| Xsight |
This appendix is adapted from the documentation for the MADSYS program provided by Dr. Hao Wu of Dr. Wayne Hendrickson's laboratory.
The series of MADSYS programs developed in Hendrickson's laboratory over the years has been put into one entity under the name of MADSYS. The current program is structured so that the logic of the old MADSYS is preserved, but one can either stop at intermediate steps or proceed to the final phase in one run. The connection of MADSYS to the previous scaling programs is through F2ANO. Any scaling output that contains non-merged non-reduced h, k, l, batch_number, i, sigi can be accepted into F2ANO by specifying the format of the file in a standard Fortran format statement. Specifically, output from SCALEPACK or CCP4 AGROVATA (a version modified locally to output original indices and completely non-merged data) is also programed as two special cases (see the keyword format below). After this point, the program is self contained. It should be noted that in scaling, one should use the same batch number for all the wavelengths at the same oscillation position. For mirror geometry, one should set the batch number according to the sequence of data collection and, for inverse beam geometry, keep the direct sweep and inverse sweep separate. One could have a mixture of mirror and inverse beam geometry in one MAD data collection.
1. Obtaining FA for determination of anomalous scatterer sites.
F2ANO --> (ANOSCL) --> WVLSCL --> MADLSQ --> MERGIT
MERGIT --> MADFAZ or
WVLSCL, MADLSQ --> MADABCD (PHASE)
Steps 1, 2, 3 above comprise the major steps of a structure determination.
4. Obtaining parameters for input into WVLSCL and MADLSQ.
5. Obtaining averaged delta(F) for an anomalous difference Patterson function.
F2ANO --> (ANOSCL) --> ANOMERGE
6. Obtaining statistics on the presence of an anomalous signal.
You can stop and start at any point.
For commands longer than four letters, only the first four letters are necessary. A ! comments out the rest of the line. The word "stop" terminates input.
absf_rms real_value
Absolute rmsF for placing data at the absolute scale.
anocut real_value
Cutoff for large anomalous differences. The set of reflections with |(F+-F-)| > anocut x rmsdel is rejected.
atom 5_real_values
Fractional atomic coordinates, b factors, occupancies of anomalous scatters.
batch_group integer integer
Lower and higher batch limits of this group. Sequential group numbers (starting from 1) are assigned to each batch_group definition.
bover real_value
Overall B factor of your structure factors.
cell 6_real_values
comment anything
copy_per_au integer
Number of copies per asymmetric unit.
cycle integer
Number of cycles of refinement in ASLSQ.
dffcut real_value
Reflections with |(F+-F-)|/F > dffcut are not included in statistics of ANOSCL.
difference_Fourier real_value integer
Do Fa difference Fourier in ASLSQ with peak height cut and number of peaks to output. (This map format is not compatible with the Xsight map format).
dispcut real_value
Differences between two wavelengths |F1-F2| > dispcut x rmsdel are rejected from WVLSCL.
error intensity/amplitude
facut real_value
faflag real_value_1 real_value_2
Reflections with fa > real_value_1 x exp(-real_value_2 . s2) are flagged.
famax real_value
famin real_value
Minimum fa cutoff used in statistics of MADFAZ.
fcscale real_value
Scale applied to calculated fa.
fdeviation real_value
|f-fave| > fdeviation x sigma will not be used in MADLSQ fitting or MADABCD.
fit scale/fp/fpp integers
Set 0/1 for each wavelength (0: fix, 1: refine).
(Refine relative scale of wavelengths 2, 3, and 4.)
(Refine f" of wavelengths 3 and 4.)
(Refine f' of wavelengths 2 and 3.)
format scalepack/ccp4 or FORTRAN_format_statement
Any FORTRAN format statement specifying h,k,l,batch,i,sigi
(Take NO MERGE ORIGINAL INDEX scaling output from scalepack)
(Take a modified output from AGROVATA, the agravata.f is distributed along with madsys which output a formatted file named AGRO_OUT. Note: AGROVATA is not part of MSI's distribution of the MADSYS program.)
fp real_values
Anomalous scattering factor f' of each wavelength.
fpp real_values
Anomalous scattering factor f" of each wavelength.
frange integer
Number of amplitude/intensity ranges for estimating lack of closure errors in madabcd.
fzcut real_value
fzmax real_value
groups_include integers
infile function_keyword filenames
Input file name for a specific function. For f2ano, anoscl, anomerge, anores, wvlscl and fa, the program expects the same number of files as the number of wavelengths. For others, one file is expected. You can split the files on several lines for those that expect the same number of files as the number of wavelengths.
absolute: protein sequence in 1- or 3-letter code.
anomerge, wvlscl: output from f2ano or anoscl.
anores: output from f2ano or anoscl.
anoscl: output from f2ano.
aslsq: output from mergit.
f2ano: scaling program output.
fa: scaling program output.
madabcd: output from madlsq and wvlscl.
madfaz: output from mergit.
madlsq: output from wvlscl.
mergit: output from madlsq.
phase: output from madlsq and wvlscl. Same as madabcd.
wvlscl: output from f2ano or anoscl.
inflate_error real_value
Inflate lack of errors by real_value-fold.
inverse 4_integers
Inverse beam geometry with starting batch # and end batch # for the direct sweep, batch difference between direct and inverse data sweep, batch tolerance in pairing.
