The following will go through converting the Crystals restraints list into
GSAS format, inputting this into GSAS format; then performing the restrained
refinement. You may find it easier to edit the following GSAS restraints as
an ASCII file, then import them in each time you make a modification (with commands
erasing the previous list of restraints)
(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)) (Refer to the CCP14 Based GSAS Tutorial Pages for download information on GSAS and EXPGUI.) At present, converting the Crystals restraints list is done manually. But parts can be done near automatically using multiple search and replaces in a program such as the freeware PFE Editor. Again, it is important that the restraint commands you generated in Crystals matches the atom numbering system in GSAS 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) ANGL 111,20= C(21) TO N(10) TO C(32) ANGL 115,20= C(21) TO N(10) TO C(33) ANGL 111,20= C(32) TO N(10) TO C(33) ANGL 118,20= O(2) TO C(12) TO C(13) ANGL 121,20= O(2) TO C(12) TO C(29) ANGL 121,20= C(13) TO C(12) TO C(29) ANGL 119,20= C(12) TO C(13) TO C(14) ANGL 122,20= C(13) TO C(14) TO C(15) ANGL 120,20= C(14) TO C(15) TO C(16) ANGL 123,20= C(15) TO C(16) TO C(17) ANGL 119,20= C(15) TO C(16) TO C(29) ANGL 117,20= C(17) TO C(16) TO C(29) ANGL 108,20= O(3) TO C(17) TO C(16) ANGL 105,20= O(3) TO C(17) TO C(18) ANGL 108,20= C(16) TO C(17) TO C(18) ANGL 110,20= O(3) TO C(17) TO C(31) ANGL 113,20= C(16) TO C(17) TO C(31) ANGL 112,20= C(18) TO C(17) TO C(31) ANGL 113,20= C(17) TO C(18) TO C(19) ANGL 109,20= C(17) TO C(18) TO C(27) ANGL 111,20= C(19) TO C(18) TO C(27) ANGL 112,20= C(18) TO C(19) TO C(20) ANGL 110,20= C(19) TO C(20) TO C(21) ANGL 110,20= C(19) TO C(20) TO C(25) ANGL 113,20= C(21) TO C(20) TO C(25) ANGL 115,20= N(10) TO C(21) TO C(20) ANGL 110,20= N(10) TO C(21) TO C(22) ANGL 117,20= C(20) TO C(21) TO C(22) ANGL 117,20= O(4) TO C(22) TO C(21) ANGL 124,20= O(4) TO C(22) TO C(23) ANGL 118,20= C(21) TO C(22) TO C(23) ANGL 121,20= C(22) TO C(23) TO C(24) ANGL 117,20= C(22) TO C(23) TO C(30) ANGL 121,20= C(24) TO C(23) TO C(30) ANGL 125,20= O(5) TO C(24) TO C(23) ANGL 120,20= O(5) TO C(24) TO C(25) ANGL 115,20= C(23) TO C(24) TO C(25) ANGL 109,20= O(6) TO C(25) TO C(20) ANGL 105,20= O(6) TO C(25) TO C(24) ANGL 110,20= C(20) TO C(25) TO C(24) ANGL 111,20= O(6) TO C(25) TO C(26) ANGL 111,20= C(20) TO C(25) TO C(26) ANGL 110,20= C(24) TO C(25) TO C(26) ANGL 113,20= O(7) TO C(26) TO C(25) ANGL 123,20= O(7) TO C(26) TO C(27) ANGL 124,20= C(25) TO C(26) TO C(27) ANGL 123,20= C(18) TO C(27) TO C(26) ANGL 118,20= C(18) TO C(27) TO C(28) ANGL 119,20= C(26) TO C(27) TO C(28) ANGL 121,20= O(8) TO C(28) TO C(27) ANGL 120,20= O(8) TO C(28) TO C(29) ANGL 119,20= C(27) TO C(28) TO C(29) ANGL 119,20= C(12) TO C(29) TO C(16) ANGL 121,20= C(12) TO C(29) TO C(28) ANGL 120,20= C(16) TO C(29) TO C(28) ANGL 118,20= O(9) TO C(30) TO N(11) ANGL 120,20= O(9) TO C(30) TO C(23) ANGL 122,20= N(11) TO C(30) TO C(23) PLANAR 0.010000 O(2) C(12) C(13) C(14) C(15) C(16) C(29) |
GSAS Restraints List in Macro FormatNotes:
It is important to know where to start the GSAS macro (using the @r GSAS "run macro file" command or just a Windows/UNIX edit/paste. If you paste the macro commands in the wrong menu item, chaos may result.
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Pasting Restraint Commands into GSASAgain, using the @r GSAS "run macro file" command or just a Windows/UNIX edit/paste, insert all the macro commands into the GSAS EXPEDT program. You can use the L (List) command to make sure restraints were inserted correctly.
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Restrained Refinement in GSASNowing, using the traditional GSAS interface or Brian Toby's EXPGUI Interface, be happy and start refining. Again, you might find it easier to edit a text file of the retraints. Normally you might start by releasing all atomic co-ordinates; but constraining all the thermals of the light atoms. For GSAS beginners, this is very easy to do in the EXPGUI program. If worried about diverging refinement, you can also initially set the Marquadt damping command:
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Running Genles
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GSAS GUI WINORTEP by Louis Farrugia to examine the Structure and reulting bond lengths and angles during the refinementUsing Ortep-3 you can quickly load the GSAS EXP 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.
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Looking at the Rietveld plot in Liveplot
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Watching the structure in Ortep-3 as restraints are slowly relaxedYou can see that the Oxygen off the Benzene ring is going a bit wrong with the angle so it could be justified putting back the relevant angle restraints. And as bond length restraints are relaxed further, bond lengths are going bad. Depending on data quality, quite large restraints may be required to keep things to reasonable values.
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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.
Again, whatever you do outside GSAS, the option of creating macros can make it relative easy to insert it into the program as per the following calculated hydrogen positions from Crystals.
i n H 0.828 0.551 0.231 1 H1 i 0.05 i n H 0.822 0.424 0.268 1 H2 i 0.05 i n H 0.693 0.317 0.076 1 H3 i 0.05 i n H 0.804 0.290 0.141 1 H4 i 0.05 i n H 0.668 0.311 0.178 1 H5 i 0.05 i n H 0.567 0.419 0.228 1 H6 i 0.05 i n H 0.608 0.463 0.070 1 H7 i 0.05 i n H -0.109 0.208 0.383 1 H8 i 0.05 i n H 0.353 0.318 0.212 1 H9 i 0.05 i n H 0.393 0.491 0.100 1 H10 i 0.05 i n H 0.456 0.376 0.094 1 H11 i 0.05 i n H -0.097 0.125 0.251 1 H12 i 0.05 i n H 0.035 0.183 0.142 1 H13 i 0.05 i n H 0.138 0.281 0.033 1 H14 i 0.05 i n H 0.269 0.338 0.018 1 H15 i 0.05 i n H 0.262 0.229 0.071 1 H16 i 0.05 |