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| == INCLAN == | | __NOTOC__ |
| | == INCLAN (INteractive Command LANguage) == |
| | |
| | * [[INCLAN Reference Manual]] |
| | |
| | == CYANA Scripts == |
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| <div style="column-count:4;-moz-column-count:4;-webkit-column-count:4"> | | <div style="column-count:4;-moz-column-count:4;-webkit-column-count:4"> |
| * [[alias]] | | * [[CYANA script: cyanaclean|cyanaclean]] |
| * [[ask]] | | * [[CYANA script: cyana|cyana]] |
| * [[break, exit, quit, return]] | | * [[CYANA script: cyanafilter|cyanafilter]] |
| * [[do]] | | * [[CYANA script: cyanajob|cyanajob]] |
| * [[echo]] | | * [[CYANA script: cyanatable|cyanatable]] |
| * [[erract]]
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| * [[eval, show, set, unset, external]]
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| * [[goto, go to]]
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| * [[if]]
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| * [[info]]
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| * [[intrinsics]]
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| * [[label]]
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| * [[nparam]]
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| * [[nproc]]
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| * [[parameter]]
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| * [[path]]
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| * [[print, error]]
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| * [[prompt]]
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| * [[protocol]]
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| * [[readline]]
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| * [[remove]]
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| * [[sleep]]
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| * [[special characters]]
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| * [[subroutine, command]]
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| * [[syntax]]
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| * [[system]]
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| * [[timing]]
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| * [[type]]
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| * [[var]]
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| </div> | | </div> |
|
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|
| == INCLAN Graphics == | | == CYANA Commands == |
| | |
| | * [[CYANA Commands]] (complete list) |
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| <div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
| | == CYANA Functions == |
| * [[plot arc]]
| | |
| * [[plot caro, plot cross, plot dot, plot plus, plot square, plot triangle]] | | * [[CYANA functions]] (complete list) |
| * [[plot clip]]
| | |
| * [[plot close]]
| | == CYANA Variables == |
| * [[plot comment]]
| | |
| * [[plot curve]]
| | * [[CYANA variables]] (complete list) |
| * [[plot errorbar]]
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| * [[plot file]]
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| * [[plot fit]]
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| * [[plot frame]]
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| * [[plot function]]
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| * [[plot label]]
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| * [[plot line]]
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| * [[plot mif, plot ps]]
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| * [[plot polygon]]
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| * [[plot rectangle]]
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| * [[plot scale]]
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| * [[plot set]]
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| * [[plot shape]] | |
| * [[plot spline]]
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| * [[plot text]]
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| * [[plot write]]
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| </div>
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|
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| == CYANA scripts == | | == Selections == |
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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"> |
| * [[cyanaclean]] | | * [[Selection rules]] |
| * [[cyana]]
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| * [[cyanafilter]]
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| * [[cyanajob]]
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| * [[cyanatable]]
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| </div> | | </div> |
|
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| == CYANA Commands ==
| | <div style="column-count:2;-moz-column-count:2;-webkit-column-count:2"> |
| | | * [[Atom selection]] |
| <div style="column-count:4;-moz-column-count:4;-webkit-column-count:4"> | | * [[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]]
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| * [[angstat clear]]
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| * [[angstat list]]
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| * [[angstat make]]
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| * [[assign]]
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| * [[atoms attach]]
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| * [[atoms calibrate]]
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| * [[atoms count]]
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| * [[atoms glomsa]]
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| * [[atoms list]]
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| * [[atoms observable]]
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| * [[atoms select]]
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| * [[atoms set]]
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| * [[atoms stereo]]
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| * [[atoms swap]]
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| * [[calibrate]]
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| * [[couplings count]]
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| * [[couplings delete]]
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| * [[couplings make]]
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| * [[couplings select]]
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| * [[couplings set]]
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| * [[distances calculate]]
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| * [[distances check]]
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| * [[distances combine]]
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| * [[distances compare]]
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| * [[distances correct]]
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| * [[distances count]]
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| * [[distances delete]]
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| * [[distances expand]]
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| * [[distances falsify]]
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| * [[distances hbond]]
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| * [[distances make]]
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| * [[distances modify]]
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| * [[distances multiple]]
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| * [[distances select]]
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| * [[distances set]]
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| * [[distances short]]
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| * [[distances split]]
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| * [[distances stat]]
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| * [[distances stereoexpand]]
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| * [[distances unique]]
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| * [[distances vdw]]
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| * [[gradient]]
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| * [[grid aco]]
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| * [[grid correlate]]
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| * [[grid fragment]]
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| * [[grid memory]]
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| * [[grid search]]
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| * [[grid swap]]
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| * [[library check]]
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| * [[library mirror]]
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| * [[library new]]
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| * [[library remove]]
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| * [[library rename]]
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| * [[library replace]]
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| * [[md]]
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| * [[minimize]]
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| * [[molecules define]]
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| * [[molecules identity]]
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| * [[molecules symdist]]
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| * [[pcs axial]]
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| * [[pcs count]]
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| * [[pcs delete]]
