1GENERAL: alias - define or list aliases for commands 1GENERAL: ask - ask for interactive input from within a macro 1GENERAL: break, exit, quit, return - exit from loops, macros, and from the program 1GENERAL: character - characters with special meaning 1GENERAL: do - unconditional or Fortran-77 do-loops 1GENERAL: echo - variable to control the echoing of commands 1GENERAL: erract - variable for error handling 1GENERAL: eval, show, set - set and show the values of variables 1GENERAL: functions - system functions 1GENERAL: goto - jump to a label within a macro 1GENERAL: help - give on-line help about commands, standard macros etc. 1GENERAL: if - Fortran-77 logical or block if statement 1GENERAL: intrinsics - intrinsic functions of the command interpreter 1GENERAL: label - labels used in macros in conjunction with goto statements 1GENERAL: macro - a file containing commands for the program 1GENERAL: parameter - give names to command line parameters for macros 1GENERAL: path - a variable that holds the search path for macros 1GENERAL: print, error - print messages 1GENERAL: subroutine, command - define subroutines or new commands within macros 1GENERAL: type - copy a macro to standard output 1GENERAL: var - declare local variables 1GENERAL: variable - string variables similar to shell variables in Unix GARANT COMMANDS: append expected peaks - append expected peaks to loaded peak list GARANT COMMANDS: append log - redirects output into a log file GARANT COMMANDS: assignment statistics - statistics of the assignment of measured peaks GARANT COMMANDS: calculate frequencies - calculate coherence ferquencies GARANT COMMANDS: check inconsistencies - check assigned peaks for inconsistencies GARANT COMMANDS: close log - redirects output to the previous destination GARANT COMMANDS: compare frequencies - differences between expected & assigned frequencies GARANT COMMANDS: compare peak assignments - compare assignments to comparison assignments GARANT COMMANDS: copyto possible assignments - copy current to possible assignments GARANT COMMANDS: criteria coherence degenerated - identify degenerate coherences (all) GARANT COMMANDS: criteria coherence interdegen - identify degenerate interresidual coherences GARANT COMMANDS: criteria coherence intradegen - identify degenerate intraresidual coherences GARANT COMMANDS: criteria coherence mapping - compare two sets of assignments GARANT COMMANDS: criteria coherence overlap - analyse overlap of assigned peaks GARANT COMMANDS: criteria coherence template - judge selected subset of peaks GARANT COMMANDS: criteria comment off - turn off the comment for the specified criterion GARANT COMMANDS: criteria comment on - turn on the comment for the specified criterion GARANT COMMANDS: criteria fragment correct - percentage of 'correct' assignments GARANT COMMANDS: criteria fragment intrainter - judge peaks in specified sequential range GARANT COMMANDS: criteria fragment mapping - compare two sets of assignments GARANT COMMANDS: criteria fragment overlap - analyse overlap of assigned peaks GARANT COMMANDS: criteria fragment SScorrect - percentage of 'correct' spinsystem assignments GARANT COMMANDS: criteria fragment template - judge selected subset of peaks GARANT COMMANDS: criteria threshold - set the thresholds t1 and t2 of the specified criterion GARANT COMMANDS: define frequency tolerance - sets the uncertainties of the assigned frequencies GARANT COMMANDS: define peak importance - set the importance of expected peaks GARANT COMMANDS: define pseudoatom correction - set correction for specified atoms GARANT COMMANDS: define secondary shifts - define shifts based on 2nd structure GARANT COMMANDS: determine equivalent peaks - find equiv. peaks in different fragments GARANT COMMANDS: evolutionary optimization - generate new resonance assignment from parents GARANT COMMANDS: filter add - adds spectrum to a filter GARANT COMMANDS: filter - compare peaks of different spectra GARANT COMMANDS: filter define - defines name of a set of spectra with common frequencies GARANT COMMANDS: initialize optimization possibilities - define size of population GARANT COMMANDS: list atoms - list the currently defined atoms matching a template GARANT COMMANDS: list expected peaks - list the currently defined expected peaks GARANT COMMANDS: list missing peaks - list expected peaks not present in the peak list GARANT COMMANDS: list peaks - lists all entries of the peaklists GARANT COMMANDS: load assignments - load peak assignments GARANT COMMANDS: load atom name library - loads library defining equivalent atom names GARANT COMMANDS: load comparison assignments - load assignments for comparions GARANT COMMANDS: load comparison coordinates - load atom coordiantes for comparison sequence GARANT COMMANDS: load comparison sequence - loads sequence to be used for comparisons GARANT COMMANDS: load coordinates - load atom coordiantes from coordinate file GARANT COMMANDS: load fragment library - loads library defining possible fragments GARANT COMMANDS: load frequencies - load frequencies from atom list GARANT COMMANDS: load peaks - read in positions of observed peaks GARANT COMMANDS: load reference peaks - load second list of measured peaks GARANT COMMANDS: load sequence - loads the (protein) sequence GARANT COMMANDS: load spin system library - loads library defining possible fragments GARANT COMMANDS: local optimization - optimizes the current resonance assignment GARANT COMMANDS: make coherences - generate expected coherences GARANT COMMANDS: make couplings - generate the expected scalar couplings GARANT COMMANDS: make distance noe - generate dipolar couplings from observed distances GARANT COMMANDS: make noe - generate the expected dipolar couplings GARANT COMMANDS: make peaks - generate expected peaks GARANT COMMANDS: make possible assignments - generate possible assignments from expected peaks GARANT COMMANDS: mark possible peaks - mark peaks that have possible assignments GARANT COMMANDS: match - calculates match between two peak lists GARANT COMMANDS: overwrite optimization possibility - save current assignment to the population GARANT COMMANDS: report calculate - analysis the assignments accoreding to defined criteria GARANT COMMANDS: report coherences - analyse assignments on the level of coherences GARANT COMMANDS: report fragments - analyse assignments on the level of fragments GARANT COMMANDS: report global - report global assignment statistics GARANT COMMANDS: reset assigned frequencies - assigned frequencies are reset GARANT COMMANDS: reset assignments - resets automatically generated assignments GARANT COMMANDS: reset possible assignments - all possible assignments are removed GARANT COMMANDS: reset user assignments - reset the user assignemts GARANT COMMANDS: seed random numbers - initialize random number generator GARANT COMMANDS: spectrum - activate spectrum of specified type GARANT COMMANDS: unfold peaks - calculate possible unfolded positions of peaks GARANT COMMANDS: write assigned peaks - write peaks marked as being assigned GARANT COMMANDS: write coherences - write coherences to a new atom list GARANT COMMANDS: write expected peaks - write expected peaks into a peak list GARANT COMMANDS: write log - redirects output into a log file GARANT COMMANDS: write peaks - write measured peaks into a peaklist GARANT COMMANDS: write possible assignments - write XEASY assignment file GARANT COMMANDS: write reference peaks - write reference peaks to a file GARANT MACROS: appNoes - interactive macro to append expected NOESY peaks GARANT MACROS: appPeaks - appends expected peaks of desired spectrum GARANT MACROS: asno - example of an asno macro GARANT MACROS: C13H1 - default set up for [13C,1H]-cosy GARANT MACROS: C13NOED2O - default set up for D2O 13C-corr. noesy spectrum GARANT MACROS: C13NOESY - default set up for 15C-correlated noesy spectrum GARANT MACROS: CBCACONH - default set up for CBCACONHN GARANT MACROS: CBCANH - default set up for CBCANHN GARANT MACROS: CCH - default set up for CCH-tocsy with long mixing time GARANT MACROS: COSY - default set up for cosy spectrum GARANT MACROS: D2OCOSY - default set up for cosy spectrum recorded in D2O GARANT MACROS: D2ONOESY - default set up for noesy spectrum recorded in D2O GARANT MACROS: D2OTOCSY - default set up for tocsy spectrum recorded in D2O GARANT MACROS: defaultreport - define default report for COSY, TOCSY and NOESY spectra GARANT MACROS: ExampleFilter - example of how to use the filter command GARANT MACROS: ExampleMatch - example of how to match two peak lists GARANT MACROS: ExampleResAss1 - example of resonance assignment with 2D spectra GARANT MACROS: ExampleResAss2 - example of resonance assignment with 3D spectra GARANT MACROS: ExampleResAss3 - example of resonance assignment with 3D spectra GARANT MACROS: genNoes - interactive macro to generate expected NOESY peaks GARANT MACROS: genPeaks - generates peak list of desired spectrum GARANT MACROS: HBHACONH - default set up for 15N-correlated tocsy spectrum GARANT MACROS: HCACO - default set up for HCACON GARANT MACROS: HCA_CO_N - default set up for HCA_CO_NN GARANT MACROS: HCCH24 - default set up for HCCH-tocsy with long mixing time GARANT MACROS: HCCH7 - default set up for HCCH-tocsy with short mixing time GARANT MACROS: HNCA - default set up for HNCAN GARANT MACROS: HN_CO_CA - default set up for HN_CO_CAN GARANT MACROS: HNCO - default set up for HNCO GARANT MACROS: HNHB - default set up for 15N-correlated HNHB spectrum GARANT MACROS: init - initialization GARANT MACROS: N15H1 - default set up for [15N,1H]-cosy GARANT MACROS: N15NOESY - default set up for 15N-correlated noesy spectrum GARANT MACROS: N15TOCSY - default set up for 15N-correlated tocsy spectrum GARANT MACROS: NOESY - default set up for noesy spectrum GARANT MACROS: opt - optimization of rasonance assignments GARANT MACROS: peaklist - load peaks with assignments from peaklist GARANT MACROS: pseudocorrection - define pseudo atom corrections for proteins GARANT MACROS: TOCSY - default set up for tocsy spectrum GARANT MACROS: writebest - example macro to write out assignments GARANT TOPICS: assignments - representation of assignments GARANT TOPICS: coherences - observable coherences GARANT TOPICS: floating assignments - definition of floating assignments GARANT TOPICS: fragment library - library defining possible fragment types GARANT TOPICS: spectra types - types of experiments defined in GARANT GARANT TOPICS: spectra variables - variables defined for each spectrum GARANT TOPICS: syntax - syntax used to specify atoms, coherences and peaks GARANT TOPICS: undocumented - undocumented commands