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Commands for controlling how SOLVE works in automated mode

This is a list of the most commonly-used keywords for SOLVE that apply to SOLVE operation in automated mode. Also see the list of all SOLVE keywords and the list of all commands .

These keywords are usually in your solve.setup file:

SYMFILE xxxxx       symmetry file for this space group
CELL   a b c alpha beta gamma
RESOLUTION dmin dmax
RES_PHASE  xx        Carry out phasing heavy-atom searches at resolution XX
                     (but write out all data in resolution range set by the
                      keyword "resolution"). Usually you should let SOLVE set this.
FFTGRID  xs xe xtotal ys ye ytotal zs ze ztotal    grid for FFT calculations
PATTGRID xs xe xtotal ys ye ytotal zs ze ztotal    grid for Patterson 
EZDGRID  xs xe    ys ye    zs ze                   grid for NEWEZD map 

These keywords are usually in your main command file:

VERBOSE                         write out a lot of output to logfile
RAWMADFILE   File will be read in as data for
                      the current mad wavelength
RAWNATIVEFILE   File & will be read in as data for
                         the native
RAWDERIVFILE   File will be read in as data for
                        the current derivative 
READ_INTENSITITES  (default)  The raw data files contain intensity measurements
READ_AMPLITUDES    The raw data files contain amplitudes (F) not intensities (I)
                   (This is valid only with READFORMATTED)

PREMERGED          The data in all RAWMADFILEs have H K L and 4 other columns:
                   I+/F+, sigma, I-/F-, sigma
UNMERGED           The data in all RAWMADFILEs have H K L and 2 other columns:
                   I/F, sigma 

READDENZO        All datafiles are written by Scalepack.  For unmerged data 
                 they will be read with the formatting:(6i4,i6,2i2,i3,2f8.0) and 
                 nsym*2+1 lines are skipped at the top of the file. For
                 merged data the formatting is:  (3i4,4f8.0) and
                 3 lines are skipped at the top of the file.

READFORMATTED      All datafiles will be read with "*" formatting and
                   contain H K L I/F sigma or H K L I+/F+ sigma I-/F- sigma

READTREK          The datafiles were written by d*trek and contain columns
                  with intensities

LABIN             specify column assignments for HKLIN in standard CCP4
                  fashion (FC=FC1 PHIC=PHIC FOM=FOM) etc

HKLIN  xxx.mtz    mtz file containing scaled amplitudes

PHASES_FORMATTED xxx.fmt   File  xxx.fmt contains H K L FC PHIC FOM and
                    the phases and fom will be used in SOLVE with
                    difference Fouriers to find initial sites

PHASES_LABIN        specification of column assignments for PHASES_MTZ file
                    Normal use is FC=FC PHIC=PHIC FOM=FOM. NOTE: MUST
                    come before PHASES_MTZ!

PHASES_MTZ xxx.mtz    as PHASES_FORMATTED, but mtz-file. FC PHIC FOM required
NSKIP n            Skip exactly n lines at the top of each data file
NSKIP 0            Do not skip any lines at the top of each data file
NSKIP -1           Skip 0 lines at the top of each data file
                    unless the keywords READDENZO and PREMERGED
                    are set in which case the default number of lines
                    are skipped (see above)

RATMIN  xx          Minumum ratio of F/sig to read in data for a
                    reflection at all is xx [default=2.0].  This is
                    useful for eliminating weak data.

FPFM_ONLY          Toss all acentric reflections where either F+
                    or F- is missing [this is the default for MAD data]

FP_OR_FM           Use F+ or F- as an estimate of Fbar if F+ and
                    F- are not both present.  This is useful if
                    your data is not that complete.  It is much
                    better to obtain complete data however.

OVERALLSCALE       Do not do local scaling; just an overall
                    scale factor for F+, F- at each wavelength.
                    Use this if you already have scaled the data
                    and you don't want any more scaling done.

