Biological Unit: Difference between revisions
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*Atomic coordinates for biological units, when specified by the authors of a published structure in REMARK 350 of the [[PDB file format]], are available from the RCSB (US) [[Protein Data Bank]]. As of April, 2010, "Biological Assemblies" were available at the bottom of the list under ''Download Files'' (upper right, near the large [[PDB code]]). | *Atomic coordinates for biological units, when specified by the authors of a published structure in REMARK 350 of the [[PDB file format]], are available from the RCSB (US) [[Protein Data Bank]]. As of April, 2010, "Biological Assemblies" were available at the bottom of the list under ''Download Files'' (upper right, near the large [[PDB code]]). | ||
*One technical problem with the files from RCSB is that when they contain more than one copy of the asymmetric unit, the duplicated chains all have identical names. RCSB offers visualization of these models in Jmol, but it is usually difficult to tell how many chains are present in the biological unit, either in the snapshot (where each chain is colored similarly in a spectral amino- to carboxy-terminal sequence) or in Jmol, where coloring by chain fails to distinguish chains with the same name. Also, the additional copies are in separate models, which often complicates visualization. In contrast, coordinates for biological units available from | *One technical problem with the files from RCSB is that when they contain more than one copy of the asymmetric unit, the duplicated chains all have identical names. RCSB offers visualization of these models in Jmol, but it is usually difficult to tell how many chains are present in the biological unit, either in the snapshot (where each chain is colored similarly in a spectral amino- to carboxy-terminal sequence) or in Jmol, where coloring by chain fails to distinguish chains with the same name. Also, the additional copies are in separate models, which often complicates visualization. In contrast, coordinates for biological units available from PISA (see below) are in a single model, and each chain is given a distinct name. RCSB also offers a viewer named Kiosk but this seems not to show the biological assembly. | ||
As for author-specified biological assemblies, sometimes the specific oligomers were not known at the time the asymmetric unit was published. Also, some authors may have failed to specify the biological unit even when it was known. Rarely, the specified biological units might be incorrect. For all these reasons, it is advisable to consult other sources in addition to REMARK 350. | As for author-specified biological assemblies, sometimes the specific oligomers were not known at the time the asymmetric unit was published. Also, some authors may have failed to specify the biological unit even when it was known. Rarely, the specified biological units might be incorrect. For all these reasons, it is advisable to consult other sources in addition to REMARK 350. | ||