Keywords

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.

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• Basic Keywords

• Advanced Keywords

• Expert Keywords

• Developer Keywords

There are equivalent Python Functions for the python interface to Phaser

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> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC>

Minimal definition of atom position

ATOM CRYSTAL <XTALID> [ELEMENT|CLUSTER] <TYPE> [ORTH|FRAC] <X Y Z> OCC <OCC> [ ISOB <ISOB> | ANOU <HH KK LL HK HL KL> | USTAR <HH KK LL HK HL KL>] FIXX [ON|OFF] FIXO [ON|OFF] FIXB [ON|OFF] BSWAP [ON|OFF] LABEL <SITE_NAME>

Full definition of atom position. B-factor defaults to isotropic and Wilson B-factor if not set and setATOM_BFACTOR_WILSON is used (the default).

ATOM CHANGE BFACTOR WILSON [ON|OFF]

Reset all atomic B-factors to the Wilson B-factor

ATOM CHANGE SCATTERER <SCATTERER>

Reset all atomic scatterers to element (or cluster) type

BFACTOR

BFACTOR WILSON RESTRAINT [ON|OFF]

Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing.

BFACTOR SPHERICITY RESTRAINT [ON|OFF]

Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing

BFACTOR REFEINE RESTRAINT [ON|OFF]

Toggle to use the restraint to zero for molecular Bfactor in molecular replacement.

BFACTOR WILSON SIGMA <SIGMA>

The sigma of the Wilson restraint.

BFACTOR SPHERICTY SIGMA <SIGMA>

The sigma of the sphericity restraint.

BFACTOR REFINE SIGMA <SIGMA>

The sigma of the sphericity restraint.

• Default: BFACTOR WILSON RESTRAINT ON
• Default: BFACTOR SPHERICITY RESTRAINT ON
• Default: BFACTOR REFINE RESTRAINT ON
• Default: BFACTOR WILSON SIGMA 5
• Default: BFACTOR SPHERICITY SIGMA 5
• Default: BFACTOR REFINE SIGMA 10

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>

Radius for the decomposition of the Patterson in Ångstroms. If it is 0, the radius defaults to 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.

• Default: CLMN LMIN 4
• Default: CLMN LMAX 100
• Default: CLMN SPHE 0

CLUSTER

CLUSTER PDB <PDBFILE>

Sample coordinates for a cluster compound for experimental phasing.

COMPOSITION

COMPOSITION BY [AVERAGE|SOLVENT|ASU]

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 [ON|OFF]

Extra verbose output for debugging

• Default: DEBUG OFF

EIGEN

EIGEN [ READ <EIGENFILE> | WRITE [ON|OFF] ]

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> PDB <PDBFILE> CARD ON

The name of a (non-standard) PDB file used to build an ENSEMBLE. The RMS deviation is parsed from the MODEL cards of the pdb file (MODEL RMS <rms>) that separate the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles.The pdb file is non-standard because of the addition of the RMS keyword to the MODEL card and also because the atom list for the different models need not be the same.

ENSEMBLE <MODLID> HKLIN <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

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

ENSEMBLE <MODLID> DISABLE CHECK [ON|OFF]

Toggle to disable checking of deviation between models in an ensemble. Use with extreme caution. Results of computations are not guaranteed to be sensible.

• Default: ENSEMBLE <MODLID> DISABLE CHECK OFF

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

HAND

HAND [ON|OFF|BOTH]

Toggle for whether or not to use other hand of space group, or both hands, in experimental phasing

• Default: HAND BOTH

HKLIN

HKLIN <FILENAME>

The mtz file containing the data

HKLOUT

HKLOUT [ON|OFF]

Flags for output of an mtz file containing the phasing information

• Default: HKLOUT ON

INTEGRATION

INTEGRATION FIXED [ON | OFF]

Fix the number of integration points or determine the number of angular steps in the integration by the variance of the function

INTEGRATION STEP <STEP>

Number of steps in angular integration of function if FIXED number of points

• Default: INTEGRATION FIXED OFF

JOBS

JOBS <NUM>

Number of processors to use in parallelized sections of code

• Default: JOBS 2

KEYWORDS

KEYWORDS [ON|OFF]

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 [ON|OFF]

Toggle for structure completion by log-likelihood gradient maps

LLGComplete SCATTERER <TYPE>

Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer

LLGComplete CLASH <CLASH>

Minimum distance between atoms in log-likelihood gradient maps (default determined by resolution, flagged by CLASH=0)

LLGComplete SIGMA <Z>

Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps

LLGComplete NCYC <NMAX>

Maximum number of cycles of log-likelihood gradient structure completion. By default, NMAX is 50, but this limit should never be reached, because all features in the log-likelihood 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 [ON|OFF]

