Examples

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Example 1

The following example shows the maximum default use of Sir2014. Most of the structures can be solved in this way. Diffraction data are in the file xanthene.hkl, in format (3i4, 2f8.2), one reflection per record. This structure has been downloaded from the Crystallography Open Database (COD, Grazulis et al., 2009).


   %structure xanthene
%job xanthene (COD 2224920)
%data
  cell 11.2438  20.1671  23.6474  90.0000  90.0000  90.0000
  space P n a 21
  cont C 220 H 320 N 4 O 44
  refl xanthene.hkl
%continue


Example 2

In the following example the experimental data are stored as |Fo| (not |Fo|2), using the free format.


   %Structure    iled

   %Job         Isoleucinomycin

   %Data

           cell             11.516  15.705  39.310  90.00  90.00  90.00 

           spacegroup    P 21 21 21

           content         C 240  H 408  N 24  O 72 

           reflections      iled.hkl

           format           free

           fobs

   %Continue


Example 3

In the following example, no space group is supplied; the program performs the automatic identification of the Laue group and of the extinction symbol from diffraction intensities.  


   %structure xanthene
%job xanthene (COD 2224920)
%data
  cell 11.2438  20.1671  23.6474  90.0000  90.0000  90.0000
  cont C 220 H 320 N 4 O 44
  refl xanthene.hkl
%continue


Example 4

In the following example, the directive spacegroup SCAN is used; the program performs the automatic identification of the Laue group and of the extinction symbol and consecutively explores (performing a complete solution run) all the selected groups.


   %structure xanthene
%job xanthene (COD 2224920)
%data
  cell 11.2438  20.1671  23.6474  90.0000  90.0000  90.0000

     Space  scan
  cont c 220 h 320 n 4 o 44
  refl xanthene.hkl
%continue

Example 5

The user wants to supply the value for the isotropic thermal factor and to set the number of strong (|Eo| value) reflections. Formula directive is used to supply the chemical cell content.


   %Structure loganin

   %Job    loganin

   %Data

           cell                 8.187  14.277  15.693  90.00  90.00  90.00 

           spacegroup     P 21 21 21

           formula           (C17  H26  O10)4  

           reflections       loganin.hkl

               fobs

           bfac                3.5

           nref                200

   %Continue


Example 6

In the following example, the Cochran formula is applied and all triplets with a concentration parameter greater than 0.4 are actively used in the phasing process, as requested by the user. The binary file "loganin.bin" must exist. Commands or directives following ">" or "!" are interpreted as a comment and will be ignored.


   %STRUCTURE LOGANIN

           >%DATA

               >CELL    8.187  14.277  15.693  90.00  90.00  90.00 

          ! spacegroup     P 21 21 21

          ! content           C 68  H 104  O 40  

          >reflections       loganin.hkl

              >FOBS

   %PHASE

           GMIN 0.4

           COCHRAN

   %END


Example 7

The user wants to explore 100 trials, starting from the trial number 132, from the phasing process up to the Fourier-Least Squares refinement. The binary file "iled.bin" must exist.


  %Structure iled

       %Phase

           MDM   100   132

        %End


Example 8

The user wants to explore only trial number 154 using 300 cycles of VLD instead of the default procedure (MDM).


   %Structure loganin

   %Phase

           VLD 300 1 154

   %End


Example 9

The program explores only the Patterson trial associated with the peak number 5; it applies the Direct Space Refinement strategy for medium size structures and stops if the final residual value (Rf %) is less than the threshold  indicated by the user.


   %Structure conotoxin

   %Phase

           Patterson  1   5

           Residual 10.0

           Size m

   %End


Example 10

In the following example the user knows a fragment and wants to complete it using the Fourier-Least Squares procedure. The  file "choror.cif" must exist.

 

       %STRUCUTRE  choror

       %Phase

             recycle   choror.cif      

       %CONTINUE

 

     


Example 11

The user wants to apply the VLD phasing approach; for proteins, like in this example, the default is Patterson.


   %Structure crambin

   %job  Crambin - PDB Code 1CNR

   %Data

            Cell   40.763 18.492 22.333 90.00 90.61 90.00

       SpaceGroup  P 21

       Content    C 406 H 776 N 110 O 131 S 12

       Reflections  crambin.hkl

   %Phase

       VLD

   %End


Example 12

Example of Sir2014 input file for electron diffraction data.


%Job charoite - Courtesy of Enrico Mugnaioli

%Structure charoite

%Data

           Cell    31.9600   19.6400    7.0900   90.0000   90.0000   90.0000

           Spacegroup  P 21/m

           Content     O 186 Na 10 Si 72 K 14 Ca 24

           Reflections charoite.hkl

           Format(3i4, 2f8.2)

           Fosq

           Wavelength  0.019700

           Electrons

   %Phase

   %End


Example 13

Example of Sir2014 input file for Simulated Annealing using electron diffraction data.


%structure cnba

%job CNBA Courtesy of Enrico Mugnaioli

%data

  cell 14.70 9.47 15.42 90 112 90

  spacegroup P21/c

  electrons

  content C 116 N 4 H 68

  reflections CNBA.hkl

%import antracene.mol

%sannel

%end



Example 14

Example of Sir2014 input file for Molecular Replacement.


%structure 2sar
%job test structure: pdb code 2sar
%data
     mtz 2sar.mtz
    label H K L FP SIGFP
    Sequence 2sar.seq
    nMolecules 1
    hetatm S 10 P 1
%remo
    model
         fragment  hetam 1ucl_mod1_lsq1.pdb
         monomers   2
         BFactor PDB
    endmodel
%end


Example 15

Example of Sir2014 input file for MAD (4 Se atoms) substructure determination.


%structure ttg_task1
%initialize
%job THERMUS THERMOPHILUS GROEL - PDB: 1SRV
%data
  mtz ttg.mtz
  label H K L FP SIGFP F(+)SE1 SIGF(+)SE1 F(-)SE1 SIGF(-)SE1 F(+)SE2 SIGF(+)SE2 F(-)SE2 SIGF(-)SE2 F(+)SE3 SIGF(+)SE3 F(-)SE3 SIGF(-)SE3 F(+)SE4 SIGF(+)SE4 F(-)SE4 SIGF(-)SE4
  nResidues 145
  nMolecules 1
  anomalous Se 3 -1.805 0.646 -8.582 3.843 -7.663 3.841 -2.618 3.578
  native
%phase
  Patterson
%end


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