View source for Keywords

<div style="margin-left: 25px; float: right;">__TOC__</div>

===Phaser Executable===

The Phaser executable runs in different modes, which perform Phaser's different functionalities. The mode is selected with the [[#MODE | MODE]] keyword. The different modes and the keywords relevant to each mode are described in [[Modes]].

Most keywords only refer to a single parameter, and if used multiple times, the parameter will take the last value input. However, some keywords are meaningful when entered multiple times. The order may or may not be important. 

*[[Image:User1.gif|link=]] [[#Basic Keywords | Basic Keywords]]

*[[Image:Output.png|link=]] [[#Output Control Keywords | Output Control Keywords]]

*[[Image:User2.gif|link=]] [[#Advanced Keywords |Advanced Keywords ]]

*[[Image:Expert.gif|link=]] [[#Expert Keywords | Expert Keywords]]

*[[Image:Developer.gif|link=]] [[#Developer Keywords | Developer Keywords]]


===Python Interface===

Phaser can be compiled as a python library. The mode is selected by calling the appropriate run-job. Input to the run-job is via input-objects, which are passed to the run-job. Setter function on the input objects are equivalent to the keywords for input to the phaser executable. The different modes and the keywords relevant to each mode are described in [[Modes]]. See [[Python Interface]] for details. 

The python interface uses standard python and cctbx/scitbx variable types.

 str          string
 float        double precision floating point
 Miller       cctbx::miller::index<int> 
 dvect3       scitbx::vec3<float> 
 dmat33       scitbx::mat3<float> 
 '''type'''_array   scitbx::af::shared<'''type'''> arrays

=Basic Keywords=
==[[Image:User1.gif|link=]]ATOM== 
; ATOM CRYSTAL <XTALID> PDB <FILENAME>
: Definition of atom positions using a pdb file.
; ATOM CRYSTAL <XTALID> HA <FILENAME>
: Definition of atom positions using 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. B-factor defaults to isotropic and Wilson B-factor. Use <TYPE>=TX for Ta6Br12 cluster and <TYPE>=XX for all other clusters. Scattering for cluster is spherically averaged.  Coordinates of cluster compounds other than Ta6Br12 must be entered with CLUSTER keyword. Ta6Br12 coordinates are in phaser code and do not need to be given with CLUSTER keyword.
; 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 including B-factor.
;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.
 setATOM_PDB(str <XTALID>,str <PDB FILENAME>)
 setATOM_IOTBX(str <XTALID>,iotbx::pdb::hierarchy::root <iotbx object>)
 setATOM_STR(str <XTALID>,str <pdb format string>)
 setATOM_HA(str <XTALID>,str <FILENAME>)
 addATOM(str <XTALID>,str <TYPE>,
   float <X>,float <Y>,float <Z>,float <OCC>)
 addATOM_FULL(str <XTALID>,str <TYPE>,bool <ORTH>,
   dvect3 <X Y Z>,float <OCC>,bool <ISO>,float <ISOB>,
   bool <ANOU>,dmat6 <HH KK LL HK HL KL>,
   bool <FIXX>,bool <FIXO>,bool <FIXB>,bool <SWAPB>,
   str <SITE_NAME>)
 setATOM_CHAN_BFAC_WILS(bool)
 setATOM_CHAN_SCAT(bool)
 setATOM_CHAN_SCAT_TYPE(str <TYPE>)

==[[Image:User1.gif|link=]]CLUSTER==      
; CLUSTER PDB <PDBFILE>
: Sample coordinates for a cluster compound for experimental phasing. Clusters are specified with type XX.  Ta6Br12 clusters do not need to have coordinates specified as the coordinates are in the phaser code. To use Ta6Br12 clusters, specify atomtypes/clusters as TX.
 setCLUS_PDB(str <PDBFILE>)
 addCLUS_PDB(str <ID>, str <PDBFILE>)

==[[Image:User1.gif|link=]]COMPOSITION==      
; COMPOSITION BY [ <sup>1</sup>AVERAGE| <sup>2</sup>SOLVENT| <sup>3</sup>ASU ]
: Alternative ways of defining composition
: <sup>1</sup> AVERAGE solvent fraction for crystals (50%)
: <sup>2</sup> Composition entered by solvent content.
: <sup>3</sup> Explicit description of composition of ASU by sequence or molecular weight
; <sup>2</sup>COMPOSITION PERCENTAGE <SOLVENT>
: Specified SOLVENT content
; <sup>3</sup>COMPOSITION PROTEIN [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM>
: Contribution to composition of the ASU. 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.
; <sup>3</sup>COMPOSITION NUCLEIC [ MW <MW> |SEQUENCE <FILE> | NRES <NRES> | STR <STR> ] NUMBER <NUM>
: Contribution to composition of the ASU. 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.
; <sup>3</sup>COMPOSITION ATOM <TYPE> NUMBER <NUM>
: Add NUM copies of an atom (usually a heavy atom) to the composition
* Default: COMPOSITION BY ASU
 setCOMP_BY(str ["AVERAGE" | "SOLVENT" | "ASU" ])
 setCOMP_PERC(float <SOLVENT>)
 addCOMP_PROT_MW_NUM(float <MW>,float <NUM>)
 addCOMP_PROT_STR_NUM(str <SEQ>,float <NUM>)
 addCOMP_PROT_NRES_NUM(float <NRES>,float <NUM>)
 addCOMP_PROT_SEQ_NUM(str <FILE>,float <NUM>)
 addCOMP_NUCL_MW_NUM(float <MW>,float <NUM>)
 addCOMP_NUCL_STR_NUM(str <SEQ>,float <NUM>)
 addCOMP_NUCL_NRES_NUM(float <NRES>,float <NUM>)
 addCOMP_NUCL_SEQ_NUM(str <FILE>,float <NUM>)
 addCOMP_ATOM(str <TYPE>,float <NUM>)

==[[Image:User1.gif|link=]]CRYSTAL==     
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN Fpos =<F+> SIGFpos=<SIG+> Fneg=<F-> SIGFneg=<SIG->
: Columns of MTZ file to read for this (anomalous) dataset
; CRYSTAL <XTALID> DATASET <WAVEID> LABIN F =<F> SIGF=<SIGF>
: Columns of MTZ file to read for this (non-anomalous) dataset. Used for LLG completion in SAD phasing when there is no anomalous signal (single atom MR protocol). Use LABIN for MR.
 setCRYS_ANOM_LABI(str <F+>,str <SIGF+>,str <F->,str <SIGF->)  
 setCRYS_MEAN_LABI(str <F>,str <SIGF>)

