The Select Command and Boolean Operators in Jmol

Unless otherwise indicated, this section of the Training Guide uses the protein Top 7 based on PDB file 1qys.pdb. Please see Getting Started with Jmol for information on how to download and open PDB files.

The Select Command

Thusfar, every command we have typed into the Command Line has affected the entire protein. However, we can specify parts of a molecule that we want to display differently by using the Select command. Below is a description of commonly used Select commands along with a Jmol button. When using the select command, Jmol will respond with '# atoms selected', where # will be the number of atoms selected. The display will NOT change until you supply additional commands, and those commands will ONLY operate on the parts of the molecule you have selected. To change another part of the molecule, you have to enter a new select command.

Please click the button after each description to see how Top 7 from 1qys.pdb will look with the selected area colored red. (Following the select command, a second command is entered to color the selected portions of the molecule.)

Select All

Select all is the default Jmol selection. With select all, every atom contained in a PDB file is selected and will be affected by future commands.

Note: When a select command is executed, Jmol displays the number of atoms selected in the Jmol Console Window. You should get a feel for whether the number of atoms selected is what you expected.

To select every atom, type:

select all

To color this selection red, type:

color red

select all; color red

Note: The Jmol buttons of Top 7 shown below have been reset before each set of commands. To do this, use the select all command followed by color gray.

Select Backbone

With select backbone, only the backbone atoms will be affected by future commands.

To select the backbone, type:

select backbone

To color this selection dodger blue, type:

color dodgerblue

Note that preset Jmol colors do not have a space between words in the command line.

select backbone; color dodgerblue

The commands above will select all atoms in the peptide backbone - so the N-C-C=O atoms. However, if you are displaying the alpha carbon backbone, in which a line (backbone) connects adjacent alpha carbon atoms (colored cyan in the backbone here: N-C-C=O), you should use the following commands:

select :a
color backbone cyan

select :a; color backbone cyan

Select Sidechain

With select sidechain, only the atoms that are part of sidechains in a protein will be affected by future commands.

To select the sidechains, type:

select sidechain

To color this selection lemon chiffon, type:

color lemonchiffon

select sidechain; color lemonchiffon

Select Hydrophobic

With select hydrophobic, only the hydrophobic amino acids in a protein will be affected by future commands.

To select hydrophobic, type:

select hydrophobic

To color this selection yellow, type:

color yellow

select hydrophobic; color yellow

Select Helix

With select helix, all atoms that are part of alpha helices will be affected by future commands.

To select alpha helices, type:

select helix

To color this selection red, type:

color red

select helix; color red

Note: Jmol does not recognize 'helices' (plural) but only 'helix' (singular).

Select Sheet

With select sheet, all atoms that are part of beta pleated sheets will be affected by future commands.

To select beta pleated sheets, type:

select sheet

To color this selection yellow, type:

color yellow

select sheet; color yellow

Select Nucleic

With select nucleic, all atoms that are part of nucleic acids (DNA, RNA) will be affected by future commands.

To select nucleic acids, type:

select nucleic

To color this selection salmon, type:

color salmon

Note: The Top 7 protein does not contain any nucleic acids and therefore nothing is colored when the select nucleic command is used. A zinc finger protein based on the file 1zaa.pdb does contain nucleic acids and therefore will have areas colored red. Click the button below to see select nucleic on a zinc finger protein.

select nucleic; color salmon - Zif268 PDB ID: 1zaa

Select Water

With select water, all water molecules will be affected by future commands.

To select water molecules, type:

select water

To display water molecules, type:

spacefill 1.2

To color this selection red, type:

color red

select water; spacefill 1.2; color red

Note: Hydrogen atoms are not displayed in pdb files that are obtained via X-ray crystallography. Therefore water molecules appear as a single oxygen atom. Since the oxygen is not visually bonded to another atom, the only way water molecules can be displayed is in spacefill format.

Select Chain

With select :, followed by the letter of the chain you would like to select, only the chain you select will be affected by future commands.

