Revision as of 11:45, 7 May 2014

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

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 <FILENAME>)
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(str <TYPE>)

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>)

COMPOSITION

COMPOSITION BY [ ¹AVERAGE| ²SOLVENT| ³ASU ]: Alternative ways of defining composition; ¹ AVERAGE solvent fraction for crystals (50%); ² Composition entered by solvent content.; ³ Explicit description of composition of ASU by sequence or molecular weight
²COMPOSITION PERCENTAGE <SOLVENT>: Specified SOLVENT content
³COMPOSITION 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.
³COMPOSITION 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.
³COMPOSITION 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>)

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>)

ENSEMBLE

ENSEMBLE <MODLID> PDB <PDBFILE> [RMS <RMS>¹ | IDENTITY <ID>² | IDHI <ID>³ | IDLO <ID>⁴ | CARD ON⁵] {PDB <PDBFILE> [RMS <RMS>¹ | IDENTITY <ID>² | IDHI <ID>³ | IDLO <ID>⁴ | CARD ON⁵}…

The names of the PDB files used to build the ENSEMBLE, and either

¹ The expected RMS deviation of the coordinates to the "real" structure

² The percent sequence identity with the real sequence, which is converted to an RMS deviation.

³ The percent sequence identity with the real sequence, which is converted to an RMS deviation sampled one standard deviation higher than the average

⁴ The percent sequence identity with the real sequence, which is converted to an RMS deviation sampled one standard deviation lower than the average

⁵ 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>: Define an ensemble as a single atom for single atom MR
ENSEMBLE <MODLID> FRACTION <FRAC_SCAT>: Fraction scattering of ensemble entered directly rather than calculated from composition
ENSEMBLE <MODLID> HETATM [ON|OFF]: Use scattering from HETATM records in pdb file. See 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_FRAC(str <MODLID>,float <FRAC_SCAT>)
setENSE_DISA_CHEC(bool)

HKLIN

HKLIN <FILENAME>: The mtz file containing the data

setHKLI(str <FILENAME>)

JOBS

JOBS <NUM>: Number of processors to use in parallelized sections of code

Default: JOBS 2

setJOBS(int <NUM>)

LABIN

LABIN F = <F> SIGF = <SIGF> PH = <PH>: Columns in mtz file. F must be given. SIGF should be given but is optional. PH is for use in the Phased Translation Function.

setLABI(str <F>,str <SIGF>)
setLABI_PH(str <PH>)

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)
ResultP_SAD r = runEP_SAD(InputEP_SAD)

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>)

SEARCH

SEARCH ENSEMBLE <MODLID> {OR ENSEMBLE <MODLID>}… NUMBER <NUM>: The ENSEMBLE to be searched for in a rotation search or an automatic search. When multiple ensembles are given using the OR keyword, the search is performed for each ENSEMBLE in turn. When the keyword is entered multiple times, each SEARCH keyword refers to a new component of the structure. If the component is present multiple times the sub-keyword NUMber can be used (rather than entering the same SEARCH keyword NUMber times).
SEARCH ORDER AUTO [ON|OFF]: Search in the "best" order as estimated using estimated rms deviation and completeness of models.
SEARCH METHOD [FULL|FAST]: Search using the "full search" or "fast search" algorithms.
SEARCH DEEP [ON|OFF]: 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 ZSCORE_CUTOFF in the first search.
SEARCH DOWN PERCENT <PERC>: Search method FAST only. Percentage to reduce rotation function cutoff if there is no TFZ over ZSCORE_CUTOFF in first search.
SEARCH BFACTOR <BFAC>: B-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

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" ])
setSEAR_DEEP(bool <DEEP>)
setSEAR_DOWN_PERC(float <PERC>)
setSEAR_BFAC(float <BFAC>)

SGALTERNATIVE

SGALTERNATIVE SELECT [¹ALL| ²HAND| ³LIST| ⁴NONE]: Selection of alternative space groups to test in translation functions i.e. those that are in same laue group as that given in SPACEGROUP; ¹ Test all possible space groups,; ² Test the given space group and its enantiomorph.; ³ Test the space groups listed with SGALTERNATIVE TEST <SG>.; ⁴ 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>)

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> <B> <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 SPACEGROUP <SG>: Space Group of the solution (if alternative spacegroups searched).
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 TRIAL ENSEMBLE <MODLID> EULER <A> <B> <C> RFZ <RFZ>: Rotation List for translation function
SOLUTION ORIGIN ENSEMBLE <MODLID>: Create solution for ensemble MODLID at the origin

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>) 
setSOLU_SPAC(str <SG>)
addSOLU_ENSE_VRMS(str <MODLID>, float_array <VARIANCES>) 
addSOLU_TRIAL_ENSE(string <MODLID>,dvect3 <A B C>,float <RFZ>)
addSOLU_ORIG_ENSE(string <MODLID>)

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>)

WAVELENGTH

WAVELENGTH <LAMBDA>: The wavelengh at which the SAD dataset was collected

setWAVE(float <LAMBDA>)

