@*~RSC_HELP_TUTORIAL_TEXSHADE

Introduction

The goal of this tutorial is to demonstrate how residue selections can be visualized in the printable PDF output. The PDF output allows to highlight annotations in different styles. As a selection criterion we will use the spatial distance of C-alpha atoms to a hetero group HTMLDOC_COMBO_CLASS:BUT_C1(Distance3DToHetero). Download PDB:1nrg

Creating PDF

The PDF-document is created with the type-setting-system WIKI:LaTeX.

Highlight spatially close residues

Open the dialog HTMLDOC_BUTTON:BUT_C1(DialogSelectionOfResidues)! and select the method HTMLDOC_COMBO_CLASS:BUT_C1(Distance3DToHetero). Select the protein and type "FMN" into the control panel. All residues in proximity to the flavin are highlighted. Use the slider to adjust the distance. Observe the effect of altering the distance in the alignment pane and the 3D backbone view. Also activate the check-box "Overview ..." left from the horizontal scrollbar.

Annotating the residue selections

From the WIKI:Context_menu use HTMLDOC_BUTTON:M_SEL_EDIT. The name, sequence positions and annotation data are shown as a table.
Figure: TEXshade command attached to the named residue selection.
HTMLDOC_JCOMPONENT:HTMLDOC_JC_ResidueAnnotation_TEXshade
Add a table row with the tool-button at the top. The figure shows the dialog for adding table rows.
Figure: Adding Pymol commands to a residue selection.
HTMLDOC_JCOMPONENT:HTMLDOC_JC_AddAnnotation
Select HTMLDOC_ICON:IC_PDFTEXshade. Choose
  \feature{top}{PROTEIN}{RESIDUES}{box[Red]}{peptide}
This TeXshade command marks the selected residues as a red box labeled with 'peptide'. This row will be inserted into the table. Click the HTMLDOC_ICON:IC_PDFTEXshade in the table row header to get a preview for one single sequence. For generating a PDF with more than one sequence, the dialog HTMLDOC_BUTTON:BUT_C1(DialogTEXshade)! is required. *@