How to: Align two or more 3D structures to a given structure

Starting with...

A PDB CODE (e.g. 1B8G)

  1. Go to the Structure Home Page.
  2. Enter the PDB code in the search box and press the Go button.
  3. Click the structure image. On the resulting page click the VAST link next to Related Structure to the right of the image.
  4. The next page lists each 3D domain in each chain of the structure. For VAST neighbors to an entire chain, click "entire chain"; for VAST neighbors for only one 3D domain, click the link for that 3D domain.
  5. Choose the structures you wish to align by checking the boxes to left of each structure. Click the "View 3D Alignment" button at the top of the report.
  6. For more information, please see the VAST help page.

A PDB-FORMAT FILE THAT IS NOT IN PDB

  1. Go to the VAST search page.
  2. Enter or browse for the PDB file name and click the Submit button.
  3. On the next page, click the Start (the VAST calculation) button at the bottom of the report. The VAST search may take several minutes to complete. When it is finished, continue with step 5 under "a PDB code" above.

A PROTEIN ACCESSION NUMBER (e.g. NP_000240) OR SEQUENCE

  1. Use the Finding a Structural Template guide to find the most appropriate PDB structure.
  2. Continue with step 1 under "a PDB code" above.
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