Using Partial Structure R1 to Do Molecular Replacement Calculations

TL;DR

This paper introduces a method using partial structure R1 maps to determine the orientation and position of missing molecular fragments, improving molecular replacement calculations through a two-step process and example demonstrations.

Contribution

It presents a novel approach that generalizes single atom R1 to partial structures, enabling efficient identification of missing fragments in molecular replacement.

Findings

Successfully applied to four data sets

Determines fragment orientation and location accurately

Reduces calculation time with predictive modeling

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.