Difference between revisions of "Keywords"
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Revision as of 10:32, 9 July 2009
Contents
 1 ATOM
 2 BFACTOR
 3 BINS
 4 BOXSCALE
 5 CELL
 6 CLMN
 7 CLUSTER
 8 COMPOSITION
 9 CRYSTAL
 10 DEBUG
 11 EIGEN
 12 ENSEMBLE
 13 FFTS
 14 GAUSS
 15 HAND
 16 HKLIN
 17 HKLOUT
 18 JOBS
 19 KEYWORDS
 20 LABIN
 21 LLGCOMPLETE
 22 MACANO
 23 MACMR
 24 MACSAD
 25 MODE
 26 MUTE
 27 NMAMETHOD
 28 NMAPDB
 29 NORMALIZATION
 30 OUTLIER
 31 PACK
 32 PARTIAL
 33 PEAKS
 34 PERMUTATIONS
 35 PTGROUP
 36 PURGE
 37 RESCORE
 38 RESHARPEN
 39 RESOLUTION
 40 ROOT
 41 ROTATE
 42 SAMPLING
 43 SCATTERING
 44 SEARCH
 45 SGALTERNATIVE
 46 SOLPARAMETERS
 47 SOLUTION
 48 SORT
 49 SPACEGROUP
 50 SUITE
 51 TARGET
 52 TITLE
 53 TOPFILES
 54 TRANSLATE
 55 VARSAD
 56 [[Image:User2.gif]link=]VERBOSE
 57 WAVELENGTH
 58 XYZOUT
Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. Some keywords are meaningful when entered multiple times. The order may or may not be important.
See also: Python Functions
Icons
 Prime Keywords
 Additional Keywords
 Expert Keywords
 Developer Keywords
ATOM
 ATOM CRYSTAL <XTALID> PDB <FILENAME> SCATTERING <ATOMTYPE>
 Definition of atom positions using a pdb file. The scattering type can be changed (for example, for SHELXD which always outputs coordinates as sulphur).
 ATOM CRYSTAL <XTALID> HA <FILENAME>
 Definition of atom positionsusing a ha file (from RANTAN, MLPHARE etc.).
 ATOM CRYSTAL <XTALID> [ELEMENTCLUSTER] <TYPE> [ORTHFRAC] <X Y Z> OCC <OCC>
 Minimal definition of atom position
 ATOM CRYSTAL <XTALID> [ELEMENTCLUSTER] <TYPE> [ORTHFRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB>  ANOU <HH KK LL HK HL KL>  USTAR <HH KK LL HK HL KL>] FIXX [ONOFF] FIXO [ONOFF] FIXB [ONOFF] BSWAP [ONOFF] LABEL <SITE_NAME>
 Full definition of atom position. Bfactor defaults to isotropic and Wilson Bfactor if not set and setATOM_BFACTOR_WILSON is used (the default).
 ATOM CHANGE BFACTOR WILSON [ONOFF]
 Reset all atomic Bfactors to the Wilson Bfactor
 ATOM CHANGE SCATTERER [ONOFF]
 Reset all atomic scatterers
 ATOM SCATTERER <SCATTERER>
 Element (or cluster) type to which all scatterers will be changed
BFACTOR
 BFACTOR WILSON [ONOFF]
 Toggle to use the Wilson restraint on the isotropic component of the atomic Bfactors.
 BFACTOR SPHERICITY [ONOFF]
 Toggle to use the sphericity restraint on the anisotropic Bfactors .
 BFACTOR SIGWILSON <SIGMA>
 The sigma of the Wilson restraint.
 BFACTOR SIGSPHERICTY <SIGMA>
 The sigma of the sphericity restraint.
 Default: BFACTOR WILSON ON
 Default: BFACTOR SPHERICITY ON
 Default: BFACTOR SIGWILSON 5
 Default: BFACTOR SIGSPHERICITY 5
BINS
 BINS {MIN <L>} {MAX <H>} {WIDTH <W>} {CUBIC <A B C>}
 The binning of the data. L = minimum number of bins, H = maximum number of bins, W = width of the bins in number of reflections, A B C are the coefficients for the binning function A(S*S*S)+B(S*S)+CS where S = (1/resolution). If N is given then the values of L and H are ignored.
