ADDSYM can be used in search of ADDitional SYMmetry for:
Missed symmetry is a serious problem. Refinement of a structure in a space group of too low symmetry may lead to poor geometry and false conclusions based on refinement artifacts.
Cases of overlooked symmetry are conveniently divided into four classes:
For a recent discussion and examples see:
See related CSD-DATA and PLATON/ADDSYM Analysis
See related paper: P1 or P-1? Or something else ? by R.E. Marsh, Acta Cryst (1999). B55, 931-936.
Major extensions to the published MISSYM (C) algorithm include:
In order not to confuse this extended implementation of the MISSYM (C) algorithm with the official (copyrighted !) MISSYM (C) implementation in the NRCVAX (C) package, it is now named ADDSYM.
Given a name.res, name.dat or name.cif formatted file, the test for possibly missed symmetry can be run (either from the keyboard or by mouse clicks on the proper menu items) as:
platon name.res
with the sole instruction:
CALC ADDSYM
The result of the analysis is displayed on the graphics window. More detailed information on the analyses can be found in the ascii window and the .lis (.lps) file.
The proposed transformation and new symmetry is written in a file with extension .eld.
See the TEST/ADDSYM_EXAMPLE subdirectory (on xraysoft.chem.uu.nl) for some examples and an additional README.
PLATON should produce a transformed shelx file with the keyboard instructions:
CALC ADDSYM SHELX
or a PLUTON DRAWING of the averaged/transformed structure with
CALC ADDSYM PLOT
or clicks on the corresponding items on the PLATON-menu.
A multi-entry CSD-CIF file (.cif) may be conveniently scanned for missed symmetry by first clicking on the SAVE-InstrS menu item (RED) before invoking ADDSYM from the main menu. Clicking on END will execute ADDSYM on the next FDAT-file entry.
where:
Note : By default up to 20 % of the atoms are allowed as mis-fits (i.e. atoms falling out of the default criteria or with missing symmetry related counterparts). The EXACT sub-keyword will put this value to zero. Other values may be set with a SET PAR instruction
(Example: SET PAR 249 40 to set the misfit % to 40).
Other Defaults:
Organic: PAR(401) = d1, PAR(402) = d2, PAR(403) = d3
Inorganic: PAR(404) = d1, PAR(405) = d2, PAR(406) = d3
In the order of 10 % of the structures published in Space group Cc can be shown to be better described with higher symmetry. A common case is the omission of an inversion centre. This example shows how to detect and correct automatically for that problem.
TITL AACRUB Cc R=0.0380 CELL 14.2460 6.9040 17.6870 90.000 97.190 90.000 CESD 0.0020 0.0010 0.0020 0.000 0.010 0.000 SPGR Cc Ru(1) 0.22852 0.15210 0.36523 Ru(2) 0.12035 0.34630 0.40847 O(1) 0.22860 0.32200 0.27210 O(2) 0.33730 0.30800 0.42380 O(3) 0.22800 -0.00410 0.45390 O(4) 0.12660 -0.00400 0.30750 O(5) 0.12440 0.52300 0.31530 O(6) 0.22860 0.49900 0.46410 O(7) 0.11900 0.17000 0.49890 O(8) 0.02400 0.17600 0.35380 O(9) 0.33580 -0.06800 0.32270 O(10) 0.00210 0.52300 0.44990 C(1) 0.18130 0.46000 0.26420 C(2) 0.17370 0.61600 0.20200 C(3) 0.31360 0.45900 0.46460 C(4) 0.39210 0.55600 0.50520 C(5) 0.17690 0.01400 0.50280 C(6) 0.16480 -0.08500 0.57740 C(7) 0.04180 0.04600 0.31500ADDSYM OUTPUT FOR EXAMPLE 1