==[[Image:User1.gif|link=]]ENSEMBLE== 
; ENSEMBLE <MODLID> PDB <PDBFILE> [RMS <RMS><sup>1</sup> | IDENTITY <ID><sup>2</sup>  | IDHI <ID><sup>3</sup> | IDLO <ID><sup>4</sup> | CARD ON<sup>5</sup>]  ''{PDB <PDBFILE> [RMS <RMS><sup>1</sup> | IDENTITY <ID><sup>2</sup>  | IDHI <ID><sup>3</sup> | IDLO <ID><sup>4</sup> | CARD ON<sup>5</sup>}…''
: The names of the PDB files used to build the ENSEMBLE, and either
:: <sup>1</sup> The expected RMS deviation of the coordinates to the "real" structure
:: <sup>2</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation.
:: <sup>3</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation sampled one standard deviation higher than the average
:: <sup>4</sup> The percent sequence identity with the real sequence, which is converted to an RMS deviation sampled one standard deviation lower than the average
:: <sup>5</sup> The RMS deviation or sequence IDENTITY is parsed from special REMARK cards of the pdb file (e.g. "REMARK PHASER ENSEMBLE MODEL 1 ID 31.2") containing the superimposed models concatenated in the one file. This syntax enables simple automation of the use of ensembles. The pdb file can be non-standard 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> ''CELL <SCALE>''
: 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. For density obtained from an EM image reconstruction, a good first guess would be to take the resolution where the FSC curve drops below 0.5 and divide by 3. The extent (difference between maximum and minimum x,y,z coordinates of region containing model density) 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. The cell scale factor defaults to 1 and can be refined (for example, if the map is from electron microscopy when the cell scale may be unknown to within a few percent).
; ENSEMBLE <MODLID> ATOM <TYPE> RMS <RMS>
: Define an ensemble as a single atom for single atom MR
; ENSEMBLE <MODLID> HELIX <NUM> 
: Define an ensemble as a helix with NUM residues
; ENSEMBLE <MODLID> HETATM [ON|OFF]
: Use scattering from HETATM records in pdb file. See [[Molecular_Replacement#Coordinate_Editing | Coordinate Editing  ]]
; 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

 addENSE_PDB_ID(str <MODLID>,str <FILE>,float <ID>) 
 addENSE_PDB_RMS(str <MODLID>,str <FILE>,float <RMS>)
 addENSE_CARD(str <MODLID>,str <FILE>,bool)
 setENSE_MAP(str <MODLID>,str <MTZFILE>,str <F>,str <PHI>,dvect3 <EX EY EZ>,
   float <RMS>,dvect3 <CX CY CZ>,float <PMW>,float <NMW>)
 setENSE_DISA_CHEC(bool)

==[[Image:User1.gif|link=]]HKLIN==
; HKLIN <FILENAME>
: The mtz file containing the data
 setHKLI(str <FILENAME>)

==[[Image:User1.gif|link=]]JOBS==      
; JOBS <NUM>
: Number of processors to use in parallelized sections of code
* Default: JOBS 2
 setJOBS(int <NUM>)

==[[Image:User1.gif|link=]]LABIN== 
; LABIN F = <F> SIGF = <SIGF> 
: Columns in mtz file. F must be given. SIGF should be given but is optional
; LABIN I = <nowiki><I></nowiki> SIGI = <SIGI> 
: Columns in mtz file. I must be given. SIGI should be given but is optional
; LABIN FMAP = <PH> PHMAP = <PHMAP> 
: Columns in mtz file. FMAP/PHMAP are weighted coefficients is for use in the Phased Translation Function.
; LABIN FMAP = <PH> PHMAP = <PHMAP> FOM = <FOM>
: Columns in mtz file. FMAP/PHMAP are the unweighted coefficients is for use in the Phased Translation Function and FOM the figure of merit for weighting
 setLABI_F_SIGF(str <F>,str <SIGF>)
 setLABI_I_SIGI(str <nowiki><I></nowiki>,str <SIGI>)
 setLABI_PTF(str <FMAP>,str <PHMAP>,str <FOM>)

 ''Data should be input to python run-jobs using one data_refl parameter''
 ''This is extracted from the ResultMR_DAT object after a call to runMR_DAT''
 setREFL_DATA(data_ref)
 ''Example:''
   i = InputMR_DAT()
   i.setHKLI("*.mtz")
   i.setLABI("F","SIGF")
   r = runMR_DAT(i)
   if r.Success():
     i = InputMR_LLG()
     i.setSPAC_HALL(r.getSpaceGroupHall())
     i.setCELL6(r.getUnitCell())
     i.setREFL_DATA(r.getDATA())
  ''See also: '' [[Python Example Scripts]]

 ''Alternatively, reflection arrays can be set using cctbx::af::shared<double>''
 setREFL_F_SIGF(float_array <F>,float_array <SIGF>)
 setREFL_I_SIGI(float_array <nowiki><I></nowiki>,float_array <SIGI>)
 setREFL_PTF(float_array <FMAP>,float_array <PHMAP>,float_array <FOM>)

==[[Image:User1.gif|link=]]MODE==
; MODE [ ANO | CCA | SCEDS | NMAXYZ | NCS | MR_AUTO | MR_GYRE | MR_ATOM | MR_ROT | MR_TRA | MR_RNP | MR_RGR | MR_OCC | MR_PAK | EP_AUTO | EP_SAD]
: The mode of operation of Phaser.  The different modes are described in a separate page on [[Keyword Modes]]
 ResultANO r = runANO(InputANO)
 ResultCCA r = runCCA(InputCCA)
 ResultNMA r = runSCEDS(InputNMA)
 ResultNMA r = runNMAXYZ(InputNMA)
 ResultNCS r = runNCS(InputNCS)
 ResultMR  r = runMR_AUTO(InputMR_AUTO)
 ResultEP r = runMR_ATOM(InputMR_ATOM)
 ResulrMR_RF r = runMR_FRF(InputMR_FRF)
 ResultMR_TF r = runMR_FTF(InputMR_FTF)
 ResultMR r = runMR_RNP(InputMR_RNP)
 ResultMR r = runMR_RGR(InputMR_RNP)
 ResultMR r = runMR_OCC(InputMR_OCC)
 ResultMR r = runMR_PAK(InputMR_PAK)
 ResultEP r = runEP_AUTO(InputEP_AUTO)
 ResultEP_SAD r = runEP_SAD(InputEP_SAD)

==[[Image:User1.gif|link=]]PARTIAL== 
; PARTIAL PDB <PDBFILE> [RMSIDENTITY] <RMS_ID>
: The partial structure for SAD refinement.
; PARTIAL HKLIN <MTZFILE> [RMS|IDENTITY] <RMS_ID>
: The partial electron density for SAD refinement.
; PARTIAL LABIN FC=<FC> PHIC=<PHIC>
: Column labels for partial electron density for SAD refinement.
 setPART_PDB(str <PDBFILE>)
 setPART_HKLI(str <MTZFILE>) 
 setPART_LABI_FC(str <FC>)
 setPART_LABI_PHIC(str <PHIC>)  
 setPART_VARI(str ["ID"|"RMS"])
 setPART_DEVI(float <RMS_ID>)

==[[Image:User1.gif|link=]]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|GYRE]
: Search using the [[Modes#Modes |full search]], [[Modes#Modes | fast search]] or [[Modes#Modes | gyration search]] algorithms.
; SEARCH DEEP [ON|OFF]
: [[#SEARCH | SEARCH METHOD FAST]] only. Flag to control whether or not the cuttoff for the peaks in the rotation function is reduced if there is no TFZ over the zscore cutoff that determines a true solution (see [[#ZSCORE | ZSCORE]]) in the first search.
; SEARCH ROTREF [ON|OFF]
: Refine the orientations after the rotation function and before the translation function.
; SEARCH DOWN PERCENT <PERC>
: [[#SEARCH | SEARCH METHOD FAST]] only. Percentage to reduce rotation function cutoff if there is no TFZ over the zscore cutoff that determines a true solution (see [[#ZSCORE | ZSCORE]]) in first search.
; SEARCH BFACTOR <BFAC>
: B-factor applied to search molecule (or atom).
; SEARCH OFACTOR <OFAC>
: Occupancy factor applied to search molecule (or atom).
* Default: SEARCH METHOD FAST
* Default: SEARCH ORDER AUTO ON
* Default: SEARCH DEEP ON
* Default: SEARCH DOWN PERCENT 25
* Default: SEARCH BFACTOR 0
* Default: SEARCH OFACTOR 1
* Default: SEARCH ROTREF OFF
 addSEAR_ENSE_NUMB(str <MODLID>,int <NUM>) 
 addSEAR_ENSE_OR_ENSE_NUMB(string_array <MODLIDS>,int <NUM>) 
 setSEAR_ORDE_AUTO(bool])
 setSEAR_METH(str [ "FULL" | "FAST" | "GYRE"])
 setSEAR_DEEP(bool <DEEP>)
 setSEAR_ROTR(bool <ROTREF>)
 setSEAR_DOWN_PERC(float <PERC>)
 setSEAR_BFAC(float <BFAC>)
 setSEAR_OFAC(float <OFAC>)

