

• pdb file in the output of a python scriptby quaeler on 2019-07-12

  forum.knime.com/p/65309

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