{"last_commit_sha":"09a86f30e42084d1657acf9d0e8d4d024e77505a","persisted":true,"title":"Tabs","content":"The `Chromatin 3D Visualizer` application contains multiple `Tabs` which represent windows with a specific function. This enables the user to access multiple features in a dedicated view. All the tabs of the application can be accessed and turned off again via the `Window` menu entry. ## The Tabs There are a few available tabs in the application. The following list provides a brief overview of the available tabs and their function: ### Viewer This is the main view of the application. In this window you can see the trajectory that is currently loaded. Via this view, the camera of the application can be controlled. This includes rotations, zooming, moving the camera and so on.
This view will be grayed out, when no trajectory has been loaded and only become available, once a trajectory has been selected and loaded.

### PBC This view contains the settings for `PBC-Trajectories` alongside some statistics obtained from the config loaded into the application.
The view contains multiple controls that influence the visualisation of the trajectory: **PBC-Mode and Container** These settings control whether the loaded trajectory will be displayed in PBC-mode and whether the PBC-container will be displayed in the main view. The additional `Color` property directly controls the color of the container, if it is displayed in the view. **Microscope Slide** The `Microscope Slide` controls influence whether a slide will be displayed in the main viewer window. Similarly to the PBC container, enabling the `Box` of the slide, will show a visualisation of the box in the main view. That view's color can also be changed. With the `Size` and `Index` controls, the slide can be increased in size and moved through the container, changing what is being included and displayed.

### Fiber Information This view contains information about the fiber that has been loaded into the application.

### Cohesin / CTCF This view contains information about hte `Cohesin` properties of the loaded fiber.

### View Settings This tab describes certain settings that directly influence the visualisation of the fiber on display. It is split into two distinct control groups: **Colors** This control directly influences the color of fiber-elements. For example, the color for the entirety of the nucleosomes can be set. **Visualization** This control group allows activating or hiding helper elements in the main view and influencing some visual properties of the displayed fiber (for example the texture).

### Configuration Player The configuration player controls which configuration will be displayed in the main view of the application. Through the tab, specific configurations can be selected or the autoplay-feature can be used, to cycle through every available config. The tab also allows for other smaller settings to influence the display of and cycling through the configurations.

### Camera Settings The camera settings mainly control the camera in the main view of the application. **Controls** This control allows switching between two different camera modes: * `First Person Perspective`, in this mode, the camera can be moved around freely * `Rotate Around The Center`, with this mode, the camera is locked to the center of the fiber **Camera** Under the `camera` portion, there are two distinct controls: * `Set Camera` allows setting different camera behaviours for when the configuration in the main view is changed * `None` this will behave the same way as `Keep Distance to Center` * `Set to Center Mass` will place the camera at the origin of the fiber whenever you change configuration * `Keep Distance to Center` will keep the camera at its current position whenever you change configuration * `Find The Fiber` is a button that will center the camera of the view on the fiber

### Nucleosomes Explorer This tab contains information about every nucleosome of the fiber loaded into the application. Through this view, every nucleosome can be selected and a custom color can be assigned.

### DNA Explorer This tab contains information about the DNA around the nucleosomes of the fiber loaded into the application. Through this tab, every piece of DNA (excluding `Linker DNA`) can be assigned a custom color.

### Linker DNA Explorer This tab contains information about the Linker DNA of the fiber loaded into the application. Through this tab, every piece of Linker DNA can be assigned a custom color.

### Cohesin/CTCF Explorer Similarly to the other explorer tabs, this tab contains information about the `Cohesin` / `CTCF` of the fiber loaded into the application. Through this tab, every `Cohesin` / `CTCF` element can be assigned a custom color.

### Tool: Color Gradient This tool allows coloring every bead of the fiber that is currently loaded into the application in a gradient based on two colors. Additionally, you can set the beginning bead id and the end bead id, which determines, which beads will be included in coloring. The same applies to the type of bead to be colored, where the different available types can be included or excluded.","front_matter":{},"format":"markdown","uploads_path":"https://gitlab.com/api/v4/projects/32582741/wikis/attachments","slug":"howto/Tabs","path":"/wedemann-group/chromatin3d-visualizer/-/wikis/howto/Tabs","wiki_path":"/wedemann-group/chromatin3d-visualizer/-/wikis/home","help_path":"/help/user/project/wiki/_index.md","markdown_help_path":"/help/user/markdown.md","markdown_preview_path":"/wedemann-group/chromatin3d-visualizer/-/wikis/howto/Tabs/preview_markdown","create_path":"/wedemann-group/chromatin3d-visualizer/-/wikis"}