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Merged
sbliven merged 22 commits into from
Jul 22, 2015
Merged

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 SEQRES
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@lafita
lafita committed Jul 22, 2015
commit bed1234c52b8bec14809884dbc042bcff2c5d945
12 changes: 5 additions & 7 deletions structure/seqres.md
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SEQRES and ATOM records, mapping to Uniprot (SIFTs)
SEQRES and ATOM Records, Mapping to Uniprot (SIFTs)
===================================================

How molecular sequences are linked to experimentally observed atoms.
Expand All @@ -16,7 +16,7 @@ As you can see, there are three PDB entries (PDB IDs [3LOH](http://www.rcsb.org/

The blue-boxes are regions for which atoms records are available. For the grey regions there is sequence information available in the PDB, but no coordinates.

## Seqres and Atom records
## Seqres and Atom Records

The sequence that has been used in the experiment is stored in the **Seqres** records in the PDB. It is often not the same sequences as can be found in Uniprot, since it can contain cloning-artefacts and modifications that were necessary in order to crystallize a structure.

Expand All @@ -40,7 +40,7 @@ The *mmCIF/PDBx* file format contains the information how the Seqres and atom re

```

## Accessing Seqres and Atom groups
## Accessing Seqres and Atom Groups

By default BioJava loads both the Seqres and Atom groups into the [Chain](http://www.biojava.org/docs/api/org/biojava/nbio/structure/Chain.html)
objects.
Expand All @@ -53,9 +53,7 @@ objects.
Groups that are part of the Seqres sequence as well as of the Atom records are mapped onto each other. This means you
can iterate over all Seqres groups in a chain and check, if they have observed atoms.



## Mapping from Uniprot to Atom records
## Mapping from Uniprot to Atom Records

The mapping between PDB and UniProt changes over time, due to the dynamic nature of biological data. The [PDBe](http://www.pdbe.org) has a project that provides up-to-date mappings between the two databases, the [SIFTs](http://www.ebi.ac.uk/pdbe/docs/sifts/) project.

Expand Down Expand Up @@ -105,7 +103,7 @@ This gives the following output:

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