Output map coefficients to mtz file

LLGComplete METHOD [IMAGINARY|ATOMTYPE]

Pick peaks from the imaginary map only or from all the completion atomtype maps

• Default: LLGCOMPLETE COMPLETE OFF
• Default: LLGCOMPLETE CLASH 0
• Default: LLGCOMPLETE SIGMA 6
• Default: LLGComplete NCYC 50
• Default: LLGComplete MAPS OFF
• Default: LLGComplete METHOD ATOMTYPE

MACANO

MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]

Protocol for the refinement of SigmaN in the anisotropy correction

MACANO ANISOTROPIC [ON|OFF] BINS [ON|OFF] SOLK [ON|OFF] SOLB [ON|OFF] {NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}

Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are performed in the order in which they are entered.

• Default: MACANO PROTOCOL DEFAULT

MACHL

MACHL PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]

Protocol for refinement of Hendrickson-Lattman coefficients

MACHL COEFFICIENTS [ON|OFF] {NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}

Macrocycle for custom refinement of Hendrickson-Lattman coefficients. Macrocycles are performed in the order in which they are entered.

• Default: MACHL PROTOCOL DEFAULT

MACMR

MACMR PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]

Protocol for refinement of molecular replacement solutions

MACMR ROT [ON|OFF] TRA [ON|OFF] BFAC [ON|OFF] VRMS [ON|OFF] {NCYCLE <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}

Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered.

• Default: MACMR PROTOCOL DEFAULT

MACNCS

MACNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]

Protocol for pseudo-translational NCS refinement.

MACNCS ROT [ON|OFF] TRA [ON|OFF] VRMS [ON|OFF] {NCYCLE <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}

Macrocycle for pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.

• Default: MACNCS PROTOCOL DEFAULT

MACSAD

MACSAD PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]

Protocol for SAD refinement.

n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details

MACSAD K [ON|OFF] B [ON|OFF] SIGMA [ON|OFF] XYZ [ON|OFF] OCCupancy [ON|OFF] BFACtor [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] {NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}

Macrocycle for SAD refinement. Macrocycles are performed in the order in which they are entered.

• Default: MACSAD PROTOCOL DEFAULT

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 a separate page on Keyword Modes

MUTE

MUTE [ON|OFF]

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 rotation-translation block method, CA uses C-alpha 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 rotation-translation 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 C-alpha atoms clash with (come within CLASH Ångstroms of) other C-alpha atoms, the distances between C-alpha atoms STRETCH too far (note that normal modes do not preserve the geometry) or the MAXRMS deviation has been reached.

NMAPDB RMS DIRECTION [FORWard|BACKward|TOFRo]

The structure is perturbed either forwards or backwards or to-and-fro (FORWARD|BACKWARD|TOFRO) along the eigenvectors of the modes specified.

NMAPDB DQ <DQ1> {DQ <DQ2>…}

Alternatively, the DQ factors (as used by the Elnemo server (K. Suhre & Y-H. 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 [ON|OFF]

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 | PERCENT | 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 C-alpha clashes within ALLOWED_CLASHES Ångstroms (ALLOW); or allow up to the ALLOWED_CLASHES percentage of C-alpha atoms of the model structure to clash; 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 right-justified (i.e. in column 20 for the single-letter names of ribonucleotides such as A, or in columns 19-20 for the two letter names of deoxyribonucleotides such as DA).

PACK CUTOFF <ALLOWED_CLASHES>

Limit on total number of clashes

PACK QUICK [ON|OFF]

Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached

PACK DISTANCE <CLASH_DISTANCE>

Distance within which C-alpha 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 PERCENT
• Default: PACK CUTOFF 5
• 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 [ROT|TRA] SELECT [ ¹PERCENT | ²SIGMA | ³NUMBER | ⁴ALL] CUTOFF <CUTOFF>

Peaks for the rotation function (ROT) or translation function (TRA) satisfying selection criteria are saved

¹Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.

