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Theses PDF data of paracetamol were collected on the XPDF beamline at Diamond. The structure of paracetamol can be found here.

Fitting without the use of a rigid body

1. Start a fresh PDF refinement using "para_100K_pdf.xy" as the filename (TOPASforPDF > 1. PDF data > Select PDF Data File) and in jEdit save the file as 'para_100K_without_rigid.inp'.

2. Enter a dQ damping with a value of 0.08 (TOPASforPDF > 2. Instrumental parameters > dQ damping).

3. Load structure from para.cif (TOPASforPDF > 3. Phase information > 3b. add new phase from CIF > i. Read a .CIF File).

4. Allow the lattice parameters to refine within the monoclinic symmetry (TOPASforPDF > 3. Phase information > 3b. add new phase from CIF > ii. constrain lattice parameters > convert to monoclinic).

5. Delete the beq 0.0789 for each atom, and instead add a beq_rcut_rlo_spherical peak shape with the default valuessome reasonable starting values such as 3.0 and 10.0; we will look at different peak shape functions in more details later on in the tutorial (TOPASforPDF > 3. Phase information > beq peak shape functions > beq spherical with min r and low r cutoffs).

6. Add view_structure to open a structure viewer where you can watch the structure as the refinement progresses (TOPASforPDF > 3. Phase information > view_structure).

7. Include output to CIF so you can compare the results in VESTA later (TOPASforPDF > 3. Phase information > outputs > output .CIF fileTOPAS_v7_Menus > Phase level - Structure > Outputs > Generate CIF output).

8. Allow all of the atomic coordinates to refine (place an @ sign after x, y and z in each site) and run the refinement in TOPAS, but when asked if you want to update the .inp file with the .out file at the end of the refinement click No. Use the structure viewer to look at how the atoms move during the refinement.

   1. How has the molecular geometry changed?

   2. Use VESTA to look  at the .cif file created, and compare it to the starting para.cif.

9. Edit the sites of the structure You hopefully observed that the structure diverged quickly from the starting model, and now looks unrealistic. Let’s try slowing down the refinement a little by damping the updates after each refinement cycle, so that the atoms will more gently move away from their starting positions. Define a new macro called “Damp” by inserting this line at the top of your inp file:

macro Damp(DampFactor) { update = Val + (Change*(1/Exp(DampFactor/2))); }

10. This macro simply allows us to change the update keyword in a more tidy manner. Add this damping to add the site x, y, z coordinates by adding Damp(5)

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10. to each of the coordinates, so each line looks like this:

    Code Block
    site C1 x @ 0.1286 Damp(5) y @ 0.1743 Damp(5) z @ -0.0080 Damp(5) occ C 1.0

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10. This Damp macro

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10. can help to keep atomic positions near their starting positions in the early stages of a refinement, but should be removed before finalising a refinement as it can prevent a refinement from converging.

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11. Change the filename for the output .cif to Out_CIF_STR("para_100K_without_rigid_damp.cif") so the previous one doesn't get overwritten.

12. Re-refine the structure and use the structure viewer to look at how the atoms move during the refinement.

    1. Use VESTA to compare the output .cif files.

    2. VESTA can be downloaded from https://jp-minerals.org/vesta/en/download.html - choose the VESTA-win64 option

    3. It does not require installation - simply extract the downloaded zip file and run the .exe file contained within