FLYA example calculations
-------------------------

23.02.2017

This directory contains FLYA automated chemical shift assignment calculations.
The main input data are unassigned experimental peak lists in the format of the 
program XEASY (*.peaks) for an SH2 domain (114 aa).

Ref.: Schmidt et al. J. Am. Chem. Soc. 134, 12817-12829 (2012).


CALC.cya: standard automated chemical shift assignment
 - specify list of input peak lists in variable 'peaks' without intervening blanks
 - specify tolerances for 1H, 13C, 15N with variables assigncs_assH, assigncs_assC assigncs_assN
 - command 'select_atoms' excludes some nuclei that are difficult to detect
 - optional parameter 'shiftreference=ref.prot' specifies reference chemical shift list, 
   used only for comparison in flya.tab, flya.txt, flya.pdf

CALCbackbone.cya: standard backbone chemical shift assignment
 - parameter 'structure=' to avoid generation of random structures, 
   which are not needed if using only through-bond spectra

CALCexperiments.cya: using modified/new experiment definitions in library
 - modified HCCHTOCSY only for aromatics (library HCCHTOCSY.lib, peak list HCCHTOCSYaro.peaks)
 - new experiment N15NOESY2D (library peak list N15NOESY2D.lib, peak list N15NOESY2D.peaks)

CALCexpfromlist.cya: read expected peaks from a peak list
 - command N15NOESY_expect, reading input peak list N15NOESY_in.peaks

CALCfixedpeaks.cya: keep input peak assignments in user peak assignments 
 - (partially) assigned input peak list N15HSQCassigned.peaks
 - parameter 'keepassigned' for loadspectra.cya

CALCfixedshifts.cya: fix input chemical shift assignments
 - input chemical shift list 'fix.prot'
 - shift error in chemical shift list specifies range for assignment

CALClabeling.cya: use of experiment-specific isotope labeling
 - command 'select_atoms' for general selection of assignable nuclei CcoNH + HSQCLEULYS
 - command '<peak list name>_select' with atom selection for a specific peak list (e.g. C13HSQC_LK.peaks) 
 - command '<peak list name>_expect' for non-standard generation of expected peaks for a given peak list 
   (e.g. CcoNH_LK.peaks with dimension-specific atom selection)

CALCnoesyonly.cya: chemical shift assignment using exclusively NOESY
 - increased population size with 'shiftassign_population=200'
 - see Schmidt et al. J. Biomol. NMR 57, 193-204 (2013)

CALCquick.cya: fast automated chemical shift assignment
 - fixed number of generations in evolutionary optimization

CALCstatistics.cya: user-defined chemical shift statistics instead of standard BMRB statistics from library
- average value and stddev from input chemical shift list 'shiftx.prot'
- 'assigncs_sd:=bmrb' to use stddev from BMRB (cyana.lib) instead of input chemical shift list
- 'assigncs_sdfactor:=0.5' to scale BMRB stddev by given factor

CALCstructcalc.cya: follow automated shift assignment by automated NOESY assignment and structure calculation
 - peak lists for distance restraint generation specified by parameter 'structurepeaks='

CALCstructure.cya: use input structure to generate expected peaks for through-space experiments
 - specify with parameter 'structure' of command 'flya'
 - if parameter 'structure' is absent, a set of random structures is generated automatically
 - if set to blank ('structure='), no random structures are generated 
   (if not needed because only through-bond spectra are used)
