CYANA 3.0 Reference Manual: Difference between revisions

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


<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[INCLAN Reference Manual]]
* [[INCLAN: alias|alias]]
* [[INCLAN: ask|ask]]
* [[INCLAN: break, exit, quit, return|break, exit, quit, return]]
* [[INCLAN: do|do]]
* [[INCLAN: echo|echo]]
* [[INCLAN: erract|erract]]
* [[INCLAN: eval, show, set, unset, external|eval, show, set, unset, external]]
* [[INCLAN: goto, go to|goto, go to]]
* [[INCLAN: if|if]]
* [[INCLAN: info|info]]
* [[INCLAN: intrinsics|intrinsics]]
* [[INCLAN: label|label]]
* [[INCLAN: nparam|nparam]]
* [[INCLAN: nproc|nproc]]
* [[INCLAN: parameter|parameter]]
* [[INCLAN: path|path]]
* [[INCLAN: print, error|print, error]]
* [[INCLAN: prompt|prompt]]
* [[INCLAN: protocol|protocol]]
* [[INCLAN: readline|readline]]
* [[INCLAN: remove|remove]]
* [[INCLAN: sleep|sleep]]
* [[INCLAN: special characters|special characters]]
* [[INCLAN: subroutine, command|subroutine, command]]
* [[INCLAN: syntax|syntax]]
* [[INCLAN: system|system]]
* [[INCLAN: timing|timing]]
* [[INCLAN: type|type]]
* [[INCLAN: var|var]]
</div>
 
== INCLAN Graphics ==
 
<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[INCLAN Graphics: plot arc|plot arc]]
* [[INCLAN Graphics: plot caro, plot cross, plot dot, plot plus, plot square, plot triangle|plot caro, plot cross, plot dot, plot plus, plot square, plot triangle]]
* [[INCLAN Graphics: plot clip|plot clip]]
* [[INCLAN Graphics: plot close|plot close]]
* [[INCLAN Graphics: plot comment|plot comment]]
* [[INCLAN Graphics: plot curve|plot curve]]
* [[INCLAN Graphics: plot errorbar|plot errorbar]]
* [[INCLAN Graphics: plot file|plot file]]
* [[INCLAN Graphics: plot fit|plot fit]]
* [[INCLAN Graphics: plot frame|plot frame]]
* [[INCLAN Graphics: plot function|plot function]]
* [[INCLAN Graphics: plot label|plot label]]
* [[INCLAN Graphics: plot line|plot line]]
* [[INCLAN Graphics: plot mif, plot ps|plot mif, plot ps]]
* [[INCLAN Graphics: plot polygon|plot polygon]]
* [[INCLAN Graphics: plot rectangle|plot rectangle]]
* [[INCLAN Graphics: plot scale|plot scale]]
* [[INCLAN Graphics: plot set|plot set]]
* [[INCLAN Graphics: plot shape|plot shape]]
* [[INCLAN Graphics: plot spline|plot spline]]
* [[INCLAN Graphics: plot text|plot text]]
* [[INCLAN Graphics: plot write|plot write]]
</div>


== CYANA Scripts ==
== CYANA Scripts ==
Line 72: Line 16:
== CYANA Commands ==
== CYANA Commands ==


