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chimerax.qmd
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# `ChimeraX` {#sec-ChimeraX .numbered}
`ChimeraX` is a widely-used, open source software package for macromolecular visualisation and analysis. It is free for academic, government, nonprofit, and personal users.
## Where can I download `ChimeraX`?
`ChimeraX` is available for download from the UC San Francisco website.
- [https://www.cgl.ucsf.edu/chimerax/download.html](https://www.cgl.ucsf.edu/chimerax/download.html)
## How do I use `ChimeraX`?
Once installed on your machine, use the `ChimeraX` application icon to start the program. You will be greeted by the standard `ChimeraX` landing screen (@fig-chimerax_landing).
{#fig-chimerax_landing width=75%}
### `ChimeraX` layout
The `ChimeraX` screen is divided into four main areas.
- Along the top of the window is a **ribbon** of icons, and a list of category buttons. Choosing buttons changes the icon/action set.
- Along the bottom of the screen is a **command line interface**, where commands can be entered to control `ChimeraX`.
- On the right hand side is the **log window** which provides useful information and outputs. This can be toggled on and off with the leftmost button at the bottom right-hand corner (or by entering the `ui windowfill toggle` command in the command line interface).
- The largest part of the screen is the **main visualisation window**, and this can be expanded to fill the full screen width by toggling the log window off.
::: {.callout-tip}
The **log window** updates with the equivalent command when icons or buttons are used. This is a useful way to learn commands for scripting `ChimeraX`.
:::
## Loading a structure
Once you have downloaded a structure from [RCSB/PDB](https://www.rcsb.org/), there are three ways to load it into `ChimeraX`.
1. Click on the `Open` icon in the **`Home` ribbon**, and use the file dialogue to select your file.
2. Use `File -> Open` in the menu bar (or Cmd-O) to bring up the file dialogue box to select your file.
3. Enter `open [PATH TO FILE]` in the **command line interface**, specifying the file you want to open.
Once the file is loaded, you will be presented with the default view, and information in the **log window** (@fig-chimerax_load). The model will also be visible in the window at the lower right of the screen.
{#fig-chimerax_load width=75%}
## Changing the appearance of the structure.
### Switching from cartoons to atoms
By default, `ChimeraX` presents a **cartoon view** of the loaded model. In the `Home` riboon, you can use the `Show` and `Hide` `Cartoons` icons to show or hide this representation, and the `Show` and `Hide` `Atoms` icons to show or hide an atom-level representation (e.g. @fig-chimerax_atoms).
::: {.callout-tip collapse="true"}
## Change from _cartoon_ to _atoms_ representation.
1. Click on `Show Atoms`
2. Click on `Hide Cartoons`
_or_ in the command line interface, enter
```text
show atoms
hide cartoons
```
:::
{#fig-chimerax_atoms width=75%}
### Changing atoms representation
The `Home` ribbon provides icons that allow switching between _ball and stick_, _space-filling_/_sphere_ (@fig-chimerax_sphere), and _stick_ representations of the atomic structure.
::: {.callout-tip collapse="true"}
## Command-line equivalents
```text
style stick
style sphere
style ball
```
:::
{#fig-chimerax_sphere width=75%}
### Changing molecule representation
The **`Molecule Display` ribbon** allows you to control the colouring and other visualisation features for the model. Clicking on the `chain` icon will colour each chain in the model differently, to help visually resolve the overall quaternary structure (@fig-chimerax_chains).
{#fig-chimerax_chains width=75%}
## Visualising Sequence Conservation
If you have a sequence alignment including the sequence of the protein(s) in your structure, then you can automatically render your model with residues coloured by the extent of sequence conservation.
### Requirements
- A structure that includes your protein of interest
- A multiple sequence alignment including your protein of interest
::: { .callout-warning }
## Your sequence alignment must meet these criteria
- The sequence corresponding to your protein **must** be the first sequence in the alignment.
- Your alignment **must** be in `CLUSTAL` format.
:::
### Loading the alignment data
The sequence alignment can be loaded using the standard `File -> Open` menu option (@fig-chimerax_open).
{#fig-chimerax_open width=75%}
Once the file dialogue opens, select the sequence alignment file and click the `Open` button (@fig-chimerax_file_dialog).
{#fig-chimerax_file_dialog width=75%}
This will open the **Sequence Viewer Window** to display your multiple sequence alignment, with a histogram of sequence conservation at the top (@fig-chimerax_sequence_viewer). The sequence associated with your protein model will be highlighted.
{#fig-chimerax_sequence_viewer width=75%}
### Visualising sequence conservation
`ChimeraX` associates the sequence conservation, as represented in the histogram in the **Sequence Viewer Window**, with a _variable_ called `seq_conservation`. `ChimeraX` can use this to change the representation of the protein model by assigning the variable to some attribute, such as `color` (for rendered colour).
We can change this attribute using the **command line interface**, by entering the command `color byattr seq_conservation` (@fig-chimerax_color_conservation_1).
{#fig-chimerax_color_conservation_1 width=75%}
This results, by default, in colouring _conserved_ sites in red (the more intense the hue, the more conserved the site), and the _variable_ sites in blue (again, the more intense the hue, the more variable the site). It can be helpful to change the model representation from space-filling _sphere_ to _cartoon_ or similar, so that the interior of the protein can be seen more clearly (@fig-chimerax_color_conservation_2).
{#fig-chimerax_color_conservation_2 width=75%}
### Selectively visualising conserved sites
We can select sites in the model by attributes, such as sequence conservation, using the `select` command. For example, to select all sites with a conservation score above 0.5 (i.e. the more conserved sites) we would use `select ::seq_conservation > 0.5` (@fig-chimerax_sel_cons).
{#fig-chimerax_sel_cons width=75%}
Executing this command will select only the sites with a sequence conservation score above 0.5, and highlight them on the current visualisation with a green outline (@fig-chimerax_sel_cons_hlt).
{#fig-chimerax_sel_cons_hlt width=75%}
With only these sites selected, we can show the atom representations for only these sites by clicking on the `Show Atoms` icon, or using the command `show sel atoms`. In (@fig-chimerax_sel_cons_spc) this represents those sites as space-filling spheres.
{#fig-chimerax_sel_cons_spc width=75%}
We can then colour the model by sequence conservation as before with `color byattr seq_conservation`, then select only the _low conservation_ sites with the commmand `select ::seq_conservation < 0.5`, and recolour them by chain (`color sel bychain`), to obtain the image in @fig-chimerax_cons_on_cartoon, where the protein chains are coloured differently, but highly-conserved residues are indicated in red and space-filling form.
{#fig-chimerax_cons_on_cartoon width=75%}