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| * [[pcs list]]
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| * [[pcs make]]
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| * [[pcs rhombic]]
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| * [[pcs select]]
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| * [[pcs set]]
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| * [[peaks backcal]]
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| * [[peaks calibrate]]
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| * [[peaks count]]
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| * [[peaks create]]
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| * [[peaks delete]]
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| * [[peaks deviations]]
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| * [[peaks distance]]
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| * [[peaks filter]]
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| * [[peaks fit]]
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| * [[peaks protonize]]
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| * [[peaks select]]
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| * [[peaks set]]
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| * [[peaks simplecal]]
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| * [[peaks split]]
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| * [[peaks unassign]]
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| * [[peaks unique]]
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| * [[randomize]]
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| * [[rdc count]]
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| * [[rdc delete]]
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| * [[rdc distance]]
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| * [[rdc fittensor]]
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| * [[rdc list]]
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| * [[rdc make]]
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| * [[rdc select]]
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| * [[rdc set]]
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| * [[rdc tensor]]
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| * [[read aco]]
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| * [[read ang]]
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| * [[read bmrb]]
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| * [[read cco]]
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| * [[read cor]]
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| * [[read lib]]
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| * [[read lol]]
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| * [[read nmrview]]
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| * [[read pcs]]
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| * [[read pdb]]
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| * [[read peaks]]
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| * [[read prot]]
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| * [[read rdc]]
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| * [[read upl]]
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| * [[read xpk]]
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| * [[read xplor]]
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| * [[shifts adapt]]
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| * [[shifts assign]]
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| * [[shifts check]]
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| * [[shifts collapse]]
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| * [[shifts consolidate]]
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| * [[shifts converge]]
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| * [[shifts d2o]]
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| * [[shifts incomplete]]
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| * [[shifts initialize]]
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| * [[shifts missing]]
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| * [[shifts randomcoil]]
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| * [[shifts renumber]]
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| * [[shifts unusual]]
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| * [[structures clear]]
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| * [[structures copy]]
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| * [[structures hbonds]]
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| * [[structures insert]]
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| * [[structures list]]
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| * [[structures mean]]
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| * [[structures overlay]]
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| * [[structures secondary]]
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| * [[structures select]]
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| * [[structures sort]]
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| * [[structures swap]]
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| * [[structures violate]]
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| * [[write aco]]
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| * [[write ang]]
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| * [[write assign]]
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| * [[write bmrb]]
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| * [[write cco]]
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| * [[write cor]]
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| * [[write lib]]
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| * [[write lol]]
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| * [[write pcs]]
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| * [[write pdb]] | |
| * [[write peaks]] | |
| * [[write prot]] | |
| * [[write rdc]] | |
| * [[write seq]] | |
| * [[write upl]] | |
| * [[write xpk]] | |
| </div> | | </div> |
|
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| | == Input files == |
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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"> |
| * [[]] | | * [[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> |
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| == CYANA Functions == | | == Nomenclature == |
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| <div style="column-count:4;-moz-column-count:4;-webkit-column-count:4">
| | * [[Standard CYANA nomenclature|Standard nomenclature for amino acids and nucleotides]] |
| * [[acoviol]] | |
| * [[anam]]
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| * [[anamlib]]
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| * [[angle]]
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| * [[anglelong]]
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| * [[atom]]
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| * [[atomlong]]
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| * [[bondangle]]
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| * [[calconst]]
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| * [[calscale]]
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| * [[cco]]
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| * [[coord]]
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| * [[cstab]]
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| * [[cyanadir]]
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| * [[dcosel]]
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| * [[derms]]
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| * [[diastereotopic]]
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| * [[dist]]
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| * [[dmax]]
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| * [[dmean]]
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| * [[dnam]]
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| * [[dnamlib]]
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| * [[drms]]
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| * [[dshift]]
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| * [[dstddev]]
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| * [[dval]]
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| * [[ekin]]
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| * [[ekmean]]
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| * [[ekrms]]
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| * [[element]]
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| * [[emean]]
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| * [[erms]]
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| * [[functions]]
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| * [[heavyatom]]
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| * [[iacod]]
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| * [[iar]]
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| * [[iaunit]]
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| * [[ibond]]
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| * [[iccoa]]
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| * [[ida]]
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| * [[idcoa]]
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| * [[idord]]
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| * [[idr]]
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| * [[ifira]]
