Secondary structure: Difference between revisions
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[[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. 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. ''This does not work in Jmol 11.8 employed in Proteopedia in June, 2011. It works in the [[Jmol/Application]] (version 12).'' You can run a Proteopedia page in Jmol 12.0 and observe the effect of this command by appending "?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar" to the url of the page and re-opening the page. The user must give permission for the signed version of Jmol to open, and when it does it has a red frank, whereas in the unsigned version is grey. Following the directions on how to use the Jmol [[Scene_authoring_tools#Using_Jmol.27s_Command_Language|command language]] enter the commands: select protein; calculate structure; cartoon; color structure and then click run. | 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. ''This does not work in Jmol 11.8 employed in Proteopedia in June, 2011. It works in the [[Jmol/Application]] (version 12).'' You can run a Proteopedia page in Jmol 12.0 and observe the effect of this command by appending "?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar" to the url of the page and re-opening the page. The user must give permission for the signed version of Jmol to open, and when it does it has a red frank, whereas in the unsigned version it is grey. Following the directions on how to use the Jmol [[Scene_authoring_tools#Using_Jmol.27s_Command_Language|command language]] enter the commands: select protein; calculate structure; cartoon; color structure and then click run. | ||
If the above series of commands are applied when the structure of a human transferrin n-lobe mutant is displayed, you will see that in additional to the sheets and the <font color=#FF0080>alpha helices</font> being displayed the <font color=#A00080>3<sub>10</sub> helices</font> and different types of turns in blue are also shown. If the above series of commands are applied when the structure of glycogen phosphorylase (domain 2) is displayed, all four chains will be initially displayed but clicking the 'domain 2 of glycogen phosphorylase' green link will display only domain 2 of chain A. You will observe all three types of helices, and the turns will be colored blue. More detail on how calculate structure determines helices, strands and turns is at [[Calculate structure]]. | If the above series of commands are applied when the structure of a human transferrin n-lobe mutant is displayed, you will see that in additional to the sheets and the <font color=#FF0080>alpha helices</font> being displayed the <font color=#A00080>3<sub>10</sub> helices</font> and different types of turns in blue are also shown. If the above series of commands are applied when the structure of glycogen phosphorylase (domain 2) is displayed, all four chains will be initially displayed but clicking the 'domain 2 of glycogen phosphorylase' green link will display only domain 2 of chain A. You will observe all three types of helices, and the turns will be colored blue. More detail on how calculate structure determines helices, strands and turns is at [[Calculate structure]]. | ||