 Constraint: CUBIC coefficients restricted to monotonically increasing function: A >0, B >0, C >0 and either (a) A=B=0 or (b) A=0 or (c) B=0
 Default: BINS MIN 6 MAX 50 WIDTH 500 CUBIC 0 1 0
BOXSCALE
 BOXSCALE <BS>
 Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BS.
 Constraint: BS > 2.4
 Default: BOXSCALE 4
CELL
 CELL <A B C ALPHA BETA GAMMA>
 Unit cell dimensions
 Constraint: A>0,B>0,C>0,ALPHA>0,BETA>0,GAMMA>0
 Default: Cell read from MTZ file
CLMN
 CLMN SPHERE <SPHERE>
 SPHERE is the radius for the decomposition of the Patterson in Ångstroms. Default value is twice the mean radius of the ENSEMBLE.
 CLMN LMIN <LMIN>
 Lower limit of L values.
 CLMN LMAX <LMAX>
 Upper limit of L values. The largest L value used in the calculation is the minimum of LMAX and 2π * SPHERE/dmin.
 Constraint: SPHERE>5
 Constraint: LMAX>LMIN
 Constraint: LMIN>0
 Default: CLMN LMIN 4
 Default: CLMN LMAX 100
CLUSTER
 CLUSTER ID <ID> PDB <PDBFILE>
 Sample coordinates for a cluster compound for experimental phasing. The ID must be two characters long and not one of the periodic table element symbols.
COMPOSITION
 COMPOSITION BY [AVERAGESOLVENTASU]
 Alternative way of defining composition,by average solvent fraction for crystals (50%)
 COMPOSITION PERCENTAGE <SOLVENT>
 Composition entered by solvent content.
 COMPOSITION PROTEIN [ MW <MW> SEQUENCE <FILE>  NRES <NRES>  STR <STR> ] NUMBER <NUM>
 Composition of the crystals. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of protein in the asymmetric unit.
 COMPOSITION NUCLEIC [ MW <MW> SEQUENCE <FILE>  NRES <NRES>  STR <STR> ] NUMBER <NUM>
 Composition of the crystals. The number of copies NUM of molecular weight MW or SEQ given in fasta format (in a file FILE) or number of residues <NRES> or a sequence string (no spaces) of nucleic acid in the asymmetric unit.
 COMPOSITION ATOM <TYPE> NUMBER <NUM>
 Add NUM copies of an atom (usually a heavy atom) to the composition
 Constraint: MW>0
 Default: COMPOSITION SOLVENT 0.5
CRYSTAL
 CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F> SIGFneg=<SIG>
 Columns of MTZ file to read for this (anomalous) dataset
DEBUG
 DEBUG [ONOFF]
 Extra verbose output for debugging
 Default: DEBUG OFF
EIGEN
 EIGEN [ READ <EIGENFILE>  WRITE [ONOFF] ]
 Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the atomic Hessian are read from the file generated by a previous run, rather than calculated. This option must be used with the job that generated the eigenfile and the job reading the eigenfile must have identical (or default) input for keyword NMAMethod. Use WRITe to control whether or not the eigenfile is written when not using the READ mode.
 Default: EIGEN WRITE ON
ENSEMBLE
 ENSEMBLE <MODLID> PDB <PDBFILE> [RMS <RMS>IDENTITY <ID>] {PDB <PDBFILE> [RMS <RMS>IDENTITY <ID>] }…
 The names of the PDB files used to build the ENSEMBLE, and either the expected RMS deviation of the coordinates to the "real" structure or the percent sequence identity with the real sequence.
 ENSEMBLE <MODLID> MAP <MTZFILE> F=<F> PHI=<PHI> EXTENT <EX EY EZ> RMS <RMS> CENTRE <CX CY CZ> PROTEIN MW <PMW> NUCLEIC MW <NMW>
 An ENSEMBLE defined from a map (via an mtz file). The molecular weight of the object the map represents is required for scaling. The effective RMS coordinate error is needed to judge how the map accuracy falls off with resolution. The extent is needed to determine reasonable rotation steps, and the centre is needed to carry out a proper interpolation of the molecular transform. The extent and the centre are both given in Ångstroms.
