Secondary structure: Difference between revisions

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<table width='410' align='right' cellpadding='10'><tr><td bgcolor='#eeeeee'><center>'''Secondary Structures of Examples'''<scene name='Secondary_structure/1dtg_ss/1'> (Initial scene)</scene></center></td></tr></table>

==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]]). 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, 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.

When the PDB file lacks HELIX and SHEET records, Jmol will determine secondary structure using objective criteria (see [http://chemapps.stolaf.edu/jmol/docs/#calculate calculate structure].

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. Here are the commands to do that:

*calculate structure

== External Links ==

For more information, see [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure].

Secondary structure: Difference between revisions

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@@ Line 13: / Line 13: @@
 <table width='410' align='right' cellpadding='10'><tr><td bgcolor='#eeeeee'><center>'''Secondary Structures of Examples'''<scene name='Secondary_structure/1dtg_ss/1'> (Initial scene)</scene></center></td></tr></table>
 {{Clear}}
-==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]]). 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, 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.
+When the PDB file lacks HELIX and SHEET records, Jmol will determine secondary structure using objective criteria (see [http://chemapps.stolaf.edu/jmol/docs/#calculate calculate structure].
+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. Here are the commands to do that:
+*calculate structure
 == External Links ==
 For more information, see [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure].