To activate model functions, read a file with the "Model/Read model"
menu item or select the model tool (linked components icon). A new
window will open with settings for components and links.
- Model menu:
- Read model - reads a model of components and links from a file (STAR, PDB, CMM).
- Write model - writes a model to a file (STAR, PDB, CMM).
- Edit model - A primitive text editor to read and fix a model file.
- Delete all components - deletes all model elements in memory (no recovery!).
- Delete non-selected components - deletes components deselected by the FOM cutoff (no recovery!).
- Add or update component type - adds or changes a component type.
- Extract marked panels - extracts panels from multi-level masks marked by components.
- Generate particles - generates particles from the component locations.
- Help - activates on-line help.
- Parameters:
- Components - number of components and the selected subset.
- Links - number of links and the selected subset.
- Distance - between the last two components selected.
- Radiobuttons to display/hide components and labels, and set the display line width.
- Select - sets the selection according to pull-down list value.
- Component radius - sets the component radius to value.
- Link radius - sets the link radius to the value.
- Color - Sets the color according to the pull-down list value.
- FOM cutoff slider - selects components for display, non-selected componets can be deleted.
- Table of component types - used for selecting types.
Mouse controls:
- Left button: create a component
- Right button: create a link from the last selected component
- Shift - left button: delete a component
- Shift - right button: delete a link
Clicking the left mouse button in an empty region on the image creates
a new component. Clicking it close to a component will select that component.
Only one component is selected at any time. A component can be dragged within the xy
plane. To move a component up or down slices, use the "u" or "d" keys,
respectively.
To jump to the selected component, use the "s" key.
Clicking the right mouse button in an empty region creates a link
from the last selected component. If there is no component selected, nothing will
happen. Clicking close to an existing component creates a link from the last
selected component to that one.
To delete a component, hold down the shift key and click the left button
on the component. All links associated with the component will also be
deleted.
To delete a link, hold the shift key and click the right button close to the link.
Saving and reading models:
The model of components and links can be saved in a model file with the menu option
"Model/Write model" and read back with the menu option "Model/Read model
". The formats acceptable for models are a STAR format with model tags, molecular files and Chimera model files (cmm).