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NMR vs X-Ray Structures
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In the PDB, it’s possible to find structures solved by X-ray crystallography and NMR (around 15% of the deposited structures). Structures solved by X-ray crystallography are considered to be of higher quality, and thus, when available are preferable to use. However, it’s not always easy or possible to crystallize the proteins.
You can learn more about the limitations of the X-ray difraction as a technique for solving macromolecular structures.
In this module we will explore the aforementioned differences. We will perform global and local structural alignments of proteins solved by both techniques. The concept of RMSD to assess differences between different conformations will be introduced. The capabilities to do distance and angle measurements in PyMOL will be explored. Some of these tasks, are suitable for automation: we will learn how to use the scripting capabilities in PyMOL to increase productivity in repetitive tasks. Finally, the concept of “scenes” will be explored, as the basis for making small movies.
A general insight on the topic can also be found on the PDB website.
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