==[[Image:User1.gif|link=]]SGALTERNATIVE==
; SGALTERNATIVE SELECT [<sup>1</sup>ALL| <sup>2</sup>HAND| <sup>3</sup>LIST| <sup>4</sup>NONE]
: Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in [[#SPACEGROUP | SPACEGROUP]]
: <sup>1</sup> Test all possible space groups, 
: <sup>2</sup> Test the given space group and its enantiomorph.
: <sup>3</sup> Test the space groups listed with SGALTERNATIVE TEST <SG>.
: <sup>4</sup> Do not test alternative space groups.
; SGALTERNATIVE TEST <SG>
: Alternative space groups to test. Multiple test space groups can be entered.
* Default: SGALTERNATIVE SELECT HAND
 setSGAL_SELE(str [ "ALL" | "HAND" | "LIST" | "NONE" ]) 
 addSGAL_TEST(str <SG>)

==[[Image:User1.gif|link=]]SOLUTION==
; SOLUTION SET <ANNOTATION>
: Start new set of solutions 
; SOLUTION TEMPLATE <ANNOTATION>
: Specifies a template solution against which other solutions in this run will be compared. Given in place of SOLUTION SET. Template rotation and translations given by subsequent SOLUTION 6DIM cards as per SOLUTION SETS.
; SOLUTION 6DIM ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> [ORTH|FRAC] <X> <Y> <Z> ''FIXR [ON|OFF] FIXT [ON|OFF] FIXB [ON|OFF] BFAC <BFAC> MULT <MULT>''
: This keyword is repeated for each known position and orientation of an ENSEMBLE MODLID. A B G are the Euler angles (z-y-z convention) 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. BFAC default to 0, MULT (for multiplicity) defaults to 1.
; SOLUTION ENSEMBLE <MODLID> VRMS DELTA <DELTA> RMSD <RMSD>
: Refined RMS variance terms for pdb files (or map) in ensemble MODLID. RMSD is the input RMSD of the job that produced the sol file, DELTA is the shift with respect to this RMSD. If given as part of a solution, these values overwrite the values used for input in the ENSEMBLE keyword (if refined).
; SOLUTION ENSEMBLE <MODLID> CELL SCALE <SCALE>
: Refined cell scale factor. Only applicable to ensembles that are maps
; SOLUTION TRIAL ENSEMBLE <MODLID> EULER <A> <nowiki><B></nowiki> <C> RFZ <RFZ>
: Rotation List for translation function
; SOLUTION ORIGIN ENSEMBLE <MODLID>
: Create solution for ensemble MODLID at the origin
; SOLUTION SPACEGROUP <SG>
: Space Group of the solution (if alternative spacegroups searched)
; SOLUTION RESOLUTION <HIRES>
: High resolution limit of data used to find/refine this solution
; SOLUTION PACKS <PACKS>
: Flag for whether solution has been retained despite failing packing test, due to having high TFZ
 addSOLU_SET(str <ANNOTATION>) 
 addSOLU_TEMPLATE(str <ANNOTATION>) 
 addSOLU_6DIM_ENSE(str <MODLID>,dvect3 <A B C>,bool <FRAC>,dvect3 <X Y Z>,
   float <BFAC>,bool <FIXR>,bool <FIXT>,bool <FIXB>,int <MULT>) 
 addSOLU_ENSE_VRMS(str <MODLID>, float_array <VARIANCES>) 
 addSOLU_ENSE_CELL(str <MODLID>, float <SCALE>)
 addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <A B C>,float <RFZ>)
 addSOLU_ORIG_ENSE(string <MODLID>)

 setSOLU_SPAC(str <SG>)
 setSOLU_RESO(float <HIRES>)
 setSOLU_PACK(bool <PACKS>)

==[[Image:User1.gif|link=]]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 can be entered in one of three ways
#The Hermann-Mauguin symbol e.g. P212121 or P 21 21 21 (with or without spaces)
#The international tables number, which gives standard setting e.g. 19 
#The Hall symbols e.g. P 2ac 2ab
* Default: Read from MTZ file
 setSPAC_NUM(int <NUM>)
 setSPAC_NAME(string <HM>)
 setSPAC_HALL(string <HALL>)

==[[Image:User1.gif|link=]]WAVELENGTH==  
; WAVELENGTH <LAMBDA> 
: The wavelengh at which the SAD dataset was collected
 setWAVE(float <LAMBDA>)
<br>
<br>

=Output Control Keywords=
==[[Image:Output.png|link=]]DEBUG==     
; DEBUG [ON|OFF]
: Extra verbose output for debugging
* Default: DEBUG OFF
 setDEBU(bool) 

==[[Image:Output.png|link=]]EIGEN==
; EIGEN WRITE [ON|OFF]
; EIGEN READ <EIGENFILE>
: Read or write a file containing the eigenvectors and eigenvalues. If reading, the eigenvalues and eigenvectors of the 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 input for the ENM parameters. Use WRITE to control whether or not the eigenfile is written when not using the READ mode.
* Default: EIGEN WRITE ON
 setEIGE_WRIT(bool)
 setEIGE_READ(str <EIGENFILE>)

==[[Image:Output.png|link=]]HKLOUT==    
; HKLOUT [ON|OFF]
: Flags for output of an mtz file containing the phasing information
* Default: HKLOUT ON
 setHKLO(bool) 

==[[Image:Output.png|link=]]KEYWORDS==  
; KEYWORDS [ON|OFF]
: Write output Phaser .sol file (.rlist file for rotation function)
* Default: KEYWORDS ON
 setKEYW(bool)

==[[Image:Output.gif|link=]]LLGMAPS==
; LLGMAPS [ON|OFF]
: Write log-likelihood gradient map coefficients to MTZ file
* Default: LLGMAPS OFF
 setLLGM(bool <True|False>)

==[[Image:Output.png|link=]]MUTE==     
; MUTE [ON|OFF]
: Toggle for running in silent/mute mode, where no logfile is written to ''standard output''.
* Default: MUTE OFF
 setMUTE(bool) 

==[[Image:Output.png|link=]]KILL==     
; KILL TIME [MINS]
: Kill Phaser after MINS minutes of CPU have elapsed, provided parallel section is complete
; KILL FILE [FILENAME]
: Kill Phaser if file FILENAME is present, provided parallel section is complete
* Default: KILL TIME 0  ''Phaser runs to completion''
* Detaulf: KILL FILE ""  ''Phaser runs to completion''
 setKILL_TIME(float) 
 setKILL_FILE(string)

==[[Image:Output.png|link=]]TITLE==
; TITLE <TITLE>
: Title for job
* Default: TITLE [no title given]
 setTITL(str <TITLE>)

==[[Image:Output.png|link=]]TOPFILES==     
; TOPFILES <NUM>
: Number of top pdbfiles or mtzfiles to write to output.
* Default: TOPFILES 1
 setTOPF(int <NUM>) 

