CellDesigner Help

All the proteins in a model can be checked in the "Proteins" list window.

ID of each Protein is allocated automatically by CellDesigner.
The name is attached in accordance with the input when you create the SpeciesAlias.

To edit the contents of the protein:

1. Double click the item in the Proteins tab in the List area.
2. Or, in the Draw area, click the Protein with the right mouse button, then select Edit Protein menu.
3. The Protein dialog appears.

Note: You can edit some of the items directly inline on the list.
If you click on the item which cannot be edited inline, a dialog will pop-up.

4. 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 class.
   residues/regions	When you click add... button, the circle symbol which represent a residue will display 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.

5. Close the subdialog by pressing Close button.
6. The residues added here can be directly dragged and arranged in the preview window.
7. When you finish editing, click [Update] button in the dialog.
8. The edited data will be updated to the model.
9. Close the dialog when you have finished editing the protein.

Note: 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.

Note: When you finish editing the protein, the data of all the SpeciesAlias which refer to the protein will be updated.

To edit the residues already added:

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

To delete the residue:

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

Caution: The name of the protein can be changed at any time. However, you cannot use the same name already specified to other protein. This is due to the fact that CellDesigner identify the proteins by name. Please refer to the Modeling Guide for details.

Caution: 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.