<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[CYANA Commands]] (complete list)
* [[CYANA Command: angles count|angles count]]
* [[CYANA Command: angles delete|angles delete]]
* [[CYANA Command: angles flip|angles flip]]
* [[CYANA Command: angles ramachandran|angles ramachandran]]
* [[CYANA Command: angles select|angles select]]
* [[CYANA Command: angles set|angles set]]
* [[CYANA Command: angles split|angles split]]
* [[CYANA Command: angstat clear|angstat clear]]
* [[CYANA Command: angstat list|angstat list]]
* [[CYANA Command: angstat make|angstat make]]
* [[CYANA Command: assign|assign]]
* [[CYANA Command: atoms attach|atoms attach]]
* [[CYANA Command: atoms calibrate|atoms calibrate]]
* [[CYANA Command: atoms count|atoms count]]
* [[CYANA Command: atoms glomsa|atoms glomsa]]
* [[CYANA Command: atoms list|atoms list]]
* [[CYANA Command: atoms observable|atoms observable]]
* [[CYANA Command: atoms select|atoms select]]
* [[CYANA Command: atoms set|atoms set]]
* [[CYANA Command: atoms stereo|atoms stereo]]
* [[CYANA Command: atoms swap|atoms swap]]
* [[CYANA Command: calibrate|calibrate]]
* [[CYANA Command: couplings count|couplings count]]
* [[CYANA Command: couplings delete|couplings delete]]
* [[CYANA Command: couplings make|couplings make]]
* [[CYANA Command: couplings select|couplings select]]
* [[CYANA Command: couplings set|couplings set]]
* [[CYANA Command: distances calculate|distances calculate]]
* [[CYANA Command: distances check|distances check]]
* [[CYANA Command: distances combine|distances combine]]
* [[CYANA Command: distances compare|distances compare]]
* [[CYANA Command: distances correct|distances correct]]
* [[CYANA Command: distances count|distances count]]
* [[CYANA Command: distances delete|distances delete]]
* [[CYANA Command: distances expand|distances expand]]
* [[CYANA Command: distances falsify|distances falsify]]
* [[CYANA Command: distances hbond|distances hbond]]
* [[CYANA Command: distances make|distances make]]
* [[CYANA Command: distances modify|distances modify]]
* [[CYANA Command: distances multiple|distances multiple]]
* [[CYANA Command: distances select|distances select]]
* [[CYANA Command: distances set|distances set]]
* [[CYANA Command: distances short|distances short]]
* [[CYANA Command: distances split|distances split]]
* [[CYANA Command: distances stat|distances stat]]
* [[CYANA Command: distances stereoexpand|distances stereoexpand]]
* [[CYANA Command: distances unique|distances unique]]
* [[CYANA Command: distances vdw|distances vdw]]
* [[CYANA Command: gradient|gradient]]
* [[CYANA Command: grid aco|grid aco]]
* [[CYANA Command: grid correlate|grid correlate]]
* [[CYANA Command: grid fragment|grid fragment]]
* [[CYANA Command: grid memory|grid memory]]
* [[CYANA Command: grid search|grid search]]
* [[CYANA Command: grid swap|grid swap]]
* [[CYANA Command: library check|library check]]
* [[CYANA Command: library mirror|library mirror]]
* [[CYANA Command: library new|library new]]
* [[CYANA Command: library remove|library remove]]
* [[CYANA Command: library rename|library rename]]
* [[CYANA Command: library replace|library replace]]
* [[CYANA Command: md|md]]
* [[CYANA Command: minimize|minimize]]
* [[CYANA Command: molecules define|molecules define]]
* [[CYANA Command: molecules identity|molecules identity]]
* [[CYANA Command: molecules symdist|molecules symdist]]
* [[CYANA Command: pcs axial|pcs axial]]
* [[CYANA Command: pcs count|pcs count]]
* [[CYANA Command: pcs delete|pcs delete]]
* [[CYANA Command: pcs list|pcs list]]
* [[CYANA Command: pcs make|pcs make]]
* [[CYANA Command: pcs rhombic|pcs rhombic]]
* [[CYANA Command: pcs select|pcs select]]
* [[CYANA Command: pcs set|pcs set]]
* [[CYANA Command: peaks backcal|peaks backcal]]
* [[CYANA Command: peaks calibrate|peaks calibrate]]
