Selecting
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Selecting can be done via atom expressions or based on topology or geometry.
Atom expressions in Jmol can be used in "select", "display", "hide" commands, as well as many others.
Contents
Atom expressions
In the reference the full list of atom expressions can be found. Common examples:
- display *.CA displays all C-alpha atoms.
- select _C selects all carbon atoms, usually (but not necessarily) equivalent to select *.C?? (the first identifies the element, the second just the atomm names and is only good for pdb files)
- select [ALA] selects all atoms in alanine residues (pdb file format)
- display 1, this will display only the first amino acid residue and/or molecule. If a file contains various molecules, and they are all numbered starting from 1, this will display only all first molecules or first residues of peptide strings.
- display 1:A, if multiple chains are present, this will display only atoms in residue 1 of chain A.
Geometric expressions
Of course one can select based on distances:
- display within(3.0,hydrophobic) displays only all atoms of hydrophobic residues (pdb file format), and all atoms within 3.0 Angstroms from these residues.
It is for the newest versions of Jmol also possible to select atoms according to plane selections.
One can select atoms within 0.01 angstrom distance within a plane (and by combining two of these selections, on a line). To display atoms up to 6 Angstrom away from a surface with Miller index 1 1 1, use:
- display within (-6, hkl, {1 1 1})
Using a plane definition instead, for example by defining two atoms and one xyz coordinate (in angstroms).
- display within (3, PLANE, (atomno=5) (atomno=40) {0 0 0})
Or it is possible to draw a plane, define it, make it invisible, and then re-use the plane definition later on:
- draw plane1 (atomno=10) (atomno=40) {0 0 0};
- draw plane1 off;
- display within (-6, PLANE, $plane1)
One can first define two planes, then define the atoms enclosed by the two planes:
- draw plane1 (atomno=5) (atomno=40) {0 0 0};
- draw plane1 off;
- draw plane2 (atomno=5) (atomno=40) {20 20 20};
- draw plane2 off;
- display (within (-3, PLANE, $plane1) and within (3, PLANE, $plane2))
Topology expressions
Some examples of using topologies as selection criteria: (check the reference for more options)
- select molecule = 1 selects the first set of covalently bound atoms in the file.
- select connected(3) selects all atoms that are connected by bonds to 3 other atoms.
- select substructure("C(O)C") selects all ketone groups in the system. Any substructure strings in the SMILE format are accepted.
Combining selection statements
The combination of selection statements in Jmol is based on Boolean logic, using the statements And, Or, and Not, in a slightly different way than these are used in conversational language.
Example: We have a system consisting of water and a peptide chain. We are interested in selecting oxygen atoms. Let's call the set of atoms in the peptide chain A, and all oxygen atoms B.
Select A
Selects all atoms in the peptide chain
Select A or B
Selects all atoms in the peptide chain, and all oxygen atoms, including the oxygen atoms in the water molecules.
Synonym: Select A,B
Select A and B
Selects only the atoms that are both belonging to the peptide chain, and oxygen atoms. Therefore it selects only the oxygen atoms in the chain.
Select A and not B
Selects the atoms in the peptide chain, except those that are oxygen atoms.
Select (A or B ) and not (A and B)
Selects all the peptide chain atoms and all the oxygen atoms, but not the oxygen atoms in the peptide chain.
