List of the directives associated to the commands
Only directives marked in red are mandatory.
CELL a b c α β γ
Cell dimensions: a, b and c are in Å, α, β and γ in degrees.
ERRORS esd(a) esd(b) esd(c) esd(α) esd(β) esd( γ)
Estimated standard deviations for the unit cell dimensions.
String is the symbol or the number of the space group, according to International Tables (1974). Blanks are necessary among the terms constituting the space group symbol (see Examples). If no space group is supplied, the program performs the automatic identification of the Laue group and of the extinction symbol from diffraction intensities. If the string SCAN is supplied, the program consecutively explores (performing a complete solution run) all the allowed space groups, related to the most probable extinction group.
FORMULA (El1n1El2n2El3n3 …)Z
Unit cell content. Eli is the chemical symbol of atomic type i, ni is the corresponding number of atoms in the chemical formula, Z is the number of molecules in the unit cell. To avid ambiguities, the two-characters elements must have the second character in lower case i.e. formula (BaSO4)4.
CONTENT El1 n1 El2 n2 El3 n3 ….
Unit cell content. Eli is the chemical symbol of atomic type i, ni is the corresponding number of atoms in the unit cell. The items in this directive must be separated by blanks. i.e. CONTENT C 68 H 104 O 40
Up to a maximum of 18 atomic species are allowed. For each chemical element up to Californium (Cf, Z=98) X-Ray, electrons and neutrons scattering factor constants for are stored, together with information on the atomic number and weight, covalent and Van-der-Waals radii, etc. in the file Sir.xen provided with the program.
SFACTORS El a1 b1 a2 b2 a3 b3 a4 b4 c
Scattering factors for species El. If more lines are necessary, use character = at the end of the line.
String is the name of the reflections file. Each records contains: Miller indices h,k,l, |Fo|, σ(Fo) (or |Fo|2, σ(Fo2) where h,k,l are integer (up to 512). The end of reflections is detected using one of the following:
– blank record.
– end of file.
Negative values of |Fo| are allowed; negative values of σ(Fo) are forbidden.
String is the run time format to read reflections. Default value for string is (3I4,2F8.2). If String is equal to free, blank delimited values are expected in the reflections file.
To be used when σ(Fo) values are meaningless or not available.
Program assumes h,k,l, |Fo|, σ(Fo). |Fo|2 and σ(Fo2) are expected as default.
Program assumes h,k,l, |Fo|2and σ(Fo2) (default choice).
To set a suitable phasing strategy. The possible values for String are: s, m, l. Default procedure is automatically chosen by the program, on the basis of the structural complexity.
Maximum value of (sinθ/λ)2 accepted for reflections to be used. In default all the data are accepted.
Maximum value of resolution (in Å) accepted for reflections to be used. In default all the data are accepted.
Minimum value of resolution (in Å) accepted for reflections to be used. In default all the data are accepted.
The program generates non-measured reflections beyond and behind the experimental resolution limit up to the specified maximum resolution value (in Å). Unobserved values are actively used in the DSR procedures. If x value is not supplied, the default resolution limit is settled by the program. Generate is a default option for macromolecules, if data at non atomic resolution are supplied.
The program does not generate (and use in active way) non-measured reflections beyond and behind the experimental resolution limit (as request by the default DSR procedures).
WAVE string or x
Nevertheless the wavelength is not used during the structure solution stage, it is necessary for the LSQ-refinement and its value is also written in CIF file produced by the program. Possible values for string are: Cu, Mo or a numeric value. Default wavelength is Mo. It is possible to supply a numeric value for the wavelength used (in Å).
Number of active reflections with largest |E| values (up to 4000) subject to a minimum value of |E| = 1.2. Default number is computed by the program.
Overall isotropic thermal factor, if the user wants to supply it. (The scale factor is assumed equal to 1).
This directive specifies that electron diffraction data will be used.
This directive specifies that neutron diffraction data will be used.
String is the name of the reflections file in MTZ format.
Strings are the names of columns in the MTZ reflections file.
String is the name of the sequence file (FASTA format).
Number of residues in the asymmetric unit.
Molecular weight (in Dalton) in the asymmetric unit.