* [[CYANA Command: peaks count|peaks count]]
* [[CYANA Command: peaks create|peaks create]]
* [[CYANA Command: peaks delete|peaks delete]]
* [[CYANA Command: peaks deviations|peaks deviations]]
* [[CYANA Command: peaks distance|peaks distance]]
* [[CYANA Command: peaks filter|peaks filter]]
* [[CYANA Command: peaks fit|peaks fit]]
* [[CYANA Command: peaks protonize|peaks protonize]]
* [[CYANA Command: peaks select|peaks select]]
* [[CYANA Command: peaks set|peaks set]]
* [[CYANA Command: peaks simplecal|peaks simplecal]]
* [[CYANA Command: peaks split|peaks split]]
* [[CYANA Command: peaks unassign|peaks unassign]]
* [[CYANA Command: peaks unique|peaks unique]]
* [[CYANA Command: randomize|randomize]]
* [[CYANA Command: rdc count|rdc count]]
* [[CYANA Command: rdc delete|rdc delete]]
* [[CYANA Command: rdc distance|rdc distance]]
* [[CYANA Command: rdc fittensor|rdc fittensor]]
* [[CYANA Command: rdc list|rdc list]]
* [[CYANA Command: rdc make|rdc make]]
* [[CYANA Command: rdc select|rdc select]]
* [[CYANA Command: rdc set|rdc set]]
* [[CYANA Command: rdc tensor|rdc tensor]]
* [[CYANA Command: read aco|read aco]]
* [[CYANA Command: read ang|read ang]]
* [[CYANA Command: read bmrb|read bmrb]]
* [[CYANA Command: read cco|read cco]]
* [[CYANA Command: read cor|read cor]]
* [[CYANA Command: read lib|read lib]]
* [[CYANA Command: read lol|read lol]]
* [[CYANA Command: read nmrview|read nmrview]]
* [[CYANA Command: read pcs|read pcs]]
* [[CYANA Command: read pdb|read pdb]]
* [[CYANA Command: read peaks|read peaks]]
* [[CYANA Command: read prot|read prot]]
* [[CYANA Command: read rdc|read rdc]]
* [[CYANA Command: read upl|read upl]]
* [[CYANA Command: read xpk|read xpk]]
* [[CYANA Command: read xplor|read xplor]]
* [[CYANA Command: shifts adapt|shifts adapt]]
* [[CYANA Command: shifts assign|shifts assign]]
* [[CYANA Command: shifts check|shifts check]]
* [[CYANA Command: shifts collapse|shifts collapse]]
* [[CYANA Command: shifts consolidate|shifts consolidate]]
* [[CYANA Command: shifts converge|shifts converge]]
* [[CYANA Command: shifts d2o|shifts d2o]]
* [[CYANA Command: shifts incomplete|shifts incomplete]]
* [[CYANA Command: shifts initialize|shifts initialize]]
* [[CYANA Command: shifts missing|shifts missing]]
* [[CYANA Command: shifts randomcoil|shifts randomcoil]]
* [[CYANA Command: shifts renumber|shifts renumber]]
* [[CYANA Command: shifts unusual|shifts unusual]]
* [[CYANA Command: structures clear|structures clear]]
* [[CYANA Command: structures copy|structures copy]]
* [[CYANA Command: structures hbonds|structures hbonds]]
* [[CYANA Command: structures insert|structures insert]]
* [[CYANA Command: structures list|structures list]]
* [[CYANA Command: structures mean|structures mean]]
* [[CYANA Command: structures overlay|structures overlay]]
* [[CYANA Command: structures secondary|structures secondary]]
* [[CYANA Command: structures select|structures select]]
* [[CYANA Command: structures sort|structures sort]]
* [[CYANA Command: structures swap|structures swap]]
* [[CYANA Command: structures violate|structures violate]]
* [[CYANA Command: write aco|write aco]]
* [[CYANA Command: write ang|write ang]]
* [[CYANA Command: write assign|write assign]]
* [[CYANA Command: write bmrb|write bmrb]]
* [[CYANA Command: write cco|write cco]]
* [[CYANA Command: write cor|write cor]]
* [[CYANA Command: write lib|write lib]]
* [[CYANA Command: write lol|write lol]]
* [[CYANA Command: write pcs|write pcs]]
* [[CYANA Command: write pdb|write pdb]]
* [[CYANA Command: write peaks|write peaks]]
* [[CYANA Command: write prot|write prot]]
* [[CYANA Command: write rdc|write rdc]]
* [[CYANA Command: write seq|write seq]]
* [[CYANA Command: write upl|write upl]]
* [[CYANA Command: write xpk|write xpk]]
</div>
 
