Secondary structure: Difference between revisions
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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 files|PDB data 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 files|PDB data format]], TURN records were abolished.) | ||
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''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 (lower right corner), whereas in the unsigned version it is grey. Click on the ''Jmol frank'', in the ''main menu'' which opens click on ''Console'', in the bottom box enter the commands: select protein; calculate structure; cartoon; color structure and then click ''Run''. | ''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 (lower right corner), whereas in the unsigned version it is grey. Click on the ''Jmol frank'', in the ''main menu'' which opens click on ''Console'', in the bottom box enter the commands: | ||
<center> | |||
select protein; calculate structure; cartoon; color structure | |||
</center> | |||
and then click ''Run''. See also [[Calculate structure]]. | |||
</blockquote> | </blockquote> | ||
