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.
Activate all in BUTTON:UserProfile#newButton()!.
As a selection criterion we will use the spatial distance of C-alpha atoms
to a hetero group COMBO:Distance3DToHetero.
Download PDB:1nrg
Highlight spatially close residues
Open the dialog BUTTON:DialogSelectionOfResiduesMain! and select
the method COMBO:Distance3DToHetero.
Select the protein and type "FMN" into the control panel.
All residues in proximity to the flavine are highlighted.
Dragging the slider to the left less amino acids are selected and dragging the slider to the right more positions are highlighted.
This is best observed in the JCOMPONENT:StrapView#button(BUT_WIRE)!.
Creating an annotated selection
The selection belongs to the type of computed residue selections.
Therefore it cannot hold annotations such as WIKI:LaTeX expressions for the PDF output
nor rendering commands for external protein viewers.
Conversion into an annotated residue selection is required.
The respective menu item is located in the WIKI:Context_menu:
BUTTON:ResidueSelectionPopup#ACTION_convertToResidueAnnotation.
As a result an annotated residue selection with at the same
sequence positions is created and shown as a table. After closing
the dialog that computed the residue selection, the annotated
selection will persist and will be saved when the alignment is
saved.
Creating PDF
The PDF-document is created with the type setting system WIKI:LaTeX which is usually part of Unix or Linux based computer systems.
Creating a PDF document with the dialog BUTTON:Texshade! requires 3 steps:
-
At first STRAP creates a multiple sequence alignment file (MSF) and
a WIKI:LaTeX source file. The LaTeX-package TeXshade is used.
-
The program WIKI:pdflatex creates a PDF-document.
-
The PDF-file is shown.
TeXshade commands in annotations
Now we consider the table of annotations.
Each annotation is shown in one table row.
The left column contains the type of annotation and the right column the textural contents.
A new table row for TeXshade-commands can be added
with the button LABEL:ResidueAnnotationView#BUT_LAB_ton.
It brings up a dialog where you can select an annotation type and a text string (figure below).
Select ICON:IC_PDFTexshade.
A list of TeXshade expressions is presented:
TEXT_LINES:Texshade#getCustomizableExamples()
Chose the TeXshade expression
\feature{top}{PROTEIN}{RESIDUES}{box[Red]}{peptide}
Its semantic meaning is obvious:
It marks the selected residues as a red box labeled with 'peptide'.
You can click the ICON:IC_PDFTexshade in the table row header of the residue selection to compute a preview for one single protein.
For generating a PDF with more than one protein, the dialog BUTTON:Texshade! is required.