== CYANA Macros ==
 
<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[CYANA Macro: anneal|anneal]]
* [[CYANA Macro: calc_all|calc_all]]
* [[CYANA Macro: caliba|caliba]]
* [[CYANA Macro: calibration|calibration]]
* [[CYANA Macro: cashiftaco|cashiftaco]]
* [[CYANA Macro: cashiftplot|cashiftplot]]
* [[CYANA Macro: cisprocheck|cisprocheck]]
* [[CYANA Macro: coco|coco]]
* [[CYANA Macro: cyscheck|cyscheck]]
* [[CYANA Macro: dcostat|dcostat]]
* [[CYANA Macro: dcotab|dcotab]]
* [[CYANA Macro: deposit|deposit]]
* [[CYANA Macro: dinucleotide|dinucleotide]]
* [[CYANA Macro: flip|flip]]
* [[CYANA Macro: forall|forall]]
* [[CYANA Macro: garant|garant]]
* [[CYANA Macro: graf|graf]]
* [[CYANA Macro: gridplot|gridplot]]
* [[CYANA Macro: habas|habas]]
* [[CYANA Macro: hbond|hbond]]
* [[CYANA Macro: init|init]]
* [[CYANA Macro: initsafe|initsafe]]
* [[CYANA Macro: karplus|karplus]]
* [[CYANA Macro: kringle|kringle]]
* [[CYANA Macro: longrangeplot|longrangeplot]]
* [[CYANA Macro: loop|loop]]
* [[CYANA Macro: makeaco|makeaco]]
* [[CYANA Macro: noeassign|noeassign]]
* [[CYANA Macro: onelettercode|onelettercode]]
* [[CYANA Macro: opalprefine|opalprefine]]
* [[CYANA Macro: overlay|overlay]]
* [[CYANA Macro: overview|overview]]
* [[CYANA Macro: peakcheck|peakcheck]]
* [[CYANA Macro: prolinebond|prolinebond]]
* [[CYANA Macro: ramaaco|ramaaco]]
* [[CYANA Macro: ramaplot|ramaplot]]
* [[CYANA Macro: random_all|random_all]]
* [[CYANA Macro: rdcdistances|rdcdistances]]
* [[CYANA Macro: read_all|read_all]]
* [[CYANA Macro: readdata|readdata]]
* [[CYANA Macro: redac|redac]]
* [[CYANA Macro: renumber|renumber]]
* [[CYANA Macro: rmsd|rmsd]]
* [[CYANA Macro: rotameraco|rotameraco]]
* [[CYANA Macro: savestereo|savestereo]]
* [[CYANA Macro: seqplot|seqplot]]
* [[CYANA Macro: ssbond|ssbond]]
* [[CYANA Macro: stereoassign|stereoassign]]
* [[CYANA Macro: structcalc|structcalc]]
* [[CYANA Macro: sugarbond|sugarbond]]
* [[CYANA Macro: sugarring|sugarring]]
* [[CYANA Macro: syscheck|syscheck]]
* [[CYANA Macro: talosaco|talosaco]]
* [[CYANA Macro: taloslist|taloslist]]
* [[CYANA Macro: threelettercode|threelettercode]]
* [[CYANA Macro: translate|translate]]
* [[CYANA Macro: vtfmin|vtfmin]]
* [[CYANA Macro: watsoncrick|watsoncrick]]
* [[CYANA Macro: write_all|write_all]]
</div>


