New page: =A simple GUI for protein structure alignment= BioJava (in SVN) contains a simple GUI for easier working with protein structure alignments. The following code launches the user interface:...

andreasprlic · andreasprlic · commit 27f3a7019a5b · 2016-04-09T10:58:02.000-07:00
diff --git a/_wikis/BioJava:CookBook:PDB:alignGUI.md b/_wikis/BioJava:CookBook:PDB:alignGUI.md
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+---
+title: BioJava:CookBook:PDB:alignGUI
+---
+
+A simple GUI for protein structure alignment
+============================================
+
+BioJava (in SVN) contains a simple GUI for easier working with protein
+structure alignments. The following code launches the user interface:
+
+<java> import org.biojava.bio.structure.gui.\*;
+
+public static void main(String[] args){
+
+`   new AlignmentGui(); `
+
+} </java>
+
+In the user interface specify 2 PDB files (and optionally chain IDs)
+that should be superimposed.
+
+![](AlignmentGui.jpg "AlignmentGui.jpg")
+
+After pressing the \*Submit\* button, the alignment is calculated. A new
+frame pops up that shows the alternative solutions for this alignment:
+
+![](AltAligFrame.jpg "AltAligFrame.jpg")
+
+The columns in this table are:
+
+    #1    the number of the alternative alignment
+    eqr   the number of structurally equivalent residues
+    score the score for this alternative alignment
+    rms   root mean sqare
+    gaps  number of gaps in the alignment
+
+The \*Show in Jmol\* button allows to display this alternative alignment
+in Jmol, if it can be found on the classpath.
+
+![](AlignmentJmol.jpg "AlignmentJmol.jpg")
+
+The \*Distance Matrix\* button shows the distance matrix that is used
+for the alignment and the path that has been choosen.
+
+### Configure PDB installation (Optional)
+
+If you have a PDB installation that contains all PDB files in a single
+directory you can configure the System property PDB\_DIR to point to
+this directory. (e.g. at startup specify -DPDB\_DIR=path/to/PDB/files )
diff --git a/_wikis/BioJava:CookBook:PDB:alignGUI.mediawiki b/_wikis/BioJava:CookBook:PDB:alignGUI.mediawiki
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+=A simple GUI for protein structure alignment=
+
+BioJava (in SVN) contains a simple GUI for easier working with protein structure alignments.
+The following code launches the user interface:
+
+<java>
+import org.biojava.bio.structure.gui.*;
+
+public static void main(String[] args){
+	new AlignmentGui();	
+}
+</java>
+
+In the user interface specify 2 PDB files (and optionally chain IDs) that should be superimposed.
+
+[[Image:AlignmentGui.jpg]]
+
+After pressing the *Submit* button, the alignment is calculated. A new frame pops up that shows the alternative solutions for this alignment:
+
+[[Image:AltAligFrame.jpg]]
+
+The columns in this table are:
+<pre>
+#1    the number of the alternative alignment
+eqr   the number of structurally equivalent residues
+score the score for this alternative alignment
+rms   root mean sqare
+gaps  number of gaps in the alignment
+</pre>
+
+The *Show in Jmol* button allows to display this alternative alignment in Jmol, if it can be found on the classpath.
+
+[[Image:AlignmentJmol.jpg]]
+
+The *Distance Matrix* button shows the distance matrix that is used for the alignment and the path that has been choosen.
+
+
+===Configure PDB installation (Optional)===
+If you have a PDB installation that contains all PDB files in a single directory you can configure the System property PDB_DIR to point to this directory. (e.g. at startup specify -DPDB_DIR=path/to/PDB/files )
