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| * [[INCLAN]] (INteractive Command LANguage)
| | __NOTOC__ |
| * [[CYANA scripts]]
| | == INCLAN (INteractive Command LANguage) == |
| * [[CYANA commands]]
| |
| * [[CYANA functions]]
| |
| * [[CYANA variables]]
| |
|
| |
|
| | * [[INCLAN Reference Manual]] |
|
| |
|
| | == CYANA Scripts == |
| | |
| | <div style="column-count:4;-moz-column-count:4;-webkit-column-count:4"> |
| | * [[CYANA script: cyanaclean|cyanaclean]] |
| | * [[CYANA script: cyana|cyana]] |
| | * [[CYANA script: cyanafilter|cyanafilter]] |
| | * [[CYANA script: cyanajob|cyanajob]] |
| | * [[CYANA script: cyanatable|cyanatable]] |
| | </div> |
| | |
| | == CYANA Commands == |
| | |
| | * [[CYANA Commands]] (complete list) |
|
| |
|
| == 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: anamo|anamo]]
| |
| * [[CYANA Function: angle|angle]]
| |
| * [[CYANA Function: anglelong|anglelong]]
| |
| * [[CYANA Function: asel|asel]]
| |
| * [[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: anam|anam]]
| |
| * [[CYANA Function: dsel|dsel]]
| |
| * [[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: npcs|npcs]]
| |
| * [[CYANA Function: npeaks|npeaks]]
| |
| * [[CYANA Function: npkl|npkl]]
| |
| * [[CYANA Function: nr|nr]]
| |
| * [[CYANA Function: nrdc|nrdc]]
| |
| * [[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: psel|psel]]
| |
| * [[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]] | | * [[Selection rules]] |
| | </div> |
| | |
| | <div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"> |
| * [[Atom selection]] | | * [[Atom selection]] |
| * [[Angle selection]] | | * [[Angle selection]] |
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| == Input files == | | == Input files == |
|
| |
|
| <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"> |
| * [[Residue library file]] (.lib) | | * [[Residue library file]] (.lib) |
| * [[Sequence file]] (.seq) | | * [[Sequence file]] (.seq) |
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| * [[XEASY peak list file]] (.peaks) | | * [[XEASY peak list file]] (.peaks) |
| * [[NMRView peak list file]] (.xpk) | | * [[NMRView peak list file]] (.xpk) |
| | * [[auto-relaxation and I(0) values]] (.rho) |
| </div> | | </div> |
| | |
| | == Nomenclature == |
| | |
| | * [[Standard CYANA nomenclature|Standard nomenclature for amino acids and nucleotides]] |
|
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| == Algorithms == | | == Algorithms == |
|
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| <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"> |
| * [[Coordinate generation]] | | * [[Coordinate generation]] |
| * [[Target function]] | | * [[Target function]] |