Output Control Keywords

DEBUG

DEBUG [ON|OFF]: Extra verbose output for debugging

Default: DEBUG OFF

setDEBU(bool)

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>)

HKLOUT

HKLOUT [ON|OFF]: Flags for output of an mtz file containing the phasing information

Default: HKLOUT ON

setHKLO(bool)

KEYWORDS

KEYWORDS [ON|OFF]: Write output Phaser .sol file (.rlist file for rotation function)

Default: KEYWORDS ON

setKEYW(bool)

LLGMAPS

LLGMAPS [ON|OFF]: Write log-likelihood gradient map coefficients to MTZ file

Default: LLGMAPS OFF

setLLGM(bool <True|False>)

MUTE

MUTE [ON|OFF]: Toggle for running in silent/mute mode, where no logfile is written to standard output.

Default: MUTE OFF

setMUTE(bool)

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)

TITLE

TITLE <TITLE>: Title for job

Default: TITLE [no title given]

setTITL(str <TITLE>)

TOPFILES

TOPFILES <NUM>: Number of top pdbfiles or mtzfiles to write to output.

Default: TOPFILES 1

setTOPF(int <NUM>)

ROOT

ROOT <FILEROOT>: Root filename for output files (e.g. FILEROOT.log)

Default: ROOT PHASER

setROOT(string <FILEROOT>)

VERBOSE

VERBOSE [ON|OFF]: Toggle to send verbose output to log file.

Default: VERBOSE OFF

setVERB(bool)

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)

Advanced Keywords

ELLG

ELLG USE [ON|OFF]: Use expected LLG to determine resolution limits and search order (explained here)
ELLG TARGET <TARGET>: Target value for expected LLG for determining resolution limits and search order

Default: ELLG USE ON
Default: ELLG TARGET 120

setELLG_USE(bool <True|False>)
setELLG_TARG(float <TARGET>)

HAND

HAND [ ¹ON| ²OFF| ³BOTH]: Hand of heavy atoms for experimental phasing; ¹Phase using the given hand of heavy atoms; ²Phase using other hand of heavy atoms; ³Phase using both hands of heavy atoms

Default: HAND BOTH

setHAND(str [ "OFF" | "ON" | "BOTH" ])

LLGCOMPLETE

LLGComplete COMPLETE [ON|OFF]: Toggle for structure completion by log-likelihood gradient maps
LLGComplete SCATTERER <TYPE>: Atom/Cluster type(s) to be used for log-likelihood gradient completion. If more than one element is entered for log-likelihood gradient completion, the atom type that gives the highest Z-score for each peak is selected. Type = "RX" is a purely real scatterer and type="AX" is purely anomalous scatterer
LLGComplete CLASH <CLASH>: Minimum distance between atoms in log-likelihood gradient maps 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"])

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>)

PACK

PACK SELECT [ ¹BEST | ²ALLOW | ³PERCENT | ⁴ALL ]: ¹Allow the best packing solutions only, provided the total number of clashes does not exceed ALLOWED_CLASHES; ²Allow all solutions that pack with number of C-alpha clashes less than ALLOWED_CLASHES; ³Allow up to the ALLOWED_CLASHES percentage of C-alpha atoms of the model structure to clash; ⁴Allow 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 (ZSCORE keyword).
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 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
PACK TRACE [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.

Default: PACK SELECT PERCENT
Default: PACK CUTOFF 5
Default: PACK QUICK ON
Default: PACK COMPACT ON
Default: PACK DISTANCE 3.0

setPACK_SELE(str ["BEST"|"ALLOW"|"PERCENT"|"ALL"]) 
setPACK_CUTO(float <ALLOWED_CLASHES>)
setPACK_QUIC(bool)
setPACK_COMP(bool)
setPACK_DIST(float <DISTANCE>)
setPACK_TRAC(bool)

PEAKS

PEAKS TRA SELECT [ ¹PERCENT | ²SIGMA | ³NUMBER | ⁴ALL]
PEAKS ROT SELECT [ ¹PERCENT | ²SIGMA | ³NUMBER | ⁴ALL]: 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 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>)

PERMUTATIONS

PERMUTATIONS [ON|OFF]: Only relevant to SEARCH MEHOD FULL. Toggle for whether the order of the search set is to be permuted.

Default: PERMUTATIONS OFF

setPERM(bool <PERMUTATIONS>)

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>)

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.
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.
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>)

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.
RESOLUTION SEARCH HIGH [ON|OFF]: Search to full resolution if high TFZ solution not found during FAST search.

