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  1. 0660103030566
  2. 9[........................................................]
  3. ******************************************************************
  4. Molecule3DisaPublicDomainShare-warereleasefromWest
  5. Germany.Youarewelcometocopythisprogramanddistributeit
  6. aslongasitisnotsoldandthisdocumentationremainswithit.
  7. Theauthoris:üRainerPaape
  8. Paschenburgstr.67
  9. 2800Bremen1
  10. WestGermany
  11. Ç(Thenewestupdatemaybepurchasedfromhim)
  12. Thedocumentationwasimportedandtranslatedby:
  13. ü
  14. RobertZimmerer
  15. 131W2ndStreet
  16. PortAngeles,WA98362
  17. (206)452-7529
  18. Ç
  19. Ifyouareinterestedinmoresoftwarefromgermanyandfor
  20. detailsaboutthisandotherprogrrams,feelfreetocallorwrite
  21. me.                                    *Seeadendumformoreinfo.
  22. ******************************************************************
  23.  
  24.  
  25. üMolecule3D InfoÇ
  26. ë
  27. üëYoumusthavethefollowingfilesinafoldernamedMOLEKUELon
  28. üëyourdiskinorderfortheprogramtowork:
  29. ê
  30. Ç -ü MOLEKUEL.PRG Ç (containsthe program)
  31.  
  32.  - üMOLEKUEL.DATÇ  (containstheprogramlogo)
  33.  
  34.  - üRADIEN.DAT Ç   (contains Atom-, Ion- and v.d. Waals-Radii)
  35.  
  36.  - üFARBEN.DAT Ç   (containsgraphicsforcolorcoordination)
  37.  
  38.  -ü RGB.DATÇ       (containsdataforcolorcoordination)
  39. ê
  40. Thefollowingfilesarealsouseful:
  41. Ç
  42.  - DEMO.KOO      (Demo-file for coordinates)
  43.  
  44.  - DEMO.BIN      (includefileofbondsforDEMO.KOO)
  45.  
  46.  - DEMOx.PI2     (Demographics for high resolution)
  47.  
  48.  - DEMOx.PI1     (Demographics for mediumresolution)
  49.  
  50.  - TEST.KOO      (Demo-file for positionsofaxiinspace)    
  51.  
  52.  - TEST.BIN      (includefileofbondsforTEST.KOO)
  53.  
  54.  - Molecule.DOC  (Thisfilein1st-Wordformat)
  55.  
  56.  - Molecule.TXT   (ThisfileinASCII)
  57.  
  58. ë
  59. Generalnotes:
  60. Ç
  61. Two sets of information are necessary for molecule representation. 
  62.  
  63.  -ü Atomsymbols and X,Y and Z-coordinatesÇ
  64.  
  65.  -ü Binding list of the atomsÇ
  66.  
  67. 
  68. Up to 216 atomic coordinates and 216 bonds can be defined.The
  69. maximumnumberofpicturesinasequencedependsontheamountof
  70. freememory.Theprogramdeterminesthemaximumnumberof
  71. picturesallowed,eachrequiringaboutê19KbytesofRAMÇ.Around
  72. 40picturescanbemadeusinga1040ST(or520STwith1Megabyteof
  73. RAM)havingwithTOSinROM.Afterabout30picturesthegoing
  74. getsprettyslow.
  75.  
  76. TheprogramoperatesinëhighÇandëmediumÇresolution!
  77.  
  78.  
  79. Sëtartingtheprogram:Ç
  80.  
  81.      OnceyouareintheMolculefolder,double-klickon
  82. ü"MOLEKUEL.PRG"Ç tostarttheprogram.Ifthenecessaryfilesare
  83. notinorderanerrormessagewillappearandyouwillbereturned
  84. tothedesktop.
  85.      Ifallgoeswell,youwillbegivenamenu.Thebottomof
  86. thescreendisplaysmemoryanddatainformationaswellasthe
  87. freespaceonthediskinthedrive.Thedriveshownisthe
  88. defaultdrive,fromwhichtheprogramwasinitiated.Ifyouwant
  89. tochangedrivespecifications(toaseconddiskdrive,aRAMdisk
  90. orHarddisk),clickontherightorleftarrowuntilyouareat
  91. thedrive.
