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. '[[Calculate structure]]' is the Jmol command which does this re-determination. The complete script required to display the ''Secondary Structure'' color scheme and hydrogen bonds (hbonds) contained in the secondary structures is 'select protein; calculate structure; cartoon; color structure; calculate hbonds structure'. At the present time 'calculate hbonds structure' messes up the post-processing by Proteopedia, and any scene whose script contains this command is not displayed. The above scenes which colors the helices, sheets and turns without displaying the hbonds were constructed using only 'select protein; calculate structure; cartoon; color structure'. If 'calculate hbonds strucutre' is run through the Jmol console as described below, the hbonds in these three types of structures will be displayed. | 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. '[[Calculate structure]]' is the Jmol command which does this re-determination. The complete script required to display the ''Secondary Structure'' color scheme and hydrogen bonds (hbonds) contained in the secondary structures is 'select protein; calculate structure; cartoon; color structure; calculate hbonds structure'. At the present time 'calculate hbonds structure' messes up the post-processing by Proteopedia, and any scene whose script contains this command is not displayed. The above scenes which colors the helices, sheets and turns without displaying the hbonds were constructed using only 'select protein; calculate structure; cartoon; color structure'. If 'calculate hbonds strucutre' is run through the Jmol console as described below, the hbonds in these three types of structures will be displayed. | ||
<blockquote> | <blockquote> | ||
Hbonds in secondary structures can be displayed by clicking on the ''Jmol frank'' which opens the ''main menu'', clicking on ''Console'', in the bottom console box entering the | Hbonds in secondary structures can be displayed by clicking on the ''Jmol frank'' which opens the ''main menu'', clicking on ''Console'', in the bottom console box entering the commands: <span style='background-color:yellow;'>select protein; calculate hbonds structure</span> | ||
and then clicking ''Run''.</blockquote> | and then clicking ''Run''.</blockquote> | ||
<blockquote> | <blockquote> | ||
If a Proteopedia page does not contain the more detailed ''Secondary Structure'' information, it can be displayed by running the script: | If a Proteopedia page does not contain the more detailed ''Secondary Structure'' information, it can be displayed by running the script: | ||