explaining chain -> seqres -> atom groups

andreasprlic · andreasprlic · commit c1c45fbcc578 · 2013-09-19T19:58:59.000-07:00
diff --git a/structure/seqres.md b/structure/seqres.md
@@ -22,6 +22,11 @@ The sequence that has been used in the experiment is stored in the **Seqres** re
 
 The **Atom** records provide coordinates where it was possible to observe them.
 
+<pre>
+    Seqres groups -> sequence that has been used in the experiment
+    Atom groups   -> subset of Seqres groups for which coordinates could be obtained
+</pre>    
+
 The *mmCIF/PDBx* file format contains the information how the Seqres and atom records are mapped onto each other. However the *PDB format* does not clearly specify how to resolve this mapping. BioJava contains a utility class that maps the Seqres to the Atom records when parsing PDB files. This class performs an alignment using dynamic programming, which can slow down the parsing process. If you do not require the precise Seqres to Atom mapping, you can turn it off like this:
 
 ```java
@@ -35,6 +40,21 @@ The *mmCIF/PDBx* file format contains the information how the Seqres and atom re
             
 ```
 
+## Accessing Seqres and Atom groups
+
+By default BioJava loads both the Seqres and Atom groups into the [Chain](http://www.biojava.org/docs/api/org/biojava/bio/structure/Chain.html) 
+objects.
+
+<pre>
+    Chain   -> Seqres groups
+            -> Atom groups
+</pre>
+
+Groups that are part of the Seqres sequence as well as of the Atom records are mapped onto each other. This means you
+can iterate over all Seqres groups in a chain and check, if they have observed atoms.
+
+
+
 ## Mapping from Uniprot to Atom records 
 
 The mapping between PDB and UniProt changes over time, due to the dynamic nature of biological data. The [PDBe](http://www.pdbe.org) has a project that provides up-to-date mappings between the two databases, the [SIFTs](http://www.ebi.ac.uk/pdbe/docs/sifts/) project. 
