 | Acta Crystallographica Section A Acta Crystallographica Section A FOUNDATIONS AND ADVANCES |
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![[Figure 7]](ae5140fig7mag.jpg)
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Figure 7
A general flowchart of applying the sR1 method for solving an unknown structure. Step 1: the starting model, which is either a single atom that is arbitrarily positioned, or a known fragment that is also arbitrarily positioned but is correctly oriented by pR1 of a free-standing fragment. After defining a new sR1 the calculation moves on to step 2: set up a grid within the cell with step size 0.4 Å. Note that whenever defining a new sR1 the known model up to that point is used. Step 3: discover sR1 holes. A grid point (colored blue) with an sR1 value smaller than all its six neighbors (colored red) marks an sR1 hole. Step 4: use a local grid with halved step size to refine the location of the sR1 holes. The local grid point with the lowest sR1 is accepted as the improved location of the hole. After repeating step 4 one more time, the 5N of the deepest holes are adopted as the candidate locations; here N is the number of atoms expected in the unit cell. Step 5: locate atom j. First, the candidate locations are filtered by applying rules excluding ghost atoms. The filtered candidate locations are shown as colored balls. Calculate sR1 over these candidate locations and assign the one (colored blue) with the smallest sR1 to atom j. The precision of this location is refined to 0.001 Å. After defining the new sR1 repeat step 5. In total, step 5 is executed Ni times. Note that Ni represents one number from a set of N1, N2, N3, …, and this set constitutes a calculation strategy. For example, for sample 3, the set of Ni's is 9, 20, 50, 76. Note that N1 + N2 + N3 + … = N − N0, where N0 is the number of atoms in the starting model. After finishing Ni cycles of step 5, with a newly defined sR1, the calculation goes back to steps 2, 3, 4, then executes the next Ni cycles of step 5. Repeat this until all Ni's in the set N1, N2, N3, …, are finished. At that point, one reaches step 6: the tentative full model. With the user's help to delete ghost atoms, one moves on to step 7: the intermediate partial model. After defining a new sR1, the calculation goes back to steps 2, 3, 4, and then repeats step 5 for certain cycles, and then goes back to step 2 again etc., until a new tentative solution is produced. If the new tentative solution still has many ghost atoms, the above calculations will again be repeated. Once the new tentative solution has high quality, one reaches step 8: the final model. |
![[Figure 7]](ae5140fig7.jpg)
| FOUNDATIONS ADVANCES |
ISSN: 2053-2733
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