More manual fixes

Author: josemduarte

_wikis/BioJava:CookBook:PDB:bioassembly.md

@@ -22,36 +22,36 @@ Here some example code how to load the biological assembly:
 
 ```java
 
-`           // good examples: 1stp 1gav 1hv4 1hho 7dfr 3fad  1qqp`
-
-`           // assembly 0 ... asym Unit`  
-`           // assembly 1 ... the first bio assembly`  
-`           // example 1fah has  2 assemblies (two copies of the assembly in asymmetric unit)`  
-`           `  
-`           `  
-`           // Various interesting symmetries: (see Lawson, 2008)`  
-`           // Circular    - 1TJA`  
-`           // Dihedral    - 1ei7`  
-`           // Icosahedral - 1a34`  
-`           // Helical     - 1cgm`  
-`           `  
-`           `  
-`           // DNA 173D .. 2`  
-`           `  
-`           // we load the bio assembly info out of the PDB files`  
-`           BioUnitDataProviderFactory.setBioUnitDataProvider(BioUnitDataProviderFactory.pdbProviderClassName);`
-
-`           //Structure bioAssembly = StructureIO.getBiologicalAssembly("4A1I",2);  `  
-`           `  
-`           Structure bioAssembly = StructureIO.getBiologicalAssembly("1ei7",1);`  
-`                                   `  
-`           StructureAlignmentJmol jmolPanel = new StructureAlignmentJmol();`  
-`           //jmolPanel.evalString("set autobond=false");`  
-`           jmolPanel.setStructure(bioAssembly);`
-
-`           // send some commands to Jmol`  
-`           jmolPanel.evalString("select * ; color structure ; spacefill off; wireframe off; backbone off; cartoon on; select ligands ; spacefill 0.4; color cpk;");`  
-`           `  
-`           System.out.println("done!");`
+           // good examples: 1stp 1gav 1hv4 1hho 7dfr 3fad  1qqp
+
+           // assembly 0 ... asym Unit  
+           // assembly 1 ... the first bio assembly  
+           // example 1fah has  2 assemblies (two copies of the assembly in asymmetric unit)  
+             
+             
+           // Various interesting symmetries: (see Lawson, 2008)  
+           // Circular    - 1TJA  
+           // Dihedral    - 1ei7  
+           // Icosahedral - 1a34  
+           // Helical     - 1cgm  
+             
+             
+           // DNA 173D .. 2  
+             
+           // we load the bio assembly info out of the PDB files  
+           BioUnitDataProviderFactory.setBioUnitDataProvider(BioUnitDataProviderFactory.pdbProviderClassName);
+
+           //Structure bioAssembly = StructureIO.getBiologicalAssembly("4A1I",2);    
+             
+           Structure bioAssembly = StructureIO.getBiologicalAssembly("1ei7",1);  
+                                     
+           StructureAlignmentJmol jmolPanel = new StructureAlignmentJmol();  
+           //jmolPanel.evalString("set autobond=false");  
+           jmolPanel.setStructure(bioAssembly);
+
+           // send some commands to Jmol  
+           jmolPanel.evalString("select * ; color structure ; spacefill off; wireframe off; backbone off; cartoon on; select ligands ; spacefill 0.4; color cpk;");  
+             
+           System.out.println("done!");
 
 ```