Updated README.

Author: iamazeem

README.md

@@ -1,66 +1,67 @@
 # BioJava-Spark
-Algorithms that are built around BioJava and are running on Apache Spark
 
+Algorithms that are built around BioJava and are running on Apache Spark
 
 [![Build Status](https://travis-ci.org/biojava/biojava-spark.svg?branch=master)](https://travis-ci.org/biojava/biojava-spark)
 [![License](http://img.shields.io/badge/license-LGPL_2.1-blue.svg?style=flat)](https://github.com/biojava/biojava/blob/master/LICENSE)
 [![Status](http://img.shields.io/badge/status-experimental-red.svg?style=flat)](https://github.com/biojava/biojava-spark)
 [![Version](http://img.shields.io/badge/version-0.2.1-blue.svg?style=flat)](https://github.com/biojava/biojava-spark/)
 
-# Starting up
+## Starting up
 
 ### Some initial instructions can be found on the mmtf-spark project
-https://github.com/rcsb/mmtf-spark
+https://github.com/sbl-sdsc/mmtf-spark
+
 ## First download and untar a Hadoop sequence file of the PDB (~7 GB download) 
+
 ```bash
 wget http://mmtf.rcsb.org/v1.0/hadoopfiles/full.tar
 tar -xvf full.tar
 ```
 Or you can get a C-alpha, phosphate, ligand only version (~800 Mb download)
+
 ```bash
 wget http://mmtf.rcsb.org/v1.0/hadoopfiles/reduced.tar
 tar -xvf reduced.tar
 ```
 ### Second add the biojava-spark dependecy to your pom
 
 ```xml
-		<dependency>
-			<groupId>org.biojava</groupId>
-			<artifactId>biojava-spark</artifactId>
-			<version>0.2.1</version>
-		</dependency>
+<dependency>
+	<groupId>org.biojava</groupId>
+	<artifactId>biojava-spark</artifactId>
+	<version>0.2.1</version>
+</dependency>
 ```
 
-
-
 ## Extra Biojava examples
 
 ### Do some simple quality filtering
 
 ```java
-	float maxResolution = 3.0f;
-	float maxRfree = 0.3f;
-	StructureDataRDD structureData = new StructureDataRDD("/path/to/file")
-				.filterResolution(maxResolution)
-				.filterRfree(maxRfree);
+float maxResolution = 3.0f;
+float maxRfree = 0.3f;
+StructureDataRDD structureData = new StructureDataRDD("/path/to/file")
+			.filterResolution(maxResolution)
+			.filterRfree(maxRfree);
 ```
 
 ### Summarsing the elements in the PDB
+
 ```java
-	Map<String, Long> elementCountMap = BiojavaSparkUtils.findAtoms(structureData).countByElement();
+Map<String, Long> elementCountMap = BiojavaSparkUtils.findAtoms(structureData).countByElement();
 ```
 
 ### Finding inter-atomic contacts from the PDB
 
 ```java
-		Double mean = BiojavaSparkUtils.findContacts(structureData,
-				new AtomSelectObject()
-						.groupNameList(new String[] {"PRO","LYS"})
-						.elementNameList(new String[] {"C"})
-						.atomNameList(new String[] {"CA"}),
-						cutoff)
-				.getDistanceDistOfAtomInts("CA", "CA")
-				.mean();
-		System.out.println("\nMean PRO-LYS CA-CA distance: "+mean);
+Double mean = BiojavaSparkUtils.findContacts(structureData,
+		new AtomSelectObject()
+				.groupNameList(new String[] {"PRO","LYS"})
+				.elementNameList(new String[] {"C"})
+				.atomNameList(new String[] {"CA"}),
+				cutoff)
+		.getDistanceDistOfAtomInts("CA", "CA")
+		.mean();
+System.out.println("\nMean PRO-LYS CA-CA distance: " + mean);
 ```
-