SWAP_ANO            Swap H K L -> -H -K -L as data are read in to
                    SOLVE in scale_native, scale_derivative, and
                    scale_mad. This is to correct for a detector or indexing
                    that swapped F+ for F-

The atom types recognized by SOLVE are: 
H, H-1, He, Li, Li+1, Be, Be+2, B, C, Cv, N, O, O-1,
F, F-1, Ne, Na, Na+1, Mg, Mg+2, Al, Al+3, Si, Siv, Si+4,
P, S, Cl, Cl-1, Ar, K, K+1, Ca, Ca+2, Sc, Sc+3, Ti, Ti+2,
Ti+3, Ti+4, V, V+2, V+3, V+5, Cr, Cr+2, Cr+3, Mn, Mn+2, Mn+3,
Mn+4, Fe, Fe+2, Fe+3, Co, Co+2, Co+3, Ni, Ni+2, Ni+3, Cu,
Cu+1, Cu+2, Zn, Zn+2, Ga, Ga+3, Ge, Ge+4, As, Se, Br,
Br-1, Kr, Rb, Rb+1, Sr, Sr+2, Y, Y+3, Zr, Zr+4, Nb, Nb+3,
Nb+5, Mo, Mo+3, Mo+5, Mo+6, Tc, Ru, Ru+3, Ru+4, Rh, Rh+3,
Rh+4, Pd, Pd+2, Pd+4, Ag, Ag+1, Ag+2, Cd, Cd+2, In, In+3,
Sn, Sn+2, Sn+4, Sb, Sb+3, Sb+5, Te, I, I-1, Xe, Cs, Cs+1,
Ba, Ba+2, La, La+3, Ce, Ce+3, Ce+4, Pr, Pr+3, Pr+4, Nd,
Nd+3, Pm, Pm+3, Sm, Sm+3, Eu, Eu+2, Eu+3, Gd, Gd+3, Tb,
Tb+3, Dy, Dy+3, Ho, Ho+3, Er, Er+3, Tm, Tm+3, Yb, Yb+2,
Yb+3, Lu, Lu+3, Hf, Hf+4, Ta, Ta+5, W, W+6, Re, Os, Os+4,
Ir, Ir+3, Ir+4, Pt, Pt+2, Pt+4, Au, Au+1, Au+3, Hg, Hg+1,
Hg+2, Tl, Tl+1, Tl+3, Pb, Pb+2, Pb+4, Bi, Bi+3, Bi+5, Po,
At, Rn, Fr, Ra, Ra+2, Ac, Ac+3, Th, Th+4, Pa, U, U+3, U+4,
U+6, Np, Np+3, Np+4, Np+6, Pu, Pu+3, Pu+4, Pu+6, Am, Cm, Bk, Cf

newatomtype xxxx    define scattering properties of atom xxxx not recognized 
                    by SOLVE
                    HINT: to get the aval, bval, cval values from Int tables
                    for atoms recognized by SOLVE, type mad_atom [atomname] and
                    SOLVE will list them for you.
aval a1 a2 a3 a4    4 real numbers (a1,a2,a3,a4)  from International Tables for             
                     the most recently defined newatomtype
bval b1 b2 b3 b4     b values for newatomtype
cval c              c value for newatomtype
fprimv xx           f' value for newatomtype
fprprv xx           f" value for newatomtype

                    For CLUSTERS, follow the instructions in

mad_atom  xxxx   name of the anomalously scattering atom is xxxx.  If SOLVE does
                 not recognize this atom, first input its scattering parameters
                 with newatomtype
fprimv_mad       f' value for anomalously scattering atom
                 at this wavelength (must be input after each wavelength)
fprprv_mad       f" value for this wavelength

FIXSCATTFACTORS     Fix scattering factors at their input values.
                    This is a good idea if you have a reasonable
                    idea of the f' and f" values.  [this is the

REFSCATTFACTORS     refine scattering factors f' and f".  If you
                    refine them, be sure to look at their new
                    values at the end of the routine MADMRG and
                    verify that they are reasonable.

derivative n        begin input of information for derivative/wavelength n
                    This command is used to start entering information on a
                    derivative.  If you want to modify something after you've
                    gone on to another derivative then you need to use the 
                    command GOTODERIV
lambda n            identical to derivative n

nsolsite_deriv      Maximum number of sites for this derivative 
                    (overrides nsolsite)

cutoff_deriv 200 3.5   resolution limits for this derivative/wavelength only

RES_PHASE 2.8   high-resolution limit for phasing only
SN_MIN    Set RES_PHASE so that signal-to-noise is bigger than this 
SN_RATIO_MIN    Set RES_PHASE so that signal-to-noise is bigger than this 
                    ratio times the value at low-resolution 