Number of equal molecules in the asymmetric unit if SEQUENCE has been used.
HETATOMS El1 n1 El2 n2 El3 n3 ….
Heterogenic atoms content. Eli is the chemical symbol of atomic type i, ni is the corresponding number of atoms in the asymmetric unit.
ANOMALOUS El n f’1 f”1 [f’2 f”2 …]
El is the chemical symbol of the anomalous scatterer, n is the corresponding number of atoms in the asymmetric unit cell, f’ and f” are the values corresponding to the first wavelength used. Up to four wavelengths are allowed. This directive is used for SAD/MAD data. If more than one anomalous scatterer is used, the ANOMALOUS directive has to be repeated for all of them.
Used when also the native data are supplied in the reflections file.
The following directives can be used also in Phase routine
Triplets with G < x are not actively used. Default threshold value is computed by the program (in any case x > 0.1).
The program uses the Cochran distribution. (P10 formula is used by default).
The program does not actively use negative quartet relationships.
The program does not actively use PSI-zero triplet relationships.
MDM [n1 n2]
The program applies the Modern Direct Methods procedure to n1 sets of random phases. Default n1 value is automatically chosen by the program, on the basis of the structural complexity. The program starts from the MDM n2th trial (default n2 = 1).
SDM [n11 n12 …. ni1 ni2]
The program applies the Standard Direct Methods procedure. If n11 and n12 (or more pairs) are supplied by the user, the program explores blocks (up to 10) of n1 tangent trials and then selects the most promising n2 (up to 500) phase sets (those with the highest eFOM score) to perform DSR procedure. Default n1 and n2 values are automatically selected by the program, on the basis of the structural complexity.
VLD [n1 n2 n3]
The program applies the VLD procedure. n1 is the number of cycles per trial, n2 is the number of trials, n3 is starting trial. Default values for n1 , n2 , n3 are 300, 20, 1 respectively.
PATTERSON [n1 n2]
The program applies the Patterson procedure. n1 is the total number of Patterson trials explored by the program. Default n1 value is automatically chosen by the program, on the basis of the structural complexity. The program starts from the Patterson n2th trial (default n2 = 1).
The program stores the n best trials in terms of R factor. Default n = 1 for X-Ray data, n = 5 for electron diffraction data.
The program stops if the final crystallographic residual factor (Rf%) is less than x. The default value is 25% for X-Ray data, is 0% for electron diffraction data. This directive is meaningless for macromolecules.
Used to visualize a known model. String is the name of the coordinates file (*.cif, *.res, *.ins, *.pdb).
Used to refine and complete a known fragment. String is the name of the coordinates file (*.cif, *.res, *.ins, *.pdb).
The program will produce the coordinates output file in SHELX format.
The program will produce the coordinates output file in CRYSTALS format.
To modify the number of Simulated Annealing runs. The default is 10 runs.
To modify the number of moves for each temperature step. In default the number of moves is automatically calculated.
To define the maximum resolution used by Simulated Annealing. The default is x=2.0 Å.
To modify the initial temperature. In default the initial temperature is automatically calculated.
x ranges between 0 and 1 and determines the cooling rate. The default value is 0.90.
FIXROTATION n1 n2
To fix the internal DOF. n1 and n2 are the atoms associated to the DOF. This directive is useful when relying on the prior chemical knowledge of the structure to fix some of its internal DOFs. For example, double bonds in conjugated acyclic systems, triple bonds, nitrilic bonds, etc.
To fix the translation of fragment containing n atom, where n is the order number of any atom in the fragment. This directive is repeated in case of fixing the translation of different fragments.
To fix the rotation of fragment containing n atom, where n is the order number of any atom in the fragment. This directive is repeated in case of fixing the rotation of different fragments.
To refine the thermal parameters.
SHIFT_ATOM x or SHIFT_ATOM x n1 n2 n3 …
To refine the atomic parameters by applying shifts (up to x) on the atoms with respect to the center of gravity of the fragment. The suggested x is 0.02. Add n1 , n2 , n3 ,… to refine only some specific atoms.
To choose the cost function: 1 for R structure factor, 2 for R intensities. The default is 1.
