Controller assisted reconfiguration of an articulated instrument during movement into and out of an entry guide

A medical robotic system comprising:

• an entry guide;
• an articulated instrument having a distal tip extending out of the entry guide;
• and
• a processor;
• the medical robotic system being programmed such that:
• when the medical robotic system is operating in a retraction mode and in response to a user-commanded translational movement of the articulated instrument in a retraction direction into the entry guide, the processor automatically commands one or more rotational joints of the articulated instrument to be rotated from a deployed state, in which the articulated instrument is not fully retractable into the entry guide, to an entry state of the one or more rotational joints, in which the articulated instrument is fully retractable into the entry guide;
• and
• when the medical robotic system is operating in a surgical mode and in response to a user-commanded input to surgically manipulate the articulated instrument, the processor commands one or more of the rotational joints of the articulated instrument to position the distal tip of the articulated instrument to perform a surgical operation.