Default for molecular replacement: Set by 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_SEAR_HIGH(bool)
setRESO(float <HIRES>,float <LORES>)

ROTATE

ROTATE VOLUME FULL: Sample all unique angles
ROTATE VOLUME AROUND EULER <A> <B> <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>)

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>)

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>)

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_ROT(str ["FAST"|"BRUTE"])
setTARG_TRA(str ["FAST"|"BRUTE"|"PHASED"])

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)

TRANSLATE

TRANSLATE VOLUME [ ¹FULL | ²REGION | ³LINE | ⁴AROUND ]): Search volume for brute force translation function.; ¹ Cheshire cell or Primitive cell volume.; ² Search region.; ³ Search along line.; ⁴ Search around a point.
^{1 2 3}TRANSLATE START <X Y Z>
^{1 2 3}TRANSLATE END <X Y Z>: Search within region or line bounded by START and END.
⁴TRANSLATE POINT <X Y Z>
⁴TRANSLATE 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>)

ZSCORE

ZSCORE USE [ON|OFF]: Use the TFZ tests. Only applicable with 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 HIGH <ZSCORE_HIGH>: Set the TFZ that terminates the deep search of rotation peaks in the translation function. Must be higher than ZSCORE_SOLVED
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 HIGH 12
Default: ZSCORE HALF ON
Default: ZSCORE STOP ON

setZSCO_USE(bool <True=ON False=OFF>)
setZSCO_SOLV(floatType ZSCORE_SOLVED)
setZSCO_HIGH(floatType ZSCORE_HIGH)
setZSCO_HALF(bool <True=ON False=OFF>)
setZSCO_STOP(bool <True=ON False=OFF>)

Expert Keywords

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"])

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"])

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 <B>,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"])

MACTNCS

MACTNCS PROTOCOL [DEFAULT|CUSTOM|OFF|ALL]: Protocol for pseudo-translational NCS refinement.
MACTNCS ROT [ON|OFF] TRA [ON|OFF] VAR [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"])

OCCUPANCY

OCCUPANCY ELLG <ELLG>: Target eLLG for determining number of residues in window for occcupancy 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 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.

Default: OCCUPANCY ELLG 5
Default: OCCYPANCY NRES 0

setOCCU_ELLG(float <ELLG)
setOCCU_NRES(int <NRES>)

ROTREF

ROTREF [ON|OFF]: Toggle for refining rotations with Wilson likelihood target prior to translation function in MR_AUTO mode with SEARCH METHOD FAST

Default: ROTREF ON

setROTR(bool)

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 MR_AUTO with search method SEARCH METHOD FAST or with SEARCH METHOD FULL, or running the translation function separately MODE MR_FTF. For SEARCH METHOD FAST the default also depends on whether or not the expected LLG target ELLG TARGET <TARGET> value is reached.

setRESC_ROTA(bool)
setRESC_TRAN(bool)

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>)

SAMPLING

SAMPLING ROT
SAMPLING 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.

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)

setSAMP_ROTA(float )
setSAMP_TRAN(float )

Developer Keywords

BINS

BINS DATA [ ¹MIN <L> | ²MAX <H> | ³WIDTH <W> ]: The binning of the data.; ¹ L = minimum number of bins; ² H = maximum number of bins.; ³ W = width of the bins in number of reflections
BINS ENSE [ ¹MIN <L> | ²MAX <H> | ³WIDTH <W> ]: The binning of the calaculated structure factos for the ensembles.; ¹ L = minimum number of bins; ² H = maximum number of bins.; ³ 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>)

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 molecular Bfactor 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 sphericity restraint.

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

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>)

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>)

CELL

Python Only: Unit cell dimensions

Default: Cell read from MTZ file

setCELL(float <A>,float <B>,float <C>,float <ALPHA>,float <BETA>,float <GAMMA>)
setCELL6(float_array <A B C ALPHA BETA GAMMA>)

CLMN

CLMN SPHERE <SPHERE>: Radius for the decomposition of the Patterson in Ångstroms. If it is 0, the radius defaults to twice the mean radius of the ENSEMBLE.
CLMN LMIN <LMIN>: Lower limit of L values.
CLMN LMAX <LMAX>: Upper limit of L values. The largest L value used in the calculation is the minimum of LMAX and 2π * SPHERE/dmin.

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

setCLMN_SPHE(float <SPHERE>) 
setCLMN_LMIN(float <LMIN>) 
setCLMN_LMAX(float <LMAX>)

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>)

ENM

ENM OSCILLATORS [ ¹RTB | ²CA | ³ALL ]: Define the way the atoms are used for the elastic network model.; ¹Use the rotation-translation block method.; ²Use C-alpha atoms only to determine the modes.; ³Use 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>)

NORMALIZATION

Python Only: 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>)

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>)

REFLECTIONS

Python Only: For setting reflection data from arrays in memory, Python only

setREFL(miller_array,float_array,float_array);
setREFL_ID(std::string,std::string);

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>)

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>)

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>)

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)

TNCS

TNCS ROTATION ANGLE <A> <B> <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>)

VARSAD

Python Only: 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>

@@ Line 102: / Line 102: @@
 :: <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 the average
+:: <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 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>''

Difference between revisions of "Keywords"

Revision as of 11:45, 7 May 2014

Contents

Phaser Executable

Python Interface

Basic Keywords

ATOM

CLUSTER

COMPOSITION

CRYSTAL

ENSEMBLE

HKLIN

JOBS

LABIN

MODE

PARTIAL

SEARCH

SGALTERNATIVE

SOLUTION

SPACEGROUP

WAVELENGTH

Output Control Keywords

DEBUG

EIGEN

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