Seeing the Invisible: 50 Years of Macromolecular Visualization

Interacting with a Structure

Graphics provided by the NGL viewer. Read more at: https://academic.oup.com/nar/article/43/W1/W576/2467902

Building a Protein Structure

Protein and nucleic acid molecules are chains of small, connected subunits in a linear sequence that fold up into three dimensional structures. Finding out the three dimensional structures of these molecules aids in our understanding of life, disease, and medicine. This video shows a brief overview of the process of determining the structure of a protein molecule using X-ray crystallography.

Read more about the structure used in these videos: http://m.jbc.org/content/277/50/48596

Checking for Errors

Because X-ray crystallography (and other structure determination methods) can’t directly show the atoms without some interpretation, the structures determined by these methods can often contain local errors. For correctly understanding the function of these structures, it is important to check for these errors, most of which are straightforward to find using the MolProbity website. Entering a structure file and going through the various pages as shown will give a variety of reports and scores about what kinds of errors are in the structure. Looking at the structure in interactive three-dimensional with visual indicators of the errors is important to finding and fixing the errors.

Read more about MolProbity at: https://onlinelibrary.wiley.com/doi/full/10.1002/pro.3330

Fixing Errors

This video shows an example of finding errors within a structure and rebuilding that part of the structure in order to fix the problems. Viewing the structure (PDB file 1lpl) with the experimental electron density data revealed that two atom groups had been incorrectly swapped. Switching them to the correct positions allowed another turn of helix to be added to the structure.

Read more about other corrections made to the 1lpl structure at: https://link.springer.com/article/10.1007/s10969-005-3138-4