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Merged
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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509057f
Adding basic alignmentcode page with MultipleStructureAlignment proposal
sbliven Jul 10, 2014
e60bfea
Explanation for AFPChain Data Model
lafita Jul 21, 2015
30a0202
Update references and section template
lafita Jul 21, 2015
f095f28
Explain MultipleAlignment object hierarchy
lafita Jul 21, 2015
ac15b5d
Include examples for the two data models
lafita Jul 21, 2015
fa0fae2
Change protein references to structure
lafita Jul 22, 2015
a45465c
Add figures for multiple GUI
lafita Jul 22, 2015
34a1a4d
Change multiple figures
lafita Jul 22, 2015
dd2b482
Describe the GUI for multiple alignments
lafita Jul 22, 2015
3e2f422
Update structure reference in README
lafita Jul 22, 2015
3118385
Update structure references in Structure modules
lafita Jul 22, 2015
9b6123b
Update first steps
lafita Jul 22, 2015
1990920
Update structure data model
lafita Jul 22, 2015
13b8380
Update caching
lafita Jul 22, 2015
ba593eb
Update chemcomp.md
lafita Jul 22, 2015
77fc195
Update mmCIF explanation
lafita Jul 22, 2015
bed1234
Update SEQRES
lafita Jul 22, 2015
b1b8204
Explain utility methods for MSTA manipulation
lafita Jul 22, 2015
b6b0a01
Description of the MultipleMC algorithm
lafita Jul 22, 2015
99c7cc2
Footer script compatible with python 2.6
lafita Jul 22, 2015
40b7c4d
Merge remote-tracking branch 'origin/multiplealignment' into multiple…
lafita Jul 22, 2015
bbc77f4
Update footers
lafita Jul 22, 2015
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Update structure references in Structure modules
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lafita committed Jul 22, 2015
commit 311838523c1b3b0238f75ea846e775d135056728
22 changes: 11 additions & 11 deletions structure/README.md
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The Protein Structure Modules of BioJava
The Structure Modules of BioJava
=====================================================

A tutorial for the protein structure modules of [BioJava](http://www.biojava.org)
A tutorial for the structure modules of [BioJava](http://www.biojava.org)

## About
<table>
Expand Down Expand Up @@ -32,35 +32,35 @@ Chapter 1 - Quick [Installation](installation.md)

Chapter 2 - [First Steps](firststeps.md)

Chapter 3 - The [data model](structure-data-model.md) for the representation of macromolecular structures.
Chapter 3 - The [Structure Data Model](structure-data-model.md), for the representation of macromolecular structures

Chapter 4 - [Local installations](caching.md) of PDB
Chapter 4 - [Local Installations](caching.md) of PDB

Chapter 5 - The [Chemical Component Dictionary](chemcomp.md)

Chapter 6 - How to [work with mmCIF/PDBx files](mmcif.md)
Chapter 6 - How to [Work with mmCIF/PDBx Files](mmcif.md)

Chapter 7 - [SEQRES and ATOM records](seqres.md), mapping to Uniprot (SIFTs)
Chapter 7 - [SEQRES and ATOM Records](seqres.md), mapping to Uniprot (SIFTs)

Chapter 8 - Protein [Structure Alignments](alignment.md)
Chapter 8 - [Structure Alignments](alignment.md)

Chapter 9 - [Biological Assemblies](bioassembly.md)

Chapter 10 - [External Databases](externaldb.md) like SCOP &amp; CATH

Chapter 11 - [Accessible Surface Areas](asa.md)

Chapter 12 - [Contacts within a chain and between chains](contact-map.md)
Chapter 12 - [Contacts Within a Chain and between Chains](contact-map.md)

Chapter 13 - Finding all interfaces in crystal: [crystal contacts](crystal-contacts.md)
Chapter 13 - Finding all Interfaces in Crystal: [Crystal Contacts](crystal-contacts.md)

Chapter 14 - Protein Symmetry

Chapter 15 - Bonds

Chapter 16 - [Special Cases](special.md)

Chapter 17 - [Lists](lists.md) of PDB IDs and PDB [status information](lists.md).
Chapter 17 - [Lists](lists.md) of PDB IDs and PDB [Status Information](lists.md)


### Author:
Expand Down Expand Up @@ -88,7 +88,7 @@ The content of this tutorial is available under the [CC-BY](http://creativecommo

Navigation:
[Home](../README.md)
| Book 3: The Protein Structure modules
| Book 3: The Structure modules

Prev: [Book 2: The Alignment module](../alignment/README.md)

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