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If the project has a department as the project team, the rate associated with the department is either a Project Rate or Department Rate which is applied for all the users within that department. If you want to enable a Role/Rate or a User Rate just for one user or couple of users in that department and do not want the Project Rate or Department Rate to be associated with these users, you can add the user(s) individually to the Project Team and assign the Role or a User Rate to them.