Python Functions

From Phaserwiki

Contents

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.

Python variable types

  • Miller = cctbx::miller::index<int>
  • dvect3 = scitbx::vec3<floatType>
  • dmat33 = scitbx::mat3<floatType>
  • type_array = scitbx::af::shared<type> arrays

Icons

  • Basic Functions
  • Advanced Functions
  • Expert Functions
  • Developer Functions

There are equivalent Keywords for the stand-alone executable of Phaser

ATOM

setATOM_PDB(string <XTALID>,string <FILENAME>)
Definition of atom positions using a pdb file.
setATOM_HA(string <XTALID>,string <FILENAME>)
Definition of atom positions using a ha file (from RANTAN, MLPHARE etc.)
addATOM(string <XTALID>,string <TYPE>,float <X>,float <Y>,float <Z>,float <OCC>)
Minimal definition of atom position.
setATOM_FULL(string <XTALID>,string <TYPE>,bool <True=ORTH False=FRAC>,dvect3 <X Y Z>,float <OCC>,bool <True=ISO False=ANO>,float <ISOB>,bool <T=ANOU F=USTAR>,dmat6 <HH KK LL HK HL KL>,bool <True=FIXX False=REFX>,bool <True=FIXO False=REFO>,bool <True=FIXB False=REFB>,bool <True=SWAPB False=!SWAPB>,string <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).
setATOM_CHAN_BFAC_WILS(bool <True|False>)
Reset all atomic B-factors to the Wilson B-factor
setATOM_CHAN_SCAT(string <TYPE>)
The scattering type of the PDB can be changed (for example, for SHELXD which always outputs coordinates as sulphur).

BFACTOR

setBFAC_WILS_REST(bool <True|False>)
Toggle to use the Wilson restraint on the isotropic component of the atomic B-factors in SAD phasing
setBFAC_SPHE_REST(bool <True|False>)
Toggle to use the sphericity restraint on the anisotropic B-factors in SAD phasing
setBFAC_REFI_REST(bool <True|False>)
Toggle to use the restraint on molecular B-factors for molecular replacement
setBFAC_WILS_SIGM(float <SIGMA>)
The sigma of the Wilson restraint.
setBFAC_SPHE_SIGM(float <SIGMA>)
The sigma of the Sphericity restraint.
setBFAC_REFI_SIGM(float <SIGMA>)
The sigma of the refinement restraint.
  • Default: setBFAC_WILS_REST(True)
  • Default: setBFAC_SPHE_REST(True)
  • Default: setBFAC_REFI_REST(True)
  • Default: setBFAC_WILS_SIGM(5)
  • Default: setBFAC_SPHE_SIGM(5)
  • Default: setBFAC_REF|I_SIGM(10)

BINS

setBINS_MINI(float <L>)
L = minimum number of bins.
setBINS_MAXI(float <H>)
H = maximum number of bins.
setBINS_WIDT(float <W>)
W = width of the bins in number of reflections.
setBINS_CUBI(dvect3 <A B C>)
A B C are the coefficients for the binning function A(S*S*S)+B(S*S)+CS where S = (1/resolution). 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: setBINS_MINI(6)
  • Default: setBINS_MAXI(50)
  • Default: setBINS_WIDT(500)
  • Default: setBINS_CUBI(0 1 0)

BOXSCALE

setBOXS(float <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: setBOXS(4)

CELL

setCELL(float <A>,float <B>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)
Unit cell dimensions
setCELL6(float_array <A B C ALPHA BETA GAMMA>)
Unit cell dimensions
  • Constraints: A>0,B>0,C>0,ALPHA>0,BETA>0,GAMMA>0

CLMN

setCLMN_SPHE(float <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.
setCLMN_LMIN(float <LMIN>)
The minimum L values for the decomposition of the Patterson
setCLMN_LMAX(float <LMAX>)
The minimum L values for the decomposition of the Patterson
  • Default: setCLMN_LMIN(4)
  • Default: setCLMN_LMAX(100)
  • Default: setCLMN_SPHE(0)

CLUSTER

setCLUS_PDB(string <pdbfile>
Sample coordinates for a cluster compound for experimental phasing. The sites are indicated with the type XX.

