CYANA 3.0 Reference Manual: Difference between revisions

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Cyana 3.0
__NOTOC__
== INCLAN (INteractive Command LANguage) ==


== INCLAN ==
* [[INCLAN Reference Manual]]


<div style="column-count:3;-moz-column-count:3;-webkit-column-count:3">
== CYANA Scripts ==
* [[alias]]
 
* [[ask]]
<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[break, exit, quit, return]]
* [[CYANA script: cyanaclean|cyanaclean]]
* [[do]]
* [[CYANA script: cyana|cyana]]
* [[echo]]
* [[CYANA script: cyanafilter|cyanafilter]]
* [[erract]]
* [[CYANA script: cyanajob|cyanajob]]
* [[eval, show, set, unset, external]]
* [[CYANA script: cyanatable|cyanatable]]
* [[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]]
</div>
</div>


== INCLAN Graphics ==
== CYANA Commands ==
 
* [[CYANA Commands]] (complete list)
 
== CYANA Functions ==
 
* [[CYANA functions]] (complete list)
 
== CYANA Variables ==


<div style="column-count:3;-moz-column-count:3;-webkit-column-count:3">
* [[CYANA variables]] (complete list)
* [[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]]
</div>


== CYANA scripts ==
== Selections ==


<div style="column-count:3;-moz-column-count:3;-webkit-column-count:3">
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
* [[cyanaclean]]
* [[Selection rules]]
* [[cyana]]
* [[cyanafilter]]
* [[cyanajob]]
* [[cyanatable]]
</div>
</div>


== CYANA Commands ==
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
 
* [[Atom selection]]
<div style="column-count:3;-moz-column-count:3;-webkit-column-count:3">
* [[Angle selection]]
* [[angles count]]
* [[Peak selection]]
* [[angles delete]]
* [[Distance restraint selection]]
* [[angles flip]]
* [[Scalar coupling selection]]
* [[angles ramachandran]]
* [[Residual dipolar coupling selection]]
* [[angles select]]
* [[Pseudocontact shift selection]]
* [[angles set]]
* [[Structure selection]]
* [[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]]
</div>
</div>


== Input files ==


<div style="column-count:3;-moz-column-count:3;-webkit-column-count:3">
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
* [[]]
* [[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)
* [[auto-relaxation and I(0) values]] (.rho)
</div>
</div>


== CYANA Functions ==
== Nomenclature ==


<div style="column-count:3;-moz-column-count:3;-webkit-column-count:3">
* [[Standard CYANA nomenclature|Standard nomenclature for amino acids and nucleotides]]
* [[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]]
</div>


== CYANA Variables ==
== Algorithms ==


<div style="column-count:3;-moz-column-count:3;-webkit-column-count:3">
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
* [[aco_type]]
* [[Coordinate generation]]
* [[combine_oi]]
* [[Target function]]
* [[corr14]]
* [[Torsion angle dynamics]]
* [[cross_oi_rdc]]
* [[Momenta compensation]]
* [[cut_aco]]
* [[Simulated annealing]]
* [[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]]
</div>
</div>

Latest revision as of 13:22, 17 January 2019

INCLAN (INteractive Command LANguage)

CYANA Scripts

CYANA Commands

CYANA Functions

CYANA Variables

Selections

Input files

Nomenclature

Algorithms

Retrieved from "https://cyana.org/w/index.php?title=CYANA_3.0_Reference_Manual&oldid=8873"