ADDSYM

ADDSYM : An extended version of the MISSYM (C) tool

PLATON incorporates a significantly modified, extented and automated implementation of the powerful MISSYM (C) algorithm for the detection of possibly MISsed ADDitional SYMmetry in a given coordinate set, invented and published by Y. Le Page, [J. Appl. Cryst. (1987), 20, 264-269; J. Appl. Cryst. (1988), 21, 983-984].

ADDSYM can be used in search of ADDitional symmetry for:

Coordinate sets derived from an X-ray structure determination (e.g.CIF, RES or SPF style)
Coordinate sets obtained from ab-initio modelling and energy minimalization.

Missed symmetry is a serious problem. Refinement of a structure in a space group with 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:

Change of Crystal System (e.g. Monoclinic to Trigonal/Rhombohedral)
Change of Laue Class without change of Crystal System (e.g. Low Tetragonal to High Tetragonal)
Addition of an Inversion Centre (e.g. Cc to C2/c)
Additional Translational Symmetry (e.g. 1/2, 1/3, 1/4 or 1/8 volume primitive subcell)

Classes 1, 2 & 3 describe the more common cases in X-ray structure analysis. Class 4 is common for energy minimised structure.

For a recent discussion and examples see:

D.Marsh, Acta Cryst. (1997). B53, 317-322.
More Space-Group Corrections: From Triclinic to Centric Monoclinic and to Rhombohedral; Also From P1 to P-1 and Cc to C2/c.
by F.H. Herbstein & R.E. Marsh, Acta Cryst (1998) B54, 677-686.

See related CSD-DATA and PLATON/ADDSYM Analysis
PLATON/ADDSYM analysis of all 1970 Cc structures in the CSD (Apr 1999).
PLATON/ADDSYM analysis of all 1848 P1 structures in the CSD (Oct 1999).
See related paper: P1 or P-1? Or something else ? by R.E. Marsh, Acta Cryst (1999). B55, 931-936.
R.E.Marsh & A.L.Spek, Acta Cryst. B57, (2001), 800-805. Use of software to search for higher symmetry: space group C2.

Major extensions to the published MISSYM (C) algorithm include:

Explicit transformation matrices and origin shifts to the revised description.
Proposed alternative space group (name)
Detection of missed lattice centering and cell halving.
The detection of approximate higher symmetry due to either missing atoms or a few atoms that do not comply with the higher symmetry (either real or refinement artifact).
Generation of new 'shelx.res'
PLUTON presentation of the transformed (averaged) structure.

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.

Optional Keyboard Instructions

CALC ADDSYM (element_name/EQUAL) (EXACT) (SHELX/PLOT) (ang d1 d2 d3)

where:

element_name - Search for higher symmetry for specified element only.
EQUAL - Search with all atom type treated as equivalent.
EXACT - All atoms should fit for given criteria.
SHELX - A new shelxl.res file is generated for the proposed space group
PLOT - A PLUTON-plot of the averaged structure in the proposed space group is generated.
ang - Angle criterium in search for metrical symmetry of the lattice (default 1.0 degree).
d1 - Distance criterium for coinciding atoms for non-inversion (pseudo)symmetry elements (default 0.25 Angstrom).
d2 - Distance criterium for coinciding atoms for (pseudo) inversion symmetry (default 0.45, 0.25 Angstrom).
d3 - Distance criterium for coinciding atoms for (pseudo) translation symmetry (default 0.45, 0.25 Angstrom).

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

Missed Symmetry Examples

Example 1

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  0.31500 

 ADDSYM 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 2

This 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
END


ADDSYM 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




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27-Jun-2023 A.L.Spek