  92.      Tocheckhowmuchfreespaceyouhaveontheselecteddrive,
  93. clickontheü"FreierSpeicher"Çbox(totheleftofthedrive
  94. selectionbox)
  95.  
  96. ë1      Data       (Daten)Ç
  97.  
  98. ê1.1    EditingthecoordinatesÇ(üKoordinateneditierenÇ)
  99.  
  100.      Inordertoeditthecoordinatevaluesofthemolecule,pull
  101. downthemenuitemlabeled"üDaten"Çandclickonthe
  102. ü"KOORDINATEN  EDITIEREN"Çentery.  Thistakesyoutoaneditor
  103. displayingthedataentriesinaledgerformat.
  104.      Onceintheeditor,youmayeditanycolumnbyclickingon
  105. theentry.The<Return>keywilltakeyoutothenextlineofthe
  106. columnandwritethenewinformationtothatlineofthecolumn.
  107. Whenyouarefinishedenteringdatainthecolumn,pressthe<Esc>
  108. key.(Besuretopress<Return>towritetheinformationbefore
  109. pressing<Esc>)
  110.      Tomovethroughthelist,clickonthearrowsymbolsatthe
  111. topofthescreen.Thesinglearrowsmovethelistoneentryin
  112. eitherdirection,thedoublearrowsmoveit15.
  113.      Thecolumnlabeledü"Art"Ç isfortheatomicsymbol,andthe
  114. coordinatesofthemoleculegointheX, Y and Zcolumns.Inthe
  115. linemarkedü"Molekül"Ç youmayenterthenameofthemolecule.
  116.      Clickingontheboxmarked"Menue"returnsyoutothemain
  117. menue.
  118.  
  119. ê1.2    EditingbondsÇ(üBindungeneditierenÇ)
  120.  
  121.      Hereyoumayenter/changethebondslist.Enteringand
  122. editingthedatafollowsthesamerulesinwiththecoordinate
  123. editingsection.
  124.      Afterenteringtheatompairs,thetypeofbondwillbeshown
  125. (eg.C-C).Thebondlengthsarealsocalculatedanddisplayed.
  126. Thisallowsyoutochecktheaccuracyofyourentriesandfind
  127. bondsthataretoshortorlong.Theprogramalsochecksifthe
  128. atomsareavailable.If,forexample,37atomiccoordinateswere
  129. definedandabondbetweenatoms34and38wereentered,abond
  130. between"34+0"wouldbedisplayed.Itisthereforeimportantto
  131. enterorloadtheatomiccoordinates.
  132.  
  133. ê1.3   Savingcoordinates/bondsÇ(üKoordinaten/BindungenspeichernÇ)
  134.  
  135.  
  136.      Whenyouarefinishedenteringthedatayoushouldalways
  137. saveitrightaway.Clickontheboxesmarkedü"KOORDINATENÇ
  138. üSPEICHERN"Çandü"BINDUNGEN  SPEICHERN"Çtosavecoordinatesand
  139. bondsrespectively.Theextensionsshouldbeü".KOO"Çfor
  140. coordinatedataandü".BIN"Çforbondingdata.(fromthegerman
  141. KOOrdinatenandBINdungen)
  142.  
  143. ê1.4    Loadingcoordinates/bondsÇ(üKoordinaten/BindungenladenÇ)
  144.  
  145.  
  146.  
  147.      InordertoloadaCoordinateorBondsfile,clickonthe
  148. entriesü"KOORDINATENLADEN"Ç forcoordinatedataandü"BINDUNGENÇ
  149. üLADEN"Çforbondsintheü"Daten"Çdropdownmenu.
  150.  
  151. ê1.5  DeletingCoordinate/BondingÇ(üKoordinaten/BindungenlöschenÇ)
  152.  
  153.      Whenyouclickontheentriesü"KoordinatenLöschen"Çor
  154. ü"BindungenLöschen"Ç,allthedataiserasedfrommemory.
  155.  
  156. ê1.6    MergingCoordinates/BondsÇ(üKoordinaten/BindungenmischenÇ)
  157.  
