Secondary structure: Difference between revisions
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==How Jmol Determines Secondary Structure== | ==How Jmol Determines Secondary Structure== | ||
[[PDB files]] usually contain HELIX, SHEET, and sometimes contain TURN records, in their headers. These represent the authors' determinations, and when present, Jmol obeys them (see [[Help:Color Keys#Secondary Structure|secondary structure colors]]). | [[PDB files]] usually contain HELIX, SHEET, and sometimes contain TURN records, in their headers. These represent the authors' determinations, and when present, Jmol obeys them (see [[Help:Color Keys#Secondary Structure|secondary structure colors]]). Secondary structure assignments are somewhat arbitrary. Proteins are not rigid (unlike PDB files!), and phi/psi angles may change from instant to instant. For example, there may be an alpha helix with a small kink in the middle. Objective software may determine that this represents two alpha helices, while the authors may specify it as a single helix. | ||
When the PDB file lacks HELIX and SHEET records, Jmol will determine secondary structure using objective criteria. | |||
== External Links == | == External Links == | ||
For more information, see [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure]. | For more information, see [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure]. | ||