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| * [[ifird]]
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| * [[indco]]
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| * [[inpk]]
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| * [[interval]]
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| * [[intervals]]
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| * [[ipa]]
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| * [[ipel]]
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| * [[iprev]]
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| * [[irnum]]
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| * [[istruct]]
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| * [[lda]]
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| * [[libdir]]
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| * [[magnitude]]
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| * [[matchangle]]
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| * [[matchatom]]
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| * [[naa]]
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| * [[naco]]
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| * [[na]]
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| * [[narmsd]]
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| * [[nassign]]
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| * [[nbond]]
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| * [[ncco]]
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| * [[nconf]]
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| * [[ndcdis]]
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| * [[ndco]]
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| * [[ndcres]]
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| * [[nd]]
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| * [[ndfree]]
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| * [[ndim]]
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| * [[nlevel]]
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| * [[nlol]]
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| * [[nmol]]
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| * [[npeaks]]
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| * [[npkl]]
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| * [[nr]]
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| * [[nsel]]
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| * [[nseldis]]
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| * [[nshifts]]
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| * [[nstructall]]
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| * [[nstruct]]
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| * [[numpro]]
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| * [[nupl]]
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| * [[orientations]]
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| * [[pi]]
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| * [[pseudoatom]]
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| * [[rad]]
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| * [[rhombicity]]
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| * [[rid]]
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| * [[rmsdcurr]]
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| * [[rmsdmax]]
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| * [[rmsdmean]]
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| * [[rmsdmin]]
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| * [[rmsdpair]]
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| * [[rmsdstd]]
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| * [[rnam]]
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| * [[rnamlib]]
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| * [[rnum]]
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| * [[seldis]]
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| * [[selected]]
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| * [[selrange]]
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| * [[selrangeshort]]
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| * [[shift]]
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| * [[stereopartner]]
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| * [[tfcalc]]
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| * [[tf]]
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| * [[tfmax]]
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| * [[tfmin]]
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| * [[tfres]]
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| * [[timestep]]
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| * [[tolcco]]
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| * [[tor]]
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| </div>
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|
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|
| == CYANA Variables == | | == 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"> |
| * [[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]]
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| * [[cut_pcs]]
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| * [[cut_rdc]]
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| * [[cut_tflocal]]
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| * [[cut_upl]]
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| * [[cut_vdw]]
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| * [[expand]]
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| * [[gridpoints]]
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| * [[gridtime]]
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| * [[hb_ang]]
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| * [[hb_len]]
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| * [[level]]
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| * [[nstep]]
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| * [[obsdis]]
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| * [[oie_k1]]
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| * [[oie_k2]]
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| * [[oi_k1]]
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| * [[oi_k2]]
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| * [[oip_end]]
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| * [[oip_max]]
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| * [[oip_min]]
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| * [[oip_scaling]]
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| * [[oip_start]]
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| * [[ois_k1]]
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| * [[ois_k2]]
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| * [[opt_tensor_count]]
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| * [[opt_tensor]]
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| * [[opt_tensor_start]]
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| * [[opt_tensor_treshold]]
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| * [[pcs_end_k1]]
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| * [[pcs_start_k1]]
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| * [[pcs_ws_on]]
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| * [[positive_gyros]]
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| * [[pseudo]]
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| * [[rdc_potential]]
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| * [[rdc_vas1_on]]
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| * [[rdc_vas2_on]]
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| * [[rdc_vts_on]]
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| * [[seed]]
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| * [[soft_aco]]
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| * [[soft_cco]]
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| * [[soft_lol]]
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| * [[soft_upl]]
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| * [[soft_vdw]]
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| * [[swap]]
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| * [[tf_asymptote]]
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| * [[tf_offset]]
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| * [[tf_type]]
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| * [[tolerance]]
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| * [[tolpeak]]
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| * [[trad_end_k1]]
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| * [[trad_start_k1]]
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| * [[upl_values]]
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| * [[use_svd]]
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| * [[variables]]
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| * [[vdw_power]]
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| * [[viocap]]
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| * [[weight_aco]]
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| * [[weight_cco]]
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| * [[weight_ide]]
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| * [[weight_lol]]
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| * [[weight_pcs]]
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| * [[weight_rdc]]
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| * [[weight_sym]]
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| * [[weight_upl]]
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| * [[weight_vdw]]
| |
| </div> | | </div> |