All keywords for SOLVE
This is a list of all the keywords for SOLVE. Keywords set values of parameters (number of heavy atom sites, f' value), while commands cause SOLVE to do something (solve a structure, scale data, search for heavy atoms, draw a map)
Also see the list of common keywords that apply to automated SOLVE operation and the list of all commands.
The keywords for SOLVE are listed here in the following groups:
VERBOSE write out a lot of output to logfile NSHELLS n Number of shells for analysis [default=10]. Does not apply to heavy atom refinement (fixed at 8). SAVE_FILES Save scratch files instead of cleaning upCrystal data (cell, resolution, etc)
SYMFILE xxxxx symmetry file for this space group CELL a b c alpha beta gamma RESOLUTION dmin dmax TITLE xxxxx CCP4 overall Title (60 characters, spaces allowed) PROJECTNAME xxxxx CCP4 Project Name (20 characters, no spaces) CRYSTALNAME xxxxx CCP4 Crystal Name (20 characters, no spaces) DATASETNAME xxxxx CCP4 Dataset Name (20 characters, no spaces)
RES_PHASE XX Just use data up to XX in phasing and heavy-atom searches, write out all data defined by dmin and dmax NRES n # of residues in asymmetric unit [default=100]. Used to estimate overall scale and (along with nanomalous) how big Fa values might be. NANOMALOUS n # of anomalously scattering atoms in asymmetric unit. Used to estimate how big the Fa values might be 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 = 0.1Reading in scaling, and rejecting data
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
READCCP4_UNMERGED All datafiles will be read as CCP4 mtz files assuming that LABIN is defined as I=I SIGI=SIGI. No LABIN lines are allowed (you cannot redefine LABIN).
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 or I/sig to read in data for a reflection at all is xx [default=2.0]. This is used to eliminate weak data.
SIGMA_I_RATIO XX Data read in with "premerged" will be given sigmas of at least XX. Default=0.0 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. 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- 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. KEEPALL keep reflections even with high differences TOSSBAD (default)Toss reflections if differences between native and derivative are more than 3 * the rms found for other reflections. Note: KEEPALL and TOSSBAD apply to MERGE, LOCALSCALE, SCALE_MAD, SCALE_MIR, SCALE_NATIVE. This is the place to reject derivative reflections with very large del F if you want to reject them at all. ANCUT minimum # of reflections to use to scale a reflection (30.) RATMIN minimum ratio of F/sigma to include (default=2) NOBFACTOR if specified, do not apply overall Wilson scaling before doing local scaling. Generally used only along with DAMPING=0. BFACTOR undoes NOBFACTOR. Do apply Wilson scaling before local scaling DAMPING xx scale factor (after Wilson scaling) is damped by taking it to the power xx. Generally used with NOBFACTOR and a value of 0 to not do any scaling at all. NODAMPING undoes DAMPING by resetting damping factor to 1.0 OVERALLSCALE just get 1 scale factor for the whole dataset. No local scaling, no wilson scaling. Same as NOBFACTOR + DAMPING 0.0 NOOVERALLSCALE undoes OVERALLSCALE. SAME AS BFACTOR + DAMPING 1.0 KEEPFIRSTCYCLE 1 On first cycle of scale_mad, do not reject any reflections RATIO_OUT 3.0 Reject reflections with iso or ano diff > ratio_out*rms diff in shell REQUIRE_NAT If native is missing, toss derivative too IKEEPFLAG 1 Keep reflections in merge even if large deviations from expected (default=0; reject them) ID_SCALE_REF 2 Use wavelength 2 as reference in scaling (default=1)Specifying file names
LOGFILE xx name of output file for summary of results is SYMFILE xxxxx symmetry file for this space group INFILE data.drg Standard datafile for input. Some routines require that other input file names are specified. OUTFILE data.xplor Standard output file. Some routines require that other output file names are specified. RAWMADFILE xxx.int read in xxx.int as data for the current mad wavelength RAWNATIVEFILE xxx.int read xxx.int as data for the native RAWDERIVFILE xxx.int read xxx.intas data for the current derivative EXPORTFILE xxx Formatted file with Fp,phase, m, and Hendrickson- Lattman coefficients will be written to this file at the end of SOLVE. Only the top solution will be written out in this way. The file has a header that you can edit and make into a little script file that will read the data into ccp4 format. Default is phases-hl.export PHASEFILE binary .drg file with the same data as the EXPORTFILE Default is phases-hl.drg NEWSCRIPTFILE script file that