COMPOSITION

setCOMP_AVERAGE()
Use average solvent content (50%)
setCOMP_SOLVENT()
Composition entered by solvent content
setCOMP_ASU()
Composition entered by components of asymmetric unit
addCOMP_PROT_MW_NUM(float <MW>,float <NUM>)
The number of copies NUM of protein molecular weight MW
Constraint: MW>0
addCOMP_PROT_STR_NUM(string <SEQ>,float <NUM>)
The number of copies NUM of protein sequence SEQ (in single letter code)
addCOMP_PROT_NRES_NUM(float <NRES>,float <NUM>)
The number of copies NUM of the number protein residues
addCOMP_PROT_SEQ_NUM(string <FILE>,float <NUM>)
The number of copies NUM of protein sequence given in fasta format (in a file FILE)
addCOMP_NUCL_MW_NUM(float <MW>,float <NUM>)
The number of copies NUM of nucleic acid molecular weight MW
Constraint: MW>0
addCOMP_NUCL_STR_NUM(string <SEQ>,float <NUM>)
The number of copies NUM of nucleic acid sequence SEQ (in single letter code)
addCOMP_NUCL_NRES_NUM(float <NRES>,float <NUM>)
The number of copies NUM of the number nucleic acid residues
addCOMP_NUCL_SEQ_NUM(string <FILE>,float <NUM>)
The number of copies NUM of nucleic acid sequence given in fasta format (in a file FILE)
addCOMP_ATOM(string <TYPE>,float <NUM>)
Add NUM copies of a atom (usually a heavy atom) to the composition
addCOMP_NUCL_NRES(float <NRES>)
The number nucleic acid resides
addCOMP_NUCL_FASTA_NUM(string <FILE>,float <NUM>)
The number of copies NUM of nucleic acid sequence given in fasta format (in a file FILE)
addCOMP_ENSE_FRAC(string <MODLID>,float)
Alternative way of defining composition. Fraction scattering is entered explicitly for MODLID.
  • Constraint: 0<FRAC<=1

CRYSTAL

setCRYS_SAD_LABI(string <F+>,string <SIGF+>,string <F->,string <SIGF->)
Column of MTZ file used for data, and/or names for output columns
addCRYS_SAD_DATA(miller_array <MILLER>,float_array <F+>,float_array <SIGF+>,bool_array <PRESENT+>,float_array <F->,float_array <SIGF->,bool_array <PRESENT->)
Arrays of data

DEBUG

setDEBU(bool <True=ON False=OFF>)
Extra verbose output for debugging
  • Default: setDEBU(False)

EIGEN

setEIGE_READ(string <FILE>)
Read a file containing the eigenvectors and eigenvalues. 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.
setEIGE_WRIT(bool <True=Do False=Don't Write>)
Control whether or not the eigenfile is written (when not using the READ mode).
  • Default: setEIGE_WRIT(True)

ENSEMBLE

addENSE_PDB_RMS(string <MODLID>,string <FILE>,float <RMS>)
Add a model in pdb format FILE to the ensemble MODLID with the expected RMS deviation of the coordinates from the "real" structure. First call initiates the MODLID.
addENSE_CARD(string <MODLID>,string <FILE>,bool)
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.
addENSE_PDB_ID(string <MODLID>,string <FILE>,float <ID>)
Add a model in pdb format FILE to the ensemble MODLID with the sequence identity ID to the "real" structure. First call initiates the MODLID.
setENSE_MAP(string <MODLID>,string <HKLIN>,string <SF>,string <PHASE>,dvect3 <EXTENT>,float <RMS>,dvect3 <CENTRE>,float <PROTMW>,float <NUCL MW>)
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.
setENSE_FRAC(string <MODLID>,float <frac>)
Fraction scattering of ensemble entered directly rather than calculated from composition
  • Constraint: ID=%
addENSE_HKL(string <MODLID>,string <MTZFILE>,float <SCAT>,dvect3 <EX EY EZ>,dmat33 <P1 P2 P3 P4 P5 P6 P7 P8 P9>,dvect3 <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
setENSE_BINS_MIN(string <MODLID>,float <L>)
L = minimum number of bins.
setENSE_BINS_MAX(string <MODLID>,float <H>)
H = maximum number of bins.
setENSE_BINS_NUM(string <MODLID>,float <N>)
N = number of bins. If N is given then the values of L and H are ignored.
setENSE_BINS_WIDTH(string <MODLID>,float <W>)
W = width of the bins in number of reflections.
setENSE_BINS_CUBIC(string <MODLID>,dvect3 <A B C>)
A B C are the coefficients for the binning function A(S*S*S)+B(S*S)+CS where S = (1/resolution). 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: setENSE_BINS_MIN(<MODLID>,6)
  • Default: setENSE_BINS_MAX(<MODLID>,200)
  • Default: setENSE_BINS_WIDTH(<MODLID>,1000)
  • Default: setENSE_BINS_CUBIC(<MODLID>,0 1 0)

