The PDB Residue Editor and The PDB Secondary Structure Editor
Examining and modifying structures imported from PDB files may be made easier by the PDB Residue Editor and PDB Secondary Structure Editor, reached via the correspondingly named items on the menu. They are illustrated below.
The PDB Residue and PDB Secondary Structure Editors
The PDB Residue
Editor (top) and PDB Secondary Structure Editor (bottom)
provide mainly read-only views of residue and other data assigned in
PDB files.
The PDB Residue Editor (top) and PDB Secondary Structure Editor provide mainly read-only views of residue and other data assigned in PDB files. The column can be used to hide the atoms in certain residues/secondary structures for easier viewing of the molecule’s key features. The column can be used to highlight the atoms corresponding to the selected item. In this example, we have highlighted residue 12 in chain A, making it easy to locate in the View window below. In the Secondary Structure Editor, selecting a chain will also select its helix—although, the reverse is not the case.
The menus in these editors are very similar to those in the Atom List Editor discussed in the previous section. Briefly, they are:
The
menu includes items related to saving and printing the data in the table:: Contains menu items allow you to modify the contents of the molecule specification:
: Atoms can be difficult to distinguish, as they are already highlighted and thus blue. Use this menu’s controls over atom highlighting to alleviate this problem. Each item in the first section is a toggle, and a check mark next to it within the menu indicates that it is enabled:
: Controls whether some or all atoms within the molecule are visible in the table and also provides shortcuts for selecting groups of atoms:
: Allows you to specify which columns appear in the table on an individual column basis via checking or unchecking their respective boxes.