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While creating instruments method u have given gradient program but selected pump mode Isocratic..u should select pump mode as gradient....good tutorial
Gradient mode is actually refers to time program. meaning change of either mobile phase or flow rate. But in isocratic you still can select the ratio of more than 1 mobile phase but it will remain the same throughout the run.
If its a standalone Empower you need to manually backup the project as per your required frequency. For that open 'configure system'. Select the required project Right click select Backup and press next, select the destination / folder and click finish. it will start the backup process.
Its good to have database backup for disaster recovery but there is no proper script to backup database on standalone system. So project backup is enough.