  158.      Thismenuentryallowsfortheunionoftwoormoredata
  159. groups.Forexample,ifyouwantedtocomparetwomolecules
  160. togetheronthesamescreenyouwould:firstloadinthe
  161. coordinatedataofthefirstmoleculefollowedbyitsbonding
  162. data.Nextmergethecoordinatedataofthesecondmoleculewith
  163. themenuentryü"Koordinatenmischen"Ç.Followthisbymergingthe
  164. bondingdataofthesecondmoleculewiththemenuentryü"BindungenÇ
  165. ümischen"Ç.
  166.      Youmaymergeasmanymoleculesasyouwant,solongasthere
  167. isenoughspaceinthememory.(seeaboveformaximumvalues)
  168.      Itisveryimportantthatyouarecarefultofollowthis
  169. procedureexactly,alwaysalternatebetweenloadingcoordinates
  170. andbonds!
  171.  
  172. ê1.7    EditingRadiiÇ(üRadieneditierenÇ)
  173.  
  174.      Togetintotheradiuseditor,clickonthemenuentrymaked
  175. "RadienEditieren".(Seeaboveforeditorcontrols)
  176.      Theelementalsymbol"CA"standsforcarboninaromatic
  177. orbits,and"CM"standsforcarboninmethylenegroups.
  178.      ThisdistinctionisonlymeaningfulinthevanderWaals-
  179. radius.Alltheradiiaregiveninunitsofthecoordinatesystem
  180. (Angstoms).
  181.  
  182. ê1.8    SavingRadiiÇ (üRadienspeichernÇ)
  183.  
  184.      Tosaveradiusdata,thedisketteinthedefaultdrivemust
  185. containthefolderü"MOLEKUEL"Çsincethedataisalwayssavedto
  186. thefileü"RADIEN.DAT"Çinthefolderü "MOLEKUEL"Ç.  Ifthefolderis
  187. notfound,error#-34(pathnamenotfound)occurs.
  188.      Thisdataisautomaticallyloadedatthebeginningbythe
  189. programsinceallthnecessaryinformationforthediagramofthe
  190. radiiiscontainedinit.Greatcareshouldbetakentoensure
  191. thatthisdataisnotlost!
  192.  
  193. ê2.      ImportingdataÇ(üInportÇ)
  194.  
  195.      Sincetheatomiccoordinatescomeoriginallyfromamini
  196. computer,youshouldtrytoportcoordinatedatafromamini
  197. computerthroughtheRS-232portiftheopportunityshoildpresent
  198. itself.Thiswillsaveyouthetimeconsumingand"typo"-full
  199. taskofenteringallthedatabyhand.Dataentryroutineswill
  200. bereleasedfornormalcalculations.
  201.  
  202. ê2.1    LoadingMNDO-DataÇ(üMNDO-DatenladenÇ)
  203.  
  204.      IfyouwanttoloadatomiccoordinatedatafromanMNDOlist
  205. (üMNDO-RechnungÇ),thedatamusthavethefollowingstructure:
  206.  
  207.      Row1     Column1-80:   Molcule'sname(comments)
  208.  
  209.      Row2-n   Symbolandcoordinatesoftheatom,withthe
  210.                followingrequirements:
  211.  
  212.                Columns16-17:atomicsymbolornumberupto20
  213.                Columns21-30:X-coordinates
  214.                Columns31-40:Y-coordinates
  215.                Columns41-50:Z-coordinates
  216.  
  217.      Rown+1   Columns1-2:/*
  218.  
  219.      Rown+2   Columns1-2://
  220.  
  221. Theformatofrows2tonareintheformoftheoutputfromthe
  222. "MOPAC"programinversion2.00.Rows1,n+1andn+2mustbe
  223. filledoutbyhandpriortoloading.
  224.  
  225. ê2.2    Loading"Ab-Initio-Daten"Ç(üAb-Initio-DatenladenÇ)
  226.  
  227.      Thisfeaturehasn'tbeenimplementedyet!
  228.  
  229. ê2.3    Loading"Gauss80-Daten"Ç(üGauss80-DatenladenÇ)
  230.  
  231.      Thisfeaturehasn'tbeenimplementedeither!
  232.  
  233. ë3      Graphics   (Grafik)Ç
  234.  
  235. ê3.1    ViewÇ        (üZeigenÇ)
  236.  
  237.      Showsthelastcalculatedorloadedgraphic.
  238.  