FFTS

setFFTS_MINI(float <ATOMS_MIN>)
setFFTS_MAXI(float <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: setFFTS_MINI(20)
  • Default: setFFTS_MAXI(80)

HAND

setHAND(string ["OFF"|"ON"|"BOTH"])
Use the given hand of heavy atoms
Use other hand of heavy atoms
Phase using both hands of heavy atoms
  • Default: setHAND("OFF")

HKLIN

setHKLI(string <FILENAME>)
The mtz file containing the data

HKLOUT

setHKLO(bool <True=ON False=OFF>)
Flag for output of an mtz file containing the phasing information
  • Default: setHKLO(True)

INTEGRATION

setINTE_FIXE(bool True|False)
Determine the number of angular steps in the integration by the variance of the function (False) or use a fixed number of steps (True)
setINTE_STEP(float <STEP>)
Number of steps in angular integration of function if the number of points is fixed
  • Default: setINTE_FIXE(False)

JOBS

setJOBS(float <NUM>)
Number of processors to use in parallelized sections of code
  • Default: JOBS 2

KEYWORDS

setKEYW(bool <True=ON False=OFF>)
Write Phaser script file
  • Default: setKEYW(True)

LABIN

setLABI(string <F>,string <SIGF>)
Columns in mtz file. F must be given. SIGF should be given but is optional.

LLGCOMPLETE

setLLGC_COMP(bool <True=Do False=Don't Complete>)
Toggle for structure completion by log-likelihood gradient maps
addLLGC_SCAT(string)
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.
setLLGC_CLAS(float <CLASH>)
Minimum distance between atoms in log-likelihood gradient maps. If zero, distance determined by resolution.
setLLGC_SIGM(float <Z>)
Z-score (sigma) for accepting peaks as new atoms in log-likelihood gradient maps
setLLGC_NCYC(int <NCYC>)
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.
setLLGC_MAPS(bool <ON|OFF>)
Output map coefficients to mtz file
setLLG_METH(string <METHOD> = ["IMAGINARY"|"ATOMTYPE"])
Pick peaks from the imaginary map only or from all the completion atomtype maps.
  • Default: setLLGC_COMP(False)
  • Default: setLLGC_CLAS(0)
  • Default: setLLGC_SIGM(6)
  • Default: setLLGC_NCYC(50)
  • Default: setLLGC_MAPS(False)
  • Default: setLLGC_METH("ATOMTYPE")

MACANO

setMACA_PROT(string ["DEFAULT"|"CUSTOM"|"OFF"|"ALL"])
Protocol for the refinement of SigmaN in the anisotropy correction
addMACA(bool <True=REFINE False=FIX ANISO>,bool <True=REFINE False=FIX BINS>,bool <True=REFINE False=FIX SOLK>,bool <True=REFINE False=FIX SOLB>,int <NCYC>,string <MINIMISER="BFGS"|"NEWTON"|"DESCENT">)
Macrocycle for the custom refinement of SigmaN in the anisotropy correction. Macrocycles are added in the order in which they are entered.
  • Default: setMACA_PROT("DEFAULT")

MACHL

setMACH_PROT(string ["DEFAULT"|"CUSTOM"|"OFF"|"ALL"])
Protocol for the refinement of Hendrickson-Lattman coefficients
addMACH(bool <True=REFINE False=FIX COEFF>,int <NCYC>,string <MINIMISER="BFGS"|"NEWTON"|"DESCENT">)
Macrocycle for custom refinement of Hendrickson-Lattman coefficients. Macrocycles performed added in the order in which they are entered.
  • Default: setMACH_PROT("DEFAULT")

