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andreasprlic merged 13 commits into from
Aug 6, 2015
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Symmetry Chapter #6

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34ba644
Update Structure readme
lafita Aug 5, 2015
dd114d0
Capitalize titles in front page
lafita Aug 5, 2015
24584ea
fix typos in structure data model
lafita Aug 5, 2015
921d825
Symmetry chapter template
lafita Aug 5, 2015
e18b322
Symmetry images
lafita Aug 5, 2015
a485322
Explain quaternary symmetry detection
lafita Aug 5, 2015
8e4e7f0
Point Group image
lafita Aug 5, 2015
70a9a06
Merge branch 'symmetry' of https://github.com/lafita/biojava-tutorial…
lafita Aug 5, 2015
5606056
CeSymm description
lafita Aug 6, 2015
317bd76
Explain symmetry GUI
lafita Aug 6, 2015
7176268
Explain combined quat and internal symmetries
lafita Aug 6, 2015
b49ea81
Update footers
lafita Aug 6, 2015
ef991d3
typo fix
lafita Aug 6, 2015
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lafita committed Aug 6, 2015
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6 changes: 3 additions & 3 deletions alignment/README.md
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Expand Up @@ -59,8 +59,8 @@ The content of this tutorial is available under the [CC-BY](http://creativecommo

Navigation:
[Home](../README.md)
| Book 2: The Alignment module
| Book 2: The Alignment Module

Prev: [Book 1: The Core module](../core/README.md)
Prev: [Book 1: The Core Module](../core/README.md)

Next: [Book 3: The Structure modules](../structure/README.md)
Next: [Book 3: The Structure Modules](../structure/README.md)
2 changes: 1 addition & 1 deletion alignment/installation.md
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Expand Up @@ -41,5 +41,5 @@ If you run

Navigation:
[Home](../README.md)
| [Book 2: The Alignment module](README.md)
| [Book 2: The Alignment Module](README.md)
| Chapter 1 : Installation
4 changes: 2 additions & 2 deletions core/README.md
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Expand Up @@ -55,6 +55,6 @@ The content of this tutorial is available under the [CC-BY](http://creativecommo

Navigation:
[Home](../README.md)
| Book 1: The Core module
| Book 1: The Core Module

Next: [Book 2: The Alignment module](../alignment/README.md)
Next: [Book 2: The Alignment Module](../alignment/README.md)
2 changes: 1 addition & 1 deletion core/installation.md
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Expand Up @@ -42,7 +42,7 @@ If you run

Navigation:
[Home](../README.md)
| [Book 1: The Core module](README.md)
| [Book 1: The Core Module](README.md)
| Chapter 1 : Installation