 ENSEMBLE <MODLID> FRACTION <FRAC_SCAT>
 Fraction scattering of ensemble entered directly rather than calculated from composition
 Constraint: ID=%
 ENSEMBLE <MODLID> HKL <MTZFILE> SCATTERING <SCAT> EXTEnt <EX EY EZ> PR <P1 P2 P3 P4 P5 P6 P7 P8 P9> PT <TX TY TZ>
 This option can be used to read back a molecular transform computed in an earlier Phaser job run in the MR_ENS mode. May be useful if the spherical harmonic decomposition is very long. This can only be used when repeating the search for a component of the asymmetric unit with no (or the same) known fixed structure as part of the search.
 ENSEMBLE <MODLID> BINS {MIN <L>} {MAX <H>} {NUM <N>} {WIDTH <W>} {CUBIC <A B C>}
 Bins for the MODLID
 Default: ENSEMBLE <MODLID> BINS MIN 5 MAX 200 WIDTH 1000 CUBIC 0 1 0
FFTS
 FFTS MIN [ATOMS_MIN] MAX [ATOMS_MAX]
 The minimum and maximum number of atoms of the range between which direct summation and fft methods are tested to see which is faster for structure factor and gradient calcuation (for this unit cell and resolution). For a number of atoms below ATOMS_MIN direct structure factor calculation is always used, and for a number of atoms above ATOMS_MAX ffts are always used for the structure factor calculation and the gradient calculations. Direct summation is always used for the curvatures. Use FFTS MIN 0 MAX O to always use ffts.
 Default: FFTS MIN 20 MAX 80
GAUSS
 GAUSS INTEGRATION [VARIABLE  FIXED]
 Determine the number of angular steps in the integration by the variance of the function
 GAUSS STEP <STEP>
 Number of steps in angular integration of function if FIXED number of points
 Default: GAUSS INTEGRATION VARIABLE
HAND
 HAND [ONOFFBOTH]
 Toggle for whether or not to use other hand of space group, or both hands, in experimental phasing
 Default: HAND OFF
HKLIN
 HKLIN <FILENAME>
 The mtz file containing the data
HKLOUT
 HKLOUT [ONOFF]
 Flags for output of an mtz file containing the phasing information
 Default: HKLOUT ON
JOBS
 JOBS <NUM>
 Number of processors to use in parallelized sections of code
 Default: JOBS 2
KEYWORDS
 KEYWORDS [ONOFF]
 Write Phaser script file
 Default: KEYWORDS ON
LABIN
 LABIN F = <F> SIGF = <SIGF>
 Columns in mtz file. F must be given. SIGF should be given but is optional
LLGCOMPLETE
 LLGComplete COMPLETE [ONOFF]
 Toggle for structure completion by loglikelihood gradient maps
 LLGComplete [ELEMENTCLUSTER] <TYPE>
 Atom type(s) to be used for loglikelihood gradient completion. If more than one element is entered for loglikelihood gradient completion, the atom type that gives the highest Zscore for each peak is selected.
 LLGComplete REAL [ONOFF]
 Complete the model using a purely real scatterer
 LLGComplete ANOMALOUS [ONOFF]
 Complete the model using a purely imaginary (anomalous) scatterer
 LLGComplete CLASH DEFAULT [ONOFF]
 LLGComplete CLASH DISTANCE <CLASH>
 Minimum distance between atoms in loglikelihood gradient maps (default determined by resolution)
 LLGComplete SIGMA <Z>
 Zscore (sigma) for accepting peaks as new atoms in loglikelihood gradient maps
 LLGComplete NCYC <NMAX>
 Maximum number of cycles of loglikelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the loglikelihood gradient maps should be assigned well before 50 cycles are finished. This keyword should be used to reduce the number of cycles to 1 or 2.
