CYANA 3.0 Reference Manual: Difference between revisions

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* [[CYANA variables]]
* [[CYANA variables]]


== CYANA Commands ==


<div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
* [[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 sparky|write sparky]]
* [[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 ==

Revision as of 15:16, 11 August 2009


CYANA Functions

CYANA Variables

Selections

Input files

Algorithms

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