Secondary structure: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eran Hodis, Karl Oberholser, Eric Martz, Wayne Decatur, Karsten Theis, Joel L. Sussman

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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 files|PDB data format]], TURN records were abolished.)
+When the PDB file lacks HELIX and SHEET records (Many PDB files used to contain TURN records, but in revision 3.2 of the  [[PDB files|PDB data format]], TURN records were abolished.), 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. '[[Calculate structure]]' is the Jmol command which does this re-determination. Several other commands are required to display the ''Secondary Structure'' color scheme and hydrogen bonds contained in the secondary structures. The script is 'select protein; calculate structure; cartoon; color structure; calculate hbonds structure'.
 <blockquote>
-''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 reloading 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:
+If a Proteopedia page does not contain this more detailed ''Secondary Structure'' information, it can be displayed by clicking on the ''Jmol frank'' which opens the ''main menu'', clicking on ''Console'', in the bottom console box entering the script:
-<center>
+<span style='background-color:yellow;'>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</span>
-select protein; calculate structure; cartoon; color structure
+and then clicking ''Run''. See also [[Calculate structure]].
-</center>
-and then click ''Run''. See also [[Calculate structure]].
 </blockquote>