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The window for complex editing
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graphical layout window section
This window section shows the graphical layout of the current complex.
The next section describes how to change molecule component states and binding site status through right mouse click.
Mouseover the graphical items may display its name(s) and/or state/status as tooltips.
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Molecule component
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Molecule component state tag
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Binding site status
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Complex molecule component tag states and binding status window section
This window section displays the complex hiearchy structure and the molecule component state and binding status information. The first column contains the complex structure information, including the names of each molecule component state tag or the binding site name. The second column contains the state of each molecule component tag : "
On", "Off", or "Don't Care" and the binding status of each binding site: "Bound", "Unbound" or "Don't Care". To make a change, the user can double click the state/status and activate a dropdown menu. Once the status is changed, the corresponding tag will be updated in the graphical layout window section.Or, the user may use mouse right click on the tag/binding site in the graphical view window section.
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Property window section
The properties of a complex include:
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"
Complex Name"Similar to the
short name of a molecule. -
"
Species Name"The
short nameof the related complex species. -
"
Annotation"Similar to the
annotation in the molecule property window section. -
"
Display in Complex List" checkbox.Specify whether the complex should be displayed in complex lists. See "
Display Hidden Complexes" in the model summary page.
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Relations" side window section
This window section is similar to the "
Relations" side window section in the complex species editing window, except that the content of the list is based on the current complex, rather than a complex species. -
Control buttons
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"
Save" buttonWhen this button is clicked, the modeler application saves the data of the current complex to the model file.
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"
Back" buttonWhen this button is clicked, the modeler application goes back to the previous window.
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"
Delete" buttonThis button is provided here for convenience. It has the same functionality as the "
Delete" button in the complex side window section when a complex is highlighted.
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Start
Click "
New" button in the "Relations" window section of the complex species editing window. -
Change state of a molecule component tag, change status of a binding site
The user can change the state of a molecule component tag or the status of a binding site in the
complex molecule component tag states and binding status window section. The modeler application will check if there is a complex with the same complex species, molecule component tag states and binding status defined before. If so, it will load it from the model file. -
Edit properties
The user can change the properties in the
property window section. -
Save data
Click the "
Save". -
Load a complex for editing
The user can load an existing complex:
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From the "
Complexes" side window section in the complex species editing window, double-click a complex, or highligh a complex and click the "View" button. -
From the "
Relations" side window section int the complex species editing window, double-click a complex, or highlight a complex and click the "View" button. -
From the
model summary window, double-click a complex.
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