**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 xxx.int File xxx.int will be read in as data for the current mad wavelength RAWNATIVEFILE xxx.int File &xxx.int& will be read in as data for the native RAWDERIVFILE xxx.int File xxx.int 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 all_keywords. 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 default] 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 nsolsite_deriv nseedtest xx Number of seeds per derivative to try (before sorting) 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 [default=off] checksolve Compare all solutions to input solution [default=off] 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