will run HEAVY and write out a new EXPORTFILE,PHASEFILE, and NEWSCRIPTFILE. Default name is "phases-hl.script". All this script file does is calculate phases. The file does contain the final heavy atom parameters. If you want to take the heavy atom parameters and continue in SOLVE with them (i.e., running ADDSOLVE or ANALYZE_SOLVE), you should copy these heavy atom parameters into the solve_mad.script or solve_mir.script file that was written by "ANALYZE_MAD" or "ANALYZE_MIR" and make a new script file this way. MADFBARFILE xx.scl Output file from SCALE_MAD with (Fbar,sigma,DelAno,sigma) for each wavelength will be xx.scl (DEFAULT="mad_fbar.scl") MADFPFMFILE yy.scl Output file from SCALE_MAD with (F+,sigma,F-,sigma) for each wavelength will be yy.scl (DEFAULT="mad_fpfm.scl") madmrgfile xxx.out SIRAS-like MAD dataset from MADMRG [ default="madmrg.out"] madbstfile yyy.out coefficients for a Bayesian Patterson to yyy.out from MADBST [default="madbst.out"] SOLVEDATAFILE xxx Output datafile with MADMRG and MADBST data NEWFILE xx file with updated script file for HEAVY OUTFILE xx output file name for HEAVY, required if KOUT is not 0 FFTFILE xx name of FFT-containing file EZDMAPFILE xx name of output EZD format map file CCP4MAPFILE xx name of output ccp4 format map file MAPVIEWFILE xx name of output MAPVIEW format file COMPARISONFILE xx name of file with FFT to be compared with all native fouriers from trial solutions (goes with checksolve). FILETITLE xxx optional title for a fileColumn numbers for data in data files
NNATF n column # for F of native data NNATS n column # of sigma of F of native data NDERF n column # for F of deriv data NDERS n column # for sigma of F of deriv data NANOF n column # of anomalous difference (Fplus-Fminu) of deriv data NANOS n column # of sigma of anomalous difference NCOLF_MERGE n column number in input file for F (default = 1) NCOLSIG_MERGE n column number in input file for sigma of F (default =2) NCOLFBAR n Fbar for this wavelength NCOLSFBAR n sigma of Fbar NCOLDELF n Del F ano (Fplus - Fminus) NCOLSDELF n sigma of del F ano NCOLFPLUS column number for Fplus NCOLSIGPLUS column number for sigma of Fplus NCOLFMINUS column number for Fminus NCOLSIGMINUS column number for sigma of Fminus NCOLFC n WT Fc (WT Fcalc) for Fdiff NCOLFOWT n WT Fo (WT Fobs) for Fdiff NCOLSWT n sigma of WT Fo for Fdiff NCOLFOMUT n MUT Fo (MUT Fobs) for Fdiff NCOLSMUT n sigma of MUT Fo for Fdiff NCOLFCMUT n MUT Fc for Fdiff NCOLRTEST n RTEST indicator (0 if missing) for Fdiff NXPLORF n column for F in drgtoxplor NXPLORSIG n column for sigma in drgtoxplor JSTD n wavelength ID for wavelength to be considered the STANDARDControl parameters for SOLVE structure determination
new_dataset Used to identify the beginning of a new dataset in combination with COMBINE_ALL_DATA. Cannot be used with mtz files. ntopfour xx Number of Fourier peaks to pick from a map ntopderiv xx Number of Fourier peaks to be tested for 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_fom do not use figure of merit in SOLVE scoring (this is default in P1 where figure of merit is poorly estimated) no_patterson do not use patterson in SOLVE scoring no_fourier do not use cross-validation difference fouriers in scoring no_native_fourier do not use analysis of native fourier in SOLVE scoring [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] full_inverse if inverse is set, calculate all scores for inverse, do not copy over patterson and cross-validation difference fourier 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.
QUICKER Go with the best solution at each stage, but try all seeds , unless a very good solution is found.
VERYQUICK SOLVE will go with the best solution at each step, even if it is not very good. This will speed up SOLVE a lot for good data.
THOROUGH keep looking anyways until a limit set by ntopsolve, nseedsolve, etc is reached. Opposite of QUICK. FINISH control parameter for solve.control file indicating that SOLVE should finish up as soon as possible without looking for any new solutions. RESOLUTION_STEPS number of steps of resolution to use in the search for heavy-atom solutions. Default=3. If you specify 0 or 1 it will go right to the highest resolution available 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]
CUT_DELETE xx Only sites with free-difference Fourier peak heights less than XX *sigma of map will be will be considered for removal in generating new test solutions. Default = 5.0 bayes Use Bayesian MAD phasing at the very end of SOLVE. (This is the default) nobayes Use the compressed MADMRG datafile for all phasing when program gets to SOLVE.
