CellDesigner Help

Edit the contents of Species (The Change identity of the species dialog)

As for the Species, to modify symbolic type and name, homodimer value and to decorate to the protein residue etc., the special modification dialogue is utilized. .

To edit the property of SpeciesAlias

  1. Select a SpeciesAlias.
  2. Select Component - Change Identity menu.
  3. or right-click on a Species, then select Change Identity menu.
  4. If Residues Caution message pops up, select Close or click Never show this button.

  5. Change identity of the species dialog will appear.

Description on each property


Pull-down to modify class symbolic type.
* The below-mentioned residues menu becomes available only when "PROTEIN" is selected here.


Click the radio button when the Species is hypothetical (something in regard to imagination).
When this is being selected, the shape of the Species remain the same, but the external line is modified from the solid line to the dotted line.


Input, or modifies name of the Species.

When PROTEIN is selected as above-mentioned class, here it is not possible to input name.
This is because CellDesigner uses the name of Species to the Protein name.


Specify optional numerical value to "homomultimer". This can be specified regardless if the target is protein or non protein.


* The following items can only be available when the PROTEIN is selected with the above-mentioned class.


The top item "protein" is pull-down menu to specify the type of the protein.
The type displayed here is the current selection of the target Species.
From here, it is possible to change the protein type referred by this SpeciesAlias.


Note: You cannot edit the name and the class of the protein from here.
To change the name, class of the protein, you should go to the Protein list window to edit the properties.


To add new residue to the protein:

1. Select Add button.
The ModificationResidue/BindingRegion dialog will popup.

2. Input the name (e.g. Thrxx), Specify the side and the angle.
3. Select Close when you finish editing.
See Also: "Create a Modification Residue/Region" for more details on the Protein residue.

To change the residue state:

1. Select the target residue (circle) in the preview window.
2. Select the appropriate residue state from the modification pull down menu.
The changes are reflected in the preview window.


To change the protein state:

1. Select the appropriate protein state from the state pull down menu.
The changes are reflected in the preview window.


To change the protein state:

1. Select user defined text from the state pull down menu.
2. Input state to text input field.
3. The changes are reflected in the preview window.


In case of editing an Existing Protein

When you select the existing protein from the pull-down menu here, name, class of that protein will be displayed in the following section.

If the referred protein has the residues, they will be displayed in the below preview window as the circular sign and the name associated with them. You can change the residue state.
If the protein referred to has no residues, the items for the residues cannot be edited from here.

In case of creating New Protein

When you select New Protein from pull-down here, new protein is created which does not exist in <Protein> list.
On creation of new protein, you can set the modification states in this dialog simultaneously.
Moreover, attributes such as name, class and the residue etc. of that protein can be compiled freely.
Be careful, however, when you specify the name, not to overlap with the existing proteins.

The reason why you cannot edit name or class, or residues in this Change Identity of the Species dialog is that the dialog is designed to edit the Species identity, and the identification of the Species here is judged by the modification states of the protein residue.
If you edit both Protein (referred-to) and Species (referrd-by) in the same dialog, there will be no distinctions identified between the Protein and Species by comparing the protein modification status. Thus there would be some conflicts among the SpeciesAliases and Species of no distinction.
To avoid such complicated situation, CellDesigner adopts this specification to separate the dialogs to edit the protein residues and the general attributes of the Species.

However, in case of creating a new protein, CellDesigner can guarantee there will be no such existing Species that refer to the newly created protein, CellDesigner allows the user to edit the protein properties freely in the Change Identity of the Species dialog.

3. When all the editing is completed, press "Apply" button.
All the modifications specified in the dialog is now reflected on the logical structure of the model and the network diagram on screen.

* If there is any other alias which refers to the same Species in the model, the message box will prompted to confirm if you want to reflect the modifications specified here to all the aliases.
Click Yes to reflect the changes to the target SpeciesAlias only. As a result, it will become a new alias which point to another Species different from the original one.

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