SIR92 Examples

Examples of input for SIR


Example 1

The following example shows the maximum default use of SIR. Most of the structures can be solved in this way. Diffraction data are in the file BOBBY.HKL in format (3I4,2F8.2), one reflection per record.

             %DATA
              CELL   9.626 9.626 9.626 90 90 90
              SPACEGROUP P 21 3
              CONT  H 24  C 24  N 4  O 24  NA 4  CA 4
              REFLECTIONS  BOBBY.HKL
             %CONTINUE

Example 2 User wants to use in the phasing process the pseudotranslational symmetry (eventually identified in a previous run). Diffraction data follow commands with format (2(3I4,F10.4,F1.0)), two per record. Sigma(F) values are not in input file.

              %WINDOW
              %STRUCTURE FEGAS
              %INIT
              %JOB    FE2GA2S5 2H P63/MMC
              %DATA
              CELL 3.651 3.651 29.745  90.   90.    120.
              SPACE      P 63/M M C
              CONT    FE 4     GA 4      S 10
              REFLECTIONS FOLLOW
              NOSIGMA
              RECORD 2
              FORMAT   (2(3I4,F10.4,F1.0))
              %NORMAL
              PSEUDO
              %CONTINUE
                 0   0   4   21.10900   0   0   6   82.16260
                 0   0   8  139.48620   0   0  10   31.70140
                 0   0  12   63.81540   0   0  14   48.66780
              ..............................................
                 5   0   6   19.55970   5   0   7     .00000
                 5   0   8    6.31500   5   0   9   28.76280

Example 3

The following example shows how to run partial procedure after that a complete run of SIR has been performed.

              %STRUCTURE CEPHAL
              %JOB   PARTIAL PROCEDURE RUN
              %NORMAL
              PARTIAL   C          .3824     .1494     .2856
                        C          .4344     .1415     .1688
                        C          .3675     .1102     .2789
                        C          .3866     .1546     .5060
                        C          .4153     .0957     .1638
                        C          .4088     .1654     .1820
               - Note that invariants and eventually seminvariants
               - need not to be recomputed
              %PHASE
              %CONTINUE

Example 4

The following example shows how to use the partial procedure when a molecular fragment is located from other sources (i.e. Patterson method).

              %WINDOW
              %STRUCTURE CEPHAL
              %INIT
              %JOB       - CEPHALOTAXIN  C 2 -
              %DATA
              CELL   22.840    8.150     19.540    90.    117.7    90.
              SPACEGROUP C 2
              CONT   C 144   H 168   O  32   N   8
              REFLECTIONS CEPHAL.HKL
              RECORD 3
              FORMAT    (3(3I3,F7.2,1.0))
              NOSIGMA
              %NORMAL
              PARTIAL
              O    .06760   -.76129    .88547  1.0
              O    .10620   -.53535    .97020  1.0
              C    .05235   -.61801    .84287  1.0
              C    .07655   -.48284    .89316  1.0
              C    .09666   -.71719    .96485  1.0
              %CONTINUE

Example 5

In the following example the use of one and two-phase seminvariants is requested together with 7 symbols to permute in PHASE routine. It is assumed that SIR92 was already run before (thus normalization and invariants are not needed).

              %STRUCTURE BOBBY
              %SEMINVARIANTS
              %PHASE
               SYMBOLS 7
              %CONTINUE 

Example 6

In the following example only the E-map of the set number 7 and the complete FOURIER/LEAST-SQUARES procedure for set number 9 are requested by the user.

              %WINDOW 850 800
              %STRUCTURE BOBBY
              %FOURIER
              SET 7
              RECYCLE 0
              %FOURIER
              SET 9
              %CONTINUE 

Example 7

The user wants only view and eventually modify the structure previously produced by FOURIER routine and create a complete input file for CRYSTALS named CEPHAL.QCK.

              %STRUCTURE CEPHAL
              %WINDOW
              %EXPORT
              CRYSTALS CEPHAL.QCK
              COMPLETE
              %END 

Example 8

In this example random approach is used and the best 200 sets, over 2000 trials, of phases are retained in the direct access file. No Fourier is required.

              %NOWINDOW
              %STRUCTURE CEPHAL
              %PHASE
              RANDOM
              MAXTRIALS 2000
              MINFOM 1.0 200
              %END

Example 9

In the following example the user just knows a fragment provided by a previous Fourier procedure and wants to delete some peaks and modify the atomic species of others.

              %STRUCTURE AZET
              %WINDOW
              %RESTART
              DELETE Q56
              DELETE Q55
              DELETE Q54
              RELABEL Q48 C
              RELABEL N6 C
              %CONTINUE 

Example 10

In the following example the user knows a fragment and wants to complete it using FOURIER/LEAST-SQUARES procedure.The binary file "azet.bin" must exist.

              %Window
              %Structure azet
              %Fourier
                fragment azet.frg
              %Continue
 
      Coordinates are in the file "azet.frg" which contains
 
               Cl     .02944    .72012    .08865
               Cl     .23727    .78692    .30869