== CYANA Functions ==
== CYANA Functions ==


<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[CYANA functions]] (complete list)
* [[CYANA Function: acoviol|acoviol]]
* [[CYANA Function: anam|anam]]
* [[CYANA Function: anamlib|anamlib]]
* [[CYANA Function: angle|angle]]
* [[CYANA Function: anglelong|anglelong]]
* [[CYANA Function: atom|atom]]
* [[CYANA Function: atomlong|atomlong]]
* [[CYANA Function: bondangle|bondangle]]
* [[CYANA Function: calconst|calconst]]
* [[CYANA Function: calscale|calscale]]
* [[CYANA Function: cco|cco]]
* [[CYANA Function: coord|coord]]
* [[CYANA Function: cstab|cstab]]
* [[CYANA Function: cyanadir|cyanadir]]
* [[CYANA Function: dcosel|dcosel]]
* [[CYANA Function: derms|derms]]
* [[CYANA Function: diastereotopic|diastereotopic]]
* [[CYANA Function: dist|dist]]
* [[CYANA Function: dmax|dmax]]
* [[CYANA Function: dmean|dmean]]
* [[CYANA Function: dnam|dnam]]
* [[CYANA Function: dnamlib|dnamlib]]
* [[CYANA Function: drms|drms]]
* [[CYANA Function: dshift|dshift]]
* [[CYANA Function: dstddev|dstddev]]
* [[CYANA Function: dval|dval]]
* [[CYANA Function: ekin|ekin]]
* [[CYANA Function: ekmean|ekmean]]
* [[CYANA Function: ekrms|ekrms]]
* [[CYANA Function: element|element]]
* [[CYANA Function: emean|emean]]
* [[CYANA Function: erms|erms]]
* [[CYANA Function: functions|functions]]
* [[CYANA Function: heavyatom|heavyatom]]
* [[CYANA Function: iacod|iacod]]
* [[CYANA Function: iar|iar]]
* [[CYANA Function: iaunit|iaunit]]
* [[CYANA Function: ibond|ibond]]
* [[CYANA Function: iccoa|iccoa]]
* [[CYANA Function: ida|ida]]
* [[CYANA Function: idcoa|idcoa]]
* [[CYANA Function: idord|idord]]
* [[CYANA Function: idr|idr]]
* [[CYANA Function: ifira|ifira]]
* [[CYANA Function: ifird|ifird]]
* [[CYANA Function: indco|indco]]
* [[CYANA Function: inpk|inpk]]
* [[CYANA Function: interval|interval]]
* [[CYANA Function: intervals|intervals]]
* [[CYANA Function: ipa|ipa]]
* [[CYANA Function: ipel|ipel]]
* [[CYANA Function: iprev|iprev]]
* [[CYANA Function: irnum|irnum]]
* [[CYANA Function: istruct|istruct]]
* [[CYANA Function: lda|lda]]
* [[CYANA Function: libdir|libdir]]
