OASIS and molecular-replacement model completion
OASIS and molecular-replacement model completion
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DOI：
10.1107/s0907444907023451
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发表时间：
2007-07-01
影响因子：
2.2
通讯作者：
Fan, Hai-Fu
中科院分区：
文献类型：
--
作者：
He, Yao;Yao, De-Qiang;Fan, Hai-Fu
提出了一种基于ARP/wARP、REFMAC、OASIS和DM程序的双空间分子置换模型补全方法，在ARP/wARP建立的模型的基础上，利用OASIS在互易空间进行相位细化。为此，重新定义了打破SAD/SIR相位模糊的直接方法概率公式。在相位细化时，表达式phi(h)中的phi(h) = phi(h) +/-竖条Delta phi(h)竖条被重新定义为从当前结构模型中随机选择5%的原子计算得出的参考相位，而竖条Delta phi(h)竖条被定义为当前模型的相位与phi(h)的绝对差值。概率公式P (+)(Delta phi(h))= 1/2 + 1/2 tanh {sin竖条Delta phi(h)竖条x [Sigma(h)m(h)m(h) - (h ')kappa(h,h ') sin (phi(3)' + Delta phi(h ' best) + Delta phi(h-h ' best)) + chi sin Delta (h)]}然后用于推导Delta phi(h)的符号。这样，‘0-2 ’相位问题就简化为‘正负’符号问题。重新定义意味着，在细化阶段，接近真实值的值可能保持不变，而远离真实值的值可能会发生很大的变化。这是相细化所需要的特性。该程序已测试使用蛋白衍射数据没有SAD/SIR信号。结果表明，使用OASIS的双空间mr模型完井比不使用OASIS的效率要高得多。
A method of dual-space molecular-replacement model completion has been proposed which involves the programs ARP/wARP, REFMAC, OASIS and DM. OASIS is used in reciprocal space for phase refinement based on models built by ARP/wARP. For this purpose, the direct-method probability formula of breaking SAD/SIR phase ambiguities has been redefined. During the phase refinement, phi(h)'' in the expression phi(h)'' = phi(h)''+/-vertical bar Delta phi(h)vertical bar is redefined as a reference phase calculated from a randomly selected 5% of the atoms in the current structure model, while vertical bar Delta phi(h)vertical bar is defined as the absolute difference between the phase of the current model and phi(h)''. The probability formula P (+)(Delta phi(h))= 1/2 + 1/2 tanh {sin vertical bar Delta phi(h)vertical bar x [Sigma(h)m(h)m(h) - (h ')kappa(h,h ') sin (Phi(3)' + Delta phi(h ' best) + Delta phi(h-h ' best)) + chi sin delta(h)]} is then used to derive the sign of Delta phi(h). In this way the '0-2 pi' phase problem is reduced to a 'plus or minus' sign problem. The redefinition implies that during the refinement phases close to the true values will probably be kept unchanged, while those distant from the true values will probably undergo a large shift. This is the desired property of phase refinement. The procedure has been tested using protein diffraction data without SAD/SIR signals. The results show that dual-space MR-model completion making use of OASIS is much more efficient than that without.