CYANA 3.0 Reference Manual: Difference between revisions
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<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4"> | <div style="column-count:4;-moz-column-count:4;-webkit-column-count:4"> | ||
* [[Coordinate generation]] | * [[Coordinate generation]] | ||
* [[Target function]] | |||
* [[Torsion angle dynamics]] | * [[Torsion angle dynamics]] | ||
* [[Simulated annealing]] | |||
</div> | </div> | ||
Revision as of 18:31, 8 February 2009
INCLAN
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
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 Macros
- anneal
- calc_all
- caliba
- calibration
- cashiftaco
- cashiftplot
- cisprocheck
- coco
- cyscheck
- dcostat
- dcotab
- deposit
- dinucleotide
- flip
- forall
- garant
- graf
- gridplot
- habas
- hbond
- init
- initsafe
- karplus
- kringle
- longrangeplot
- loop
- makeaco
- noeassign
- onelettercode
- opalprefine
- overlay
- overview
- peakcheck
- prolinebond
- ramaaco
- ramaplot
- random_all
- rdcdistances
- read_all
- readdata
- redac
- renumber
- rmsd
- rotameraco
- savestereo
- seqplot
- ssbond
- stereoassign
- structcalc
- sugarbond
- sugarring
- syscheck
- talosaco
- taloslist
- threelettercode
- translate
- vtfmin
- watsoncrick
- write_all
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
Selections
Input files
- Residue library file (.lib)
- Sequence file (.seq)
- Distance restraint file (.upl, .lol)
- Torsion angle restraint file (.aco)
- Residual dipolar coupling restraint file (.rdc)
- Pseudocontact shift restraint file (.pcs)
- DG Cartesian coordinate file (.cor)
- PDB coordinate file (.pdb)
- Torsion angle file (.ang)
- XEASY chemical shift list file (.prot)
- BMRB chemical shift list file (.bmrb)
- XEASY peak list file (.peaks)
- NMRView peak list file (.xpk)