* [[CYANA Function: magnitude|magnitude]]
* [[CYANA Function: matchangle|matchangle]]
* [[CYANA Function: matchatom|matchatom]]
* [[CYANA Function: naa|naa]]
* [[CYANA Function: naco|naco]]
* [[CYANA Function: na|na]]
* [[CYANA Function: narmsd|narmsd]]
* [[CYANA Function: nassign|nassign]]
* [[CYANA Function: nbond|nbond]]
* [[CYANA Function: ncco|ncco]]
* [[CYANA Function: nconf|nconf]]
* [[CYANA Function: ndcdis|ndcdis]]
* [[CYANA Function: ndco|ndco]]
* [[CYANA Function: ndcres|ndcres]]
* [[CYANA Function: nd|nd]]
* [[CYANA Function: ndfree|ndfree]]
* [[CYANA Function: ndim|ndim]]
* [[CYANA Function: nlevel|nlevel]]
* [[CYANA Function: nlol|nlol]]
* [[CYANA Function: nmol|nmol]]
* [[CYANA Function: npeaks|npeaks]]
* [[CYANA Function: npkl|npkl]]
* [[CYANA Function: nr|nr]]
* [[CYANA Function: nsel|nsel]]
* [[CYANA Function: nseldis|nseldis]]
* [[CYANA Function: nshifts|nshifts]]
* [[CYANA Function: nstructall|nstructall]]
* [[CYANA Function: nstruct|nstruct]]
* [[CYANA Function: numpro|numpro]]
* [[CYANA Function: nupl|nupl]]
* [[CYANA Function: orientations|orientations]]
* [[CYANA Function: pi|pi]]
* [[CYANA Function: pseudoatom|pseudoatom]]
* [[CYANA Function: rad|rad]]
* [[CYANA Function: rhombicity|rhombicity]]
* [[CYANA Function: rid|rid]]
* [[CYANA Function: rmsdcurr|rmsdcurr]]
* [[CYANA Function: rmsdmax|rmsdmax]]
* [[CYANA Function: rmsdmean|rmsdmean]]
* [[CYANA Function: rmsdmin|rmsdmin]]
* [[CYANA Function: rmsdpair|rmsdpair]]
* [[CYANA Function: rmsdstd|rmsdstd]]
* [[CYANA Function: rnam|rnam]]
* [[CYANA Function: rnamlib|rnamlib]]
* [[CYANA Function: rnum|rnum]]
* [[CYANA Function: seldis|seldis]]
* [[CYANA Function: selected|selected]]
* [[CYANA Function: selrange|selrange]]
* [[CYANA Function: selrangeshort|selrangeshort]]
* [[CYANA Function: shift|shift]]
* [[CYANA Function: stereopartner|stereopartner]]
* [[CYANA Function: tfcalc|tfcalc]]
* [[CYANA Function: tf|tf]]
* [[CYANA Function: tfmax|tfmax]]
* [[CYANA Function: tfmin|tfmin]]
* [[CYANA Function: tfres|tfres]]
* [[CYANA Function: timestep|timestep]]
* [[CYANA Function: tolcco|tolcco]]
* [[CYANA Function: tor|tor]]
</div>


