The abbey church was a structure of great size and of beautiful architecture. It consisted of the usual divisions, having nave, choir, and transepts, with aisles and probably a lady chapel to the east, two western towers, and a tower over the crossing. But of all that splendid structure there now only remain the ruins of the nave and one western tower. The abbey and palace were frequently attacked and burnt by the English, particularly under Hertford in 1544, and the abbey was again destroyed by Somerset in 1547. At the latter date the monks had left the abbey, and the invaders stripped the lead off the roofs of the buildings. These “visitations” seem to have led to the serious injury of the choir; but the choir and transept do not appear to have been completely ruined till after 1569. At that date, Adam, Bishop of Orkney and Commendator of Holyrood, stated to the General Assembly that “the Abbay Church of Halyrud house hath been these 20 years bygane ruinous, through decay of two principall pillars, so that none were assured under it ... he purposed to provide the means that the superfluous ruinous parts to wit the Queir and Croce Kirk might be disponed to faithfull men to repair the remanent sufficiently.”[33] The bishop’s proposal was apparently carried out, and the materials of the choir and transept were demolished and sold “to provide funds for converting the nave into the Parish Kirk of the Canongate.” The two pillars referred to by the bishop as unsafe were probably the east pillars of the crossing, which are now removed, but the two west pillars still stand. They form the east end of the existing nave. Sir D. Wilson believes that, when the choir was taken down, the vault which contained the remains of the kings and queens of Scotland was built in the south-east angle of the nave, and their coffins transferred into it. Holyrood Palace was the principal residence in Scotland of James VI. and Charles I. The latter took considerable interest in the church, and wished to restore it as the chapel royal. He had the west end re-edified, as the style of the architecture of the upper portion and the inscriptions thereon bear witness.