²Select peaks by taking all peaks with a Z-score greater than CUTOFF

³Select peaks by taking top CUTOFF

⁴Select all peaks

PEAKS [ROT|TRA] CLUSTER [ON|OFF]

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 [ON|OFF]

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 ENABLE [ON|OFF]

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 ENABLE ON PERCENT 75

RESCORE

RESCORE [ROT|TRA] [ON|OFF]

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 B-factor in the direction of lowest fall-off (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 final 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 for molecular replacement: RESOLUTION 2.5 for all calculations, except anisotropy correction and final rigid-body refinement.
• Default for molecular replacement: all data used for final rigid-body refinement (if no RESOLUTION AUTO command given)
• Default for experimental phasing: use all data

ROOT

ROOT <FILEROOT>

Root filename for output files (e.g. FILEROOT.log)

• Default: ROOT PHASER

ROTATE

ROTATE VOLUME FULL

Sample all unique angles

ROTATE VOLUME AROUND EULER <A B G> RANGE <RANGE>

Restrict the search to the region of +/- RANGE degrees around orientation given by EULER

• Constraint: RANGE>0
• Default: ROTATE VOLUME FULL

SAMPLING

SAMPLING [ROT|TRA]

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 TYPE <TYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF|EDGE]

Measured scattering factors for a given atom type, from a fluorescence scan. FIX EDGE (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIX ON or FIX OFF does not depend on proximity of edge.

SCATTERING RESTRAINT [ON|OFF]

use Fdp restraints

SCATTERING SIGMA <SIGMA>

Fdp restraint sigma used is SIGMA multiplied by initial fdp value

• Default: SCATTERING SIGMA 0.2
• Default: SCATTERING RESTRAINT 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 sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).

SEARCH ORDER AUTO [ON|OFF]

Search in the "best" order as estimated using estimated rms deviation and completeness of models.

SEARCH METHOD [FULL|FAST]

Search using the "full search" or "fast search" algorithms.

SEARCH DEEP [ON|OFF]

Flag to control whether or not the cuttoff for the peaks in the rotation function is reduced if there is no TFZ over ZSCORE_CUTOFF in the first search. Search method FAST only.

SEARCH DOWN PERCENT <PERC>

Percentage to reduce rotation function cutoff if there is no TFZ over ZSCORE_CUTOFF in first search Search method FAST only.

• Default: SEARCH METHOD FULL
• Default: SEARCH ORDER AUTO ON
• Default: SEARCH DEEP ON
• Default: SEARCH DOWN PERCENT 10

SGALTERNATIVE

SGALTERNATIVE SELECT [ALL|HAND|LIST|NONE]

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 [ON|OFF]

Sort alternative space group list in order of frequency of occurrence

• Default: SGALTERNATIVE SELECT HAND
• Default: SGALTERNATIVE SORT ON

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 TEMPLATE

Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET

SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A B G> [ORTH|FRAC] <X Y Z> FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC>

This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. 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 ENSEMBLE <MODLID> VRMS <V1> <V2> ...

Refined RMS variance terms for pdb files (or map) in ensemble MODLID. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword.

SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A B G> {SCORE <SCORE>}

Rotation List for translation function

SOLUTION ORIGIN ENSEMBLE <MODLID>

Create solution for ensemble MODLID at the origin

SORT

SORT [ON|OFF]

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

TARGET

TARGET FRF [LERF1|LERF2|CROWTHER]

Target function for fast rotation searches (2)

TARGET FTF [LETF1|LETF2|LETFL|LETFQ|CORRELATION]

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]

TNCS

TNCS TRA VECTOR <x y z>

Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.

TNCS ROT ANGLE <rotx roty rotz>

Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes.

TNCS ROT RANGE <angle>

Maximum deviation from initial rotation from which to look for rotational deviation. The best refined rotational angle will be selected.

TNCS ROT SAMPLING <sampling>

Sampling for rotation search. By default the sampling depends on the resolution and the estimated molecular radius.

TNCS VARIANCE RMS <num>

Input estimated rms deviation between pseudo-translational symmetry vector related molecules.

TNCS VARIANCE FRAC <num>

Input estimated fraction of cell content that obeys pseudo-translational symmetry.

• Default: TNCS VARIANCE RMS 0.5
• Default: TNCS VARIANCE FRAC 1
• Default: TNCS ROT ANGLE 0 0 0
• Default: TNCS ROT RANGE 0

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 [ORTH|FRAC] START <XS YS ZS> END <XE YE ZE>

Search volume for brute force translation function. Search along line.

TRANSLATE VOLUME REGION [ORTH|FRAC] START <XS YS ZS> END <XE YE ZE>

Search volume for brute force translation function. Search region.

TRANSLATE VOLUME AROUND [ORTH|FRAC] 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 B-factor (B) for the anomalous scatterer model, the overall scale (PK) and B-factor (PB) for the partial structure (if given), and sigma-scale (SIGMA).

VERBOSE

VERBOSE [ON|OFF]

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 [ON|OFF]

Toggle for output coordinate files.

• Default: XYZOUT OFF (Rotation functions)
• Default: XYZOUT ON (all other relevant modes)

ZSCORE

ZSCORE SOLVED <ZSCORE_SOLVED>

Set the translation function Z-score that indicates a definite solution. Enter 0 to turn off zscore tests.

• Default: ZSCORE SOLVED 8