This manual details algorithms and usage controls behind a series of Xtal programs last released in Xtal3.2 (1992). The Xtal system grew explosively in functionality up to this point, with the Xtal coordinators finding they could no longer answer queries regarding the use and functionality of many of the protein and maximum entropy programs described herein. Envisioning a drastic change in future design The Xtal System rediscovered its roots in small molecule crystallography, and the programs described below were dropped from the publicly released versions from Xtal3.4 onwards. Sadly the expected radical changes in design did not come to fruition, with the consequence that the unsupported programs detailed below remain completely compatable with core Xtal3.6 routines.

The program descriptions were prepared by the program authors listed under the program name and header of each chapter. If you experience difficulties with a program, or require further information, please try to contact the author(s) indicated. The Xtal Coordinators have extremely limited knowledge of these programs, but may be contacted as a last resort.

Program Summary

The following is a summary of the state of The Xtal System as of version 3.2.

The descriptions of the individual programs are preceded by an overview of the calculations. There is a brief summary of each program grouped according to their basic function. Note that there is some overlap of calculations. In several cases two programs do essentially the same calculation (e.g. BONDLA and REGFE). In general, however, there are significant differences between programs performing equivalent tasks. Users must learn by experience which program best suits their specific needs. Note that the programs intended primarily for macromolecular calculations have been flagged with a  '⋄'. 

Processing raw diffraction data

	STARTX:	Creates or updates a standard archival binary data file. Storesinformation pertaining to the crystal, cell and symmetry. Spherical scatteringfactors and dispersion corrections automatic.
	LATCON:	Determines lattice parameters and their esd's from the 2θ anglesof indexed reflections. The crystal system constraints are included andsystematic errors in the zero values can be corrected.
	DIFDAT:	Processes diffractometer data to produce reflection intensities andvariances. CAD, Siemens, Rigaku and Tsukuba files are treated automatically. Arange of scaling and smoothing functions may be applied. Corrections for thebeam instability can be calculated.
	REFCAL:	Processes diffractometer data entered primarily from the standaloneprogram Difrac (Flack).
	NICNAK:	Transfers reflection data from a Nicolet diffractometer file to a bdf.No data treatment based on standards is performed.
⋄	ADDMUL:	Stores onto lrrefl: |F| or data from a Siemensarea detector which has been processed and reduced by the XENGEN system.Friedel reflections can be stored on the same packets.
	ABSORB:	Corrects I, or |F| data, from any shaped crystal, forabsorption by the gaussian or analytical methods. Bisecting and azimuthal scandata from many diffractometer systems are allowed. Tbar can be calculated andstored. Spherical crystals are treated separately.
	LSABS:	Applies analytical and Gaussian absorption corrections to diffraction data.
⋄	ABSCAL:	Empirically corrects for absorption by the capillary, motherliquor and the crystal. Decay of the crystal is empirically corrected by use ofstandards.
	PERFAC:	Estimates the monochromator perfection factor C, required in thecorrection for polarisation, from Ni filtered and graphite monochromatedCuKα data sets.
	ADDREF:	Adds information to the reflection record either ab initio or inupdate mode. Data can be converted to I, or |F|. X-ray andneutron Lp corrections for a variety of diffraction geometries are available.Options include: form factors stored in lrrefl:, Bayesian treatment ofweak data, removal of systematic absences and separate storage of Friedelpairs.
	SORTRF:	Sorts reflections into any desired hkl order. Multiple and symmetryequivalent I, or |F| (one only) can also be averaged. Outliersfrom averages may treated by a choice of algorithms. Friedel pairs can betreated separately.
	BAYEST:	Determines the Bayesian posterior estimate of I, |F|, σ(I) andσ(|F|) from the intensity distribution. This approach is useful in thetreatment of weak and negative intensities.
⋄	SCALE1:	Scales multiple-observation sets of intensity data by themethod of Monohan, Schiffer and Schiffer.
⋄	FINDKB:	Determines a linear scale and exponential thermal factorwhich places the structure factors for two derivatives on the same scale. Achoice of two algorithms is available.
	XTINCT:	Calculates the extinction coefficient from the diffraction datameasured from and irregular crystal.