ADDSYM - CHECK (cf. MISSYM (C): Le Page, Y., J. Appl. Cryst. (1987), 20, 264-269; J. Appl. Cryst. (1988), 21, 983-984) ------------------------------------------------------------------------------ - This ADDSYM Search is run on ALL NON-H Chemical Types - Number of Input Atoms Included in Search = 25 - The Structure implies the following Symmetry Elements subject to the Criteria: 1.00 Deg., (metric) 0.25 Ang. (distances) and 0.45 Ang. (inv. and transl.) Symm. Input Reduced (Ang) (Deg) (Ang) Input Cell Elem Cell Row Cell Row d Type Dot Angle Max. dev. x y z -------------------------------------------------------------------------------- c [ 0 1 0] [-1 0 0] 6.903 2 2 0.00 0 through 0 0 0 Glide = 0 0 1/2 -1 * ====================================== 0.270 at 0.174 0.249 0.387 F3 -F4 Reduced->Convent Input->Reduced T = Input->Convent: a' = T a -------------------------------------------------------------------------------- ( -1 2 0 ) ( 0 1 0 ) ( 1 0 0 ) Det(T) ( 1 0 0 ) X ( 1/2 1/2 0 ) = ( 0 1 0 ) = ( 0 0 -1 ) ( 0 0 -1 ) ( 0 0 1 ) 1.000 Cell Lattice a b c alpha beta gamma Volume CrystalSystem Laue -------------------------------------------------------------------------------- Input mC 14.246 6.904 17.687 90.00 97.19 90.00 1726 Monoclinic 2/m Reduced P 6.903 7.915 17.687 83.53 90.00 64.15 863 Convent mC 14.246 6.904 17.687 90.00 97.19 90.00 1726 Monoclinic 2/m Conventional, New or Pseudo Symmetry ================================================================================ Space Group C2/c No: 15, Laue: 2/m [Hall: -C 2yc ] Lattice Type mC, Centric, Monoclinic, Order 8( 2) [Shoenflies: C2h^6 ] Nr ***** Symmetry Operation(s) ***** 1 X , Y , Z 2 X , - Y , 1/2 + Z 3 - X , - Y , - Z 4 - X , Y , 1/2 - Z 5 1/2 + X , 1/2 + Y , Z 6 1/2 + X , 1/2 - Y , 1/2 + Z 7 1/2 - X , 1/2 - Y , - Z 8 1/2 - X , 1/2 + Y , 1/2 - Z :: Origin shifted to: 0.424, 0.499, 0.387 after transformation :: * Symmetry Elements preceded by an Asterisk are New and indicate :: Missed/Pseudosymmetry Summary :: M/P AACRUB Cc R=0.0380 mC => mC 0.000 0.00 0.500 100% C2/c :: note: glide plane codes are with reference to input cell !! :: An SPF-style file is written to be used for the cell transformation.
Example 2This example shows how to detect and correct for missed symmetry for a structure initially solved and refined as a structure in space group Cc. The structure is actually taken from the Cambridge Crystallographic Database and was shown by Marsh & Herbstein (Acta Cryst (1988), B44, 77-88) to be better described in space group Fdd2.
TITL CcToFdd2 Cc (Anonymous Example from CSD) CELL 0.71073 6.6260 41.0800 6.6000 90.000 120.110 90.000 ZERR 1 0.0030 0.0200 0.0030 0.000 0.050 0.000 LATT -7 SYMM X , - Y , 0.50000 + Z SFAC C H S UNIT 56 80 16 S1 3 0.21990 0.21930 0.19410 11.0000 0.1000 S2 3 0.57670 0.14380 -0.14760 11.0000 0.1000 C1 1 0.31270 0.19010 -0.11180 11.0000 0.1000 C2 1 0.10530 0.19950 -0.09000 11.0000 0.1000 C3 1 0.50640 0.19980 0.31840 11.0000 0.1000 C4 1 0.53620 0.19040 0.11230 11.0000 0.1000 C5 1 0.68580 0.16180 0.14100 11.0000 0.1000 C6 1 0.29050 0.16190 -0.27040 11.0000 0.1000 C7 1 0.49320 0.21550 -0.06860 11.0000 0.1000 H1 2 -0.00400 0.18300 -0.11100 11.0000 0.0500 H2 2 -0.01900 0.22400 -0.20400 11.0000 0.0500 H3 2 0.58900 0.21600 0.41300 11.0000 0.0500 H4 2 0.50900 0.18200 0.38400 11.0000 0.0500 H5 2 0.64100 0.14200 0.24000 11.0000 0.0500 H6 2 0.81500 0.16700 0.19300 11.0000 0.0500 H7 2 0.25600 0.16600 -0.43500 11.0000 0.0500 H8 2 0.15500 0.14300 -0.31100 11.0000 0.0500 H9 2 0.44100 0.23600 -0.07100 11.0000 0.0500 H10 2 0.61400 0.21300 -0.14300 11.0000 0.0500 S3 3 0.56400 0.03100 -0.11710 11.0000 0.1000 S4 3 1.26330 0.10620 0.22630 11.0000 0.1000 C8 1 0.96450 0.05950 0.19380 11.0000 0.1000 C9 1 0.73190 0.05000 0.16440 11.0000 0.1000 C10 1 0.73020 0.04990 -0.23680 11.0000 0.1000 C11 1 0.95900 0.05970 -0.03760 11.0000 0.1000 C12 1 1.08120 0.08900 -0.06300 11.0000 0.1000 C13 1 1.09330 0.08840 0.34010 11.0000 0.1000 C14 1 1.09940 0.03490 0.14280 11.0000 0.1000 H11 2 0.73700 0.04400 0.31000 11.0000 0.0500 H12 2 0.64900 0.07000 0.15800 11.0000 0.0500 H13 2 0.76500 0.03100 -0.33000 11.0000 0.0500 H14 2 0.66400 0.06800 -0.31900 11.0000 0.0500 H15 2 0.96400 0.10000 -0.20500 11.0000 0.0500 H16 2 1.15500 0.08300 -0.11000 11.0000 0.0500 H17 2 1.17300 0.08100 0.47500 11.0000 0.0500 H18 2 0.93000 0.10400 0.32300 11.0000 0.0500 H19 2 1.02700 0.02000 0.09600 11.0000 0.0500 H20 2 1.26800 0.04000 0.26600 11.0000 0.0500 HKLF 4 1 1.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00 1.00 ENDADDSYM OUTPUT for Example 2:
ADDSYM - CHECK (cf. MISSYM (C): Le Page, Y., J. Appl. Cryst. (1987), 20, 264-269; J. Appl. Cryst. (1988), 21, 983-984) -------------------------------------------------------------------------- - This ADDSYM Search is run on ALL NON-H Chemical Types - Number of Input Atoms Included in Search = 18 - The Structure implies the following Symmetry Elements subject to the Criteria: 1.00 Deg., (metric) 0.25 Ang. (distances) and 0.45 Ang. (inv. and transl.) Symm. Input Reduced (Ang) (Deg) (Ang) Input Cell Elem Cell Row Cell Row d Type Dot Angle Max. dev. x y z -------------------------------------------------------------------------------- n [ 0 1 0] [ 1 1 2] 41.080 2 2 0.00 0 through 0 3/4 0 Glide = 1/2 0 1/2 d * [ 1 0 2] [ 1-1 0] 11.418 2 2 0.02 0.026 through 0.894 0 0.788 C13 -C6 Glide = 1/4 1/4 0 2 * [ 1 0 0] [-1-1 0] 6.626 2 2 0.02 0.026 through 0.269 1/8 0.538 C13 -C6 Reduced->Convent Input->Reduced T = Input->Convent: a' = T a -------------------------------------------------------------------------------- ( 1 1 2 ) ( 0 0 -1 ) ( 0 -1 0 ) Det(T) ( -1 1 0 ) X ( 1 0 1 ) = ( 1 0 2 ) = ( -1 -1 0 ) ( -1/2 -1/2 0 ) ( -1 0 0 ) 2.000 Cell Lattice a b c alpha beta gamma Volume CrystalSystem Laue -------------------------------------------------------------------------------- Input mC 6.626 41.080 6.600 90.00 120.11 90.00 1554 Monoclinic 2/m Reduced P 6.600 6.602 20.806 94.59 94.58 119.75 777 Convent oF 41.080 11.419 6.626 90.02 90.00 90.00 3108 Orthorhombic mmm :: Cell Angles differ 0.02 Deg. from (90/120) Conventional, New or Pseudo Symmetry ================================================================================ Space Group Fdd2 No: 43, Laue: mmm [Hall: F 2 -2d ] Lattice Type oF, Acentric, Orthorhombic, Order 16( 4) [Shoenflies: C2v^19 ] CHIRAL - See P.G. Jones, Acta Cryst. (1986), A42, 57. Nr ***** Symmetry Operation(s) ***** 1 X , Y , Z 2 - X , - Y , Z 3 3/4 - X , 3/4 + Y , 1/4 + Z 4 1/4 + X , 1/4 - Y , 1/4 + Z 5 X , 1/2 + Y , 1/2 + Z 6 - X , 1/2 - Y , 1/2 + Z 7 3/4 - X , 1/4 + Y , 3/4 + Z 8 1/4 + X , 3/4 - Y , 3/4 + Z 9 1/2 + X , Y , 1/2 + Z 10 1/2 - X , - Y , 1/2 + Z 11 1/4 - X , 3/4 + Y , 3/4 + Z 12 3/4 + X , 1/4 - Y , 3/4 + Z 13 1/2 + X , 1/2 + Y , Z 14 1/2 - X , 1/2 - Y , Z 15 1/4 - X , 1/4 + Y , 1/4 + Z 16 3/4 + X , 3/4 - Y , 1/4 + Z :: Origin shifted to:-0.125, 0.269, 0.000 after transformation :: * Symmetry Elements preceded by an Asterisk are New and indicate :: Missed/Pseudosymmetry Summary :: M/P CcToFdd2 Cc (Anonymous ExamC => oF 0.000 0.02 0.026 100% Fdd2 :: note: glide plane codes are with reference to input cell !! :: An SPF-style file is written to be used for the cell transformation. :: Change of Crystal System indicated. (Maxdev. = 0.026 Ang.)
See also applications from the modelling realm:Example 3 for a model in P1 that transforms to a description in space group P-3m1
Example 4 for a model in P1 that transforms to I4/mmm.
Both examples are taken from J. Appl. Cryst. (1998), 31, 922-928.
Example 5 Case of subcell symmetry: P1 to P21/c (1/8 subcell !)
See also Abstract ACA97-Talk on MISSED SYMMETRY
SYMMETRY TOOLS PLATON HOMEPAGE
14-Dec-2024 A.L.Spek