  239. ê3.2    InvertingÇ  (üInvertierenÇ)
  240.  
  241.      Showsthelastcalculatedorlastloadedgraphicin
  242. invertedform.
  243.  
  244. ê3.3    HardcopyÇ
  245.  
  246.      Printsacopyofthelastshowngraphic.Theoperating
  247. systemsprintingroutineisusedforthis.Ifyourprinterisn't
  248. supported,youmustfirstloadtheappropriateprinterdriverfor
  249. yourmachine.Thehardcopycanbeprintedthenthroughthescreen
  250. dumpcommand(<Alt><Help>).
  251.  
  252. ê3.4    LoadingÇ    (üLadenÇ)
  253.  
  254.      Loadsapreviouslysavedgraphic.
  255.  
  256. ê3.5    SavingÇ     (üSpeichernÇ)
  257.  
  258.      Thissavesthelastcalculatedandshowngraphicasanentire
  259. screen.Inmonochromethepictureshavetheextensionü".PI2"Çand
  260. canbeloadedintoandmodifiedbygraphicsprogramsthathandle
  261. monochrome.Whensavedfromacolormonitorsystem,thecolor
  262. informationisn'tsaved.Youcanuse"PAINTER.ST"tomodifythese
  263. pictures.
  264.  
  265. ê4      ColorsÇ     (üFarbenÇ)
  266.  
  267.      Thismenuselectioncanonlybeselectedfrommedium
  268. resolution.
  269.  
  270. ê4.1    SettingRGBvaluesÇ(üRGB-Werte einstellenÇ)
  271.  
  272.      Thismenuselectionallowsyoutoadjustthesettingsofthe
  273. red,greenandblueforthedisplay.Bywearingapairof
  274. red/greenglassesandloadingthefilecalled"FARBEN.DAT",you
  275. cangetthereal"3D"effect.
  276.  
  277. ê4.2    Loading/SavingColorsettingsÇ(RüGB-Werte laden/speichernÇ)
  278.  
  279.      Withthesemenuselections(üRGB-Werte laden/RGB-WerteÇ
  280. üSpeichernÇ),thecolorsettingscanbeloadedandsaved.
  281.   
  282. ê5      GraphicsCalculationsÇ(üMenue_2 / Grafik BerechnenÇ)
  283.  
  284.      Hereyougetanewdropdownmenuwhichallowsallthe
  285. parametersfortherepresentationofthemoleculetobelaidout
  286. andadjusted.Thismenuwillonlybeselectableaftercoordinates
  287. andbondsareavailable(havingbeenenteredorloaded).This
  288. screencontainsawindow(2/3thescreen)fordisplayingthe
  289. molecule,andagroupofparametercontrolboxesontheright.
  290.  
  291. ê5.1    ModesÇ      (üModiÇ)
  292.  
  293. ê5.1.1  RotationaroundOriginal/ActualAxisÇ
  294.                         (üRotation um Ursprungs/aktuelle AchseÇ)
  295.  
  296.      Whenrotatingaroundtheoriginalaxis,themoleculeis
  297. turnedaroundtheX,YorZaxis.Theseaxiiarehorizontaland
  298. verticlefromtheobserver'sperspective.Whenrotatingaround
  299. theactualaxis,thechosenspinistakenintoconsiderationfor
  300. theXandYaxiirespectively.(sebelowfordetails)Thedefault
  301. isrotationabouttheoriginalaxis.
  302.  
  303. ê5.1.2  RotationaroundtheX,YorZaxisÇ
  304.                            (üRotation um die X, Y oder Z-AchseÇ)
  305.  
  306.      Determineswhichofthethreeaxiitherotationwillbe
  307. around.ThedefaultistheXaxis.
  308.  
  309. ê5.1.3  ProjectionÇ(üProjektionÇ)
  310.  
  311.      Withverticle(üsenkrechterÇ)projectionthemoleculeis
  312. representedwithoutdistortions.Perspective(üperspektivischerÇ)
  313. projectiondistortsobjectswhicharecloserintheviewmorethan
  314. theobjectswhicharefurtheraway.Thedefaultisü"senkrechte"Ç
  315. projection.
  316.  
  317. ê5.2    GraphicsÇ   (üGrafikÇ)
  318.  
