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gpcrdb_data/docs/tutorial_structures.rst

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Structures Structure statistics Question Structure browser Question Structure superposition Example 1 Example 2 Example 3 Generic numbering of PDB files
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Structures

Structure statistics

This video demonstrates how to view statistics based on available structure data in GPCRdb.

  • The statistics are automatically generated, and always reflect the latest version of the database.
  • By moving the pointer over the plot, more information can be displayed.
  • All plots can be downloaded.

Question

  • How many structures were published in 2014?

Structure browser

This video demonstrates how to use the structure browser to gain an overview of the available structural data in GPCRdb.

  • The structural data is displayed in a table format.
  • The table can be filtered and sorted on any column.
  • The "Show representative" button shows only one selected structure for each protein.
  • To use the "Superpose structures" button, first select (check box) structures to superpose, and highlight (click on the row) the reference structure (the selected structure will be superposed on this structure).
  • To use the "Download" and "Align" buttons, first select (tick box) structures to download or align.

Question

How many structures from Class B are available?

Structure superposition

The following three videos demonstrate how to superpose structures in GPCRdb.

Example 1

  • Only one structure can be selected as a reference, and all selected structures will be superposed on this structure.
  • It is possible to select many structures to superpose using the "Structure(s) to superpose" button (hold down Control on Windows/Linux and Command on Mac while selecting).
  • It is possible to select which parts of the sequence (e.g. all TMs or only TM5) to superpose on.
  • After the structures have been superposed, you can download the full structures, or only a specific part of the sequence (e.g. TM5). In this video, the user downloads the full structure.

Example 2

  • Only one structure can be selected as a reference, and all selected structures will be superposed on this structure.
  • It is possible to select many structures to superpose using the "Structure(s) to superpose" button (hold down Control on Windows/Linux and Command on Mac while selecting).
  • It is possible to select which parts of the sequence (e.g. all TMs or only TM5) to superpose on.
  • After the structures have been superposed, you can download the full structures, or only a specific part of the sequence (e.g. TM5). In this video, the user downloads only a part of the sequence.

Example 3

  • It is also possible to select structures to superpose from the structure browser.
  • First select the structures that should be superposed using the check boxes to the left of each row.
  • To select the reference structure, highlight it by click anywhere on its row (it turns blue).
  • Click "Superpose structures" and continue the superposition workflow as before.

Generic numbering of PDB files

This video demonstrates how to add generic residue numbers to a PDB file using GPCRdb, and visualize the numbers in PyMOL.

  • Upload any PDB file (also homology models).
  • It is possible to download the full structure, or subset of its sequence.
  • On the results page, download the PyMOL visualization script at the bottom of the page.
  • Load the downloaded PDB file into PyMOL.
  • Drag the downloaded script file onto the PyMOL window.
  • Press F2 to view the generic residue numbers (F1 removes the numbers again).