== CYANA Variables ==
== CYANA Variables ==


<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[CYANA variables]] (complete list)
* [[CYANA Variable: aco_type|aco_type]]
* [[CYANA Variable: combine_oi|combine_oi]]
* [[CYANA Variable: corr14|corr14]]
* [[CYANA Variable: cross_oi_rdc|cross_oi_rdc]]
* [[CYANA Variable: cut_aco|cut_aco]]
* [[CYANA Variable: cut_cco|cut_cco]]
* [[CYANA Variable: cut_lol|cut_lol]]
* [[CYANA Variable: cut_pcs|cut_pcs]]
* [[CYANA Variable: cut_rdc|cut_rdc]]
* [[CYANA Variable: cut_tflocal|cut_tflocal]]
* [[CYANA Variable: cut_upl|cut_upl]]
* [[CYANA Variable: cut_vdw|cut_vdw]]
* [[CYANA Variable: expand|expand]]
* [[CYANA Variable: gridpoints|gridpoints]]
* [[CYANA Variable: gridtime|gridtime]]
* [[CYANA Variable: hb_ang|hb_ang]]
* [[CYANA Variable: hb_len|hb_len]]
* [[CYANA Variable: level|level]]
* [[CYANA Variable: nstep|nstep]]
* [[CYANA Variable: obsdis|obsdis]]
* [[CYANA Variable: oie_k1|oie_k1]]
* [[CYANA Variable: oie_k2|oie_k2]]
* [[CYANA Variable: oi_k1|oi_k1]]
* [[CYANA Variable: oi_k2|oi_k2]]
* [[CYANA Variable: oip_end|oip_end]]
* [[CYANA Variable: oip_max|oip_max]]
* [[CYANA Variable: oip_min|oip_min]]
* [[CYANA Variable: oip_scaling|oip_scaling]]
* [[CYANA Variable: oip_start|oip_start]]
* [[CYANA Variable: ois_k1|ois_k1]]
* [[CYANA Variable: ois_k2|ois_k2]]
* [[CYANA Variable: opt_tensor_count|opt_tensor_count]]
* [[CYANA Variable: opt_tensor|opt_tensor]]
* [[CYANA Variable: opt_tensor_start|opt_tensor_start]]
* [[CYANA Variable: opt_tensor_treshold|opt_tensor_treshold]]
* [[CYANA Variable: pcs_end_k1|pcs_end_k1]]
* [[CYANA Variable: pcs_start_k1|pcs_start_k1]]
* [[CYANA Variable: pcs_ws_on|pcs_ws_on]]
* [[CYANA Variable: positive_gyros|positive_gyros]]
* [[CYANA Variable: pseudo|pseudo]]
* [[CYANA Variable: rdc_potential|rdc_potential]]
* [[CYANA Variable: rdc_vas1_on|rdc_vas1_on]]
* [[CYANA Variable: rdc_vas2_on|rdc_vas2_on]]
* [[CYANA Variable: rdc_vts_on|rdc_vts_on]]
* [[CYANA Variable: seed|seed]]
* [[CYANA Variable: soft_aco|soft_aco]]
* [[CYANA Variable: soft_cco|soft_cco]]
* [[CYANA Variable: soft_lol|soft_lol]]
* [[CYANA Variable: soft_upl|soft_upl]]
* [[CYANA Variable: soft_vdw|soft_vdw]]
* [[CYANA Variable: swap|swap]]
* [[CYANA Variable: tf_asymptote|tf_asymptote]]
* [[CYANA Variable: tf_offset|tf_offset]]
* [[CYANA Variable: tf_type|tf_type]]
* [[CYANA Variable: tolerance|tolerance]]
* [[CYANA Variable: tolpeak|tolpeak]]
* [[CYANA Variable: trad_end_k1|trad_end_k1]]
* [[CYANA Variable: trad_start_k1|trad_start_k1]]
* [[CYANA Variable: upl_values|upl_values]]
* [[CYANA Variable: use_svd|use_svd]]
* [[CYANA Variable: variables|variables]]
* [[CYANA Variable: vdw_power|vdw_power]]
* [[CYANA Variable: viocap|viocap]]
* [[CYANA Variable: weight_aco|weight_aco]]
* [[CYANA Variable: weight_cco|weight_cco]]
* [[CYANA Variable: weight_ide|weight_ide]]
* [[CYANA Variable: weight_lol|weight_lol]]
* [[CYANA Variable: weight_pcs|weight_pcs]]
* [[CYANA Variable: weight_rdc|weight_rdc]]
* [[CYANA Variable: weight_sym|weight_sym]]
* [[CYANA Variable: weight_upl|weight_upl]]
* [[CYANA Variable: weight_vdw|weight_vdw]]
</div>


== Selections ==
== Selections ==


<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
* [[Selection rules]]
</div>
 
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
* [[Atom selection]]
* [[Atom selection]]
* [[Angle selection]]
* [[Angle selection]]
Line 504: Line 41:
* [[Pseudocontact shift selection]]
* [[Pseudocontact shift selection]]
* [[Structure selection]]
* [[Structure selection]]
</div>
== Input files ==
<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>
== Nomenclature ==
* [[Standard CYANA nomenclature|Standard nomenclature for amino acids and nucleotides]]
== Algorithms ==
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">
* [[Coordinate generation]]
* [[Target function]]
* [[Torsion angle dynamics]]
* [[Momenta compensation]]
* [[Simulated annealing]]
</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"