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Methods, Problems and Solutions

Restrained Rietveld Structure Refinement of Organics

Using Crystals Generated Restraints Commands for Restrained Refinement in GSAS

(Not including hydrogen placement)

The CCP14 Homepage is at http://www.ccp14.ac.uk
[Back to Problems and Solutions] | [Back to Restrained Rietveld Refinement of Organics Page]| [Back to GSAS Tutorials Page]
[The reference to use for GSAS in any resulting publications is: A.C. Larson and R.B. Von Dreele, "General Structure Analysis System (GSAS)", Los Alamos National Laboratory Report LAUR 86-748 (1994).]
[The reference to cite in any resulting publications for using EXPGUI is: B. H. Toby, EXPGUI, a graphical user interface for GSAS, J. Appl. Cryst. (2001). 34, 210-213]

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 page

DIST   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 Format

Notes:

  • d 1:1000 deletes the list of relevant restraints already in GSAS
  • F sets the weighting for each restraint type. As the refinement converges, the idea is to try lower this so you reply less on the restraints and more on the powder diffraction data.
  • After initially putting and refining with the bond-angle restraints in, you may like to delete the bond-angle restraints and see how the refinement goes.

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. 

y 
l s 
d
d 1:1000
F 1000
R 1.5
i 1.352 .01 2 12
Y
i 1.432 .01 2 12
Y
i 1.259 .01 4 22
Y
i 1.234 .01 5 24
Y
i 1.422 .01 6 25
Y
i 1.330 .01 7 26
Y
i 1.276 .01 8 28
Y
i 1.313 .01 9 30
Y
i 1.494 .01 10 21
Y
i 1.490 .01 10 32
Y
i 1.491 .01 10 33
Y
i 1.301 .01 11 30
Y
i 1.386 .01 12 13
Y
i 1.405 .01 12 29
Y
i 1.357 .01 13 14
Y
i 1.399 .01 14 15
Y
i 1.375 .01 15 16
Y
i 1.534 .01 16 17
Y
i 1.422 .01 16 29
Y
i 1.540 .01 17 18
Y
i 1.516 .01 17 31
Y
i 1.526 .01 18 19
Y
i 1.512 .01 18 27
Y
i 1.534 .01 19 20
Y
i 1.538 .01 20 21
Y
i 1.522 .01 20 25
Y
i 1.522 .01 21 22
Y
i 1.403 .01 22 23
Y
i 1.427 .01 23 24
Y
i 1.435 .01 23 30
Y
i 1.552 .01 24 25
Y
i 1.508 .01 25 26
Y
i 1.354 .01 26 27
Y
i 1.445 .01 27 28
Y
i 1.451 .01 28 29
Y
X

A
d 1:1000
f 1000
i  111 20   21 10 32 
i  115 20   21 10 33 
i  111 20   32 10 33 
i  118 20   2 12 13 
i  121 20   2 12 29 
i  121 20   13 12 29 
i  119 20   12 13 14 
i  122 20   13 14 15 
i  120 20   14 15 16 
i  123 20   15 16 17 
i  119 20   15 16 29 
i  117 20   17 16 29 
i  108 20   3 17 16 
i  105 20   3 17 18 
i  108 20   16 17 18 
i  110 20   3 17 31 
i  113 20   16 17 31 
i  112 20   18 17 31 
i  113 20   17 18 19 
i  109 20   17 18 27 
i  111 20   19 18 27 
i  112 20   18 19 20 
i  110 20   19 20 21 
i  110 20   19 20 25 
i  113 20   21 20 25 
i  115 20   10 21 20 
i  110 20   10 21 22 
i  117 20   20 21 22 
i  117 20   4 22 21 
i  124 20   4 22 23 
i  118 20   21 22 23 
i  121 20   22 23 24 
i  117 20   22 23 30 
i  121 20   24 23 30 
i  125 20   5 24 23 
i  120 20   5 24 25 
i  115 20   23 24 25 
i  109 20   6 25 20 
i  105 20   6 25 24 
i  110 20   20 25 24 
i  111 20   6 25 26 
i  111 20   20 25 26 
i  110 20   24 25 26 
i  113 20   7 26 25 
i  123 20   7 26 27 
i  124 20   25 26 27 
i  123 20   18 27 26 
i  118 20   18 27 28 
i  119 20   26 27 28 
i  121 20   8 28 27 
i  120 20   8 28 29 
i  119 20   27 28 29 
i  119 20   12 29 16 
i  121 20   12 29 28 
i  120 20   16 29 28 
i  118 20   9 30 11 
i  120 20   9 30 23 
i  122 20   11 30 23 
x

p
d 1:1000
f 100000
i 0.01 2 12 13 14 15 16 29
0
x

Pasting Restraint Commands into GSAS

Again, 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.

About to paste GSAS Macro Commands

GSAS Restraint commands all go in

Restrained Refinement in GSAS

Nowing, 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:

  • L - Least squares refinement set up
  • L - Edit least squares controls
  • D d - Marquardt factor

EXPGUI Atom list refinement Interface

EXPGUI constraints interface

Running Genles

Genles running

GSAS GUI WINORTEP by Louis Farrugia to examine the Structure and reulting bond lengths and angles during the refinement

Using 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.

Ortep-3 with a GSAS structure file

Ortep-3 with a GSAS structure file

Looking at the Rietveld plot in Liveplot

Examining the Rietveld plot in Liveplot

Watching the structure in Ortep-3 as restraints are slowly relaxed

You 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.

Ortep-3 with a GSAS structure file

Ortep-3 with a GSAS structure file

Ortep-3 with a GSAS structure file

Further Options

You 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

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