A robotic system includes a master device and a slave manipulator configured to support an instrument. The instrument includes an instrument shaft having a proximal end and a distal end, and an end effector coupled to the distal end. The instrument shaft is optionally configured to be inserted into an inserted position through a port so as to provide the end effector with access to a site. A control system is operably coupled to the master device and to the slave manipulator. In response to input at the master device, the control system controls the slave manipulator to move the instrument based on modeling the end effector as being positioned along a line coincident with a longitudinal axis of the distal end of the instrument shaft. The line does not intersect the port when the instrument shaft is in the inserted position through the port. Methods relate to robotic systems.