==[[Image:Output.png|link=]]ROOT==    
; ROOT <FILEROOT>
: Root filename for output files (e.g. FILEROOT.log)
* Default: ROOT PHASER
 setROOT(string <FILEROOT>)

==[[Image:Output.png|link=]]VERBOSE==  
; VERBOSE [ON|OFF] 
: Toggle to send verbose output to log file.
* Default: VERBOSE OFF
 setVERB(bool) 

==[[Image:Output.png|link=]]XYZOUT==  
; XYZOUT [ON|OFF] ''ENSEMBLE [ON|OFF]''
: Toggle for output coordinate files. If the optional ENSEMBLE keyword is ON, then each placed ensemble is written to its own pdb file. The files are named FILEROOT.#.#.pdb with the first # being the solution number and the second # being the number of the placed ensemble (representing a SOLU 6DIM entry in the .sol file). 
* Default: XYZOUT OFF (Rotation functions)
* Default: XYZOUT ON ENSEMBLE OFF (all other relevant modes)
 setXYZO(bool) 
 setXYZO_ENSE(bool)
<br>
<br>

=Advanced Keywords=
==[[Image:User2.gif|link=]]ELLG==
([[Molecular_Replacement#Should_Phaser_Solve_It.3F|explained here]])
; ELLG TARGET <TARGET>
: Target value for expected LLG for determining resolution limits and search order
<!--; ELLG HIRES <HIRES> Internal control only-->
* Default: ELLG TARGET 120
 setELLG_TARG(float <TARGET>)

==[[Image:User2.gif|link=]]HAND==
; HAND [ <sup>1</sup>ON| <sup>2</sup>OFF| <sup>3</sup>BOTH]
: Hand of heavy atoms for experimental phasing
: <sup>1</sup>Phase using the given hand of heavy atoms 
: <sup>2</sup>Phase using other hand of heavy atoms 
: <sup>3</sup>Phase using both hands of heavy atoms
* Default: HAND BOTH
 setHAND(str [ "OFF" | "ON" | "BOTH" ])

==[[Image:User2.gif|link=]]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 REAL ON
; Use a purely real scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER RX)
; LLGCOMPLETE ANOMALOUS ON
; Use a purely anomalous scatterer for log-likelihood gradient completion (equivalent to LLGCOMPLETE SCATTERER AX)
; LLGCOMPLETE CLASH <CLASH> 
: Minimum distance between atoms in log-likelihood gradient maps and also the distance used for determining anisotropy of atoms (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 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 METHOD ATOMTYPE
 setLLGC_COMP(bool <True|False>) 
 setLLGC_CLAS(float <CLASH>) 
 setLLGC_SIGM(float <Z>)  
 setLLGC_NCYC(int <NMAX>)
 setLLGC_METH(str ["IMAGINARY"|"ATOMTYPE"])

==[[Image:User2.gif|link=]]NMA==  
; NMA  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. The first 6 modes are the pure rotation and translation modes and do not lead to perturbation of the structure. If the number M is less than 7 then M is interpreted as the first M modes starting at 7, so for example, MODE 5 would give modes 7 8 9 10 11.
; NMA COMBINATION <NMAX>
: Controls how many modes are present in any combination.
* Default: NMA MODE 5
* Default: NMA COMBINATION 2
 addNMA_MODE(int <MODE>) 
 setNMA_COMB(int <NMAX>)

==[[Image:User2.gif|link=]]PACK==
; PACK SELECT [ <sup>1</sup>BEST | <sup>2</sup>ALLOW | <sup>3</sup>PERCENT | <sup>4</sup>ALL ]
: <sup>1</sup>Allow the best packing solutions only, provided the total number of clashes does not exceed ALLOWED_CLASHES
: <sup>2</sup>Allow all solutions that pack with number of C-alpha clashes less than ALLOWED_CLASHES
: <sup>3</sup>Allow up to the ALLOWED_CLASHES percentage of C-alpha atoms of the model structure to clash
: <sup>4</sup>Allow all solutions (no packing test)
: 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 (or percent) of clashes 
; PACK QUICK [ON|OFF]
: Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached. However, all clashes are found when the solution has a high Z-score (see [[#ZSCORE | ZSCORE]]).
; PACK COMPACT [ON|OFF]
: Pack ensembles into a compact association (minimize distances between centres of mass for the addition of each component in a solution).
; PACK KEEP HIGH TFZ [ON|OFF]
: Solutions with high tfz (see [[#ZSCORE | ZSCORE]]) but that fail to pack are retained in the solution list.
; PACK OCCUPANCY <CUTOFF>
: Atoms with an occupancy less that <CUTOFF> are excluded from the packing test.
;[[Image:Expert.gif|24px]] PACK DISTANCE <DISTANCE>
: Distance within which C-alpha atoms clash given by 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
;[[Image:Expert.gif|24px]] PACK TRACE USE [ON|OFF]
: Toggle whether or not to only use Trace atoms (C-alpha atoms in proteins and P in RNA/DNA) for packing analysis, or all atoms. Only recommended to be OFF for use with small fragments.
;[[Image:Expert.gif|24px]] PACK TRACE MAX <TRACEMAX>
:If the trace length exceeds TRACEMAX atoms then the molecule(s) will be sampled on a hexagonal grid and the clash distance increased in proportion to the size of the hexagonal grid sampling
* Default: PACK SELECT PERCENT
* Default: PACK CUTOFF 5
* Default: PACK QUICK ON
* Default: PACK KEEP OFF
* Default: PACK KEEP OFF
* Default: PACK OCCUPANCY 0.3
* Default: PACK DISTANCE 3.0
* Default: PACK TRACE USE ON
* Default: PACK TRACE MAX 1000
 setPACK_SELE(str ["BEST"|"ALLOW"|"PERCENT"|"ALL"]) 
 setPACK_CUTO(float <ALLOWED_CLASHES>)
 setPACK_QUIC(bool)
 setPACK_KEEP_HIGH(bool)
 setPACK_OCCU(float)
 setPACK_COMP(bool)
 setPACK_DIST(float <DISTANCE>)
 setPACK_TRAC_USE(bool)
 setPACK_TRAC_MAX(int)

==[[Image:User2.gif|link=]]PEAKS==
; PEAKS TRA SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL] 
; PEAKS ROT SELECT [ <sup>1</sup>PERCENT | <sup>2</sup>SIGMA | <sup>3</sup>NUMBER | <sup>4</sup>ALL]
: Peaks for individual rotation functions (ROT) or individual translation functions (TRA) satisfying selection criteria are saved. To be used for subsequent steps, peaks must also satisfy the overall PURGE selection criteria, so it will usually be appropriate to set only the PURGE criteria (which over-ride the defaults for the PEAKS criteria if not explicitly set).
: <sup>1</sup> Select peaks by taking all peaks over CUTOFF percent of the difference between the top peak and the mean value.
: <sup>2</sup> Select peaks by taking all peaks with a Z-score greater than CUTOFF.
: <sup>3</sup> Select peaks by taking top CUTOFF.
: <sup>4</sup> Select all peaks.
; PEAKS ROT CUTOFF <CUTOFF>
; PEAKS TRA CUTOFF <CUTOFF>
: Cutoff value for the rotation function (ROT) or translation function (TRA) peak selection criteria.
: If selection is by percent and PURGE PERCENT is changed from the default, then the PEAKS percent value is set to the lower PURGE percent value.
; PEAKS ROT CLUSTER [ON|OFF] 
; PEAKS TRA CLUSTER [ON|OFF]
: Toggle selects clustered or unclustered peaks for rotation function (ROT) or translation function (TRA).
* Default: PEAKS ROT SELECT PERCENT
* Default: PEAKS TRA SELECT PERCENT
* Default: PEAKS ROT CUTOFF 75
* Default: PEAKS TRA CUTOFF 75
* Default: PEAKS ROT CLUSTER ON
* Default: PEAKS TRA CLUSTER ON
 setPEAK_ROTA_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"]) 
 setPEAK_TRAN_SELE(str ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])
 setPEAK_ROTA_CUTO(float <CUTOFF>)
 setPEAK_TRAN_CUTO(float <CUTOFF>) 
 setPEAK_ROTA_CLUS(bool <CLUSTER>) 
 setPEAK_TRAN_CLUS(bool <CLUSTER>)

