Title: Using Partial Structure R1 to Do Molecular Replacement Calculations Show Chinese title

Title: 使用部分结构R1进行分子置换计算

Abstract: The concept of partial structure R1 (pR1) is a generalization of the concept of single atom R1 (sR1) (Zhang & Donahue, 2024). The hypothesis is that the deepest hole of a pR1 map determines the orientation and location of a missing fragment. In current implementation, the calculation is divided into two steps. The first step is to detect possible orientations of all missing fragments by the holes of a pR1 map of a free-standing fragment in a 3-dimensional orientation space. The second step is to determine the orientation and location of a missing fragment. To this end, if done strictly, all the candidate orientations are tried. With each candidate orientation, the best choice of location of the missing fragment is determined by the deepest hole of a pR1 map in a 3-dimensional location space. This best choice is combined with the trial orientation to form one candidate orientation-location. After trying all candidate orientations, a list of candidate orientation-locations are formed, from which, the one with the lowest R1 determines the orientation and location of a missing fragment. Then a newer pR1 is defined by including the atoms of this newly determined fragment into the known atoms. This newer pR1 is used to determine the next missing fragment in the same way. To shorten the calculation time, the possible locations of all missing fragments can be predicted by the holes of a pR1 map of a completely disoriented model of a fragment. All these ideas of using pR1 to do molecular replacement calculations have been demonstrated by four example data sets. Show Chinese abstract

Abstract: 部分结构R1（pR1）的概念是对单原子R1（sR1）概念的推广（Zhang & Donahue, 2024）。 假设是，pR1图中的最深空穴决定了缺失片段的方向和位置。 在当前的实现中，计算分为两个步骤。 第一步是通过自由存在的片段的pR1图中的空穴，在三维方向空间中检测所有缺失片段的可能方向。 第二步是确定缺失片段的方向和位置。 为此，如果严格进行，所有的候选方向都会被尝试。 对于每个候选方向，通过三维位置空间中pR1图的最深空穴确定缺失片段的最佳位置。 这个最佳位置与试验方向结合，形成一个候选方向-位置。 在尝试所有候选方向后，会生成一个候选方向-位置列表，其中R1最低的那个确定缺失片段的方向和位置。 然后通过将新确定的片段的原子包含到已知原子中来定义一个新的pR1。 这个新的pR1以同样的方式用于确定下一个缺失片段。 为了缩短计算时间，可以通过片段完全无取向模型的pR1图中的空穴预测所有缺失片段的可能位置。 所有使用pR1进行分子替换计算的想法已经通过四个示例数据集得到了验证。