NO_ANISOTROPIC_B no anisotropic b used in automated structure determination no_duplicate_sites Do not allow the same site to appear in more than one derivative.(default=off) CONTINUE_SAD Continuing a SAD dataset (keyword used by SOLVE in solve_fast_sad.script
CONTINUE_MAD Continuing a SAD dataset (keyword used by SOLVE in solve_mad.script
USE_INPUT_PHASES Using input phases (must be defined in input file) (keyword used by SOLVE in solve_mad.script and solve_mir.script)Defining heavy atom scattering factors
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
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 (NOTE: not the same as BVALUE).
cval c c value for newatomtype
fprimv xx f' value for newatomtype
fprprv xx f" value for newatomtype
Where the fo scattering from this atom is:
cval + sum_{i=1 to 4} (aval(i)*exp(-bval(i)*(sin(theta)/lambda)**2)
and the f" value is fprimv and the f"" value is fprprv
For CLUSTER compounds, you may wish to specify instead fprimv, fprprv,
plus 3 separate formulas, one for the f_o part of the scattering factor,
1 for NORMALIZED f", and one for NORMALIZED f"".
All three of these quantities will depend strongly on scattering angle.
NOTE: when you put in a cluster compound, it is a good idea to look at
the form factors as a function of sin(theta)/lambda using the keyword
plot_formfactors xxxx
The formulas used are:
f_o formula:
The "clus_aval",
"clus_bval","clus_cval(1)" values
will be used almost as for regular atoms, but with 2 additional
factors cval(2) and cval(3) that put in a sinc function as described
in Fu et al., Cell 98, 799 (1999):
clus_aval 4 real numbers (a1,a2,a3,a4)
clus_bval 4 real numbers
clus_cval 3 real numbers
fo= clus_cval(1) +
sinc(clus_cval(2)*(sin(theta)/lambda)**clus_cval(3))**2 *
[sum_{i=1 to 4} (clus_aval(i)*exp(-bval(i)*(sin(theta)/lambda)**2)]
Note the sinc function multiplies the whole sum over the aval/bval terms
but NOT the cval(1) term (it is unclear how this was done
in the Fu et al paper).
f" and f"" formulas
clus_fp_aval 4 real numbers (a1,a2,a3,a4) for f"
clus_fp_bval 4 real numbers
clus_fp_cval 3 real numbers
clus_fpp_aval 4 real numbers (a1,a2,a3,a4) for f""
clus_fpp_bval 4 real numbers
clus_fpp_cval 3 real numbers
The formulas for f" and f"" are a little different so as to
preserve compatibility with the definitions for normal atoms. The
definitions here are not used in the Fu et al article mentioned above.
In each case, the value used for f" and f""
in all the routines is equal to their INPUT values (fprimv and fprprv or
fprimv_mad and fprprv_mad)
TIMES an overall form factor given by (for f"):
form_factor= clus_fp_cval(1) +
clus_fp_cval(2)*sinc((sin(theta)/lambda)**clus_fp_cval(3))**2 *
[sum_{i=1 to 4} (clus_fp_aval(i)*exp(-bval(i)*(sin(theta)/lambda)**2)]
and for f"":
form_factor= clus_fpp_cval(1) +
clus_fpp_cval(2)*sinc((sin(theta)/lambda)**clus_fpp_cval(3))**2 *
[sum_{i=1 to 4} (clus_fpp_aval(i)*exp(-bval(i)*(sin(theta)/lambda)**2)]
Example of CLUSTER form factor input:
newatomtype wclu
fprimv 100.0 ! fprime value, to be multiplied by clus_fp form factor
fprprv 50.0 ! fprime value, to be multiplied by clus_fpp form factor
clus_aval 2093 5109.4 -1197.1 5254.3 ! form factors for f_o scattering
clus_bval 509.3 -37.8 849.4 108.5
clus_cval 184 30 1.2
clus_fp_aval 0.185886 0.453782 -0.10632 0.466651 ! form factors for fprime
clus_fp_bval 509.3 -37.8 849.4 108.5
clus_fp_cval 184 30 1.2
clus_fpp_aval 0.185886 0.453782 -0.10632 0.466651 !form factors, fdoubleprime
clus_fpp_bval 509.3 -37.8 849.4 108.5
clus_fpp_cval 184 30 1.2
Example of CLUSTER form factor input for mad atom:
Same as above for the newatomtype. Then specify:
mad_atom wclu
and for each wavelength specify (just as usual)
fprimv_mad 100.
fprprv_mad 50.