To select chain A, type:

select :a

To color this selection green, type:

coor green

Note: The Top 7 protein is a protein with only a single chain, so all atoms are colored red with the commands used above. Hemoglobin based on the file 1a3n.pdb contains four chains so the commands above will only color a portion of the structure. Click the button below to see select :a on hemoglobin.

select :a; color green - hemoglobin PDB ID: 1a3n

Select Residue Number

With the Residue Number select command, you can select a specific amino acid or a range of amino acids that all future commands will affect.

To select residue number 58, type:

select 58

To color this selection purple, type:

color purple

select 58; color purple

Note: You can also select an amino acid by its three letter abbreviation followed by the residue number. For example, instead of select 58 as shown above, you could also use select lys58 because the amino acid at residue number 58 in the Top 7 protein is lysine. There are two advantages to including the residue name. First, if you accidentally mistype the residue number, if there is a mismatch between the residue name and number, Jmol will return '0 atoms selected'. Second, if you keep a record of your work, including the residue name may be helpful in remembering why you displayed the residue. For more information on documenting your model design, see the tutorial Maintaining a Record of Your Work.

To select residues 20 through 30, type:

select 20-30

To color this selection orange, type:

color orange

select 20-30; color orange

Select Atom Number

With the Atom Number select command, you can select a specific atom number or range of atoms that all future commands will affect.

To select atom number 317, type:

select atomno=317
or you may use the shortcut:
select @317

To color this selection magenta, type:

color magenta

select @317; color magenta

Select a Range of Atoms

With an alteration to the Atom Number select command, you can select a range of atoms that all future commands will affect.

To select atom number 303 through 410, type:

select atomno>=303 and atomno<=410

Note that the shortcut @ does NOT work with this selection!

To color this selection lawn green, type:

color lawngreen

select atomno>=303 and atomno<=410; color lawngreen

Note: If you do not know the Residue Number, Chain, Amino Acid Type, or the Atom Number you want to select, you can click on the residue in the Display Window. Jmol will provide information on the Console Window regarding the atom you clicked. The image below decodes this information in detail:

Boolean Operators

Once you are comfortable using the Select command, you can begin to link together selections by using Boolean Operators. Imagine you are working with two predefined sets, for example, helix and backbone which are illustrated in the Venn diagram below.

You can select just the helices. This set includes all the alpha helices (including any backbone atoms that happen to be in alpha helices). The area with the hatched lines represents what is selected.

select helix

You can also select backbone. This set includes all the atoms that are part of the backbone (including any alpha helix atom that also happen to be backbone atoms).

select backbone

Or Operator

You can use the or Boolean Operator to select all the amino acids that are either part of alpha helices or the atoms that are part of the backbone.

select helix or backbone

The phrase 'select helix or backbone' means 'select all atoms that are either a helix or in the backbone (or both)'.

Jmol shortcut: Instead of using the operator or, you may also separate items with a comma:

select helix, backbone
is equivalent to:
select helix or backbone

And Operator

You can use the and Boolean Operator to select all the amino acids that are both backbone amino acids as well as amino acids in alpha helices.

select helix and backbone

The phrase 'select helix and backbone' means 'select all atoms that are both part of a helix AND part of the backbone'.

Not Operator

You can use the not Boolean Operator to select only the atoms that are not part of helices and not part of the backbone.

select not helix and not backbone /span>

The phrase 'select not helices and not backbone' means 'select all atoms that are neither a helix nor part of the backbone'.

No Atoms Selected

When using select and Boolean operators in Jmol, occasionally '0 atoms selected' will be displayed in the Console Window. This means the selection is invalid. Consider for instance, the command:

select helix and sheet

The phrase 'select helix and sheet' means 'select all the atoms that are BOTH helices AND sheets'. In the diagram below, you'll see that these are two mutually exclusive sets of atoms. There are no atoms that fulfill this selection, and Jmol will diplay '0 atoms selected'.

Use of Parentheses

Parentheses can be used in a select command when combining operators to insure that the proper selection occurs. Here are some sample commands that are frequently used in designing models:

select :b and (his63 or his92) and (sidechain or alpha)

This selects the sidechain and alpha carbon atoms in two residues, his63 and his92, on chain b of the protein.

select (:a or :c) and sheet

This command selects the sheets in chains a and c of the molecule.