This page is supposed to provide an overview over the structure and meaning of
the most essential XML parameters for a valid fibre file that can be loaded and
parsed by the _Chromatin 3D Visualizer_.

In general, all parameters are optional. Even an XML file without
any parameters can be understood and parsed by the program. However, this leads
to the parameters being initialized with standard values, which means, that data displayed
within the application might be lacking. As a consequence there are some
values that should be set for an optimal user experience.

> **Note:** "parameters" in this text refers strictly to the entries of the `parameters` block
in the fibre XML file.
>
> Also: It is possible to overwrite the parameters set globally in the `parameters` block
for each configuration via the
>
> ```xml
> <overwrite_parameters>
>   ...
> </overwrite_parameters>
> ```
> block. This way, certain parameters can be specifically altered for certain configurations.

### Chapters

* [Parameters](#parameters)
  * [Radius DNA](#radius-dna)
  * [Nucleosome Radius](#nucleosome-radius)
  * [Nucleosome Height](#nucleosome-height)
  * [PBC Container Start Dimension](#pbc-container-start-dimension)
  * [Cohesin Head Radius](#cohesin-head-radius)
  * [Ring Thickness](#ring-thickness)
  * [Ring Radius](#ring-radius)

## Parameters

All the parameters are stored within the `parameters` block

```xml
<parameters>
    <parameter>...</parameter>
    <parameter>...</parameter>
    ...
</parameters>
```

The `parameter` blocks all have the same structure:

```xml
<parameter>
    <name>name</name>
    <value>value</value>
</parameter>
```
<br />
<br />

-----

### Radius DNA

Name (XML): `RadiusDNA`

#### Description

Provides the radius of the linker DNA (thereby controlling the visualization in the 
application).

#### Type

* Number (float)

#### Sample Value

Typically, made up of relatively small numbers.

* 1.2
<br />
<br />

-----

### Nucleosome Radius

Name (XML): `NucleosomeRadius`

#### Description

Provides the radius of the nucleosomes (thereby controlling the visualization in the
application).

#### Type

* Number (float)

#### Sample Value

Typically, made up of relatively small numbers.

* 5.5
  <br />
  <br />

-----

### Nucleosome Height

Name (XML): `NucleosomeHeight`

#### Description

Provides the height of the nucleosomes (thereby controlling the visualization in the
application).

#### Type

* Number (float)

#### Sample Value

Typically, made up of relatively small numbers.

* 2.0
  <br />
  <br />

-----

### PBC Container Start Dimension

Name (XML): `PBCContainerStartDimension`

#### Description

Provides the dimensions of the PBC container. Since this is a cube, only one 
dimension has to be provided and from said value, the entire cube is created.
If this parameter is omitted or set to `-1`, PBC mode is deactivated for that fibre.

#### Type

* Number
 
#### Sample Value

Typically, made up of relatively big numbers.

* 300
  <br />
  <br />

-----

### Cohesin Head Radius

* Name (XML): `CohesinHeadRadius`

#### Description

If cohesin is part of the fibre, this parameter states the radius of the cohesin heads and 
should not be omitted, since this could lead to unexpected behaviour in the visualization.

#### Type

* Number (float)

#### Sample Value

Typically, made up of relatively small numbers.

* 2.0
  <br />
  <br />

-----

### Ring Thickness

* Name (XML): `ringThickness`

#### Description

Describes the thickness of the cohesin ring. This should not be omitted, if there is a cohesin ring 
present in the fibre, since this could lead to unexpected behaviour in the visualization.

#### Type

* Number (float)

#### Sample Value

Typically, made up of relatively small numbers.

* 1
  <br />
  <br />

-----

### Ring Radius

Name (XML): `ringRadius`

#### Description

Describes the radius of the cohesin ring. Should not be omitted, if there is a cohesin ring
present in the fibre, since this could lead to unexpected behaviour in the visualization.

#### Type

* Number (float)

#### Sample Value

Typically, made up bigger numbers than radii of the dna or nucleosomes (since it is a bigger object).

* 20
  <br />
  <br />