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Using SAINT Using SADABS File Name Confusion

Data Reduction. Using SAINT Using SADABS File Name Confusion. SAINT Now and Then. There was a time before GUIs where SAINT did not run on PCs. One had to call SAINT from the command line. Like so: saint /l1:1023 /l2:768 /k1:1 /k2:3 /bg:2 /h:2.

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Using SAINT Using SADABS File Name Confusion

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  1. Data Reduction • Using SAINT • Using SADABS • File Name Confusion

  2. SAINT Now and Then There was a time before GUIs where SAINT did not run on PCs. One had to call SAINT from the command line. Like so: saint /l1:1023 /l2:768 /k1:1 /k2:3 /bg:2 /h:2 This translates to: run SAINT, treat everything as constant during integration, allow everything but crystal translations and goniometer zeros to be refined in post-refinement, assume triclinic Laue symmetry during integration, assume monocinic Laue symmetry in post-refinement, assume low background noise level, assume small allocated memory. There were more qualifiers for special cases (like very weak diffraction, etc.).

  3. SAINT The Old Days

  4. SAINT The Old Days

  5. SAINT 32: The Main Menu • Define Project. • Initialize (answer YES to all questions) • Execute • Give correct Laue group • Give Resolution (at 5.0 cm, 2Θ = -30  dmax = 0.70 Å) • Check for correct file names • Do not integrate the zero frames • Click on “Integrate” in upper right corner

  6. SAINT 32: Integrate • Give a sensible box size. • Do not apply decay correction. • Do not constrain metric cell symmetry in pre-refinement unless you have a problem with cell-refinement. • Do constrain metric cell symmetry in post-refinement. • Do not refine Goniometer Zeros or Crystal Translationsunless you have a very good crystal. • Do refine the other parameters. • Don’t even click on “Advanced Integrate” in lower left corner unless you want to do something extravagant.

  7. SAINT 32: Integrate • Give a sensible box size Sensible starting values are around 0.6 or 0.7 or so for all three parameter (x, y and z). But SAINT is good in refining them. The Box

  8. SAINT 32: Integrate • Give a sensible box size. • Do not apply decay correction. • Do not constrain metric cell symmetry in pre-refinement unless you have a problem with cell-refinement. • Do constrain metric cell symmetry in post-refinement. • Do not refine Goniometer Zeros or Crystal Translationsunless you have a very good crystal. • Do refine the other parameters. • Don’t even click on “Advanced Integrate” in lower left corner unless you want to do something extravagant.

  9. SAINT 32: Integrate • Give a sensible box size. • Do not apply decay correction. • Do not constrain metric cell symmetry in pre-refinement unless you have a problem with cell-refinement. • Do constrain metric cell symmetry in post-refinement. • Do not refine Goniometer Zeros or Crystal Translationsunless you have a very good crystal. • Do refine the other parameters. • Don’t even click on “Advanced Integrate” in lower left corner unless you want to do something extravagant.

  10. SAINT 32: Advanced Integrate • In most cases: Don‘t change anything here • Do not blend the 9 profiles • For very week data from a very good crystal> lower the I/sigma lower limit to 5.0> lower the I/sigma threshold to 4.0 • Instrument:Do no change the Base Offset per Readout unless you have a darn good reason.

  11. SAINT The GUI

  12. SAINT: Data Flow 04000-1.raw 04000-1._ls (…) 04000-5.raw 04000-5._ls 04000-m.raw 04000-m._ls 04000-m.p4p 04000-1.001 04000-1.002 (…) 04000-5.800 04000-1.p4p SAINT Raw files & Refined cell Frames & Initial cell C:\frames\04000\work C:\frames\04000

  13. SADABS: Default Magic (The Wizzard of Göttingen) • Always use SADABS • Generally SADABS comes right after SAINT • You can use all defaults except for one: the LAUE symmetry • Look at the SADABS output (sad.eps) • Use the corrected data (sad.hkl) to go into XPREP, not the 04000-m.raw Absorption (and other) corrections from equivalents

  14. SADABS: The Laue Symmetry The answer to the third question in SADABS is critical. You must give the same Laue symmetry and setting you used in SAINT, even if you happen to know that this is not the true Laue symmetry. What you should do in such a case is go back to SMART find an orientation matrix in the correct Laue symmetry, repeat the integration in SAINT with this matrix and then run SADABS.

  15. SADABS SADABS: Data Flow 04000-1.raw (…) 04000-5.raw or 04000-m.raw sad.hkl sad.abs sad.eps

  16. SADABS: Not Very Graphical Open SADABS either from the SAINTPLUS interface by clicking on SADABS (will open a DOS window) or directly from a DOS-prompt. And then just follow the Yellow Brick Road.

  17. SADABS: Lets Look at an Example MS-DOS window Ghostview

  18. Information about Laue symmetry or lattice centering SMART SADABS SAINT copy to sad.p4p XPREP SHELX Editor or XP Data Flow 04000-n.xxx 04000-1.p4p 04000-n.raw 04000-n._ls 04000-m.p4p sad.hkl sad.abs sad.prp name.ins name.hkl name.ins name.res name.lst

  19. The new HOMEPAGE is growingalmost by the day. Visit it frequently. http://web.mit.edu/x-ray

  20. Next Meeting Tuesday November 9,11:00 a.m. AMDUR room (here) Space Group Determination and other things you can do in XPREP

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