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
%CONTINUEExample 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 28.76280Example 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
%CONTINUEExample 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
%CONTINUEExample 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
%ENDExample 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