PDB Structure Editor

Access: CP::Editor::PDB

Molecular Structure Display

The PDB-Editor displays and renders molecular structures at the atomic detail.  Designed to be simple and light, the editor has a capacity for eight molecules.  To load a PDB structure,

1. Select a PDB file from the PDB button;
2. Name the molecule at the Molecular Name box;
3. Load and display the atomic model via the Add button.

The name of the molecule will appear in the list at the upper-left of the page, together with the total atom count and the molecular weight.  A selected structure (mouse LeftClick in the list to high-light) can be centered in the display window by the Center button, or be deleted from the list by the Close button.  The graphics rendering of a molecular structure can be customized at the Graphics Style and Quality menu, including an option to hide via Invisible (the molecule remains in the editor).  Note that increasing graphics quality entails higher computational complexity in the rendering, which might slow down interactive display.

Synthetic Map from PDB

A resolution-dependant density map can be calculated for the assembly of all visible molecules in the editor according to the user-defined Map Resolution, Voxel Size, and Boundary Margin (all in Å).  Activating the Map button will generate the synthetic density map and display it in CP::Editor::MAP.

Molecular Structure Modeling

When an EM density map for a macromolecular assembly has been reconstructed at sub-nanometer or near-atomic resolution, structure modeling of the molecular complex becomes feasible when facilitated by folding prediction and PDB-map docking.

(To be documented.)