==[[Image:User2.gif|link=]]PERMUTATIONS==    
; PERMUTATIONS [ON|OFF]
: Only relevant to [[#SEARCH | SEARCH METHOD FULL]]. Toggle for whether the order of the search set is to be permuted.
* Default: PERMUTATIONS OFF
 setPERM(bool <PERMUTATIONS>)

==[[Image:User2.gif|link=]]PERTURB==  
; PERTURB RMS STEP <RMS>
: Increment in rms Ångstroms between pdb files to be written. 
; PERTURB RMS CLASH <CLASH> 
; PERTURB RMS STRETCH <STRETCH> 
; PERTURB 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.
; PERTURB 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.
; PERTURB INCREMENT [RMS| DQ] 
: Perturb the structure by rms devitations along the modes, or by set dq increments
; PERTURB 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: PERTURB INCREMENT RMS
* Default: PERTURB RMS STEP 0.2
* Default: PERTURB RMS STRETCH 5.0 
* Default: PERTURB RMS CLASH 2.0
* Default: PERTURB RMS MAXRMS 0.3
* Default: PERTURB RMS DIRECTION TOFRO
 setPERT_INCR(str [ "RMS" | "DQ" ])
 setPERT_RMS_CLAS(float <CLASH>) 
 setPERT_RMS_STRE(float <STRETCH>) 
 setPERT_RMS_MAXI(float <MAX>)
 setPERT_RMS_DIRE(str [ "FORWARDS" | "BACKWARDS" | "TOFRO" ]) 
 addPERT_DQ(float <DQ>)

==[[Image:User2.gif|link=]]PURGE==  
; PURGE ROT ENABLE [ON|OFF]
; PURGE TRA ENABLE [ON|OFF]
; PURGE RNP ENABLE [ON|OFF]
: Toggle for whether to purge the solution list from the RF or TF and after the refinement (RNP) steps (in AUTO mode) according to the best solution found so far. If there are a number of RF or TF searches with different partial solution backgrounds, the PURGE is applied to the total list of peaks.
; PURGE ROT PERCENT <PERC>
; PURGE TRA PERCENT <PERC>
; PURGE RNP PERCENT <PERC>
: PERC is the percent of the difference between the top solution and the mean at which to purge the solutions. Note that this criterion is applied subsequent to any selection criteria applied through the PEAKS command.  If only the PURGE command is given, this over-rides the default for PEAKS.
; PURGE ROT NUMBER <NUM>
; PURGE TRA NUMBER <NUM>
; PURGE RNP NUMBER <NUM>
: NUM is the number of solutions to retain in purging. If NUMBER is given (non-zero) it overrides the PERCENT option.
* Default: PURGE ROT ENABLE ON 
* Default: PURGE ROT PERC 75
* Default: PURGE ROT NUM 0
* Default: PURGE TRA ENABLE ON
* Default: PURGE TRA PERC 75
* Default: PURGE TRA NUM 0
* Default: PURGE RNP ENABLE ON
* Default: PURGE RNP PERC 75
* Default: PURGE RNP NUM 0
 setPURG_ROTA_ENAB(bool <ENABLE>)
 setPURG_TRAN_ENAB(bool <ENABLE>) 
 setPURG_RNP_ENAB(bool <ENABLE>)
 setPURG_ROTA_PERC(float <PERC>) 
 setPURG_TRAN_PERC(float <PERC>) 
 setPURG_RNP_PERC(float <PERC>)
 setPURG_ROTA_NUMB(float <NUM>) 
 setPURG_TRAN_NUMB(float <NUM>)
 setPURG_TRAN_NUMB(float <NUM>)
 setPURG_RNP_NUMB(float <NUM>)

==[[Image:User2.gif|link=]]RESOLUTION==     
; RESOLUTION HIGH <HIRES> 
: High resolution limit in Ångstroms. 
; RESOLUTION LOW <LORES>
: Low resolution limit in Ångstroms.
; RESOLUTION AUTO HIGH <HIRES> 
: High resolution limit in Ångstroms for final high resolution refinement in MR_AUTO mode.
* Default for molecular replacement:  Set by [[#ELLG | ELLG TARGET]] for structure solution, final refinement uses all data
* Default for experimental phasing: All data used
 setRESO_HIGH(float <HIRES>) 
 setRESO_LOW(float <LORES>)
 setRESO_AUTO_HIGH(float <HIRES>) 
 setRESO_AUTO_LOW(float <LORES>)
 setRESO(float <HIRES>,float <LORES>)

==[[Image:User2.gif|link=]]ROTATE==  
; ROTATE VOLUME FULL
: Sample all unique angles 
; ROTATE VOLUME AROUND EULER <A> <nowiki><B></nowiki> <C> RANGE <RANGE> 
: Restrict the search to the region of +/- RANGE degrees around orientation given by EULER
 setROTA_VOLU(string ["FULL"|"AROUND"|) 
 setROTA_EULE(dvect3 <A B C>) 
 setROTA_RANG(float <RANGE>)

==[[Image:User2.gif|link=]]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
 addSCAT(str <TYPE>,float <FP>,float <FDP, string <FIXFDP>) 
 setSCAT_REST(bool) 
 setSCAT_SIGM(float <SIGMA>)

==[[Image:User2.gif|link=]]SCEDS==  
; SCEDS NDOM <NDOM>
:Number of domains into which to split the protein
; SCEDS WEIGHT SPHERICITY <WS>
: Weight factor for the the Density Test in the SCED Score. The Sphericity Test scores boundaries that divide the protein into more spherical domains more highly.
; SCEDS WEIGHT CONTINUITY <WC>
: Weight factor for the the Continuity Test in the SCED Score. The Continuity Test scores boundaries that divide the protein into domains contigous in sequence more highly. 
; SCEDS WEIGHT EQUALITY <WE>
: Weight factor for the the Equality Test in the SCED Score. The Equality Test scores boundaries that divide the protein more equally more highly.
; SCEDS WEIGHT DENSITY <WD>
: Weight factor for the the Equality Test in the SCED Score. The Density Test scores boundaries that divide the protein into domains more densely packed with atoms more highly. 
* Default: SCEDS NDOM 2
* Default: SCEDS WEIGHT EQUALITY 1
* Default: SCEDS WEIGHT SPHERICITY 4  
* Default: SCEDS WEIGHT DENSITY 1
* Default: SCEDS WEIGHT CONTINUITY 0
 setSCED_NDOM(int <NDOM>) 
 setSCED_WEIG_SPHE(float <WS>) 
 setSCED_WEIG_CONT(float <WC>)
 setSCED_WEIG_EQUA(float <WE>) 
 setSCED_WEIG_DENS(float <WD>)

