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sbliven merged 22 commits into from
Jul 22, 2015
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Extend structure alignment page with multiple alignments #5

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Adding basic alignmentcode page with MultipleStructureAlignment proposal
sbliven Jul 10, 2014
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Explanation for AFPChain Data Model
lafita Jul 21, 2015
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Update references and section template
lafita Jul 21, 2015
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Explain MultipleAlignment object hierarchy
lafita Jul 21, 2015
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Include examples for the two data models
lafita Jul 21, 2015
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Change protein references to structure
lafita Jul 22, 2015
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Add figures for multiple GUI
lafita Jul 22, 2015
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Change multiple figures
lafita Jul 22, 2015
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Describe the GUI for multiple alignments
lafita Jul 22, 2015
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Update structure reference in README
lafita Jul 22, 2015
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Update structure references in Structure modules
lafita Jul 22, 2015
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Update structure data model
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Update chemcomp.md
lafita Jul 22, 2015
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Update mmCIF explanation
lafita Jul 22, 2015
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lafita Jul 22, 2015
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Explain utility methods for MSTA manipulation
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Description of the MultipleMC algorithm
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Footer script compatible with python 2.6
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Update mmCIF explanation
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lafita committed Jul 22, 2015
commit 77fc195d527d21e92367c8537061f043b75c33ca
16 changes: 8 additions & 8 deletions structure/mmcif.md
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# How to parse mmCIF files using BioJava
# How to Parse mmCIF Files using BioJava

A quick tutorial how to work with mmCIF files.

Expand All @@ -10,12 +10,12 @@ The Protein Data Bank (PDB) has been distributing its archival files as PDB file

The mmCIF file format has been around for some time (see [Westbrook 2000][] and [Westbrook 2003][] ) [BioJava](http://www.biojava.org) has been supporting mmCIF already for several years. This tutorial is meant to provide a quick introduction into how to parse mmCIF files using [BioJava](http://www.biojava.org)

## The basics
## The Basics

BioJava provides you with both a mmCIF parser and a data model that reads PDB and mmCIF files into a biological and chemically meaningful data model (BioJava supports the [Chemical Components Dictionary](mmcif.md)). If you don't want to use that data model, you can still use BioJava's file parsers, and more on that later, let's start first with the most basic way of loading a protein structure.


## First steps
## First Steps

The simplest way to load a PDB file is by using the [StructureIO](http://www.biojava.org/docs/api/org/biojava/nbio/structure/StructureIO.html) class.

Expand Down Expand Up @@ -61,7 +61,7 @@ By default BioJava is using the PDB file format for parsing data. In order to sw

As you can see, the AtomCache will again download the missing mmCIF file for 4HHB in the background.

## Low level access
## Low Level Access

If you want to learn how to use the BioJava mmCIF parser to populate your own data structure, let's first take a look this lower-level code:

Expand Down Expand Up @@ -93,13 +93,13 @@ To re-use the parser for your own datamodel, just implement the [MMcifConsumer](
parser.addMMcifConsumer(myOwnConsumerImplementation);
```

## I loaded a Structure object, what now?
## I Loaded a Structure Object, What Now?

BioJava provides a number of algorithms and visualisation tools that you can use to further analyse the structure, or look at it. Here a couple of suggestions for further reads:

+ [The BioJava Cookbook for protein structures](http://biojava.org/wiki/BioJava:CookBook#Protein_Structure)
+ How does BioJava [represent the content](structure-data-model.md) of a PDB/mmCIF file?
+ [How to calculate a protein structure alignment using BioJava](http://biojava.org/wiki/BioJava:CookBook:PDB:align)
+ How to calculate a protein structure alignment using BioJava: [tutorial](alignment.md) or [cookbook](http://biojava.org/wiki/BioJava:CookBook:PDB:align)
+ [How to work with Groups (AminoAcid, Nucleotide, Hetatom)](http://biojava.org/wiki/BioJava:CookBook:PDB:groups)

## Further reading
Expand All @@ -121,8 +121,8 @@ See the [http://mmcif.rcsb.org/](http://mmcif.rcsb.org/) site for more documenta

Navigation:
[Home](../README.md)
| [Book 3: The Protein Structure modules](README.md)
| Chapter 6 : work with mmCIF/PDBx files
| [Book 3: The Structure modules](README.md)
| Chapter 6 : Work with mmCIF/PDBx Files

Prev: [Chapter 5 : Chemical Component Dictionary](chemcomp.md)

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