A surgical robotic system comprising: a surgical instrument having a proximal end, a distal end effector suitable for insertion into a patient, an intermediate portion therebetween, and an instrument shaft (14.1) between the end effector and the proximal end; a manipulator configured to support the proximal end of the instrument so as to move the instrument from outside the patient; the manipulator and instrument having a plurality of driven joints, the joints being configured to provide sufficient degrees of freedom to allow a range of joint states for an end effector state while the intermediate portion and instrument shaft (14.1) passes through an access site; an input configured to receive a movement command to effect a desired movement of the end effector within a surgical workspace; and a processor coupling the input to the manipulator, the processor being configured to: calculate movements of the driven joints in response to the commanded movement so that the intermediate portion of the instrument is within the access site and so as to move the end effector with the desired movement by pivoting the instrument about a pivotal center of the instrument, and determine a desired location of the pivotal center adjacent the access site, wherein the calculated movement of the driven joints moves the pivotal center of the instrument towards the desired location of the pivotal center when the access site moves and achieves controlled movement of the pivotal center with the processor. a surgical instrument having a proximal end, a distal end effector suitable for insertion into a patient, an intermediate portion therebetween, and an instrument shaft (14.1) between the end effector and the proximal end; a manipulator configured to support the proximal end of the instrument so as to move the instrument from outside the patient; the manipulator and instrument having a plurality of driven joints, the joints being configured to provide sufficient degrees of freedom to allow a range of joint states for an end effector state while the intermediate portion and instrument shaft (14.1) passes through an access site; an input configured to receive a movement command to effect a desired movement of the end effector within a surgical workspace; and a processor coupling the input to the manipulator, the processor being configured to: calculate movements of the driven joints in response to the commanded movement so that the intermediate portion of the instrument is within the access site and so as to move the end effector with the desired movement by pivoting the instrument about a pivotal center of the instrument, and determine a desired location of the pivotal center adjacent the access site, wherein the calculated movement of the driven joints moves the pivotal center of the instrument towards the desired location of the pivotal center when the access site moves and achieves controlled movement of the pivotal center with the processor. calculate movements of the driven joints in response to the commanded movement so that the intermediate portion of the instrument is within the access site and so as to move the end effector with the desired movement by pivoting the instrument about a pivotal center of the instrument, and determine a desired location of the pivotal center adjacent the access site, wherein the calculated movement of the driven joints moves the pivotal center of the instrument towards the desired location of the pivotal center when the access site moves and achieves controlled movement of the pivotal center with the processor.