==[[Image:User2.gif|link=]]TARGET==
; TARGET ROT [FAST | BRUTE]
: Target function for fast rotation searches (2). BRUTE searches all angles on a grid with the full rotation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these rotations with the full rotation likelihood target.
; TARGET TRA [FAST | BRUTE | PHASED]
: Target function for fast translation searches (3). BRUTE searches all positions on a grid with the full translation likelihood target. FAST uses a fast fft approximation to the likelihood target and only rescores the highest scoring of these positions with the full translation likelihood target. PHASED select the "phased translation function".
* Default: TARGET ROT FAST
* Default: TARGET TRA FAST
 setTARG_ROTA(str ["FAST"|"BRUTE"])
 setTARG_TRAN(str ["FAST"|"BRUTE"|"PHASED"])

==[[Image:User2.gif|link=]]TNCS==
; TNCS USE [ON|OFF]
: Use TNCS if present: apply TNCS corrections. (Note: was TNCS IGNORE [ON|OFF] in Phaser-2.4.0)
; TNCS NMOL <NMOL>
: Number of molecules/molecular assemblies related by single TNCS vector (usually only 2). If the TNCS is a pseudo-tripling of the cell then NMOL=3, a pseudo-quadrupling then NMOL=4 etc.
; TNCS RLIST ADD [ON | OFF]
: Supplment the rotation list used in the translation function with rotations already present in the list of known solutions. New molecules in the same orientation as those in the known search (as occurs with translational ncs) may not have peaks associated with them from the rotation function because the known molecules mask the presence of the ones not yet found. 
* Default: TNCS USE ON
* Default: TNCS NMOL 2
* Default: TNCS RLIST ADD ON
 setTNCS_USE(bool)
 setTNCS_NMOL(int <NMOL>)
 setTNCS_RLIS_ADD(bool)

==[[Image:User2.gif|link=]]TRANSLATE== 
; TRANSLATE VOLUME [ <sup>1</sup>FULL | <sup>2</sup>REGION | <sup>3</sup>LINE | <sup>4</sup>AROUND ])
: Search volume for brute force translation function.
: <sup>1</sup> Cheshire cell or Primitive cell volume. 
: <sup>2</sup> Search region.
: <sup>3</sup> Search along line. 
: <sup>4</sup> Search around a point.
; <sup>1 2 3</sup>TRANSLATE START <X Y Z> 
; <sup>1 2 3</sup>TRANSLATE END <X Y Z>
: Search within region or line bounded by START and END.
; <sup>4</sup>TRANSLATE POINT <X Y Z>
; <sup>4</sup>TRANSLATE RANGE <RANGE>
: Search within +/- RANGE Ångstroms (not fractional coordinates, even if the search point is given as fractional coordinates) of a point <X Y Z>.
; TRANSLATE [ORTH | FRAC]
: Coordinates are given in orthogonal or fractional values.
* Default: TRANSLATE VOLUME FULL
 setTRAN_VOLU(string ["FULL"|"REGION"|"LINE"|"AROUND"])
 setTRAN_START(dvect <START>)
 setTRAN_END(dvect <END>)
 setTRAN_POINT(dvect <POINT>)
 setTRAN_RANGE(float <RANGE>)
 setTRAN_FRAC(bool <True=FRAC False=ORTH>)

==[[Image:User2.gif|link=]]ZSCORE==   
; ZSCORE USE [ON|OFF]
: Use the TFZ tests. Only applicable with [[#SEARCH | SEARCH METHOD FAST]]. (Note Phaser-2.4.0 and below use "ZSCORE SOLVED 0" to turn off the TFZ tests)
; ZSCORE SOLVED <ZSCORE_SOLVED>
: Set the minimum TFZ that indicates a definite solution for amalgamating solutions in FAST search method. 
;ZSCORE STOP [ON|OFF]
: Stop adding components beyond point where TFZ is below cutoff when adding multiple components in FAST mode. However, FAST mode will always add one component even if TFZ is below cutoff, or two components if starting search with no components input (no input solution).
; ZSCORE HALF [ON|OFF]
: Set the TFZ for amalgamating solutions in the FAST search method to the maximum of ZSCORE_SOLVED and half the maximum TFZ, to accommodate cases of partially correct solutions in very high TFZ cases (e.g. TFZ > 16)
* Default: ZSCORE USE ON
* Default: ZSCORE SOLVED 8
* Default: ZSCORE HALF ON
* Default: ZSCORE STOP ON
 setZSCO_USE(bool <True=ON False=OFF>)
 setZSCO_SOLV(floatType ZSCORE_SOLVED)
 setZSCO_HALF(bool <True=ON False=OFF>)
 setZSCO_STOP(bool <True=ON False=OFF>)
<br>
<br>

=Expert Keywords=

==[[Image:Expert.gif|link=]]MACANO==      
; MACANO PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]
: Protocol for the refinement of SigmaN in the anisotropy correction
; MACANO ANISO [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
 setMACA_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])
 addMACA(bool <ANISO>,bool <BINS>,bool <SOLK>,bool <SOLB>,
   int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])

==[[Image:Expert.gif|link=]]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] ''CELL [ON|OFF] LAST [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. For description of VRMS see the [[FAQ]]. CELL is the scale factor for the unit cell for maps (EM maps). LAST is a flag that refines the parameters for the last component of a solution only, fixing all the others.
* Default: MACMR PROTOCOL DEFAULT
 setMACM_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])
 addMACM(bool <ROT>,bool <TRA>,bool <BFAC>,bool <VRMS>,bool <CELL>bool <LAST>,
   int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])

==[[Image:Expert.gif|link=]]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] OCC [ON|OFF] BFAC [ON|OFF] FDP [ON|OFF] SA [ON|OFF] SB [ON|OFF] SP [ON|OFF] SD [ON|OFF] ''{PK [ON|OFF]} {PB [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
 setMACS_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])
 addMACS(bool <K>,bool <nowiki><B></nowiki>,bool <SIGMA>,
   bool <XYZ>,bool <OCC>,bool <BFAC>,bool <FDP>
   bool <SA>,bool <SB>,bool <SP>,bool <SD>,
   bool <PK>, bool <PB>,
   int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])

==[[Image:Expert.gif|link=]]MACTNCS==     
; MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]
: Protocol for pseudo-translational NCS refinement.
; MACTNCS 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: MACTNCS PROTOCOL DEFAULT
 setMACT_PROT(str [ "DEFAULT" | "CUSTOM" | "OFF" | "ALL" ])
 addMACT(bool <ROT>,bool <TRA>,bool <VRMS>,
    int <NCYC>,str [BFGS"|"NEWTON"|"DESCENT"])

