CellDesigner Help

The Protein Dialog (Gene|RNA|Antisense RNA Dialog)

If you are working on a Gene/RNA/Antisense RNA, replace the word "Protein" with "Gene/RNA/Antisense RNA" as you read through.

All the Proteins in a model can be viewed in the Proteins list in the List Area.
ID of each Protein is automatically assigned by CellDesigner.
The name has been given when you created the SpeciesAlias for the Protein.
The name of a Protein can be changed at any time.

In the Protein dialog, however, you cannot change the name to the one already given to another Protein. This is due to the fact that CellDesigner identifies a Protein by its name. Please refer to the Modeling Guide for details.
In order to change a Protein name to the one already given to another Protein, use the Change identity of the species dialog. As a result, these two Proteins will become one. Although there seem to be two Proteins on Canvas, or two SpeciesAliases, they are one Species.

If you are working on a Gene/RNA/Antisense RNA, replace the word "Protein" with "Gene/RNA/Antisense RNA" as you read through.

To open the Protein dialog

Select a Protein.
Do one of the followings:

In the List Area, click Proteins tab, select the Protein to which you want to add the residue, and click Edit button.
Click the right mouse button on the target Protein, then select Edit Protein menu.

Protein dialog will pop-up.

To edit the contents of the Protein

Double-click the item in the Proteins list in the List Area.
Or, in the Draw Area, click the Protein with the right mouse button, then select Edit Protein menu.
The Protein dialog appears.

You can edit some of the properties directly inline in the list.
If you double-click on the property which cannot be edited inline, the Protein dialog will pop-up.

Edit the data.

name

Edit the name of the Protein.

type

Specify the type of the Protein. Select from GENERIC, RECEPTOR, ION_CHANNEL, TRUNCATED. The shape will be changed automatically in accordance with the change of the type.

residues/regions

When you click add... button, the circle symbol which represents a residue will be added to the Protein in the preview window, and the sub-dialog ModificationResidue/BindingRegion will pop-up.

id	Assigned automatically.
name	Specify the name of the residue (3 letters + residue position number as specified in IUPAC Recommendations 1997)
type	Select residue or binding region. Selecting binding region changes the shape from a circle to a rectangle in the Protein dialog's preview window.
size	Enabled when the type is binding region. Used to change the width of the rectangle in the preview window.
side	Enabled when the type is residue. If the Protein is transmembrane, specify the position of the residue against the compartment.
angle	Specify the position of the residue in the Protein. move slide bar while viewing the position in the Protein dialog.

Close the subdialog by pressing Close button.
The residues added here can be directly dragged and arranged in the preview window.
When you finish editing, click Update button in the dialog.
The edited data will be updated in the model.
Close the dialog when you have finished editing the Protein.

If you want to continue to edit the other proteins, keep open the dialog. The data of the newly selected Protein will be displayed in the Protein dialog.

When you finish editing the Protein, the data of all the SpeciesAliases which refer to the Protein will be updated.

To edit the residues already added

In the Protein dialog, click the target residue or binding region, then click the edit.. button.
The ProteinModificationResidue/BindingRegion sub-dialog will pop-up.

To delete the residue

In the Protein dialog, select the target residue or binding region.
Click del.. button or press [Delete] key or [Backspace] key.

When you delete the residues or binding region of the Protein, all the list that the SpeciesAliases have will be shrunk according to the decreased number of the residues.
In result, there are some cases in which the Species once distinct becomes identical. For details, please check the Modeling Guide.