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PDB Utitity Servers
Selection of Residues and Atoms

pdbUtilNight PDB Utitity Servers
Selection of Residues and Atoms

Contact:
Frank Delaglio delaglio@nih.gov

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PDB Utility Servers - Selection of Residues and Atoms in a PDB Structure

Some of the PDB Utility servers provide an option to select which residues of the molecule will be included in a calculation. The selection is specified as a list of residue IDs or ranges separated by spaces. The keywords First and Last are used for the lowest and highest residue IDs in the molecule, respectively, while the Keyword All is used to select all residues. The keyword to is used to specify a range of residues. So, for example, the following two specification both include all residues, i.e., all residues from the lowest residue ID to the highest residue ID in the molecule (this is usually the default selection in the PDB Utilities):

first to last
all

Likewise, a specific range of residues can be specified, for example:

22 to 34

Multiple ranges can be specified, as well as individual residues. For example, the following specification selects residues 10 and 13 as well as the range of residues 22 to 34 and the range of residues 40 to 50:

10 13 22 to 34 40 to 50
The specifications can include commas for clarity, but the commas are ignored. So, the following two specification lines select the same residues:
10, 13, 22 to 34, 40 to 50
10 13 22 to 34 40 to 50

The keywords chain and seg are used to specify residues in systems with multiple chains or segments, for example:

chain A 30 to 40

After a given chain or segment is specified, that selection applies to all residues that follow, until a new chain or segment is specified. For example, the following specification selects residues 30 to 40 from chain A, ranges 50 to 60 and 80 to 90 from chain B, and residues 10 to 20 from chain C:

chain A 30 to 40 chain B 50 to 60 80 to 90 chain C 10 to 20.

By default, both ATOM and HETATM entries in the PDB input will be processed. The Keywords atom noatom hetatm nohetatm are used to toggle whether or not ATOM or HETATM entries are included in the selections which follow the Keyword. For example, to select only the HETATMs:

noatom all
To select only the ATOM residues 10 to 20 plus all of the HETATMS:
nohetatm 10 to 20 noatom hetatm all.
To select only the ATOM residues 10 to 20 and all of the HETATMS:

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last update: Feb 9 2012