Then the clus_fp_aval etc will be applied to the fprimv_mad value, and the
clus_fpp_aval etc will be applied to the fprprv_mad value as a function
of sin(theta)/lambda.
mad_atom xxxx name of the anomalously scattering atom is xxxx.
fprimv_mad f' value for anomalously scattering atom at a particular
wavelength (must be input after each wavelength)
fprprv_mad f" value for a particular wavelength
FIXSCATTFACTORS Fix scattering factors at their input values [default]
REFSCATTFACTORS refine scattering factors f' and f".
Heavy atom parameters
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
gotoderiv n go to previously specified derivative (wavelength) n
and get readyto read some modifications of the parameters
for this derivative.
LABEL text label for this wavelength
IEGROUP n Group of correlated derivatives that this derivative
belongs to. Determined automatically if GETGROUPS is set
DERSCALE Dividing scale factor applied to all this derivative data
after overall scale factor has been applied. DEFAULT=1.0
DERTEMP Dividing B-factor to apply to deriv data. DEFAULT =0.
SIGDERSCALE Scale factor to apply to derivative sigmas after all above
scaling is applied. DEFAULT = 1.0
ATOMNAME XXXX XXXX is the atom type of an atom to be refined.
Please note: the f' and f" values in SOLVE's database are
for lambda=1.54 A. If you collected MIR data at a
synchrotron then you should define a new atom type with
NEWATOMTYPE and input the correct f' and f" values.
HINT: you can get the aval, bval, and cval values for an
atom recognized by SOLVE by typing madatom [atom name].
When you type ATOMNAME, SOLVE assumes you are typing in a new
atom and it zeroes out all the parameters for this new atom.
If you want to go back to this atom later (i.e., in another
cycle) use the keywords GOTODERIV and GOTOATOM to identify
this atom.
When you have multiple sites for a particular derivative,
use ATOMNAME XXXX for the first, then input all the data on
that site, then start the next site with ATOMNAME YYYY, and
so forth.
gotoatom n go to the n'th atom in this derivative/wavelength
and get ready to read some modifications of its parameters
OCCUPANCY x Fractional occupancy of this atom
Note: if occupancy is equal to 0.000 or refines to 0.000,
the atom is ignored in refinement.
BVALUE b Temperature factor for this atom. Anisotropic temperature
factors are also supported (just input 6 numbers.)
NOTE: bval is not the same as bvalue. BVAL refers to
scattering factors for a newatomtype.
XYZ x y z Fractional coordinates of this atom
Note: if coordinates move dramatically during refinement,
the occupancy is set to zero and the atom ignored.
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.
Control parameters for HEAVY atom refinement
and phasing
NO_SIM Do not use Sim weighing with heavy-atom structure factors in SAD CORRELPHASE Use Bayesian correlated MIR phasing (default) GETGROUPS Automatically get groups of correlated derivatives for correlated MIR phasing IMADPHASE n wavelength to phase using Bayesian MAD phasing (default =0, no Bayesian MAD phasing). See description below. n refers to the wavelength to be defined as a reference. Note that you cannot refine with madphase, you can only phase. Note: Flags for refinement of a heavy atom are cumulative, so you can refine x and y using REFINEX and REFINEY. Note: Flags for refinement of a heavy atom do not apply when the keyword SOLVE is used (only with HEAVY) REFINENONE Don't refine anything...reset all the refinement flags to zero REFINEALL Refine x,y,z,occupancy, and B REFINEOCCB Refine occupancy and B REFINEXYZ Refine x,y,z REFINEX Refine x REFINEY Refine y REFINEZ Refine z REFINEOCC Refine occupancy REFINEB Refine B NOREFINESCALE Do not refine overall scale factor. Default = refined REFINETEMP Refine B-factor applied to deriv data. DEFAULT= not refined nsolsite_deriv Maximum number of sites for this derivative only cutoff_deriv 200. 