MACMR

setMACM_PROT(string ["DEFAULT"|"CUSTOM"|"OFF"|"ALL"])
Protocol for refinement of molecular replacement solutions
addMACM(bool <True=REFINE False=FIX ROT>,bool <True=REFINE False=FIX TRA>,bool <True=REFINE False=FIX BFAC>,bool <True=REFINE False=FIX VRMS>,int <NCYC>,string <MINIMIZER="BFGS"|"NEWTON"|"DESCENT")
Macrocycle for custom refinement of molecular replacement solutions. Macrocycles are performed in the order in which they are entered.
  • Default: setMACM_PROT("DEFAULT")

MACNCS

setMACN_PROT(string ["DEFAULT"|"CUSTOM"|"OFF"|"ALL"])
Protocol for refinement of pseudo-translational NCS refinement
addMACN(bool <True=REFINE False=FIX ROT>,bool <True=REFINE False=FIX TRA>,bool <True=REFINE False=FIX DRMS>, int <NCYC>,string <MINIMIZER="BFGS"|"NEWTON"|"DESCENT")
Macrocycle for custom refinement of pseudo-translational NCS refinement. Macrocycles are performed in the order in which they are entered.
  • Default: setMACN_PROT("DEFAULT")

MACSAD

setMACS_PROT(string ["DEFAULT"|"CUSTOM"|"OFF"|"ALL"])
Protocol for refinement of SAD refinement
n.b. PROTOCOL ALL will crash phaser and is only useful for debugging - see code for details
addMACS(REF_K=<True|False>,REF_B=<True|False>,REF_SIGMA=<True|False>,REF_XYZ=<True|False>,REF_OCC=<True|False>,REF_BFAC=<True|False>,REF_FDP=<True|False>,REF_SA=<True|False>,REF_SB=<True|False>,REF_SP=<True|False>,bool REF_SD,int <NCYC>,string <MINIMIZER="BFGS"|"NEWTON"|"DESCENT">)
Macrocycle for custom refinement of SAD refinement. Macrocycles are performed in the order in which they are entered.
  • Default: setMACS_PROT("DEFAULT")

MODE

Not relevant to python scripting

MUTE

setMUTE(bool <True=ON False=OFF>)
Toggle for running in "silent" mode, with no summary, logfile or verbose output written to "standard output". Output can be extracted from Results object in python, or from XML file.
  • Default: setMUTE(False)

NMAMETHOD

setNMAM_OSCI(string ["RTB"|"CA"|"ALL"])
Use the rotation-translation block method to determine the modes
Use C-alpha atoms only to determine the mode
Use all atoms only to determine the mode (only for use on very small molecules, less than 250 atoms)
setNMAM_RTB_MAXB(float)
For the RTB analysis, number of rotation-translation blocks
setNMAM_RTB_NRES(float)
For the RTB analysis, number of residues in a rotation-translation block. By default NRES is calculated so that it is as high as it can be without reaching MAXBlocks.
  • Default: setNMAM_RTB()
  • Default: setNMAM_RTB_MAXB(250)
setNMAM_RADI(float <RADIUS>)
Elastic Network Model interaction radius (Angstroms)
setNMAM_FORC(float <FORCE>)
Elastic Network Model force constant
  • Default: setNMAM_RADI(5)
  • Default: setNMAM_FORC(1)

NMAPDB

setNMAP_PERT(string ["RMS"|"DQ"])
Tobble to use rms deviations or dq steps to perturb structure
addNMAP_MODE(float <MODE>)
Add a 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.
setNMAP_COMB(float <NMAX>)
Controls how many modes are present in any combination.
setNMAP_RMS_STEP(float <RMS>)
Increment in rms Ångstroms between pdb files to be written.
setNMAP_RMS_CLAS(float <CLASH>)
setNMAP_RMS_STRE(float <STRETCH>)
setNMAP_RMS_MAXI(float <MAX>)
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.
setNMAP_RMS_DIRE(string["FORWARDS"|"BACKWARDS"|"TOFRO"])
Direction of perturbation along the eigenvectors of the modes specified.
addNMAP_DQ(float)
Add a 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.
  • Default: addNMAP_MODE(7)
  • Default: setNMAP_COMB(3)
  • Default: setNMAP_RMS(0.3)
  • Default: setNMAP_STRE(10.0)
  • Default: setNMAP_CLAS(2.0)
  • Default: setNMAP_MAXI(0.5)
  • Default: setNMAP_RMS_TOFRO()

NORMALIZATION

setNORM(float_array <B1 B2 ...> ,dmat6 <HH KK LL HK HL KL>,float <SOLK>,float <SOLB>)
The normalization factors the 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>)