 LLGComplete MAPS [ONOFF]
 Default: LLGCOMPLETE COMPLETE OFF
 Default: LLGCOMPLETE CLASH AUTO ON
 Default: LLGCOMPLETE SIGMA 6
 Default: LLGComplete NCYC 50
MACANO
 MACANO ANISOTROPIC [ONOFF] BINS [ONOFF] SOLK [ONOFF] SOLB [ONOFF] {NCYCle <NCYC>} {MINIMIZER [BFGSNEWTONDESCENT]}
 Macrocycles for the refinement of SigmaN in the anisotropy correction
 MACANO OFF
 Turns off the anisotropy correction
 Default: MACANO ANIS ON BINS ON SOLK OFF SOLB OFF NCYC 50 MINIMIZER NEWTON
MACMR
 MACMR ROT [ONOFF] TRA [ONOFF] {NCYCLE <NCYC>} {MINIMIZER [BFGSNEWTONDESCENT]}
 Molecular replacement refinement macrocycle. The macrocycles are performed in the order that they are entered
 MACMR OFF
 Turn off molecular replacement refinement
 Default:
 MACMR ROT ON TRA ON NCYC 50 MINIMIZER BFGS
MACSAD
 MACSAD K [ONOFF] B [ONOFF] SIGMA [ONOFF] XYZ [ONOFF] OCCupancy [ONOFF] BFACtor [ONOFF] FDP [ONOFF] SA [ONOFF] SB [ONOFF] SP [ONOFF] SD [ONOFF] {NCYCle <NCYC>} {MINIMIZER [BFGSNEWTONDESCENT]}
 SAD refinement macrocycle. The macrocycles are performed in the order that they are entered
 MACSAD OFF
 Turn off SAD refinement
 Default:
 MACSAD K OFF B OFF SIGMA OFF XYZ OFF OCC ON BFAC OFF FDP ON SA OFF SB OFF SP OFF SD OFF NCYC 50 MINIMIZER BFGS
 MACSAD K OFF B OFF SIGMA OFF XYZ ON OCC ON BFAC ON FDP ON SA OFF SB OFF SP ON SD ON NCYC 50 MINIMIZER BFGS
 There are additional undocumented keywords that will crash phaser but are useful for debugging  see code for details'
MODE
 MODE [ ANO  CCA  NMA  MR_AUTO  MR_FRF  MR_FTF  MR_BRF  MR_BTF  MR_RNP  MR_LLG  MR_PAK  EP_AUTO  EP_SAD]
 The mode of operation of Phaser. The different modes are described in Phaser2.2: Modes
MUTE
 MUTE [ONOFF]
 Toggle for running in "silent" mode, with no summary, logfile or verbose output written to "standard output".
 Default: MUTE OFF
NMAMETHOD
 NMAMETHOD OSCILLATORS [RTB  CA  ALL ]
 Define the atoms used for the normal mode analysis. RTB uses the rotationtranslation block method, CA uses Calpha atoms only to determine the modes, and ALL uses all atoms to determine the modes (only for use on very small molecules, less than 250 atoms).
 NMAMETHOD MAXBLOCKS <MAXBLOCKS>
 MAXBLOCKS is the number of rotationtranslation blocks for the RTB analysis.
 NMAMETHOD NRES <NRES>
 For the RTB analysis, by default NRES is calculated so that it is as high as it can be without reaching MAXBlocks.
 Default: NMAMETHOD RTB MAXBLOCKS 250
 NMAMETHOD RADIUS <RADIUS>
 Elastic Network Model interaction radius (Angstroms)
 NMAMETHOD FORCE <FORCE>
 Elastic Network Model force constant
 Default: NMAMETHOD FORCE 1
NMAPDB
 NMAPDB PERTURB [RMS DQ]
 Perturb the structure by rms devitations along the modes, or by set dq increments
 NMAPDB MODE <M1> {MODE <M2>…}
 The MODE keyword gives the mode along which to perturb the structure. If multiple modes are entered, the structure is perturbed along all the modes AND combinations of the modes given. There is no limit on the number of modes that can be entered, but the number of pdb files explodes combinatorially.
 NMAPDB COMBination <NMAX>
 Controls how many modes are present in any combination.
 NMAPDB RMS STEP <RMS>
 Increment in rms Ångstroms between pdb files to be written.
 NMAPDB RMS CLASH <CLASH>
 NMAPDB RMS STRETCH <STRETCH>
 NMAPDB RMS MAX <MAXRMS>
 The structure will be perturbed along each mode until either the Calpha atoms clash with (come within CLASH Ångstroms of) other Calpha atoms, the distances between Calpha atoms STRETCH too far (note that normal modes do not preserve the geometry) or the MAXRMS deviation has been reached.
