Chemical crosslinking‐mass spectrometry (XL‐MS) is a valuable technique for gaining insights into protein structure and the organization of macromolecular complexes. XL‐MS data yield inter‐residue restraints that can be compared with high‐resolution structural data. Distances greater than the crosslinker spacer‐arm can reveal lowly populated “excited” states of proteins/protein assemblies, or crosslinks can be used as restraints to generate structural models in the absence of structural data. Despite increasing uptake of XL‐MS, there are few tools to enable rapid and facile mapping of XL‐MS data onto high‐resolution structures or structural models. PyXlinkViewer is a user‐friendly plugin for PyMOL v2 that maps intra‐protein, inter‐protein, and dead‐end crosslinks onto protein structures/models and automates the calculation of inter‐residue distances for the detected crosslinks. This enables rapid visualization of XL‐MS data, assessment of whether a set of detected crosslinks is congruent with structural data, and easy production of high‐quality images for publication.

中文翻译：

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PyXlinkViewer：一种灵活的工具，用于在 PyMOL 分子图形系统中可视化蛋白质化学交联数据。

化学交联质谱 (XL-MS) 是深入了解蛋白质结构和大分子复合物组织的重要技术。XL-MS 数据产生可与高分辨率结构数据进行比较的残留间限制。大于交联剂间隔臂的距离可以揭示蛋白质/蛋白质组装的低密度“激发”状态，或者在没有结构数据的情况下，交联可以用作生成结构模型的约束。尽管 XL-MS 的应用越来越多，但很少有工具能够将 XL-MS 数据快速轻松地映射到高分辨率结构或结构模型上。PyXlinkViewer 是 PyMOL v2 的用户友好插件，用于映射蛋白质内、蛋白质间、和末端交联到蛋白质结构/模型上，并自动计算检测到的交联的残基间距离。这可以快速可视化 XL-MS 数据，评估一组检测到的交联是否与结构数据一致，并轻松生成高质量的图像以供发表。