Therefore it selects only the oxygen atoms in the chain. Selects only the atoms that are both belonging to the peptide chain, and oxygen atoms. Selects all atoms in the peptide chain, and all oxygen atoms, including the oxygen atoms in the water molecules. Let's call the set of atoms in the peptide chain A, and all oxygen atoms B.
We are interested in selecting oxygen atoms. 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.Įxample: We have a system consisting of water and a peptide chain.
Any substructure strings in the SMILE format are accepted. select substructure("C(O)C") selects all ketone groups in the system.select connected(3) selects all atoms that are connected by bonds to 3 other atoms.select molecule = 1 selects the first set of covalently bound atoms in the file.Some examples of using topologies as selection criteria: (check the reference for more options) display (within (-3, PLANE, $plane1) and within (3, PLANE, $plane2)).display within (3, PLANE, (atomno=5) (atomno=40).Using a plane definition instead, for example by defining two atoms and one xyz coordinate (in angstroms). To display atoms up to 6 Angstrom away from a surface with Miller index 1 1 1, use: One can select atoms within 0.01 angstrom distance within a plane (and by combining two of these selections, on a line). It is for the newest versions of Jmol also possible to select atoms according to plane selections. 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.Of course one can select based on distances: display 1:A, if multiple chains are present, this will display only atoms in residue 1 of chain A.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, this will display only the first amino acid residue and/or molecule.select selects all atoms in alanine residues (pdb file format).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).display *.CA displays all C-alpha atoms.
#Jmol floating residue glitch full
In the reference the full list of atom expressions can be found.
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