 NMAPDB RMS DIRECTION [FORWardBACKwardTOFRo]
 The structure is perturbed either forwards or backwards or toandfro (FORWARDBACKWARDTOFRO) along the eigenvectors of the modes specified.
 NMAPDB DQ <DQ1> {DQ <DQ2>…}
 Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & YH. Sanejouand, NAR 2004 vol 32) ) by which to perturb the atoms along the eigenvectors can be entered directly.
 Default: NMAPDB MODE 7
 Default: NMAPDB COMBINATION 3
 Default: NMAPDB PERTURB RMS
 Default: NMAPDB RMS STEP 0.3
 Default: NMAPDB RMS STRETCH 10.0
 Default: NMAPDB RMS CLASH 2.0
 Default: NMAPDB RMS MAXRMS 0.5
 Default: NMAPDB RMS DIRECTION TOFRO
NORMALIZATION
 NORMALIZATION BINS <B1 B2 ...> ANISO <HH KK LL HK HL KL> SOLK <SOLK> SOLB <SOLB>
 The normalization factors that correct for anisotropy in the data
OUTLIER
 OUTLIER REJECT [ONOFF]
 Reject low probability data outliers
 OUTLIER PROB <PROB>
 Cutoff for rejection of low probablity outliers
 Default: OUTLIER REJECT ON PROB 0.000001
PACK
 PACK SELECT [ BEST  ALLOW  ALL ]
 Allow the best packing solutions provided the total number of clashes does not exceed ALLOWED_CLASHES (BEST); or allow all solutions that pack with number of Calpha clashes within ALLOWED_CLASHES Ångstroms (ALLOW); or allow all solutions (ALL).
 If the model is RNA or DNA, phosphate (P) and carbon atoms (C3* and C4*) in the phosphate backbone, and nitrogen atoms in the bases are taken as the marker atoms for clashes. The atom names must start in column 14 (leaving one space at the beginning of the field), and the residue names must be rightjustified (i.e. in column 20 for the singleletter names of ribonucleotides such as A, or in columns 1920 for the two letter names of deoxyribonucleotides such as DA).
 PACK CUTOFF <ALLOWED_CLASHES>
 Limit on total number of clashes
 PACK QUICK [ONOFF]
 Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached
 PACK DISTANCE <CLASH_DISTANCE>
 Distance within which Calpha atoms clash given by CLASH_DISTANCE Ångstroms. If the model is RNA or DNA, phosphate and carbon atoms in the phosphate backbone, and nitrogen atoms in the bases are taken as the marker atoms for clashes
 Default: PACK SELECT BEST
 Default: PACK CUTOFF 10
 Default: PACK QUICK ON
 Default: PACK DISTance 3.0
PARTIAL
 PARTIAL PDB <PDBFILE> [RMS <RMS>IDENTITY <ID>]
 The partial structure for SAD refinement
 Constraint: ID=%
PEAKS
 PEAKS [ROTTRA] SELECT [ ^{1}PERCENT  ^{2}SIGMA  ^{3}NUMBER  ^{4}ALL] CUTOFF <CUTOFF>
 Peaks for the rotation function (ROT) or translation function (TRA) satisfying selection criteria are saved
 ^{1}Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.
 ^{2}Select peaks by taking all peaks with a Zscore greater than CUTOFF
 ^{3}Select peaks by taking top CUTOFF
 ^{4}Select all peaks
 PEAKS [ROTTRA] CLUSTER [ONOFF]
 Toggle for CLUSTER selects clustered peaks
 Default: PEAKS ROT SELECT PERCENT CUTOFF 75
 Default: PEAKS TRA SELECT PERCENT CUTOFF 75
 Default: PEAKS ROT CLUSTER ON
 Default: PEAKS TRA CLUSTER ON
PERMUTATIONS
 PERMUTATIONS [ONOFF]
 Toggle for whether the order of the search set is to be permuted.