(This inverse beam data contain batches 1-40 as direct sweep, 41-80 as inverse sweep, pair any hkl/-h-k-l that are separated by 40+/-4 batches)
Iterations integer
Number of iterations of madlsq phasing.
list integer
List every integerth reflection.
local_scaling all/centrics/acentrics, group integers reso real_value real_value
(This scaling group uses both centrics and acentrics of group 1, 2, and 3 and at resolution 30 - 3.0A.)
(This scaling group uses only centric reflections for determining scale factors.)
mirror 6_integers
Mirror geometry with starting batch #, end batch #, batch tolerance in pairing, and spindle axis direction specified by three numbers along the a*, b* and c*.
(This mirror geometry data contains batches 1-82, pair any reflections related by the mirror plane at +/- 4 batches, spindle is along a*+b*.)
error intensity/amplitude
name character integer
number_wavelength integer
nstep integer
Number of steps to search at either side of Fz in a 2D phase probability distribution to obtain a best Fz and best phase probability distribution.
observations integer
Minimum number of total observations for each reflection in wvlscl before merging into other reflections.
outfile function_keyword filenames
Output file names for a specific function. You can either write out output from every function or, if you run several functions sequentially as outlined in the flow chart, you can just save the output from your final function. For F2ANO and ANOSCL, there will be same number of output files as the number of wavelengths. For others, one file is output.
absolute: no output.
anomerge: in xplor format, containing h,k,l,delta(F) and sigma. unit 41.
anores: no output.
anoscl: output after anisotropic parameterized local scaling. unit 31-30+n for n wavelengths.
aslsq: containing refined fcscale and site, b and occupancy of anomalous scatters. unit 65.
f2ano: paired reflections. unit 21-20+n for n wavelengths.
fa: merged reflections containing fz, fa, delta(phi). unit 55.
madabcd: containing phased reflections and a, b, c, d coefficients. unit 60.
madfaz: phased reflections containing fz, phi, etc. unit 55.
madlsq: unmerged reflections containing fz, fa, delta(phi). unit 45.
mergit: merged reflections containing fz, delta(phi), etc. unit 55.
phase: containing phased reflections and a, b, c, d coefficients. unit 60.
wvlscl: reflections after scaling among wavelengths. unit 40.
(Facalc/Faobs required for Fn only.)
(Ft containing the normal scattering component of the entire unit cell content)
(Fn containing only the normal scattering component of non-anomalous scatters alone.)
pmax real_value
qmax real_value
Maximum quart (a value representing goodness of madlsq fitting).
random 3_integers
Random pairing based only on batch separation is applied with low batch limit, high batch limit and batch difference allowed in pairing.
refine scale/b/occupancy
Define what to refine, position always refine.
resolution real_value real_value
Upper and lower resolution range in angstroms.
rmsdeltaF real_value
Rms(F+-F-) obtained from a previous run.
scale real_value
Relative scale between the wavelengths as obtained from ABSOLUTE.
(Relative scale between the four wavelengths.)
scattering_factor 9_real_values
Scattering factor exponentials (a(i),b(i),i=1,4),c as in International tables for Crystallography, Vol. IV.
sc_cycle integer
Number of cycles of scattering_factor_refinement in madlsq.
sequence integer
Letter code of your input amino acid sequence.
shell integer
step real_value
Step size in sigma of searching the best Fz in MADABCD.
stop
symmetry character
Space group name as it appears in International Tables for Crystallography except:
p2c: c unique p2
p21c: c unique p21
b2: c unique c2
r3r: r3 of rhombohedron setting
r32r: r32 of rhombohedron setting.
Always check the symmetry printout to make sure that they are correct since not all space groups have been extensively tested.
wave_scaling group integers resolution 2_real_values
weighting_scheme prolsq/sigma prolsq/sigma (optional) 2_real_values (optional)
xplor function_keyword filename
Output xplor filename for functions FA, MERGIT, PHASE, MADFAZ and MADABCD.
The sequence of function keywords determines the sequence of running options.
Calculate expected signal, absolute rmsF and relative scales among the different wavelengths.
Bijvoet differences are averaged among data from all the wavelengths for calculating Bijvoet difference patterson. Not tested yet.
Calculate anomalous signals present in data of each wavelength.
Parameterized anisotropic local scaling is performed to reduce noise in Bijvoet differences.
Refine anomalous scatterer sites against fa.
Observations related by a certain data collection geometry are paired. In addition, symmetry and centric/acentric codes are calculated and intensities changed into amplitudes.
FA consists of a series of functions to generating fa: F2ANO, ANOSCL, WVLSCL, MADLSQ and MERGIT.
Calculating Hendrickson-Lattman phase coefficients based on anomalous scatterer model. This is not only useful for phase combination but should also prove superior to madfaz in generating protein phases in that it generally phases more reflections and gives more realistic figure of merit.
Phiz is calculated from Delphi and Phia from input anomalous scatterer model to complete MAD phasing by outputting FZ, Phiz, fom.
Least-squares solutions to the MAD equation are performed for each observation, where FA, Delphi and FZ are derived.
Individual observations are merged to give weighted FA, Delphi, FZ.
Overall and parameterized anisotropic local scaling are performed between data from different wavelengths.