Next: [Chapter 2 : Basic Sequence types](sequences.md)
13 changes: 13 additions & 0 deletions core/readwrite.md
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Expand Up @@ -62,3 +62,16 @@ BioJava can be used to parse large FASTA files. The example below can parse a 1G
}
}
```

<!--automatically generated footer-->

---

Navigation:
[Home](../README.md)
| [Book 1: The Core Module](README.md)
| Chapter 3 : Reading and Writing sequences

Prev: [Chapter 2 : Basic Sequence types](sequences.md)

Next: [Chapter 4 : Translating](translating.md)
4 changes: 2 additions & 2 deletions core/sequences.md
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Expand Up @@ -60,9 +60,9 @@ See the Cookbook for [more details on dealing with sequences] (http://biojava.or

Navigation:
[Home](../README.md)
| [Book 1: The Core module](README.md)
| [Book 1: The Core Module](README.md)
| Chapter 2 : Basic Sequence types

Prev: [Chapter 1 : Installation](installation.md)

Next: [Chapter 4 : Translating](translating.md)
Next: [Chapter 3 : Reading and Writing sequences](readwrite.md)
4 changes: 2 additions & 2 deletions core/translating.md
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Expand Up @@ -110,7 +110,7 @@ Translated Frame:REVERSED_THREE : HRGS*AFG*LCAISSL*ANNQSHHSDGHSLSGEDSRTGQLLLRQMS

Navigation:
[Home](../README.md)
| [Book 1: The Core module](README.md)
| [Book 1: The Core Module](README.md)
| Chapter 4 : Translating

Prev: [Chapter 2 : Basic Sequence types](sequences.md)
Prev: [Chapter 3 : Reading and Writing sequences](readwrite.md)
2 changes: 1 addition & 1 deletion genomics/README.md
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Expand Up @@ -64,4 +64,4 @@ Navigation:
[Home](../README.md)
| Book 4: The Genomics Module

Prev: [Book 3: The Structure modules](../structure/README.md)
Prev: [Book 3: The Structure Modules](../structure/README.md)
4 changes: 2 additions & 2 deletions structure/README.md
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Expand Up @@ -88,8 +88,8 @@ The content of this tutorial is available under the [CC-BY](http://creativecommo

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

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

Next: [Book 4: The Genomics Module](../genomics/README.md)
2 changes: 1 addition & 1 deletion structure/alignment.md
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Expand Up @@ -385,7 +385,7 @@ Thanks to P. Bourne, Yuzhen Ye and A. Godzik for granting permission to freely u

Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| [Book 3: The Structure Modules](README.md)
| Chapter 8 : Structure Alignments

Prev: [Chapter 7 : SEQRES and ATOM Records](seqres.md)
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2 changes: 1 addition & 1 deletion structure/asa.md
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Expand Up @@ -41,7 +41,7 @@ See [DemoAsa](https://github.com/biojava/biojava/blob/master/biojava3-structure/

Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| [Book 3: The Structure Modules](README.md)
| Chapter 11 : Accessible Surface Areas

Prev: [Chapter 10 : External Databases](externaldb.md)
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2 changes: 1 addition & 1 deletion structure/bioassembly.md
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Expand Up @@ -233,7 +233,7 @@ The RCSB PDB web site has a great [tutorial on Biological Assemblies](http://www

Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| [Book 3: The Structure Modules](README.md)
| Chapter 9 : Biological Assemblies

Prev: [Chapter 8 : Structure Alignments](alignment.md)
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2 changes: 1 addition & 1 deletion structure/caching.md
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Expand Up @@ -89,7 +89,7 @@ There are quite a number of external database IDs that are supported here. See t

Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| [Book 3: The Structure Modules](README.md)
| Chapter 4 : Local Installations

Prev: [Chapter 3 : Structure Data Model](structure-data-model.md)
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2 changes: 1 addition & 1 deletion structure/chemcomp.md
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Expand Up @@ -89,7 +89,7 @@ If you want to enable the second behaviour (slow loading of all chem comps at st

Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| [Book 3: The Structure Modules](README.md)
| Chapter 5 : Chemical Component Dictionary

Prev: [Chapter 4 : Local Installations](caching.md)
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2 changes: 1 addition & 1 deletion structure/contact-map.md
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Expand Up @@ -68,7 +68,7 @@ See [DemoContacts](https://github.com/biojava/biojava/blob/master/biojava3-struc

Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| [Book 3: The Structure Modules](README.md)
| Chapter 12 : Contacts Within a Chain and between Chains

Prev: [Chapter 11 : Accessible Surface Areas](asa.md)
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4 changes: 2 additions & 2 deletions structure/crystal-contacts.md
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Expand Up @@ -65,9 +65,9 @@ One can also cluster the interfaces based on their similarity. The similarity is

Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| [Book 3: The Structure Modules](README.md)
| Chapter 13 - Finding all Interfaces in Crystal: Crystal Contacts

Prev: [Chapter 12 : Contacts Within a Chain and between Chains](contact-map.md)

Next: [Chapter 16 : Special Cases](special.md)
Next: [Chapter 14 : Protein Symmetry](symmetry.md)
2 changes: 1 addition & 1 deletion structure/externaldb.md
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Expand Up @@ -205,7 +205,7 @@ got 4 domains

Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| [Book 3: The Structure Modules](README.md)
| Chapter 10 : External Databases

Prev: [Chapter 9 : Biological Assemblies](bioassembly.md)
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2 changes: 1 addition & 1 deletion structure/firststeps.md
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Expand Up @@ -123,7 +123,7 @@ BioJava provides a number of algorithms and visualisation tools that you can use

Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| [Book 3: The Structure Modules](README.md)
| Chapter 2 : First Steps

Prev: [Chapter 1 : Installation](installation.md)
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2 changes: 1 addition & 1 deletion structure/installation.md
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Expand Up @@ -43,7 +43,7 @@ If you run

Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| [Book 3: The Structure Modules](README.md)
| Chapter 1 : Installation

Next: [Chapter 2 : First Steps](firststeps.md)
2 changes: 1 addition & 1 deletion structure/lists.md
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Expand Up @@ -26,7 +26,7 @@ The following provides information about the status of a PDB entry

Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| [Book 3: The Structure Modules](README.md)
| Chapter 17 : Status Information

Prev: [Chapter 16 : Special Cases](special.md)
2 changes: 1 addition & 1 deletion structure/mmcif.md
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Expand Up @@ -144,7 +144,7 @@ See the [http://mmcif.rcsb.org/](http://mmcif.rcsb.org/) site for more documenta

Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| [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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2 changes: 1 addition & 1 deletion structure/seqres.md
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Expand Up @@ -103,7 +103,7 @@ This gives the following output:

Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| [Book 3: The Structure Modules](README.md)
| Chapter 7 : SEQRES and ATOM Records

Prev: [Chapter 6 : Work with mmCIF/PDBx Files](mmcif.md)
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4 changes: 2 additions & 2 deletions structure/special.md
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Expand Up @@ -130,9 +130,9 @@ DYG is an unusual group - it has 3 characters as a result of .getOne_letter_code

Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| [Book 3: The Structure Modules](README.md)
| Chapter 16 : Special Cases

Prev: [Chapter 13 - Finding all Interfaces in Crystal: Crystal Contacts](crystal-contacts.md)
Prev: [Chapter 14 : Protein Symmetry](symmetry.md)

Next: [Chapter 17 : Status Information](lists.md)
2 changes: 1 addition & 1 deletion structure/structure-data-model.md
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Expand Up @@ -165,7 +165,7 @@ This prints all the compounds/entities in a structure

Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| [Book 3: The Structure Modules](README.md)
| Chapter 3 : Structure Data Model

Prev: [Chapter 2 : First Steps](firststeps.md)
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13 changes: 13 additions & 0 deletions structure/symmetry.md
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Expand Up @@ -202,3 +202,16 @@ below:

This results can gives hints about the function and evolution of proteins and biological
structures.

<!--automatically generated footer-->

---

Navigation:
[Home](../README.md)
| [Book 3: The Structure Modules](README.md)
| Chapter 14 : Protein Symmetry

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

Next: [Chapter 16 : Special Cases](special.md)