************************************************************************** define command Leif Laaksonen CSC 1996 Eero Häkkinen CSC 2002 Timm Uhlmann 2003 ************************************************************************** # # define background colour by defining a colour name or # integer or float triplet (rgb) values # defi$ne bgco$lour Colour.Name "Fred Fgreen Fblue" # # define bond display style options: # smooth (atom colour changes smoothly along the bond) # half or default (half of the bond is in the colour of the connected atom) # bondst$yle smoo$th half defa$ult # # define cell dimensions, line width and colour # cell dime$nsions Fa Fb Fc angl$es Falpha Fbeta Fgamma line$width Ivalue colour ColourName "Fred Fgreen Fblue" # # define colour mapping for values between 0.0 ... 1.0 # the scale goes from (0.0) blue to (1.0) red through green at (0.5) # colorm$apping texture rainbow # # define the display "colour" type. choose between colour and grayscale # if you choose grayscale the display will switch to grayscale. # colort$ype colo$r gray$scale # # define the length of the cross used for atom display # cros$s Fvalue # # Put the global usage of display lists on/off # disp$laylists on off # # Sets the type specific usage of display lists on/off # Global setting "off" will overwrite this. # disp$laylists on defa$ult off defa$ult disp$laylists on TypeName off TypeName # # define the draw buffer (default is back) # drawb$uffer back fron$t # # define the near plane distance and step values # near$plane step Fvalue valu$e Fvalue # # define the far plane distance and step values # farp$lane step Fvalue valu$e Fvalue # # define viewing angle for perspective projection # viewa$ngle Fvalue # # define material specular (0.0 - > 128.0) # mate$rial spec$ular Fvalue # # molecule line width in pixels # mlin$ewidth Ivalue # # not in use # node Node.Name # # contour line width in pixels # clin$ewidth Ivalue # # define licorice sphere and cylinder for the molecule display # good for the ball and stick display # the Ivalue defines the structure number # to apply for all structures use the character "*" or word "all" # licos$phere Fvalue Ivalue licos$phere Fvalue * licoc$ylinder Fvalue Ivalue licoc$ylinder Fvalue * # # define the cylinder and sphere quality # cyli$nderquality Ivalue # any number > 0 (default 10) sphe$requality Ivalue # any number > 0 (default 10) # # not in use # hurl URL.Address webb$rowser WebBrowser.Name # # define default coordinate file type and extension # defa$ult coor$dinate type ambe$r char$mm gaus$sian hype$rchem insi$ght mol2 mumo$d open$mol pdb xmol xyz yasp exte$nsion ambe$r String char$mm String gaus$sian String hype$rchem String insi$ght String mol2 String mumo$d String open$mol String pdb String xmol String xyz String yasp String # # define default trajectory file type and extension # traj$ectory type ambe$r ceri$us2 char$mm disc$over grom$os hype$rchem mumo$d xmol xplor yasp exte$nsion ambe$r String ceri$us2 String char$mm String disc$over String grom$os String hype$rchem String mumo$d String xmol String xplo$r String yasp String # # Gromos96 uses a constant with which the coordinates will be # multiplied (default = 10.0). # gromos96 coorda$mplifier Fvalue # # toggle rotations state between on/off # rota$tion stat$e on off # # toggle translation state between on/off # tran$slation stat$e on off # # activate or deavtivate the state for picking atoms # iden$ntify on off # # recalculate automatically atom reconnectivity # reco$nnectivity on off # recalculate automatically atom hydrogen bonds # hbre$connectivity on off # # defines whether the system is translated around origo or not # this is active both at reading a new structure or when there # already are structures read # syst$em tran$slation on off # # define the projection method orthographic/perspective # proj$ection orth$ographic pers$pective # # define window actions # single/multi windowing # update is automatic/manual # wind$owing sing$le multi upda$te auto$matic manu$al # # put the trajectory frame number display on/off # traj$ectory fid on off # # define the cutplane 3d magnitude. Constant with which the magnitude is # multiplied with. The range is between 0.0 and 1.0. # cutp$lane damp$ing Fvalue # # define scaling mode. It is possible to scale in "global" mode that # scales all objects equally or in an "local" mode when only # one or some of the objects are scaled. Using this mode ruins of # course the chemistry/physics of teh system. It can only be use # for display purposes. The objects are selected from the main window. # scal$ing glob$al loca$l # # put the stereo pair display mode on/off # define the distance between the objects in the stereo pair mode # define the "tilt" angle for the objects (+-) # spai$r on off distance Fvalue angle Fvalue # # put the harware stereo (stereo in a window mode on/off # define the "tilt" angle for the objects (+-) # quad$stereo on off angl$e Fvalue # # be careful with these commands ... do not use them! # # Reconnectivity defines if the atom connection table # is recalculated between the frames or not. # Hbreconnectivity defines if the atom hydrogen bond # connection table is recalculated between the frames or not. # Maxconnectivity is the max number of connections (bonds) # an atom can have # Covar radius is used while calculating connections. # atom coor$dinates Fx Fy Fy IAindex ISindex char$ge Fvalue IAindex ISindex labe$l Name IAindex ISindex resn$umber Ivalue IAindex ISindex vdw Fvalue IAindex ISindex iden$ntify on off reco$nnectivity on off hbre$connectivity on off maxc$onnectivity cova$r AtomSymbol Fradius ElementNumber Fradius resi$due labe$l Name IAindex ISindex segm$ent labe$l Name IAindex ISindex stru$cture StrucName Iatoms new appe$nd # # define atom neighbour search window (in atoms) # atom wind$ow Inumber # # # define global text string # gtext "string" # # Define light position # light diffuse color # ligh$t posi$tion c nw ne n w e sw se s diff$use red fval gree$n fval blue fval # # # Sets redisplay mode to fast or slow # redi$splay fast slow # # # Sets transformation mode # transf$ormation global local user ************************************************************************** LUL/2002 **************************************************************************