  319. ê5.2.1  RadiiÇ   (üRadienÇ)
  320.  
  321.      Determinesifandwhichradiusshouldbeattheendofbond
  322. (onlyinü"senkrechter"Çprojection).Iftheradii(üRadienÇ)is
  323. selected,theü"BINDUNGENZEICHNEN"Ç shouldfirstbedeselected.
  324. Thedefaultsettingforradiiisnoradiusü(kein RadiusÇ).
  325.  
  326. ê5.2.2  AtomsymbolsÇ(üAtomsymbolÇ)
  327.  
  328.      Determinesiftheatomsymbolwillbedisplayed.(this
  329. featureonlyworksinü"senkrechter"Çprojectionandonlywhenthe
  330. radiiarenotselected!)Thedefaultisnoatomsymbols(ükeinÇ
  331. üAtomsymbolÇ).
  332.  
  333. ê5.2.3  AtomicnumberÇ(üAtomnummerÇ)
  334.  
  335.      Thisdisplaystheatomicnumberoftheatom(same
  336. restrictionsaswithatomicsymbols).Thedefaultisnoatomic
  337. number(ükeine AtomnummerÇ).
  338.  
  339. ê5.2.4  ShowAxisÇ    (üAchsen zeichnenÇ)
  340.  
  341.      Determinesiftheaxiiofthecoordinatesystemwillbe
  342. displayedornot.Thedefaultisnoaxis(ünicht einzeichnenÇ).
  343.  
  344. ê5.2.5  ShowbondsÇ (üBindungen zeichnenÇ)
  345.  
  346.      Determinesifthebondswillbedisplayedornot.The
  347. defaultisshowbonds(üeinzeichnenÇ).
  348.  
  349. ê5.3    PicturesÇ     (üBilderÇ)
  350.  
  351. ê5.3.1  Single/AnimateÇ(üEinzelbild/BildfolgeÇ)
  352.  
  353.      Whensinglepicture(üEinzelbildÇ)isselected,onlyone
  354. moleculeisdisplayed.WhenAnimate(üBildfolgeÇ) isselected,the
  355. moleculeisrotatedaroundtheaxisselectedinMode(üModusÇ).The
  356. defaultissingle(üEinzelbildÇ).
  357.  
  358. ê5.3.2  PicturesizeÇ (üBildgrößeÇ)
  359.  
  360.      When1/1isselected,theentiredisplaywindowisusedfor
  361. themoleculediagram.When4/4isselected,thewindowisdivided
  362. intoquarters,eachshowingadifferentviewofthemolecule.The
  363. defaultis1/1.
  364.  
  365. ê5.3.3  ColorStereoPictureÇ(üFarbiges StereobildÇ)
  366.  
  367.      Thisfeaturemayonlybeselectedinmediumresolution.Two
  368. picturesaredrawn(detailedin5.5.7)whichdifferbyaspecified
  369. angle.WiththehelpofRed/Greenglassesyoucangetan
  370. appearenceofspace(see4.1).Thisonlyworksin1/1picture
  371. setting.
  372.   
  373. ê5.4    MeasureÇ      (üMaßstabÇ)
  374.  
  375.      Determineswhetherthesizeofthediagramisautomatically
  376. ormanuallyset.Defaultisautomatic.
  377.   
  378. ê5.5    SettingthenumericalParametersÇ
  379.  
  380.      Settingthenumericalparametersisdonebyclickingonthe
  381. leftorrightarrowassociatedwiththeparameter.Clickingthe
  382. rightmousebuttonwillincreaseordecreasethevaluebyten,the
  383. leftbuttonwillchangethevaluebyone.Holdingeitherbutton
  384. downwillcausethevaluetochangeuntilthebuttonisreleased.
  385.  
  386. ê5.5.1  PicturesÇ     (üBilderÇ)
  387.  
  388.      Thisisthenumberofpicturesusedinananimationsequence.
  389. Themaximumvaluedependsontheamountoffreememory.The
  390. numberofpicturesisinverselyproportionaltotherotation
  391. angle.Thedefaultisthemaximum.
  392.  
  393. ê5.5.2  RotationangleÇ(üDrehwinkelÇ)
  394.  
