Practical structure solution with ARCIMBOLDO.
Practical structure solution with ARCIMBOLDO.
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DOI：
10.1107/s0907444911056071
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发表时间：
2012-04
期刊：
影响因子：
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通讯作者：
Usón I
中科院分区：
文献类型：
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作者：
Rodríguez D;Sammito M;Meindl K;de Ilarduya IM;Potratz M;Sheldrick GM;Usón I
ARCIMBOLDO将小碎片的位置与Phaser相结合，并将所有可能的Phaser解决方案的密度修改与SHELXE相结合。通过实际的测试案例对其使用进行了解释和说明。自2009年9月发布以来，结构求解程序ARCIMBOLDO基于多溶液框架中定位小模型片段（如聚丙氨酸α-螺旋）的密度修改与程序SHELXE相结合，已经发展到包含其他立体化学或实验信息来源。可以通过在主链上模拟侧链或从低同源模型中提取侧链来提出比普遍存在的主链α-螺旋更复杂的片段，因为即使传统的分子替代方法失败，它们的局部结构也可能与未知的结构足够相似。在这种情况下，程序可以针对指定的优点并行测试一组可选模型，并继续进行选定的模型。实验信息可以通过三种方式进行整合：在ARCIMBOLDO中搜索针对异常差异或MAD数据的异常片段，或者在使用其他程序（如SHELXD）确定异常子结构或随后位于从部分片段阶段计算的异常傅立叶图中时查找模型片段。在扩展过程中，这两种信息来源可以结合在一起。在所有这些情况下，关键是控制工作流，以最大限度地提高成功的机会，同时避免创建难以处理的并行进程数量。已经实现了GUI，以帮助在各种典型场景中设置合适的策略。在目前的工作中，通过分布式测试用例描述了ARCIMBOLDO在这些场景中的实际应用。
ARCIMBOLDO combines the location of small fragments with Phaser and density modification with SHELXE of all possible Phaser solutions. Its uses are explained and illustrated through practical test cases. Since its release in September 2009, the structure-solution program ARCIMBOLDO, based on the combination of locating small model fragments such as polyalanine α-helices with density modification with the program SHELXE in a multisolution frame, has evolved to incorporate other sources of stereochemical or experimental information. Fragments that are more sophisticated than the ubiquitous main-chain α-helix can be proposed by modelling side chains onto the main chain or extracted from low-homology models, as locally their structure may be similar enough to the unknown one even if the conventional molecular-replacement approach has been unsuccessful. In such cases, the program may test a set of alternative models in parallel against a specified figure of merit and proceed with the selected one(s). Experimental information can be incorporated in three ways: searching within ARCIMBOLDO for an anomalous fragment against anomalous differences or MAD data or finding model fragments when an anomalous substructure has been determined with another program such as SHELXD or is subsequently located in the anomalous Fourier map calculated from the partial fragment phases. Both sources of information may be combined in the expansion process. In all these cases the key is to control the workflow to maximize the chances of success whilst avoiding the creation of an intractable number of parallel processes. A GUI has been implemented to aid the setup of suitable strategies within the various typical scenarios. In the present work, the practical application of ARCIMBOLDO within each of these scenarios is described through the distributed test cases.