Example 1
The following example shows the maximum default use of Sir2019. 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).
%window
%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.
%window
%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.
%window
%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.
%window
%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.
%window
%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.
%window
%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.
%window
%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).
%window
%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 R(F)% is less than the threshold (Residual) indicated by the user.
%window
%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.
%window
%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.
%window
%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 input file for electron diffraction data.
%window
%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 input file for Simulated Annealing using electron diffraction data.
%window
%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 14
Example of 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 input file for MAD (3 Se atoms) data. Buccaner will be used to build the structure.
%structure ttg
%amb Buccaneer
%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
%mad
%end