 Default: PERMUTATIONS OFF
PTGROUP
 PTGROUP COVERAGE <COVERAGE>
 Percentage coverage for two sequences to be considered in same pointgroup
 PTGROUP IDENTITY <IDENTITY>
 Percentage identity for two sequences to be considered in same pointgroup
 PTGROUP RMSD <RMSD>
 Percentage rmsd for two models to be considered in same pointgroup
 PTGROUP TOLERANCE ANGULAR <ANG>
 Angular tolerance for pointgroup
 PTGROUP TOLERANCE SPATIAL <DIST>
 Spatial tolerance for pointgroup
PURGE
 PURGE SELECT [ONOFF]
 Toggle for whether to purge the solution list from the translation function and the refinement and phasing steps (when searching multiple space groups) according to the best solution found so far.
 PURGE PERCENT <PERC>
 PERC is the percent of the difference between the top solution and the mean at which to purge the solutions.
 Default: PURGE SELECT ON PERCENT 75
RESCORE
 RESCORE [ROTTRA] [ONOFF]
 Toggle for rescoring of fast rotation function (ROT) or fast translation function(TRA) search peaks.
 Default: RESCORE ROT ON
 Default: RESCORE TRA ON
RESHARPEN
 RESHARPEN PERCENTAGE <PERC>
 Perecentage of the Bfactor in the direction of lowest falloff (in anisotropic data) to add back into the structure factors F_ISO and FWT and FDELWT so as to sharpen the electron density maps
 Default: RESHARPEN PERCENT 100
RESOLUTION
 RESOLUTION <HIRES> <LORES>
 Resolution range in Ångstroms. If only one limit is given, it is the high resolution limit; otherwise the limits can be in either order.
 Constraint: HIRES>0,LORES>0
 RESOLUTION AUTO <HIRES> <LORES>
 Resolution range in Ångstroms for high resolution refinement in MR_AUTO mode. If only one limit is given, it is the high resolution limit; otherwise the limits can be in either order.
 Constraint: HIRES>0
 Constraint: LORES>0
 Default: RESOLUTION 3 for rotation and translation functions
ROOT
 ROOT <FILEROOT>
 Root filename for output files (e.g. FILEROOT.log)
 Default: ROOT PHASER
ROTATE
 ROTATE VOLUME [FULLAROUND] EULER <A B G> RANGE <RANGE>
 Sample all unique angles (FULL) or restrict the search to the region of +/ RANGE degrees around orientation given by EULER
 Constraint: RANGE>0
 Default: ROTATE FULL
SAMPLING
 SAMPLING [ROTTRA]
 Sampling of search given in degrees for a rotation search and Ångstroms for a translation search. Sampling for rotation search depends on the mean radius of the Ensemble and the high resolution limit (dmin) of the search.
 Constraint: SAMP>0
 Default: SAMP = 2*atan(dmin/(4*meanRadius)) (MODE = MR_BRF or MR_FRF)
 Default: SAMP = dmin/5; (MODE = MR_BTF)
 Default: SAMP = dmin/4; (MODE = MR_FTF)
SCATTERING
 SCATTERING ELEMENT <ATOMTYPE> FP=<FP> FDP=<FDP> FIX [ONOFF]
 Measured scattering factors for a given atom type, from a fluorescence scan
 SCATTERING CLUSTER <ATOMTYPE> FP=<FP> FDP=<FDP> FIX [ONOFF]
 Measured scattering factors for a given cluster, from a fluorescence scan.
 SCATTERING RESTRAIN [ONOFF]
 use Fdp restraints
 SCATTERING SIGMA [ONOFF]
 Fdp restraint sigma
 Default: SCATTERING SIGMA 0.01
 Default: SCATTERING Restrain ON
SEARCH
 SEARCH ENSEMBLE <MODLID> {OR ENSEMBLE <MODLID>}… NUMBER <NUM>
 The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the subkeyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).
 SEARCH ORDER AUTO [ONOFF]
 Search in the "best" order as estimated using estimated rms deviation and completeness of models
 Default: NUM=1
 Default: SEARCH ORDER AUTO ON
SGALTERNATIVE
 SGALTERNATIVE SELECT [ALLHANDLISTNONE]
 Selection of alternative space groups to test in translation functions. ALL tests all possible space groups, HAND tests the given space group and its enantiomorph and LIST tests the space groups listed with TEST <SG>.
