CYANA 3.0 Reference Manual: Difference between revisions

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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]] (complete list)


== 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]]


== Algorithms ==
== Algorithms ==


<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]]

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

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