CYANA 3.0 Reference Manual

INCLAN

• alias
• ask
• break, exit, quit, return
• do
• echo
• erract
• eval, show, set, unset, external
• goto, go to
• if
• info
• intrinsics
• label
• nparam
• nproc
• parameter
• path
• print, error
• prompt
• protocol
• readline
• remove
• sleep
• special characters
• subroutine, command
• syntax
• system
• timing
• type
• var

INCLAN Graphics

• plot arc
• plot caro, plot cross, plot dot, plot plus, plot square, plot triangle
• plot clip
• plot close
• plot comment
• plot curve
• plot errorbar
• plot file
• plot fit
• plot frame
• plot function
• plot label
• plot line
• plot mif, plot ps
• plot polygon
• plot rectangle
• plot scale
• plot set
• plot shape
• plot spline
• plot text
• plot write

CYANA scripts

• cyanaclean
• cyana
• cyanafilter
• cyanajob
• cyanatable

CYANA Commands

• angles count
• angles delete
• angles flip
• angles ramachandran
• angles select
• angles set
• angles split
• angstat clear
• angstat list
• angstat make
• assign
• atoms attach
• atoms calibrate
• atoms count
• atoms glomsa
• atoms list
• atoms observable
• atoms select
• atoms set
• atoms stereo
• atoms swap
• calibrate
• couplings count
• couplings delete
• couplings make
• couplings select
• couplings set
• distances calculate
• distances check
• distances combine
• distances compare
• distances correct
• distances count
• distances delete
• distances expand
• distances falsify
• distances hbond
• distances make
• distances modify
• distances multiple
• distances select
• distances set
• distances short
• distances split
• distances stat
• distances stereoexpand
• distances unique
• distances vdw
• gradient
• grid aco
• grid correlate
• grid fragment
• grid memory
• grid search
• grid swap
• library check
• library mirror
• library new
• library remove
• library rename
• library replace
• md
• minimize
• molecules define
• molecules identity
• molecules symdist
• pcs axial
• pcs count
• pcs delete
• pcs list
• pcs make
• pcs rhombic
• pcs select
• pcs set
• peaks backcal
• peaks calibrate
• peaks count
• peaks create
• peaks delete
• peaks deviations
• peaks distance
• peaks filter
• peaks fit
• peaks protonize
• peaks select
• peaks set
• peaks simplecal
• peaks split
• peaks unassign
• peaks unique
• randomize
• rdc count
• rdc delete
• rdc distance
• rdc fittensor
• rdc list
• rdc make
• rdc select
• rdc set
• rdc tensor
• read aco
• read ang
• read bmrb
• read cco
• read cor
• read lib
• read lol
• read nmrview
• read pcs
• read pdb
• read peaks
• read prot
• read rdc
• read upl
• read xpk
• read xplor
• shifts adapt
• shifts assign
• shifts check
• shifts collapse
• shifts consolidate
• shifts converge
• shifts d2o
• shifts incomplete
• shifts initialize
• shifts missing
• shifts randomcoil
• shifts renumber
• shifts unusual
• structures clear
• structures copy
• structures hbonds
• structures insert
• structures list
• structures mean
• structures overlay
• structures secondary
• structures select
• structures sort
• structures swap
• structures violate
• write aco
• write ang
• write assign
• write bmrb
• write cco
• write cor
• write lib
• write lol
• write pcs
• write pdb
• write peaks
• write prot
• write rdc
• write seq
• write upl
• write xpk

• [[]]

CYANA Functions

• acoviol
• anam
• anamlib
• angle
• anglelong
• atom
• atomlong
• bondangle
• calconst
• calscale
• cco
• coord
• cstab
• cyanadir
• dcosel
• derms
• diastereotopic
• dist
• dmax
• dmean
• dnam
• dnamlib
• drms
• dshift
• dstddev
• dval
• ekin
• ekmean
• ekrms
• element
• emean
• erms
• functions
• heavyatom
• iacod
• iar
• iaunit
• ibond
• iccoa
• ida
• idcoa
• idord
• idr
• ifira
• ifird
• indco
• inpk
• interval
• intervals
• ipa
• ipel
• iprev
• irnum
• istruct
• lda
• libdir
• magnitude
• matchangle
• matchatom
• naa
• naco
• na
• narmsd
• nassign
• nbond
• ncco
• nconf
• ndcdis
• ndco
• ndcres
• nd
• ndfree
• ndim
• nlevel
• nlol
• nmol
• npeaks
• npkl
• nr
• nsel
• nseldis
• nshifts
• nstructall
• nstruct
• numpro
• nupl
• orientations
• pi
• pseudoatom
• rad
• rhombicity
• rid
• rmsdcurr
• rmsdmax
• rmsdmean
• rmsdmin
• rmsdpair
• rmsdstd
• rnam
• rnamlib
• rnum
• seldis
• selected
• selrange
• selrangeshort
• shift
• stereopartner
• tfcalc
• tf
• tfmax
• tfmin
• tfres
• timestep
• tolcco
• tor

CYANA Variables

• aco_type
• combine_oi
• corr14
• cross_oi_rdc
• cut_aco
• cut_cco
• cut_lol
• cut_pcs
• cut_rdc
• cut_tflocal
• cut_upl
• cut_vdw
• expand
• gridpoints
• gridtime
• hb_ang
• hb_len
• level
• nstep
• obsdis
• oie_k1
• oie_k2
• oi_k1
• oi_k2
• oip_end
• oip_max
• oip_min
• oip_scaling
• oip_start
• ois_k1
• ois_k2
• opt_tensor_count
• opt_tensor
• opt_tensor_start
• opt_tensor_treshold
• pcs_end_k1
• pcs_start_k1
• pcs_ws_on
• positive_gyros
• pseudo
• rdc_potential
• rdc_vas1_on
• rdc_vas2_on
• rdc_vts_on
• seed
• soft_aco
• soft_cco
• soft_lol
• soft_upl
• soft_vdw
• swap
• tf_asymptote
• tf_offset
• tf_type
• tolerance
• tolpeak
• trad_end_k1
• trad_start_k1
• upl_values
• use_svd
• variables
• vdw_power
• viocap
• weight_aco
• weight_cco
• weight_ide
• weight_lol
• weight_pcs
• weight_rdc
• weight_sym
• weight_upl
• weight_vdw