view article

Figure 6
Positioning bases in density. (a) When placing bases into density, the nucleoside base is first approximated as a 5 Å vector, shown here in transparent gray. This vector is anchored at the C1′ candidate, which is shown as a cyan sphere. The vector is then replaced by a pyrimidine base, which may be computationally mutated to a purine if desired. To align the purine with the pyrimidine, the midpoint of the purine C4—C5 bond (yellow sphere) is aligned with the 5 Å vector. (b) When flipping a pyrimidine between anti and syn configurations, the base is rotated about the C1′ atom (cyan sphere) and the midpoint of the C4—C5 bond (yellow sphere). Flipping the base in this manner ensures that it is not moved out of the electron density.

Journal logoBIOLOGICAL
ISSN: 1399-0047
Follow Acta Cryst. D
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds