molstack

Platform for sharing electron density maps and their interpretations
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Molstack is a tool that allows the visualization and analysis of multiple sets of coordinate and electron density data in stacks in dual, synchronized side-by-side windows for easy comparison.

Each stack can be used to present and analyze various data, including:

  1. atomic coordinates, 2mFc-DFo maps, and an omit map for small molecule ligands and its surrounding;
  2. alternative ligands or ligands in alternative conformations that may be used to interpret the experimental evidences for the same site;
  3. a collection of structures such as structures with different ligand, mutants of the same protein, or homologous structures from different organisms;
  4. re-interpretation, re-refinements or corrections of existing structures;
  5. supporting data like anomalous difference maps.

Molstack organizes the sharing and publication of these structural models along with their experimental evidence as an interactive session.

Molstack uses UglyMol created by Marcin Wojdyr for visualization of models and maps.

Example projects:

Unexpected ligand

This is RutR, a TetR-like transcriptional regulator that usually co-purifies with uracil under normal growth conditions.

Anomalous metal verification

Re-refinement - ligand identification

The structure 5i4f has been re-refined and the ligand density has been reinterpreted as a different disaccharide.

Dethiobiotin synthetase and its complexes

Dethiobiotin synthetase (DTBS) is involved in the biosynthesis of biotin in bacteria, fungi, and plants. This Molstack project presents the enzyme from Helicobacter pylori and its complexes with ATP, ADP and substrate analog. This work is described in: https://doi.org/10.1111/j.1742-4658.2012.08506.x .