Secondary structure: Difference between revisions
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==How Jmol Determines Secondary Structure== | ==How Jmol Determines Secondary Structure== | ||
===From PDB files=== | |||
[[PDB files]] usually contain HELIX and SHEET 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. | [[PDB files]] usually contain HELIX and SHEET 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. | ||
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===Jmol's objective calculation=== | |||
When the PDB file lacks HELIX and SHEET records, Jmol will determine secondary structure using objective criteria. Optionally, using Jmol [[Scene_authoring_tools#Using_Jmol.27s_Command_Language|command language]], you can re-determine secondary structure objectively, overriding the authors' specifications in the PDB file. Typically when you do this, and re-apply the ''Secondary Structure'' color scheme, some blue turns will appear. (Many PDB files used to contain TURN records, but in revision 3.2 of the [[PDB format]], TURN records were abolished.) | When the PDB file lacks HELIX and SHEET records, Jmol will determine secondary structure using objective criteria. Optionally, using Jmol [[Scene_authoring_tools#Using_Jmol.27s_Command_Language|command language]], you can re-determine secondary structure objectively, overriding the authors' specifications in the PDB file. Typically when you do this, and re-apply the ''Secondary Structure'' color scheme, some blue turns will appear. (Many PDB files used to contain TURN records, but in revision 3.2 of the [[PDB format]], TURN records were abolished.) | ||
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