INPHASE             include this wavelength/derivative in phasing.
NOINPHASE           do not this include this derivative/wavelength in phasing

INANO               include anomalous differences for this wavelength/deriv

noanorefine        use anomalous differences in phasing but not
                   refinement for this derivative.
                   (this is usually the best option for MIR
                   unless your anomalous differences are really
                   big, as from a synchrotron MIR dataset at an
                   absorption edge).  Note: you still have to specify
                   for each derivative "inano" to include anomalous
                   differences for that derivative.

anorefine          For this derivative with "inano" specified, use
                   anomalous differences in both refinement and phasing.
                   This is best for MAD data. (This is the default also).
                   Applies to current derivative/wavelength

ATOMNAME XXX      Start reading in information about a new site with atomname
                     "XXX" at the current wavelength/deriv. 

OCCUPANCY xx       occupancy of current atom
BVALUE xx          B-value of current atom
XYZ  xx yy zz      fractional coordinates of current atom
REFINEALL          refine x,y,z,occ and b for this atom
REFINENONE         don't refine anything for this atom

Note: Flags for refinement of a heavy atom do not apply when the keyword 
SOLVE is used (only with HEAVY) 

PDB_XYZ_IN     <filename>   PDB file with orthogonal A coordinates
                  of all heavy-atoms for this derivative/wavelength
                NOTE: you cannot use XYZ/OCC/BVALUE/REFINEMENT parameters along
                      with pdb_xyz_in.

NRES   n            # of residues in asymmetric unit  [default=100]

NANOMALOUS n        # of anomalously scattering atoms in asymmetric unit.
                    Used to estimate how big the Fa values might be.
                    Also used to set max # of heavy atoms if nsolsite is not set

nobayes        do not use Bayesian correlated phasing in SOLVE.

ntopfour xx         Number of Fourier peaks to pick from a map

ntopderiv xx        Number of Fourier peaks to be tested for
                    inclusion in the model

nsolsite xx         Maximum number of sites in a derivative unless overridden by

nseedtest xx        Number of seeds per derivative to try (before

nseedsolve xx       Number of seeds (total) to try after
                    sorting them

ntopsolve xx        Number of solutions to print out at the end
                    and number of solutions to keep track of at
                    any one time

addsolve           Add on to solution that is input
checksolve         Compare all solutions to input solution

analyze_solve      Analyze input solution without doing anything
                    else [default=off]

[no]delete          do [not] check out all solutions by testing
                    all one-site deletions [default=delete]

[no]inverse         do [not] check out all solutions by testing
                    their inverses (does not apply if a solution
                    is centrosymmetric or if anomalous differences
                    are not used). [default=inverse]

SCORING_TABLE (8 values)  Scoring table (usually generated by SOLVE) consisting
                      of mean and standard deviation of scores for trial 
                      solutions for Pattersons, Cross-fouriers, Native Fourier
                      maps, and mean figure of merit.  This keyword is useful
                      when you are running SOLVE after modifying the script
                      file it writes out at the end.

QUICK                once a plausible solution is found, don't keep looking,
                     just add on sites to it and check it at the end. [default]

THOROUGH             keep looking anyways until a limit set by ntopsolve,
                     nseedsolve, etc is reached.

NTOL_SITE            a site within ntol_site grid units of an existing site is
                     considered to be a duplicate and is ignored. [default=8]

NTOL_SOLN            a heavy-atom solution for which every site matches another
                     solution within ntol_soln grid units is considered to be 
                     a duplicate and is ignored. [default=2]

ACCEPTANCE  xx       the weighting function for scoring patterson and free-
                     difference fourier peak heights is adjusted so that a new
                     site with height relative to the previous average height
                     of ACCEPTANCE or higher will generally give a solution
                     with a higher score than the solution without this site.
                     [default =0.2]
SN_MIN  xx           Identify working resolution as the point where signal-
                     to-noise in the data goes down to about XX. Default =0.5
SN_RATIO_MIN  xx     Identify working resolution as the point where signal-
                     to-noise in the data goes down to about XX times its 
                      maximum value. Larger of value of S/N obtained by SN_MIN and 
                      SN_RATIO_MIN used. Default = 0.1
NO_SIM               Do not use Sim weighing with heavy-atom structure factors in SAD            


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