  395.      Showstheangleofrotationbetweenpicturesinananimation.
  396. Theminimumvaluedependsontheamountoffreememory.Theangle
  397. iscloselyrelatedtothenumberofpicturesintheanimation.
  398. Thedefaultisthesmallestanglepossiblefortheamountoffree
  399. memory.
  400.  
  401. ê5.5.3  X/YRotationÇ (üDrehung um X/YÇ)
  402.  
  403.      Determineshowmanydegreesthemoleculewillberotatedin
  404. space.Thedefaultis0ineachcase.
  405.  
  406. ê5.5.4  SizeinPixelsÇ(üGröße in PixelnÇ)
  407.  
  408.      Determinesthehalfsizeofthegraphicinpixels.Also
  409. workswhenthemeasureisautomaticallycalculated.Thedefault
  410. is150.
  411.  
  412. ê5.5.5  DistanceÇ     (üAbstandÇ)
  413.  
  414.      Determinesthedistancetheobserverisfromtheobject(only
  415. inperspectiveprojection).Thedefaultvalueis16.
  416.  
  417. ê5.5.6  UnityÇ        (üEinheitÇ)
  418.  
  419.      Determineshowmanypixelsaunityinthecoordinatesystem.
  420. Achangeinthisvalueonlyhasaneffectwhenthesettingforthe
  421. Measureisinmanual.thedefaultvalueis40.
  422.  
  423. ê5.5.7  StereopicturedifferenceÇ(üStereobild DifferenzÇ)
  424.  
  425.      Determineshowmanydegreesthestereopicturesareseperated
  426. fromoneanother.Thesettingisintenthsofdegrees.The
  427. defaultvalueis2.5degrees.
  428.  
  429. ê5.5.8  ShowPictureÇ (üZeige BildÇ)
  430.  
  431.        Displaysthepicturesintheanimationontheentirescreen
  432. aslongasananimationhasbeencalculated.
  433.  
  434. ê5.5.9  SpeedÇ        (üGeschwindigkeitÇ)
  435.  
  436.        Adjuststhespeedwithwhichthemoleculerotatesinan
  437. animation.
  438.  
  439. ê5.5.10 StartÇ
  440.  
  441.        Beginsthecalculationofamoleculeorshowsaprepared
  442. animation.Allofthepreviousfunctionslikecalculatingand
  443. drawingmaybecanceledbypressingtherightmousebutton.
  444.  
  445. ê5.5.10 ToMenuÇ      (üZum MenueÇ)
  446.  
  447.        Returnsyoutothemainmenu.
  448.  
  449.  
  450. êSubjecttochangew/onoticeÇ
  451.  
  452. -----------------------------------------------------------------
  453.  
  454. ê*Translater'sAdendumÇ:
  455.  
  456.        Imustapologizeforanyinaccuraciesinrelationto
  457. chemicalterminology.IhavehadtheusualHighSchoolchemistry
  458. coursesandfoundsomeofthegermantermsidentifiable.Icannot
  459. beheldresponsibleforanypossibledamageordefamationof
  460. characterthatmightbeincureduponuseofthissoftware.
  461.  
  462.        Asstatedabove,thisisPublicDomainShare-warefromWest
  463. Germany,andmaycontainreferencestoprogramsandsoftwarenot
  464. availableintheUSA.Thistranslationofthedocumentationis
  465. alsoreleasedintothePublicDomainwiththeonlyrestrictions
  466. beingthatitmaynotbesold.Copyitandpassiton.
  467.  
  468.        Ihaveorganizedadiskwhichincludes:acopyofthe
  469. originalsoftwarepackage,includinggermandocumentation,mymost
  470. recenttranslationandahandytranslationsheettohelpyouin
  471. operatingtheprogramandreadingthemenus.
  472.  
  473.        Ifyouwouldlikethedisk&translations,send$5.50(to
  474. coverdisk,shipping&handling,importcosts&translating)to:
  475.  
  476. üRobertZimmerer
  477. Diskorder
  478. 131W2ndStreet
  479. PortAngeles,WA98362
  480. Ç
  481.        FormoreinformationaboutotherPDsoftwarefromWest
  482. Germanyyoumaywritetotheaboveaddressorcallat:
  483. ü
  484. (206)452-7529Ç
  485.