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 (see [http://chemapps.stolaf.edu/jmol/docs/#calculate calculate structure]. | 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: | 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 appear to work in Jmol 11.8 employed in Proteopedia in June, 2011. It works in the [[Jmol/Application]] (version 12).'' Here are the commands to do that: | ||
*select protein | |||
*calculate structure | *calculate structure | ||
*cartoon | |||
*color structure | |||
== External Links == | == External Links == | ||
For more information, see [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure]. | For more information, see [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure]. | ||