Fourier transform calculations

	FOURR:	A reciprocal-to-real-space crystallographic Fourier calculation.Beevers-Lipson or FFT options. Transform coefficients may be standard or asdesired. Automatically generates the asymmetric unit. Output printed or writtento a file for further analysis. Maps are strictly parallel to axial thedirections.
⋄	BFOURR:	Generates transform coefficients and phases for calculating anon-standard crystallographic Fourier transform with FOURR.
⋄	CONVOL:	Performs real space convolution to smooth or shape theelectron density, by multiplication of structure factors and the desiredfunction in reciprocal space. The coefficients generated are used as input toFOURR.
	SLANT:	Produces a Fourier map in any general plane by interpolation from aFOURR output.
	PEKPIK:	Searches a Fourier density map for a unique asymmetric set of themaxima or minima. Fractional coordinates may be stored on a PEK file orpunched.
	FOGEN:	Reproduces any volume of Fourier density from a map containing aminimum of one asymmetric unit of points.
⋄	FOGNU:	Reproduces any volume of Fourier density from a map containinga unit cell of points. Both map layouts must be identical.
	FODIFF:	Performs a simple one for one subtraction of the scaled Fourierdensity points stored on separate binary data files.
⋄	FOSTAT:	Determines empirically the distribution of electron densityvalues on a Fourier density map.
	RMAP:	Calculates a linear combination of R factor and correlation coefficientas a function of the translated position of a molecular fragment. A maximumcorresponds to the optimum position in the unit cell. A map of the values canbe stored and the best solution found using PEKPIK.

Solving the phase problem

	GENEV:	Calculates normalized structure factors and sigmas. Scaling can belinear or non-linear and applied overall or to groups. Partial structureinformation can be used in normalization. Special treatment of weak data may beapplied.
	GENSIN:	Generates triplet and quartet structure invariant relationships.Parameters optionally used to define generator reflections and invariant types.Conditional probabilities phase estimate enhancement by group structure factorinformation.
	GENTAN:	Structure factor phases from triplets/quartets by the general tangentformula. Cell or enantiomorph origins can be automatic. Permuted, magic integeror random phase initialisation. Phase extension/refinement by cascade or block.Probabilistic, Hull-Irwin or modified Hull-Irwin weighting. Variety of figuresof merit employed.
	PATSEE:	Identifies molecular fragments of known geometry by using anintegrated Patterson search and structure invariant data from GENSIN. SIMPEL:Phases from normalized structure factors by applying the symbolic additionprocedure to triplet/quartet invariants. Enantiomorph origin can be automatic.Wide range of phase selection/extension options. Many procedures to determinesymbol phases and a variety of figures of merit available.
⋄	MIR:	Calculates reflection phases for native proteins by therefinement of parameters of heavy atom derivatives by the method of multipleisomorphous replacement. Phase estimation may be by the Blow-Crick or Syguschprocedures with refinement by the Bricogne method.
	REVIEW:	Analyzes the agreement between triplet/quartet structure invariantsand a given phase set. Used to examine invariant relationships of unsuccessfulsolutions.
⋄	MEPHAS:	Estimates phase using maximum entropy techniques.

Density and phase enhancement methods

⋄	APMASK:	Enhancement of the molecular contribution to the Fourierelectron by solvent flattening. Density is modified by user or program definedscales and offsets. Requires a mask to be input through MKMASK.
⋄	MKMASK:	Creates a mask to be used for separating the Fourier electrondensity into molecular and non-molecular (solvent) regions. A precursor toAPMASK.
⋄	MERUN:	Creates the input file for the maximum entropy refinement of alow resolution electron density map using the programs MEDENS and MEFFIT.
⋄	MEDENS:	Computes the constrained exponential electron densitydistribution from a low resolution electron density map. New phase estimatesfor the constrained electron density distribution are recovered by executingRFOURR.
⋄	MEFFIT:	Combines the constrained exponential electron density mapfrom MEDENS with a difference map from FOURR using the above new phaseestimates to produce a new map from which the maximum entropy phases andstructure factor moduli are determined by RFOURR.
⋄	MESTAR:	Start maximum entropy phasing process.
⋄	MEPHAS:	Ab initio maximum entropy phasing technique.