OUTLIER

setOUTL_REJE(bool <True|False>)
Reject low probability data outliers
setOUTL_PROB(float <PROB>)
Cutoff for rejection of low probablity outliers
  • Default: setOUTL_REJE(True)
  • Default: setNMAM_PROB(1.0e-06)

PACK

setPACK_SELE(string ["BEST"|"ALLOW"|"ALL"])
Allow the best packing solutions provided the total number of clashes does not exceed ALLOWED_CLASHES
Allow all solutions that pack with the total number of clashes less than ALLOWED_CLASHES
Allow all solutions (no packing test)
setPACK_CUTO(float <ALLOWED_CLASHES>)
Total number of allowed clashes
setPACK_QUIC(bool <True=ON False=OFF>)
Packing check stops when ALLOWED_CLASHES or MAX_CLASHES is reached
setPACK_DIST(float <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: setPACK_BEST()
  • Default: setPACK_CUTO(10)
  • Default: setPACK_QUIC(True)
  • Default: setPACK_DIST(3.0)

PARTIAL

setPART_PDB(string <FILENAME>)
The partial structure for SAD refinement
setPART_HKLI(string <FILENAME>)
The partial density for SAD refinement
setPART_VARI(string ["ID"|"RMS"])
setPART_DEVI(float <RMS_ID>)
The sequence identity or rms deviation between the model and target structure
  • Constraint: ID=%
  • Constraint: RMS>0
  • No Default

PEAKS

setPEAK_ROTA_SELE(string ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])
setPEAK_TRAN_SELE(string ["SIGMA"|"PERCENT"|"NUMBER"|"ALL"])
Select rotation/translation peaks by taking
peaks over CUTOFF percent of the difference between the top peak and the mean value.
peaks with a Z-score greater than CUTOFF
the top CUTOFF peaks
all peaks
setPEAK_ROTA_CUTO(float <CUTOFF>)
setPEAK_TRAN_CUTO(float <CUTOFF>)
The cutoff value for peak selection
setPEAK_ROTA_CLUS(bool <True=Do False=Don't CLUSTER>)
setPEAK_TRAN_CLUS(bool <True=Do False=Don't CLUSTER>)
Toggle for CLUSTER selects clustered peaks from translation function
  • Default: setPEAK_ROTA_SELE("PERCENT")
  • Default: setPEAK_TRAN_SELE("PERCENT")
  • Default: setPEAK_ROTA_CUTO(0.75)
  • Default: setPEAK_TRAN_CUTO(0.75)
  • Default: setPEAK_ROTA_CLUS(True)
  • Default: setPEAK_TRAN_CLUS(True)

PERMUTATIONS

setPERM(bool <True=ON False=OFF>)
Toggle for whether the order of the search set is to be permuted.
  • Default: setPERM(False)

PTGROUP

setPTGR_COVE(float <COVERAGE>)
Percentage coverage for two sequences to be considered in same pointgroup
setPTGR_IDEN(float <IDENTITY>)
Percentage identity for two sequences to be considered in same pointgroup
setPTGR_RMSD(float <RMSD>)
Percentage rmsd for two models to be considered in same pointgroup
setPTGR_TOLE_ANGU(float <ANG>)
Angular tolerance for pointgroup
setPTGR_TOLE_SPAT(float <DIST>)
Spatial tolerance for pointgroup

PURGE

setPURG_ENAB(bool <True=ON False=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.
setPURG_PERC(float <PERC>)
Percent of the difference between the top solution and the mean at which to purge the solutions.
  • Default: setPURG(True)
  • Default: setPURG_PERC(0.75)

Image:Expert.gifRESCORE

setRESC_ROTA(bool <True=ON False=OFF>)
Toggle for rescoring of fast rotation function search peaks
setRESC_TRAN(bool <True=ON False=OFF>)
Toggle for rescoring of fast translation function search peaks
setRESC_FAST(bool <True=ON False=OFF>)
Toggle for rescoring of fast translation function search peaks in FAST search mode
  • Default: setRESC_ROTA(True)
  • Default: setRESC_TRAN(True)
  • Default: setRESC_FAST(False)

RESHARPEN

setRESH_PERC(float <PERCENT>)
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: setRESH_PERC(100)