 SGALTERNATIVE TEST <SG>
 Alternative space groups to test.
 SGALTERNATIVE SORT [ONOFF]
 Sort alternative space group list in order of frequency of occurrence
SOLPARAMETERS
 SOLPARAMETERS FSOL <FSOL> BSOL <BSOL>
 Change solvent parameters for Sigma(A) curves. The results are not terribly sensitive to these parameters, which affect only lower resolution data.
 Constraint: 0<FSOL<1, BSOL>0, FSOL<BSOL
 Default: SOLPARAMETERS FSOL 0.95 BSOL 300
SOLUTION
 SOLUTION SET <ANNOTATION>
 Start new set of solutions
 SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A B G> [ORTHFRAC] <X Y Z> FIXR [ONOFF] FIXT [ONOFF] FIXB [ONOFF] BFAC <BFAC>
 This keyword is repeated for each known position and orientation of a ENSEmble ID. A B G are the Euler angles and X Y Z are the translation elements, expressed either in orthogonal Angstroms (ORTH) or fractions of a cell edge (FRAC). The input ensemble is transformed by a rotation around the origin of the coordinate system, followed by a translation.
 SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A B G> {SCORE <SCORE>}
 Rotation List for translation function
SORT
 SORT [ONOFF]
 Sort the reflections into resolution order upon reading MTZ file, for performance gain in molecular replacement
 Default: SORT ON
SPACEGROUP
 SPACEGROUP <SG>
 Space group may be altered from the one on the MTZ file to a space group in the same point group. The space group name or number can be given e.g. P 21 21 21 or 19. l.
 Default: Read from MTZ file
SUITE
 SUITE CCP4
 CCP4 style output
 SUITE PHENIX
 Phenix style output
 SUITE CIMR
 CIMR style output
 Default depends on distribution (CCP4 or Phenix)
TARGET
 TARGET FRF [LERF1LERF2CROWTHER]
 Target function for fast rotation searches (2)
 TARGET FTF [LETF1LETF2LETFLLETFQCORRelation]
 Target function for fast translation searches (3)
 Default: TARGET FRF LERF1
 Default: TARGET FTF LETF1
TITLE
 TITLE <TITLE>
 Title for job
 Default: TITLE [no title given]
TOPFILES
 TOPFILES <NUM>
 Number of top pdbfiles or mtzfiles to write to output.
 Default: TOPFILES 1
TRANSLATE
 TRANSLATE VOLUME FULL
 Search volume for brute force translation function. Cheshire cell or Primitive cell volume.
 TRANSLATE VOLUME LINE [ORTHFRAC] START <XS YS ZS> END <XE YE ZE>
 Search volume for brute force translation function. Search along line.
 TRANSLATE VOLUME REGION [ORTHFRAC] START <XS YS ZS> END <XE YE ZE>
 Search volume for brute force translation function. Search region.
 TRANSLATE VOLUME AROUND [ORTHFRAC] POINT <X Y Z> RANGE <RANGE>
 Search volume for brute force translation function. Search within +/ RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.
 Default: TRANSLATE VOLUME FULL
VARSAD
 VARSAD [ {K <N>}  {B <N>}  {SIGMA <N>}  {SA <B1 B2 …>}  {SB <B1 B2 …>}  {SP <B1 B2 …>}  {SD <B1 B2 …>}  {PK <N>}  {PB <N>}]
 SAD variance parameters SA and SB (the real and imaginary components of Sigma Minus), SP (Sigma Plus) and SD (Sigma Delta) by resolution bin, the overall scale (K) and Bfactor (B) for the anomalous scatterer model, the overall scale (PK) and Bfactor (PB) for the partial structure (if given), and sigmascale (SIGMA).
[[Image:User2.gif]link=]VERBOSE
 VERBOSE [ONOFF]
 Toggle to send verbose output to log file.
 Default: VERBOSE OFF
WAVELENGTH
 WAVELENGTH <LAMBDA>
 The wavelengh at which the SAD dataset was collected
XYZOUT
 XYZOUT [ONOFF]
 Toggle for output coordinate files.
 Default: XYZOUT OFF (Rotation functions)
 Default: XYZOUT ON (all other relevant modes)