Loading atom site data

	ADDATM:	Positional, thermal and structural parameters are loaded into thearchival binary data file either ab initio or in update mode. Specialpositions and symmetry constraints are automatically determined. User definedconstraints or soft restraints allowed.
⋄	PROATM:	Positional, thermal and structural parameters are loaded,deleted or updated into the archival binary data file or punched in a formspecified by the Protein Data Bank (PDB).
⋄	PRECED:	Loads macromolecular sequences, bonding and force restraintsand special linkage information onto the archival bdf as a precursor to CEDAR.Ensures the atom list on the input bdf is complete with respect to therestraint requirements.
	PEAKIN:	Peak sites are inserted into the into a PEK bdf as produced by PEKPIK.
⋄	PROTIN:	Sets up constraint-observational terms for PROLSQ from theatomic parameters and stereochemical information.

Structure factor calculations

	FC:	Calculates structure factors from the asymmetric set of atom sites.Optionally determines the Sim weight and corrects for dispersion and isotropicextinction.
⋄	RFOURR:	Fourier transforms a complete cell of sampled points indirect space to a unique asymmetric set of structure factors and phases inreciprocal space.
⋄	SIMWGT:	Phase probabilities are calculated and stored on the bdf.These can be used as phases for MIR or combined with the Hendrickson-Lattmancoefficients to calculate weighted Fourier syntheses.

Structure Refinement techniques

	CRYLSQ:	Least squares refinement of molecular structures. Determines generaland atomic parameters and their esd's. User defined invariants, constraints,soft restraints and rigid groups can be applied. Data is optionally culled andweighted. A choice of full matrix, block diagonal or user defined blocks used.Dispersion and various extinction models can be applied and/or refined. TheFlack absolute configuration parameter can be refined.
	LSLS:	Structure factore least squares based on I and. Permitsthe refinement of crystal shape and twin components. A wide range of restraintsare possible using the program LSRES.
	CEDAR:	Refinement of molecular structures using energy minimization anddynamics. Forces may include those from target atoms, bond lengths, bondangles, dihedral angles, interatomic distances, van der Waals interactions andpartial ionic charges. Conventional crystallographic least squares, symmetryand lattice related forces and solvent molecules may be included incalculations.
⋄	PROLSQ:	A restrained parameter sfls refinement program for largemolecules. Allows for refinement of atomic parameters which are restrained toconform to stereochemical information such as coplanarity, chirality, van derWaals distances, torsion angles, thermal shifts, interchain distances, andnon-crystallographic symmetry. This is the XTAL version of the Hendrickson andKonnert program.

Analyse molecular geometry

	PIG:	An interactive graphics routine for displaying, selecting andmanipulating atom and peak sites. Molecule or cell can be displayed. Sites canbe added, deleted, relabeled and the atom type redefined. Bond distances andangles, contact distances and torsion angles can be displayed. View can bechanged by rotation or projection onto least squares plane. Orientation issaved for ORTEP.
	BONDLA:	Calculates bond distances and angles, contact distances and dihedralangles and their esd's from the asymmetric unit of atom sites. Search includesspace group symmetry and adjacent cells.
	REGFE:	Calculates a variety of functions (bond lengths, angles, distances fromplanes etc) and their esd's from the variances and covariances of theparameters.
	MODEL:	Searches peak or atom sites for a connected molecular model based onbond lengths and angles or supplied connectivity information..
	BONDAT:	Generates the "ideal" coordinates of atoms from the geometry ofpreviously determined atoms. A general as well as a variety of specificconfigurations can be determined.
	RIGBOD:	Converts coordinates of an idealized group of atoms into coordinatesproperly located in a given cell for use with rigid group refinement in CRYLSQ.
	LSQPL:	Determines the coefficients of least squares planes and lines and theiresd's. Also calculates distances of atoms to the planes, interplanar angles andtheir esd's.
	NEWMAN:	Stereochemical Newman projections about any bond axis are calculatedand the diagrams may be printed and/or plotted. Maximum bond lengths for anatom type can be specified by the user.

Calculate charge densities and properties

	PARTN:	Hirshfeld weights are use to partition an input Fourier densityaccording to the contributions of a specific atom or of that atom and itssymmetry equivalents.
	CHARGE:	Derives the charge, according to the Hirshfeld method, associated withan atom from the difference Fourier density.
	FOURR:	Calculate electrostatic potential, field vector and field gradient anddisplay these using the programs SLANT, CONTRS and PLOTX.