RESOLUTION

setRESO_HIGH(float <HIRES>)
The high resolution limit
setRESO_LOW(float <LORES>)
The low resolution limit
setRESO_AUTO_HIGH(float <HIRES>)
The high resolution limit for high resolution refinement in MR_AUTO.
setRESO_AUTO_LOW(float <LORES>)
The low resolution limit for high resolution refinement in MR_AUTO.
setRESO(float <HIRES>,float <LORES>)
Resolution range in Ångstroms. The limits can be in either order.
setRESO_AUTO(float <HIRES>,float <LORES>)
Resolution range in Ångstroms for high resolution refinement in AutoMR. The limits can be in either order.
  • Constraint: HIRES>0
  • Constraint: LORES>0
  • Default: setRESO_HI(2.5) for rotation and translation functions only

ROOT

setROOT(string <FILEROOT>)
Root filename for output files (e.g. FILEROOT.log)
  • Default: setROOT("PHASER")

ROTATE

setROTA_VOLU(string ["FULL"|"AROUND"|)
Sample all unique angles or sample all unique angles within RANGE of EULER
setROTA_EULE(dvect3 <EULER>)
setROTA_RANG(float <RANGE>)
setROTA_VOLU_AROU_EULE_RANG(dvect3 <EULER>,float <RANGE>)
Restrict the search to the region of +/- RANGE degrees around orientation given by EULER
  • Constraint: RANGE>0
  • Default: setROTA_VOLU_FULL()

SAMPLING

setSAMP_ROTA(float <SAMP>)
Sampling of search given in degrees for a rotation search. Default sampling depends on the geometric mean radius (GMR) of the Ensemble and the high resolution limit (dmin) of the search.
setSAMP_TRAN(float <SAMP>)
Sampling of search given in Ångstroms for a translation search. Default sampling depends on the high resolution limit (dmin) of the search.
  • Constraint: SAMP>0
  • Default: SAMP = 2*atan(dmin/(4*GMR)) (MODE = MR_BRF)
  • Default: SAMP = 2*atan(dmin/(4*GMR)) (MODE = MR_FRF)
  • Default: SAMP = dmin/5; (MODE = MR_BTF)
  • Default: SAMP = dmin/3; (MODE = MR_FTF)

SCATTERING

addSCAT(string <TYPE>,float <FP>,float <FDP, string <FIXFDP>)
Measured scattering factors for a given atom type or cluster type, from a fluorescence scan. FIXFDP="EDGE" (default) fixes the fdp value if it is away from an edge, but refines it if it is close to an edge, while FIXFDP="ON" or FIXFDP="OFF" does not depend on proximity of edge.
setSCAT_REST(bool <ON|OFF>)
use Fdp restraints
setSCAT_SIGM(float <SIGMA>)
Fdp restraint sigma used is SIGMA multiplied by initial fdp value
  • Default: setSCAT_REST(True)
  • Default: setSCAT_SIGM(0.2)

SEARCH

addSEAR_ENSE_NUMB(string <MODLID>,int <NUM>)
The ENSEMBLE to be searched for in a rotation search or an automatic search. 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).
addSEAR_ENSE_OR_ENSE_NUMB(string_array <MODLIDS>,int <NUM>)
Array of alternative ensembles for a search component. 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).
setSEAR_ORDE_AUTO(bool [True|False])
Search in the "best" order as estimated using estimated rms deviation and completeness of models.
setSEAR_METH("FULL"|"FAST")
Search using the "full search" or "fast search" algorithms.
setSEAR_DEEP(bool [True|False])
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.
setSEAR_DOWN_PERC(float <PERC>)
Percentage to reduce rotation function cutoff if there is no TFZ over ZSCORE_CUTOFF in first search. Search method FAST only.
  • Default: setSEARC_METH("FULL")
  • Default: setSEARC_ORDE_AUTO(True)
  • Default: setSEAR_DEEP(True)
  • Default: setSEAR_DOWN_PERC(10)

SGALTERNATIVE

setSGAL_SELE(string ["ALL"|"HAND"|"LIST"|"NONE"])
Tests all possible space groups in the same pointgroup as the space group
Test the given space group and its enantiomorph
Test the space groups in the entered list.
Test no alternative space groups
addSGAL_NAME(string <NAME>)
Add alternative space groups to test.
setSGAL_SORT(bool [True|False])
Sort alternative space groups in order of frequency of occurrence

