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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
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Update footers
lafita Jul 22, 2015
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Update first steps
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lafita committed Jul 22, 2015
commit 9b6123b2ad7235c735210e1dfab1fbdaba4057c5
14 changes: 7 additions & 7 deletions structure/firststeps.md
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First Steps
===========

## 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 @@ -40,7 +40,7 @@ If you already have a local PDB installation, you can configure where BioJava sh
-DPDB_DIR=/wherever/you/want/
</pre>

## Memory consumption
## Memory Consumption

Talking about startup properties, it is also good to mention the fact that many PDB entries are large molecules and the default 64k memory allowance for Java applications is not sufficient in many cases. BioJava contains several built-in caches which automatically adjust to the available memory. As such, the more memory you grant your Java applicaiton, the better it can utilize the caches and the better the performance will be. Change the maximum heap space of your Java VM with this startup parameter:

Expand Down Expand Up @@ -86,7 +86,7 @@ This will result in the following view:
</tr>
</table>

## Asymmetric unit and Biological Assembly
## Asymmetric Unit and Biological Assembly

By default many people work with the *asymmetric unit* of a protein. However for many studies the correct representation to look at is the *biological assembly* of a protein. You can request it by calling

Expand All @@ -105,13 +105,13 @@ By default many people work with the *asymmetric unit* of a protein. However for

This topic is important, so we dedicated a [whole chapter](bioassembly.md) to it.

## 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)


Expand All @@ -123,9 +123,9 @@ BioJava provides a number of algorithms and visualisation tools that you can use

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

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

Next: [Chapter 3 : data model](structure-data-model.md)
Next: [Chapter 3 : Structure Data Model](structure-data-model.md)