# Difference between revisions of "Keywords"

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: 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). | : 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). | ||

− | ==[[Image:User2.gif | + | ==[[Image:User2.gif|link=]]VERBOSE== |

; VERBOSE [ON|OFF] | ; VERBOSE [ON|OFF] | ||

: Toggle to send verbose output to log file. | : Toggle to send verbose output to log file. |

## Revision as of 15:22, 20 August 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 MACHL
- 24 MACMR
- 25 MACSAD
- 26 MODE
- 27 MUTE
- 28 NMAMETHOD
- 29 NMAPDB
- 30 NORMALIZATION
- 31 OUTLIER
- 32 PACK
- 33 PARTIAL
- 34 PEAKS
- 35 PERMUTATIONS
- 36 PTGROUP
- 37 PURGE
- 38 RESCORE
- 39 RESHARPEN
- 40 RESOLUTION
- 41 ROOT
- 42 ROTATE
- 43 SAMPLING
- 44 SCATTERING
- 45 SEARCH
- 46 SGALTERNATIVE
- 47 SOLPARAMETERS
- 48 SOLUTION
- 49 SORT
- 50 SPACEGROUP
- 51 SUITE
- 52 TARGET
- 53 TITLE
- 54 TOPFILES
- 55 TRANSLATE
- 56 VARSAD
- 57 VERBOSE
- 58 WAVELENGTH
- 59 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> [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 [ON|OFF]
- Reset all atomic scatterers
- ATOM SCATTERER <SCATTERER>
- Element (or cluster) type to which all scatterers will be changed

## BFACTOR

- BFACTOR WILSON [ON|OFF]
- Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors.
- BFACTOR SPHERICITY [ON|OFF]
- Toggle to use the sphericity restraint on the anisotropic B-factors .
- 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 [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> 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 [ON|OFF|BOTH]
- 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 [ON|OFF]
- 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 [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 [ELEMENT|CLUSTER] <TYPE>
- Atom 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.
- LLGComplete REAL [ON|OFF]
- Complete the model using a purely real scatterer
- LLGComplete ANOMALOUS [ON|OFF]
- Complete the model using a purely imaginary (anomalous) scatterer
- LLGComplete CLASH DEFAULT [ON|OFF]
- LLGComplete CLASH DISTANCE <CLASH>
- Minimum distance between atoms in log-likelihood gradient maps (default determined by resolution)
- 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]

- Default: LLGCOMPLETE COMPLETE OFF
- Default: LLGCOMPLETE CLASH AUTO ON
- Default: LLGCOMPLETE SIGMA 6
- Default: LLGComplete NCYC 50

## MACANO

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

## MACHL

- MACHL COEFFICIENTS [ON|OFF]
*{NCYCle <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}* - Macrocycles for the refinement of Hendrickson-Lattman coefficients
- MACH OFF
- Turns off the Hendrickson-Lattman coefficient refinement

- Default: MACHL OFF

## MACMR

- MACMR ROT [ON|OFF] TRA [ON|OFF]
*{NCYCLE <NCYC>} {MINIMIZER [BFGS|NEWTON|DESCENT]}* - 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 [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]}* - 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 Phaser-2.2: 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 | 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 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 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 [ROT|TRA] 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 Z-score greater than CUTOFF^{3}Select peaks by taking top CUTOFF^{4}Select 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 SELECT [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 SELECT 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 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 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 ELEMENT <ATOMTYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF]
- Measured scattering factors for a given atom type, from a fluorescence scan
- SCATTERING CLUSTER <ATOMTYPE> FP=<FP> FDP=<FDP> FIX [ON|OFF]
- Measured scattering factors for a given cluster, from a fluorescence scan.
- SCATTERING RESTRAIN [ON|OFF]
- use Fdp restraints
- SCATTERING SIGMA [ON|OFF]
- 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 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

- Default: NUM=1
- Default: SEARCH ORDER AUTO ON

## 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

## 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> [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 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 [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

## 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 [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]

## 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)