中国物理B ›› 2010, Vol. 19 ›› Issue (9): 96101-096101.doi: 10.1088/1674-1056/19/9/096101

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Combining SAD/SIR iteration and MR iteration in partial-model extension of proteins

武丽杰1, 古元新1, 郑朝德1, 范海福1, 张涛2   

  1. (1)Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; (2)Research Institute of Magnetic Materials, School of Physical Sciences and Technology, Lanzhou University, Lanzhou 730000, China; Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
  • 收稿日期:2010-04-28 修回日期:2010-05-21 出版日期:2010-09-15 发布日期:2010-09-15
  • 基金资助:
    Work supported by the Innovation Project of the Chinese Academy of Sciences and by the National Basic Research Program of China (Grant No. 2002CB713801).

Combining SAD/SIR iteration and MR iteration in partial-model extension of proteins

Zhang Tao(张涛)a)b)*, Wu Li-Jie(武丽杰)b)*, Gu Yuan-Xin(古元新)b)†, Zheng Chao-De(郑朝德)b), and Fan Hai-Fu(范海福)b)‡   

  1. a Research Institute of Magnetic Materials, School of Physical Sciences and Technology, Lanzhou University, Lanzhou 730000, China; b Beijing National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
  • Received:2010-04-28 Revised:2010-05-21 Online:2010-09-15 Published:2010-09-15
  • Supported by:
    Work supported by the Innovation Project of the Chinese Academy of Sciences and by the National Basic Research Program of China (Grant No. 2002CB713801).

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摘要： There are two kinds of dual-space partial-model extensions which involve the direct-method program OASIS. The first kind, named SAD/SIR iteration, uses SAD/SIR information, while the second kind, named molecular replacement (MR) iteration, does not use that information. In general, the SAD/SIR iteration is more powerful since more experimental information is used. However, in most cases when protein structures are solved with the molecular replacement method, SAD/SIR information is not available. Thus the MR iteration is particularly useful for the completion of models from molecular replacement. The SAD/SIR iteration will be automatically used in OASIS for data sets containing SAD/SIR signals, while the MR iteration will be dedicated to data sets without SAD/SIR signals. The present paper shows that for data containing SAD/SIR signals, a combination of SAD/SIR iteration and MR iteration could lead to significantly better results than that obtained from the SAD/SIR iteration alone.

Abstract: There are two kinds of dual-space partial-model extensions which involve the direct-method program OASIS. The first kind, named SAD/SIR iteration, uses SAD/SIR information, while the second kind, named molecular replacement (MR) iteration, does not use that information. In general, the SAD/SIR iteration is more powerful since more experimental information is used. However, in most cases when protein structures are solved with the molecular replacement method, SAD/SIR information is not available. Thus the MR iteration is particularly useful for the completion of models from molecular replacement. The SAD/SIR iteration will be automatically used in OASIS for data sets containing SAD/SIR signals, while the MR iteration will be dedicated to data sets without SAD/SIR signals. The present paper shows that for data containing SAD/SIR signals, a combination of SAD/SIR iteration and MR iteration could lead to significantly better results than that obtained from the SAD/SIR iteration alone.

Key words: OASIS, dual-space phasing, model completion, proteins

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  • 6110M