3.5 resolution limits for this derivative/wavelength only RES_PHASE 2.2 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 current 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 ISOONLY use only isomorphous differences in phasing and refinement this deriv ANOONLY use only anomalous differences in phasing and refinement this deriv ISOANO use both isomorphous and anomalous differences this deriv (cancels ISOONLY and ANOONLY)(default) KOUT n type of output from HEAVY if any. DEFAULT = 0 (no binary output) KOUT...TYPE OF OUTPUT 0.... NONE 2.... DIFFERENCE FOURIER FOR KDER A=m(Fder-Fnat)cos(PhiBest) B=m(Fder-fnat)sin(PhiBest) 3.... ANOM DIFF FOURIER FOR KDER A=m(DelAno)cos(PhiBest-90) B=m(DelAno)sin(PhiBest-90) 4.... RESIDUAL MAP FOR KDER A=m(Fder-|Fnat+FH|)cos(PhiBest) B=m(fder-|Fnat+FH|)sin(PhiBest) (where Fnat+FH is the vector sum of Fnat and the heavy atom FH) 6.... NATIVE FOURIER A=m(Fnat)cos(PhiBest) B=m(Fnat)sin(PhiBest) 7.... PHASES AND FIGURE OF MERIT and fnat PhiBest (in degrees), PhiMostProbable, and figure of merit, and Fnat 8.... Fnat,phibest, phi most probable, figure of merit, HENDRICKSON-LATTMAN COEFFS 9.... HEAVY ATOM S. FACTORS FOR KDER A, B= real and imaginary parts of normal scattering from heavy atom. C, D= real and imaginary parts of anomalous scattering NOTE: m=the figure of merit, PhiBest is the "Best" phase, PhiMostProbable is the the most probable phase. KDER n derivative n is to be included in output IANGLE x phasing angle, minimum=5, default=5 INANAL n PHASE ANALYSIS. DEFAULT=0 1 for printing of extensive heavy atom statistics INRESD n RESIDUAL AND STATISTICS. DEFAULT = 0 -1 No residuals or statistics calculated. 0 zeroth cycle added before first refinement cycle. During zeroth cycle residuals and statistics are calculated and printed. No statistics are calculated on other cycles. 1 Residuals and statistics calculated every cycle and printed according to INPRNT. Note: residuals are only calculated for derivatives with INPHAS = 1. INOSIG n USE OF SIGMAS. DEFAULT = 0 (use sigmas). 1 if sigmas from input data file are not to be used. INHEND n USE OF HENDRICKSON-LATTMAN COEFFICIENTS. DEFAULT=0 (don't use) 1 if Hendrickson-Lattman coefficients are to be calculated and used for phasing instead of Blow-Crick phasing. HEAVY does not do phase combination. If KOUT=8 and INHEND=1, then standard H-L ABCD are output. If KOUT=8 and INHEND=0, then HL ABCD are fit by least squares to the phase probability distribution. INPRNT n PRINTING OF SHIFTS. DEFAULT =0 (don't print) 1 if shifts (and statistics, if any) are to be printed on every cycle. Default is to print statistics on first cycle, shifts and statistics on last. JALT n USE OF PHASES IN REFINEMENT. DEFAULT = 0 (Patterson refinement) 0 is to use origin-removed Patterson refinement. 1 is to use phase refinement at most probable phase JALT and KALT are set automatically to 0 if you use a procedure (IHEAVYPROC > 0) KALT n USE OF DERIVATIVE BEING REFINED IN PHASING. DEFAULT=0(don't use) 0 is not to use derivative being refined in phases 1 is to use all available derivatives in phasing JALT and KALT are set automatically to 0 if you use a procedure (IHEAVYPROC > 0) NCYCLE n Number of cycles of refinement to be carried out if a PROCEDURE is NOT used (see IHEAVYPROC). Maximum = 30 Default = 0 IREFCY n List of derivative numbers to be refined during the NCYCLE cycles of refinement if a procedure is NOT used. Default = 0 i.e., 1,1,1,1,0 means refine deriv #1 on cycles 1-4 and calculate phases, get residuals, figure of merit, etc on cycle #5. Note that you don't get these statistics on cycles in which you refine with Patterson refinement. IHEAVYPROC n RUN a procedure with HEAVY. Default =5 (refine everything) Available procedures: 1 = NREP cycles of refinement of each deriv that has INPHASE specified, refining only occupancy. 2 = as 1, but refining only xyz. Fixes coordinates of best atom in each deriv in polar space group in polar directions unless another atom is already fixed by user. 3 = as 2, but refining xyz and occ 4 = as 3, but refining xyz, occ, B 5 = 1, then 2, then 3, then 4 6 = phased refinement to obtain relative coordinates among derivatives for polar directions in polar space groups. Fix and phase with best derivative. Refine just coordinates in polar directions for all other derivatives with INPHASE specified. This should be followed by #5 again. Note: when you use this procedure you must still set which refinement flags you want to (ever) be refined. The procedures only turn OFF flags, they do not turn on ones you have never set. NREP n # of