Graphical output processes

	CONTRS:	Contours a Fourier density map as output by either FOURR or SLANT.Contours are determined by linear or cubic interpolation, may be smoothed ifrequired and the line type specified by the user.
	ORTEP:	Crystal structure illustrations are generated with wide variety ofdisplay options. Automatic, semi-automatic as well as manual modes can beused.
	PLOT:	Generates the display of graphical information for user specified localdevices.
	PLOTX:	Generates the display of graphical information using local plotsoftware such as GKS to generate commands for local plotting devices. Supportscolour, automatic scaling and interprets the output of programs such as ORTEP,CONTRS, NEWMAN , PIG or ABSORB.

Quality measures

	REGWT:	Analyzes the weights applied in the structure refinement for systematictrends in |F|,, I and sinθ /λ. Determinescoefficients for a weight modification expression to account for uncorrectedrandom or systematic errors.
⋄	PHACMP:	Compares reflection phases from two separate sources anddetermines mean and weighted means and esd's. Phases may exist on the same ordifferent bdf's.
	MULIST:	Produces statistics on replicated observations and reflections.
	CRITIQ:	Examines variability amongst multiply observed intensity data. Themost variable reflections are selected and five discrepancy lists prepared.CRITIQ is an alternate approach to MULIST.
	RSCAN:	Structure factor residuals and R-factors are listed as functions ofMiller indices, measured structure factors, measured intensities and(sinθ /λ)2. Overall scale, thermal displacementparameter shift and R-factor are determined.
	RCALC:	Calculates the R-factor between any two user specified items inlrrefl:.

Storing and manipulating data

	CIFIO:	Converts data on the Xtal archive file to either a standard IUCr CIFformat suitable for electronic transmission to journals or databases, or alocal ASCII archive format which can be read and manipulated with a texteditor.
	VUBDF:	Displays the contents of any bdf (archival or auxiliary) in terms ofthe packet, physical and logical record structure.
	NEWCEL:	Transform all crystallographic data for a new cell and symmetry.
	REFM90:	Converts crystallographic data from the Xtal bdf to the StandardCrystallographic File Structure, and vice versa.
	MODHKL:	Enables the modification of reflection records on the bdf. Globally,items may be removed from reflection packets, rcodes can be modified orreflections purged based on specified conditions. Specific reflections can bedeleted or modified.
	EDTBDF:	Changes, deletes or adds items to any logical record in the bdf.
	REMSET:	Removes a dataset from the bdf. The logical records modified are:lrddef:, lrexpl:, lrdset:, lratom:, andlrrefl:.
	MERGOB:	Reflection records of two individual archival binary data files areunited into one record with separate scale groups if desired.
	MERGDS:	Reflection data of an isomorph on one archival binary data file iseither added to or replaces data of the same isomorph on a second binary datafile.
	PHONYD:	Structure factor amplitudes are generated from calculated structurefactors for purpose of testing programs. Random errors are optionally applied.Intensities may be similarly generated.

Interfaces to other systems

⋄	MAKBRK:	Converts a Fourier density map written by FOURR into a randomaccess bricked density file for use by the Frodo graphics program.
	SHELIN:	Extracts from a standard Shelx input file the required commands anddata to generate the input file for STARTX, ADDREF and ADDATM and alsoautomatically initiates their calculation.
	MAPLST:	Converts map file to list file suitable for Mathematica®.
	MOGIN:	Produces atom site data for input to the molecular graphics programMogli.
	MIND:	Produces atom site data for input to the molecular graphics programMindTool.
	MOLVU:	Produces atom site data for input to the molecular graphics programMolView.
	SKLOUT:	Produces atom site data for input to the molecular graphics programSchakal.

Preparation of data for publication

	CIFIO:	Converts data on the Xtal bdf to either a standard IUCr CIF formatsuitable for electronic transmission to journals or databases.
	ATABLE:	Prints atomic coordinates and thermal parameters in a tabular formatwhich is suitable for publication.
	LISTFC:	Reflection data such as hkl, Frel, Fcal, σ(F) or the phase canbe listed in a format suitable for publication or hard-copy archiving.
	BONDLA:	Calculates bond distances and angles, contact distances and dihedralangles and their esd's from the asymmetric unit of atom sites and outputs theseinto the punch file in a format suitable for publication tables.
	REGFE:	Calculates a variety of functions (bond lengths, angles, distances fromplanes etc) and their esd's from the variances and covariances of theparameters and outputs them in a format suitable for publication tables.