==[[Image:Expert.gif|link=]]OCCUPANCY==     
; OCCUPANCY WINDOW ELLG <ELLG>
: Target eLLG for determining number of residues in window for occupancy refinement. The number of residues in a window will be an odd number. Occupancy refinement will be done for each offset of the refinement window.
; OCCUPANCY WINDOW NRES <NRES>
: As an alternative to using the eLLG to define the number of residues in window for occupancy refinement, the number may be input directly. NRES must be an odd number.
; OCCUPANCY WINDOW MAX <NRES>
: Maximum number of residues in an occupancy window (determined either by ellg or given as NRES) for which occupancy is refined. Prevents the refinement windows from spanning non-local regions of space.
; OCCUPANCY REFINE TOP [ON/OFF]
: Refine occupancy for TOPFILES number of solutions in [[#SEARCH | SEARCH METHOD FAST]]
; OCCUPANCY REFINE REJECT [ON/OFF]
: Refine occupancy for rejected solutions with high TFZ in [[#SEARCH | SEARCH METHOD FAST]]
; OCCUPANCY MIN <MINOCC> MAX <MAXOCC>
: Minimum and maximum values of occupancy during refinement, renormalized to range [0,1] after refinement
; OCCUPANCY NCYCLES <NCYCLES> 
: Number of cycles of occupancy refinement and renormalization to perform
* Default: OCCUPANCY WINDOW ELLG 10
* Default: OCCUPANCY REFINE TOP OFF
* Default: OCCUPANCY REFINE REJECT OFF
* Default: OCCUPANCY MIN 0.1 MAX 1
* Default: OCCUPANCY NCYCLES 3
 setOCCU_WIND_ELLG(float <ELLG)
 setOCCU_WIND_NRES(int <NRES>)
 setOCCU_WIND_MAX(int <NRES>)
 setOCCU_REFI_TOP(bool)
 setOCCU_REFI_REJE(bool)
 setOCCU_MIN(float)
 setOCCU_MAX(float)
 setOCCU_NCYC(float)

==[[Image:Expert.gif|link=]]RESCORE==  
; RESCORE ROT [ON|OFF]
; RESCORE 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|OFF will depend on whether phaser is running in the mode [[#MODE | MODE MR_AUTO]] with [[#SEARCH | SEARCH METHOD FAST]] or with [[#SEARCH | SEARCH METHOD FULL]], or running the translation function separately [[#MODE | MODE MR_FTF]]. For [[#SEARCH | SEARCH METHOD FAST]] the default also depends on whether or not the expected LLG target [[#ELLG | ELLG TARGET <TARGET>]] value is reached.
 setRESC_ROTA(bool)
 setRESC_TRAN(bool)

==[[Image:Expert.gif|link=]]RFACTOR==  
; RFACTOR USE [ON|OFF]
: For cases of searching for one ensemble when there is one ensemble in the asymmetric unit, the R-factor for the ensemble at the orientation and position in the input is calculated. If this value is low then MR is not performed in the MR_AUTO job in FAST search mode. Instead, rigid body refinement is performed before exiting. Note that the same R-factor test and cutoff is used for judging success in single-atom molecular replacement (MR_ATOM mode).
; RFACTOR CUTOFF <VALUE>
: Rfactor in percent used as cutoff for deciding whether or not the R-factor indicates that MR is not necessary.
* Default: RFACTOR USE ON CUTOFF 35
 setRFAC_USE(bool)
 setRFAC_CUTO(float <PERCENT>)

==[[Image:Expert.gif|link=]]SAMPLING==
; SAMPLING ROT <SAMP>
; SAMPLING TRA <SAMP>
: 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.
* Default: SAMP = 2*atan(dmin/(4*meanRadius)) (ROTATION FUNCTION)
* Default: SAMP = dmin/5; (BRUTE TRANSLATION FUNCTION)
* Default: SAMP = dmin/4; (FAST TRANSLATION FUNCTION)
 setSAMP_ROTA(float <SAMP>)
 setSAMP_TRAN(float <SAMP>)
<br>
<br>

=Developer Keywords=
==[[Image:Developer.gif|link=]]BINS==  
; BINS DATA [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]
: The binning of the data.
: <sup>1</sup> L = minimum number of bins
: <sup>2</sup> H = maximum number of bins.
: <sup>3</sup> W = width of the bins in number of reflections
; BINS ENSE [ <sup>1</sup>MIN <L> | <sup>2</sup>MAX <H> | <sup>3</sup>WIDTH <W> ]
: The binning of the calaculated structure factos for the ensembles.
: <sup>1</sup> L = minimum number of bins
: <sup>2</sup> H = maximum number of bins.
: <sup>3</sup> W = width of the bins in number of reflections
* Default: BINS DATA MIN 6 MAX 50 WIDTH 500 
* Default: BINS ENSE MIN 6 MAX 1000 WIDTH 1000 
 setBINS_DATA_MINI(float <L>)
 setBINS_DATA_MAXI(float <H>)
 setBINS_DATA_WIDT(float <W>)
 setBINS_ENSE_MINI(float <L>)
 setBINS_ENSE_MAXI(float <H>)
 setBINS_ENSE_WIDT(float <W>)

==[[Image:Developer.gif|link=]]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 REFINE RESTRAINT [ON|OFF] 
: Toggle to use the restraint to zero for the molecular B-factor in molecular replacement.
; BFACTOR WILSON SIGMA <SIGMA>
: The sigma of the Wilson restraint.
; BFACTOR SPHERICITY SIGMA <SIGMA>
: The sigma of the sphericity restraint.
; BFACTOR REFINE SIGMA <SIGMA>
: The sigma of the restraint to zero for the molecular B-factor in molecular replacement.
* 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 6
 setBFAC_WILS_REST(bool <True|False>)
 setBFAC_SPHE_REST(bool <True|False>)
 setBFAC_REFI_REST(bool <True|False>) 
 setBFAC_WILS_SIGM(float <SIGMA>) 
 setBFAC_SPHE_SIGM(float <SIGMA>) 
 setBFAC_REFI_SIGM(float <SIGMA>)

==[[Image:Developer.gif|link=]]BOXSCALE==
; BOXSCALE <BOXSCALE>
: Scale for box for calculating structure factors. The ensembles are put in a box equal to (extent of molecule)*BOXSCALE
* Default: BOXSCALE 4
 setBOXS<float <BOXSCALE>)

==[[Image:Developer.gif|link=]]CELL==
; <span style="color:darkorange">Python Only</span> 
: Unit cell dimensions
* Default: Cell read from MTZ file
 setCELL(float <A>,float <nowiki><B></nowiki>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)
 setCELL6(float_array <A B C ALPHA BETA GAMMA>)

==[[Image:Developer.gif|link=]]DDM==  
; DDM SLIDER <VAL> 
: The SLIDER window width is used to smooth the Difference Distance Matrix. 
; DDM DISTANCE MIN <VAL> MAX <VAL> STEP <VAL>
: The range and step interval, as the fraction of the difference between the lowest and highest DDM values used to step.
; DDM SEPARATION MIN <VAL> MAX <VAL>
: Through space separation in Angstroms used.
; DDM SEQUENCE MIN <VAL> MAX <VAL>
: The range of sequence separations between matrix pairs.
; DDM JOIN MIN <VAL> MAX <VAL>
: The range of lengths of the sequences to join if domain segments are discontinuous in percentages of the polypeptide chain.
* Default: DDM SLIDER 0
* Default: DDM DISTANCE MIN 1 MAX 5 STEP 50
* Default: DDM SEPARATION MIN 7  MAX 14
* Default: DDM SEQUENCE MIN 0 MAX 1
* Default: DDM JOIN MIN 2 MAX 12
 setDDM_SLID(int <VAL>) 
 setDDM_DIST_STEP(int <VAL>) 
 setDDM_DIST_MINI(int <VAL>) 
 setDDM_DIST_MAXI(int <VAL>) 
 setDDM_SEPA_MINI(float <VAL>) 
 setDDM_SEPA_MAXI(float <VAL>)
 setDDM_JOIN_MINI(int <VAL>) 
 setDDM_JOIN_MAXI(int <VAL>) 
 setDDM_SEQU_MINI(int <VAL>) 
 setDDM_SEQU_MAXI(int <VAL>)

