minor update

Andreas Prlic · Andreas Prlic · commit f575b15d8cef · 2013-09-18T17:34:36.000-07:00
diff --git a/structure/README.md b/structure/README.md
@@ -29,9 +29,9 @@ Chapter 10 - Protein Symmetry
 
 Chapter 11 - Bonds
 
-###
+### Author: 
 
-Author: [Andreas Prlic](https://github.com/andreasprlic)
+[Andreas Prli&#263;](https://github.com/andreasprlic)
 
 
 
diff --git a/structure/chemcomp.md b/structure/chemcomp.md
@@ -51,7 +51,7 @@ As you can see, although MSE is flaged as HETATM in the PDB file, BioJava still
 
 
 ### How to access Chemical Component definitions
-Bye default BioJava ships with a minimal representation of standard amino acids, however if you want to parse the whole PDB archive, it is good to tell the library to either
+By default BioJava ships with a minimal representation of standard amino acids, which is useful when you just want to work with atoms and a basic data representation. However if you want to work with a  correct representation (e.g. distinguish ligands from the polypeptide chain, correctly resolve chemically modified residues), it is good to tell the library to either
 
 1. fetch missing Chemical Component definitions on the fly (small download and parsing delays every time a new chemical compound is found), or
 2. Load all definitions at startup (slow startup, but then no further delays later on, requires more memory)
diff --git a/structure/structure-data-model.md b/structure/structure-data-model.md
@@ -4,7 +4,7 @@ A biologically and chemically meaningful data representation of PDB/mmCIF.
 
 ## The basics   
 
-BioJava at its core is a collection of file parsers and (in some cases) data models to represent frequently used biological data.  The protein-structure modules represent macromolecular data in a way that should make it easy to work with. The representation is essentially independ of the underlying file format and the user can chose to work with either PDB or mmCIF files and still get an almost identical data representation.
+BioJava at its core is a collection of file parsers and (in some cases) data models to represent frequently used biological data.  The protein-structure modules represent macromolecular data in a way that should make it easy to work with. The representation is essentially independ of the underlying file format and the user can chose to work with either PDB or mmCIF files and still get an almost identical data representation. (There can be subtile differences between PDB and mmCIF data, for example the atom indices in a few entries are not 100% identical)
 
 ## The main hierarchy
 
@@ -25,7 +25,7 @@ Structure
                  Atom(s)
 </pre>
 
-All structure objects contain one or more "models". That means also X-ray structures contain an "virtual" model which serves as a container for the chains. The most common way to access chains will be via
+All structure objects contain one or more "models". That means also X-ray structures contain a "virtual" model which serves as a container for the chains. The most common way to access chains will be via
 
 <pre>
         List < Chain > chains = structure.getChains();
@@ -47,6 +47,10 @@ If you want to directly access an array of [Atoms](http://www.biojava.org/docs/a
 
 Alternatively you can access atoms also by their parent-group.
 
+## Loop over all the data
+
+//TODO
+
 ## Working with groups
 
 The [Group](http://www.biojava.org/docs/api/org/biojava/bio/structure/Group.html) interface defines all methods common to a group of atoms. There are 3 types of Groups:
