PDB REDO: Difference between revisions
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== PDB_REDO == | == PDB_REDO == | ||
A databank with updated and optimised macromolecular X-ray diffraction structure models. [ | A databank with updated and optimised macromolecular X-ray diffraction structure models. [https://pdb-redo.eu/ pdb-redo.eu] | ||
[[Image:PDB REDO.png|right]] | [[Image:PDB REDO.png|right]] | ||
=== Why | === Why ''redo'' PDB files? === | ||
The goal of PDB_REDO is to provide optimised structure models for a wide | The goal of PDB_REDO is to provide optimised structure models for a wide | ||
range of PDB users (biologist, (bio)chemist, drug designers, teachers | range of PDB users (biologist, (bio)chemist, drug designers, teachers | ||
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hopefully be here at some point). Of course, | hopefully be here at some point). Of course, | ||
'''rebuilding can change the interpretation of the experimental data substantially''', therefore models | '''rebuilding can change the interpretation of the experimental data substantially''', therefore models | ||
redone with and without rebuilding are provided. | redone with and without rebuilding are provided. This enables the user to choose between the interpretation of the original depositor and that of PDB_REDO. | ||
''PDB_REDO: automated re-refinement of X-ray structure models in the PDB'', Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund AC, Blanchet C, Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R, Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K, Pagni M, Reichstadt M, Breton V, Tickle IJ, Vriend G (2009) JOURNAL OF APPLIED CRYSTALLOGRAPHY 42 : 376-384 | ''PDB_REDO: automated re-refinement of X-ray structure models in the PDB'', Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund AC, Blanchet C, Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R, Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K, Pagni M, Reichstadt M, Breton V, Tickle IJ, Vriend G (2009) JOURNAL OF APPLIED CRYSTALLOGRAPHY 42 : 376-384 | ||
===How To ReDo=== | |||
# Go to [https://pdb-redo.eu/ pdb-redo.eu]. | |||
# Enter the [[PDB ID]] of a published structure. | |||
# Download the re-refined and rebuilt PDB file. | |||
# [http://firstglance.jmol.org/where.htm#uploading Upload] it to [http://firstglance.jmol.org FirstGlance in Jmol] or open it in [[Molecular modeling and visualization software|another viewer]]. | |||