==[[Image:Developer.gif|link=]]ENM==    
; ENM OSCILLATORS [ <sup>1</sup>RTB | <sup>2</sup>CA | <sup>3</sup>ALL ] 
: Define the way the atoms are used for the elastic network model.
: <sup>1</sup>Use the rotation-translation block method.
: <sup>2</sup>Use C-alpha atoms only to determine the modes.
: <sup>3</sup>Use all atoms to determine the modes (only for use on very small molecules, less than 250 atoms). 
; ENM MAXBLOCKS <MAXBLOCKS>
: MAXBLOCKS is the number of rotation-translation blocks for the RTB analysis.
; ENM NRES <NRES>
: For the RTB analysis, by default NRES=0 and then it is calculated so that it is as small as it can be without reaching MAXBlocks. 
; ENM RADIUS <RADIUS>
: Elastic Network Model interaction radius (Angstroms)
; ENM FORCE <FORCE>
: Elastic Network Model force constant
* Default: ENM OSCILLATORS RTB MAXBLOCKS 250 NRES 0 RADIUS 5 FORCE 1
 setENM_OSCI(str ["RTB"|"CA"|"ALL"])
 setENM_RTB_MAXB(float <MAXB>)
 setENM_RTB_NRES(float <NRES>) 
 setENM_RADI(float <RADIUS>) 
 setENM_FORC(float <FORCE>)

==[[Image:Developer.gif|link=]]NORMALIZATION==
; <span style="color:darkorange">Python Only</span>
: The normalization factors that correct for anisotropy in the data
 setNORM_BINS(float_array <B1 B2 ...>)
 setNORM_ANIS(dmat6 <HH KK LL HK HL KL>)
 setNORM_SOLK(float <SOLK>) 
 setNORM_SOLB(float <SOLB>) 
 setNORM(float_array <B1 B2 ...> ,dmat6 <HH KK LL HK HL KL>,float <SOLK>,float <SOLB>)

==[[Image:Developer.gif|link=]]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
 setOUTL_REJE(bool) 
 setOUTL_PROB(float <PROB>)

==[[Image:Developer.gif|link=]]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
 setPTGR_COVE(float <COVERAGE>) 
 setPTGR_IDEN(float <IDENTITY>) 
 setPTGR_RMSD(float <RMSD>) 
 setPTGR_TOLE_ANGU(float <ANG>) 
 setPTGR_TOLE_SPAT(float <DIST>)

==[[Image:Developer.gif|link=]]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
 setRESH_PERC(float <PERCENT>)

==[[Image:Developer.gif|link=]]SOLPARAMETERS==
; SOLPARAMETERS SIGA FSOL <FSOL> BSOL <BSOL> MIN <MINSIGA>
: Babinet solvent parameters for Sigma(A) curves.  MINSIGA is the minimum SIGA for Babinet solvent term (low resolution only)
; SOLPARAMETERS BULK USE [ON|OFF]
: Toggle for use of Babinet solvent parameters for ensemble structure factors, applied to Fmask.
; SOLPARAMETERS BULK FSOL <FSOL> BSOL <BSOL> 
: Babinet solvent parameters for ensemble structure factors, applied to Fmask.
* Default: SOLPARAMETERS SIGA FSOL 1.05 BSOL 501 MIN 0.1
* Default: SOLPARAMETERS SIGA RESTRAINT ON
* Default: SOLPARAMETERS BULK USE OFF
* Default: SOLPARAMETERS BULK FSOL 0.35 BSOL 45
 setSOLP_SIGA_FSOL(float <FSOL>) 
 setSOLP_SIGA_BSOL(float <BSOL>)
 setSOLP_SIGA_MIN(float <MINSIGA>)
 setSOLP_BULK_USE(bool)
 setSOLP_BULK_FSOL(float <FSOL>) 
 setSOLP_BULK_BSOL(float <BSOL>)

==[[Image:Developer.gif|link=]]TARGET== 
; TARGET ROT FAST TYPE [LERF1 | CORRELATION]
: Target function type for fast rotation searches
; TARGET TRA FAST TYPE [LETF1 | LETF2]
: Target function type for fast translation searches
 setTARG_ROTA_TYPE(string TYPE)
 setTARG_TRAN_TYPE(string TYPE)

==[[Image:Developer.gif|link=]]TNCS==
; TNCS ROTATION ANGLE <A> <nowiki><B></nowiki> <C>
: Input rotational difference between molecules related by the pseudo-translational symmetry vector, specified as rotations in degrees about x, y and z axes (GRID OFF). Central value for grid search (GRID ON).
; TNCS ROTATION GRID [ON | OFF]
: Refine the initial rotation angle starting from a grid of orientations around the starting angle (default 0,0,0). Grid controlled by RANGE and SAMPLING. The best refined rotational angle will be selected.
; TNCS ROTATION RANGE <angle>
: Maximum deviation from initial rotation from which to look for rotational deviation. Value of 0 means use internally determined defaultvalue based on resolution of data and size of G-function effective molecular radius.
; TNCS ROTATION SAMPLING <sampling>
: Sampling for rotation search. Value of 0 means use internally determined defaultvalue based on resolution of data and size of G-function effective molecular radius.
; TNCS TRA VECTOR <x y z> 
: Input pseudo-translational symmetry vector (fractional coordinates). By default the translation is determined from the Patterson.
; TNCS VARIANCE RMSD <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.
; TNCS LINK RESTRAINT [ON | OFF]
: Link the occupancy of atoms related by TNCS in SAD phasing
; TNCS LINK SIGMA <sigma>
: Sigma of link restraint of the occupancy of atoms related by TNCS in SAD phasing
; TNCS PATT HIRES <hires>
: High resolution limit for Patterson calculation for TNCS detection
; TNCS PATT LORES <lores>
: Low resolution limit for Patterson calculation for TNCS detection
; TNCS PATT PERCENT <percent>
: Percent of origin Patterson peak that qualifies as a TNCS vector
; TNCS PATT DISTANCE <distance>
: Minium distance of Patterson peak from origin that qualifies as a TNCS vector
* Default: TNCS ROTATION ANGLE 0 0 0
* Default: TNCS ROTATION GRID ON
* Default: TNCS ROTATION SAMPLING 0
* Default: TNCS ROTATION RANGE 0
* Default: TNCS VARIANCE RMS 0.4 
* Default: TNCS VARIANCE FRAC 1 
* Default: TNCS LINK RESTRAINT ON
* Default: TNCS LINK SIGMA 0.1
* Default: TNCS PATT HIRES 5
* Default: TNCS PATT LORES 10
* Default: TNCS PATT PERCENT 20
* Default: TNCS PATT DISTANCE 15
 setTNCS_ROTA_ANGL(dvect3 <A B C>) 
 setTNCS_ROTA_RANG(float <RANGE>) 
 setTNCS_ROTA_SAMP(float <SAMPLING>)
 setTNCS_TRAN_VECT(dvect3 <X Y Z>) 
 setTNCS_VARI_RMSD(float <RMSD>) 
 setTNCS_VARI_FRAC(float <FRAC>)
 setTNCS_LINK_REST(bool)
 setTNCS_LINK_SIGM(float <SIGMA>) 
 setTNCS_PATT_HIRE(float <HIRES>)
 setTNCS_PATT_LORE(float <LORES>) 
 setTNCS_PATT_PERC(float <PERCENT>) 
 setTNCS_PATT_DIST(float <DISTANCE>)

==[[Image:Developer.gif|link=]]VARSAD==
; <span style="color:darkorange">Python Only</span>
: 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).
 setVARS(float_array <VARIANCES>