SOLPARAMETERS

setSOLP_FSOL(float <FSOL>)
setSOLP_BSOL(float <BSOL>)
Solvent parameters for Sigma(A) curves. The results are not terribly sensitive to these parameters, which affect only lower resolution data. FSOL and BSOL can be given in either order, the lower number being taken as FSOL.
  • Constraint: 0<FSOL<1, BSOL>0, FSOL<BSOL
  • Default: setSOLP(0.95,300)

SOLUTION

addSOLU_SET(string <ANNOTATION>)
Start new set of solutions
addSOLU_6DIM_ENSE(string <MODLID>,dvect3 <EULER>,bool <True=FRAC False=ORTH>,dvect3 <X Y Z>,float <BFAC>,bool <True=FIX False=Refine ROT>,bool <True=FIX False=Refine TRA>,bool <True=FIX False=Refine 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.
addSOLU_ENSE_VRMS(string <MODLID>, float_array <VARIANCES>)
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.
addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <EULER>, float <SCORE>)
Rotation List for translation function
addSOLU_ORIG_ENSE(string <MODLID>)
Create solution for ensemble MODLID at the origin

SORT

setSORT(bool <True=ON False=OFF>)
Sort the reflections into resolution order upon reading MTZ file, for performance gain in molecular replacement
  • Default: setSORT(True)

SPACEGROUP

setSPAC_NUM(int <NUM>)
Set the space group using the number 19 (gives standard setting).
setSPAC_NAME(string <NAME>)
Set the space group using the Hermann-Mauguin symbols eg P21 21 21
setSPAC_HALL(string <HALL>)
Set the space group using the Hall symbol

TARGET

setTARG_FRF(string ["LERF1"|"LERF2"|"CROWTHER"])
Target function for fast rotation searches.
setTARG_FTF(string ["LETF1"|"LETF2"|"CORRELATION"])
Target function for fast translation searches.
  • Default: setTARG_FRF("LERF1")
  • Default: setTARG_FTF("LETF1")

TITLE

setTITL(string <TITLE>)
Title for job
  • Default: setTITL(string "[no title given]")

TNCS

setTNCS_TRAN(dvect3 <x y z>)
Input pseudo-translational symmetry vector. By default the translation is determined from the Patterson.
setTNCS_ROTA(dvect3 <alpha beta gamma>)
Input rotational difference between molecules related by the pseudo-translational symmetry vector.
setTNCS_DRMS(float <num>)
Input estimated rms deviation between pseudo-translational symmetry vector related molecules.
setTNCS_RANG(float <angle>)
Maximum deviation from initial rotation from which to look for rotational deviation. The best refined rotational angle will be selected.
  • Default: TNCS ROT 0 0 0 DRMS 0.95 RANGE 0

TOPFILES

setTOPF(float <NUM>)
Number of top pdbfiles or mtzfiles to write to output.
  • Default: setTOPF(1)

TRANSLATE

setTRAN_VOLU(string ["FULL"|"REGION"|"LINE"|"AROUND"])
Search volume for brute force translation function. Cheshire cell or Primitive cell volume.
setTRAN_STAR(dvect <START>)
Start point for REGION and LINE
setTRAN_POIN(dvect <POINT>)
Start point AROUND
setTRAN_END(dvect <START>)
End point for REGION and LINE
setTRAN_RANG(float <RANGE>)
Range for AROUND, in Ångstroms
setTRAN_FRAC(bool <True=FRAC False=ORTH>)
Start and End points delimited in Fractional or Orthogonal coordinates.
  • Default: setTRAN_VOLU("FULL")

VARSAD

setVARS(float_array <VARIANCES>
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

setVERB(bool <True=ON False=OFF>)
Toggle to send verbose output to log file.
  • Default: setVERB(False)

WAVELENGTH

setWAVE(float <LAMBDA>)
The wavelengh at which the SAD dataset was collected

XYZOUT

setXYZO(bool <True=ON False=OFF>)
Toggle for output coordinate files.
  • Default: setXYZO(False) (Rotation functions)
  • Default: setXYZO(True) (other relevant functions)

ZSCORE

setZSCO_SOLV(floatType ZSCORE_SOLVED)
Set the translation function Z-score that indicates a definite solution. Enter 0 to turn off zscore tests.
  • Default: setZSCO_SOLV(8)
user stories