Hello Hamid,
You are quite correct that the formulas in PD 5500 do not include a joint efficiency factor for pressure parts. If you enter these values, they will not be used to determine required thickness for internal pressure.
The exception is the skirt to shell weld. Since this weld is not fully "X-ray able", its efficiency will be less than one and the appropriate efficiency should be entered into the circumferential field.
A benefit to being able to enter these values for 5500 is that when the Code is switched, this data may be used for another Code, like ASME VIII-1 for example.
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Scott MayeuxCADWorx & Analysis Solutions
Intergraph Process, Power, & Marine