The following will go through converting the Crystals restraints list into
Fullprof format, inputting this into GSAS format; then performing the restrained
refinement.
(Refer to the CCP14 Based Fullprof Tutorial Pages for download information on Fullprof) At present (October 2000), converting the Crystals restraints list is done manually and only bond-restraints are supported by Fullprof (no bond-angle restraints/planar restraints). Again, it is important that the restraint commands you generated in Crystals matches the atom labels in Fullprof or mayhem and chaos will result. Also refer to Randomly Perturbing Atomic Positions in Crystals. This can be relevant for successfully performing DLS and refinement involving pseudo-symmetry. |
Crystals Restraints List from previous tutorial pageDIST 1.352,.01= O(2) TO C(12) DIST 1.432,.01= O(3) TO C(17) DIST 1.259,.01= O(4) TO C(22) DIST 1.234,.01= O(5) TO C(24) DIST 1.422,.01= O(6) TO C(25) DIST 1.330,.01= O(7) TO C(26) DIST 1.276,.01= O(8) TO C(28) DIST 1.313,.01= O(9) TO C(30) DIST 1.494,.01= N(10) TO C(21) DIST 1.490,.01= N(10) TO C(32) DIST 1.491,.01= N(10) TO C(33) DIST 1.301,.01= N(11) TO C(30) DIST 1.386,.01= C(12) TO C(13) DIST 1.405,.01= C(12) TO C(29) DIST 1.357,.01= C(13) TO C(14) DIST 1.399,.01= C(14) TO C(15) DIST 1.375,.01= C(15) TO C(16) DIST 1.534,.01= C(16) TO C(17) DIST 1.422,.01= C(16) TO C(29) DIST 1.540,.01= C(17) TO C(18) DIST 1.516,.01= C(17) TO C(31) DIST 1.526,.01= C(18) TO C(19) DIST 1.512,.01= C(18) TO C(27) DIST 1.534,.01= C(19) TO C(20) DIST 1.538,.01= C(20) TO C(21) DIST 1.522,.01= C(20) TO C(25) DIST 1.522,.01= C(21) TO C(22) DIST 1.403,.01= C(22) TO C(23) DIST 1.427,.01= C(23) TO C(24) DIST 1.435,.01= C(23) TO C(30) DIST 1.552,.01= C(24) TO C(25) DIST 1.508,.01= C(25) TO C(26) DIST 1.354,.01= C(26) TO C(27) DIST 1.445,.01= C(27) TO C(28) DIST 1.451,.01= C(28) TO C(29) |
Restraints in Fullprof Format
The Fullprof dis parameter (to the right of the number of atoms in the phase)
is set to the number of restraints, in this case "35".
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Fullprof Input File(For comparison with single crystal results of tetracycline refer: "Tetracycline hydrochloride: a synchrotron micro-crystal study" Clegg W. & Teat S.J. Acta Cryst., C56 , 1343-1345 (2000)) Paste the restraints into the Fullprof file.
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Restrained Refinement in FullprofThe Fullprof *.out output file will tell you what is going on with respect to the bond length restraints and if you have made any obvious mistakes setting things up.=> Distance constraints: Dobs Dcalc diff/sigma (O2 - C12 ): 1.35200 1.33918 1.28200 (O3 - C17 ): 1.43200 1.44425 -1.22492 (O4 - C22 ): 1.25900 1.25923 -0.02342 (O5 - C24 ): 1.23400 1.27322 -3.92196 (O6 - C25 ): 1.42200 1.44513 -2.31262 (O7 - C26 ): 1.33000 1.37402 -4.40164 (O8 - C28 ): 1.27600 1.29485 -1.88483 (O9 - C30 ): 1.31300 1.32626 -1.32631 (N10 - C21 ): 1.49400 1.49864 -0.46387 (N10 - C32 ): 1.49000 1.48344 0.65643 (N10 - C33 ): 1.49100 1.46163 2.93682 (N11 - C30 ): 1.30100 1.34755 -4.65486 (C12 - C13 ): 1.38600 1.37961 0.63871 (C12 - C29 ): 1.40500 1.43496 -2.99565 (C13 - C14 ): 1.35700 1.35754 -0.05361 (C14 - C15 ): 1.39900 1.41365 -1.46538 (C15 - C16 ): 1.37500 1.39229 -1.72884 (C16 - C17 ): 1.53400 1.54902 -1.50199 (C16 - C29 ): 1.42200 1.45817 -3.61701 (C17 - C18 ): 1.54000 1.52876 1.12411 (C17 - C31 ): 1.51600 1.49568 2.03242 (C18 - C19 ): 1.52600 1.53847 -1.24725 (C18 - C27 ): 1.51200 1.54576 -3.37646 (C19 - C20 ): 1.53400 1.52490 0.90995 (C20 - C21 ): 1.53800 1.54776 -0.97597 (C20 - C25 ): 1.52200 1.56787 -4.58719 (C21 - C22 ): 1.52200 1.55911 -3.71107 (C22 - C23 ): 1.40300 1.44134 -3.83443 (C23 - C24 ): 1.42700 1.48698 -5.99785 (C23 - C30 ): 1.43500 1.47896 -4.39645 (C24 - C25 ): 1.55200 1.58359 -3.15930 (C25 - C26 ): 1.50800 1.53789 -2.98923 (C26 - C27 ): 1.35400 1.41101 -5.70073 (C27 - C28 ): 1.44500 1.46845 -2.34495 (C28 - C29 ): 1.45100 1.47536 -2.43574 |
GSAS GUI WINORTEP by Louis Farrugia to examine the Structure and resulting bond lengths and angles during the refinementUsing Ortep-3 you can quickly load the Fullprof *.pcr file and check that the bond length and angle restraints are doing what you think they should be doing (using the Calculate menu option). You can also keep a graphical eye on the thermals.
In the following case, thermals are quite large, possibly due to poorly defined manual background. Switching to a refined background might be a better thing to do here.
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Looking at the Rietveld plot in Winplotr
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Further OptionsYou may want to re-import the structure back into Crystals (using Ortep-3) to allow very easy placement of hydrogens (Structure, Add Hydrogens); as well as possible validation with the CSD database to check that bond-length and angles are consistent with structures already in the Cambridge Database. A "might happen" feature for a future version of Crystals is to generate idealised bond lengths and bond angles based on the cambridge database in a similar way to how Crystals presently does the CSD validation. |