refinements of each deriv in procedures with IHEAVYPROC > 0 (default=5) SMALL xx minimum ratio of derivative structure factor amplitude (F Deriv) to RMS lack-of-closure for use in refinement or residuals. DEFAULT=0. FMIN xx minimum native F for any action. Default=0. FOMMIN xx minimum figure of merit for use in phased portion of refinement. Default =0. BMAX maximum allowed bvalue default = 60 BMIN minimum allowed bvalue default = 1 THR xx Keywords to set threshold and damping factors for shifts: ACL xx if SHIFT > THR *sigma of SHIFT, SHIFT=SHIFT*ACL Defaults are 0. and 0.5 FSIGMIN xx MINIMUM ratio of F/sig to include. DEFAULT =1.0 NNATF n column number in input file for native F NNATS n column number for sigma of native F NNATF_DERIV n column number for native F that pairs with this derivative NNATS_DERIV n sigma of native F that pairs with this derivative NBST n optional column number for "best" phase in input file NMP n optional column number for most probable phase in input file NFIGM n optional column number for figure of merit in input file Note: if you set NFIGM for routine HEAVY it will be applied in MAPS too. Be sure you reset it to the value you want. INOLD n Flag for using phases from input file in phasing when they are not available from current data. default = 0. To use input phases, inold=1 ANATSCALE xx Overall scale factor applied to ALL data before any other scaling. DEFAULT = 1.0 SIGNATSCALE xx Scale factor applied to native sigmas after overall scaling DEFAULT = 1.0 EIS Optional list of estimated rms isomorphous lack-of-closure residuals in 8 resolution ranges EAD Optional list of estimated rms anomalous lack-of-closure residuals in 8 resolution ranges FPHBAR Optional list of estimated rms derivative F in 8 resolution ranges FHBAR Optional list of estimated rms heavy atom F in 8 resolution ranges SIGBAR Optional list of estimated rms derivative sigma in 8 resolution ranges
USE_F_BINS Use |F| and resolution to set bins for phasing statistics
(only used internally, does not affect printout)
NO_USE_F_BINS Use only resolution to set bins for phasing statistics
N_F_BINS Number of bins (for each resolution range) based on F for
phasingControl parameters for HASSP
searchregion region to search (xs,xe,ys,ye,zs,ze) (default = region
covered by the FFTGRID)
ihassptype n control of what is to be done (default=0)
0 search for single-site solutions, then 2-sites
2 search for single-site solutions
5 same as 0
-5 use trial solutions given in keyword trialsite
as trial cross-vectors
-6 use trial sites given in trialsite as a
trial solution. evaluate it and look for more
sites
discrm xx ratio of peak height over surroundings to use
(default=1.0)
icrmax n maximum # of peaks to try in 2-site search (default=10)
nospec n control over ignoring symmetry #'s of special positions
(default=0, do not ignore)
nsignf n 0 if significance of peaks is to be tested (default=0)
spat xx minimum probability for non-randomness to keep a peak
in routine "patpk". (default=0.0)
ssin xx as spat, but for single-site searches (default=0.0)
sdub xx as spat, for two-site searches (default=0.95)
strp xx as spat, for 3-site searches (default=0.0)
ssft xx as spat, for sifting through 3-site solutions
(default=0.95)
ihassplist print out value of patterson function
at every predicted self- and cross-vector for every
solution. this is very helpful for analyzing a
solution in detail. default =0 (not to print out).
trialsite x y z fractional coordinates of a trial site or cross vector
(read in if ihassptype < 0)
ntophassp n a maximum of n solutions will be saved in routines
that use hassp output to build up solutions
sigma_remove n peaks labelled with uvw_remove will be set to this value
uvw_remove u v w n remove this uvw peak from the Patterson (set to
sigma_remove*sigma)
Working with maps
PATTERSON this is a Patterson map FOURIER this is a fourier mapGrids used for FFT calculations
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 BOSSGRID xs xe ys ye zs ze grid for MAPVIEW map .Control parameters for GENERATE
coordinatefile pdb file with coordinates for GENERATE
percent_error % error added to intensities in GENERATE
cell_derivative a b c alpha beta gamma (only for generate_mir) cell parameters
for this derivative.