To randomize the internal and external DOFs and the atomic parameters (if refined). n is an optional parameters used as seed of random generator.
ROTAT n1 n2
To specify the internal DOF using the input file.
The pseudotranslational information will be actively used to solve the protein structure.
The program just finds the orientation of a model and stops.
The program export the output coordinates files in SHELX format (PDB format is the default).
Starts the block of directives related to each model.
Ends the block of directives related to each model.
FRAGMENT [HETAM] string
String is the name of the coordinates file (*.pdb). HETAM allows the program to use Heterogenic atoms content.
The MR model will be improved using VLD and, if the resolution is worse than 1.25 Å, by means of the Free Lunch algorithm.
The MR model will be refined by Refmac (if installed) using batches on n refinement cycles. The default is REFINE 10.
No refinement by Refmac of the MR model.
The Free Lunch algorithm will not be used.
String is the name of the file (in FASTA format) containing the alignment between the sequence of the target and the sequence of the model.
The polyalanine model will be applied.
BFACTOR x / wilson / pdb
The atomic B factors are set to x or to the Wilson B-factor or to the PDB values.
CUT n1 n2
The program removes from the model some terminal residues if they lie ‘outside’ n1 and n2 limits.
RANGE x y
Resolution range (in Å) the program will use. If only one limit is given, it is the high resolution limit; otherwise must be x < y.
THRESHOLD x y z w
The program selects the solutions to be analyzed after the rotation, the clustering, the translation and the optimization stage; the cutoff value is the maximum normalized distance from the best solution FOM. The default value is 0.1 for all the stages. In case of difficult structures with sequence identity less than 45% the values is automatically set to 0.15.
The number of monomer to search is set to n.
Sequence identity with the target sequence (between 0.0 and 1.0). In default it will be calculated by the program.
POSITION r1 r2 r3 t1 t2 t3
The rotation (r1 , r2 , r3 eulerian angles) and the translation (t1 , t2 , t3 fractional values) are applied to the model.
ROTSELECTED r1 r2 r3
The rotation (r1 , r2 , r3 eulerian angles) is applied to the model; the procedure continues normally.
TRASELECTED t1 t2 t3
The translation (t1 , t2 , t3 fractional values) is applied to the model; the procedure continues normally.
WAVE n1 n2 n3 n4
Which wavelengths will be used for substructure refinement and phase extension. The wavelength number order corresponds to that specified in %Data with the directive ANOMALOUS
WAVE 1 3 Only the first and the third wavelength will be used.
If the directive WAVE is absent all the wavelengths will be used.
SET n1 n2
Specifies the number (the range) of the substructures previously obtained.
n1, n2 = 1 , 2 … 10 (ordered by FOM_frag)
SET 1 2 the first two sets (in order of FOMfrag) will be used.
The default is SET 1 – 1, i.e. all fragments will be used.
Conditions for the refinement (LSQ) of the substructure/wavelength parameters;
n=0,1,..5 specifies the options for substructure parameters (x,y,z, B-factor, sof).
0 no refinement
1 only B-factor
2 x, y,z
3 x, y, z , B-factor
4 only sof
5 x, y, z, B-factor, sof
The default value is 5.
m specifies the options for wavelength parameter (f” , df’).
0 no refinement
3 f”, df’
The default value is 3.
LSQ 50 Refine only substructure parameters x,y,z, B-factor, sof
LSQ 53 Refine all parameters: x, y, z, B-factor, sof, f” and df’
String is the name of the file (*.pdb) which contains the coordinates of the anomalous substructure.
Default: the program will use the file structurename_SIR200x.fra written during the anomalous scatterer substructure determination.
String is the name of the coordinates file (*.pdb) where a previously created model is stored . (i.e. a Molecular Replacement result).
String is the name of the reflections file in MTZ format, if not already defined in %Data. Phase and fom columns are necessary to perform refinement.
Strings are the names of columns in the MTZ reflections file, if not already defined in %Data.
Phases have been produced by a Molecular Replacement procedure.
Phases have been produced by a MAD/SAD procedure.
Phases have been produced by an ab initio procedure.