Beilstein Commander User Guide
Contents
1. 1 2 Windows Set up The set up procedure describes the installation of the client software only For information concerning the server please consult the server guide Before you start the setup procedure we recommend that you prepare a backup copy of your set of installation disks The Setup can be stopped at any time by clicking the Cancel button You will also be able to navigate through the dialog boxes of Setup by using the Next and Back buttons until copying of the files starts 1 2 1 Start On starting SETUP EXE the following dialog box will appear Setup 0 x Beilstein Commander Application CrossFire for Windows 95 Lx Welcome to the Beilstein Commander Setup program This program will install Beilstein Commander on your computer It is strongly recommended that you exit all Windows programs before running this Setup program Click Cancel to quit Setup and then close any programs you have running Click Next to continue with the Setup program WARNING This program is protected by copyright law and international treaties Unauthorized reproduction or distribution of this program or any portion of it may result in severe civil and criminal penalties and will be prosecuted to the maximum extent possible under law Setup automatically recognizes the operating system and will install the appropriate Beilstein Commander version The headline tells you the version that will be inst2. The individual applications are described in detail in the appendix 4 3 1 Application No Application Use this option to deactivate any application This can be useful if for example the communications link has broken down and you need to start a new session Simply select No application and then select the application that you would like to re start 41 4 4 Task menu commands The Task menu offers the following commands Display Hits Fact Editor Structure Editor Browse Database Start F7 4 4 1 Task Display This option will only be available and enabled if a hit set has been created Select this option to switch to the display of search results More information about using the Display can be found in the Help for Display Hits or relevant manual section Button 4 4 2 Task Fact Editor This option will only be enabled when CrossFire is the active application Selecting this option has the same effect as double clicking the fact window and switches to the Fact Editor OLE server The current query if present will be displayed in the editor More information about the operation of the Fact Editor can be found in the relevant manual section Button 4 4 3 Task Structure Editor Selecting this option has the same effect as double clicking the structure window and switches to the Structure Editor The current query if present will be displayed in the editor More information about the operation
3. AUTONOM s success rate is up to 86 of its applications AUTONOM works with a library of more than 7 000 entries in the ring dictionary AUTONOM recognizes abnormal valences AUTONOM can name single charged compounds AUTONOM has a large database of functional groups 6 1 4 Application Sandra SANDRA your window to the Beilstein Handbook Presently the Beilstein Handbook contains carefully checked information on over 3 0 million organic compounds Without SANDRA locating information on any particular compound in the Handbook requires some knowledge of the Beilstein classification system and an appropriate search technique SANDRA relieves you of this burden and is easy to use You simply draw structural formulas using a mouse These are then entered via a fast flexible graphic input system and analyzed by SANDRA which then tells you where to look for your compound or its analogues in the Beilstein Handbook assuming the structure exists Hardware Requirements IBM PC compatible personal computer with at least 256k memory IBM and Hercules graphics card Microsoft or compatible mouse a screen dump can be made with IBM compatible printers The Beilstein Handbook of Organic Chemistry commonly referred to as Beilstein contains important information published since 1779 about the manufacture and properties of carbon compounds With over 500 single volumes 70 the Beilstein Handbook today constitutes the world s largest collection of crit
4. Copy Ctrl C Paste Ctrl 4 2 1 Undo Can t Undo command Use this command to reverse the last editing action if possible The name of the command changes depending on what the last action was The Undo command changes to Can t Undo on the menu if you cannot reverse your last action Shortcuts Keys CTRL Z or ALT BACKSPACE Macintosh 28 Z Command Z 4 2 2 Cut command Use this command to remove the currently selected data from the document and put it on the clipboard This command is unavailable if there is no data currently selected Cutting data to the clipboard replaces the contents previously stored there Shortcuts Toolbar Keys CTRL X Macintosh 38 X Command X 4 2 3 Copy command Use this command to copy selected data onto the clipboard This command is unavailable if there is no data currently selected Copying data to the clipboard replaces the contents previously stored there Shortcuts 39 Toolbar Keys CTRL C Macintosh 38 C Command C 4 2 4 Paste command Copies the contents of the clipboard to the active window This will only be available if a section of text or a structure has been copied from the Hit Display to the clipboard Shortcuts Toolbar Keys CTRL V Macintosh 38 V Command V 40 4 3 Application Menu Commands The Application menu offers the following commands Application CrossFire Current Facts Molterm FastDoc AutoNom Sandra No Application
5. release 2 0 is a windows based program for the PC and Macintosh which generates IUPAC names from graphic structures The algorithms in AUTONOM 2 0 name your structure in the same way a nomenclature specialist would first AUTONOM identifies the parent fragment of a structure by applying the appropriate IUPAC nomenclature principles it then orders the other structure fragments according to the predefined nomenclature hierarchy Next all recognized fragments of the input structure ring systems chains functional groups are related to their corresponding name fragments and finally assembled to from a complete IUPAC compatible name AUTONOM 2 0 uses the Beilstein structure editor however it can be configured to use any editor that supports MDLs sketch file format as input NEW FOR RELEASE 2 0 Two component structures are now handled previous version was limited to naming single component substances including inorganic cations anions and inorganic neutral species 69 Organic cyanamide derivatives Organic carbodiimide derivatives Carbox amidines Hydroxamic acid derivatives Phthalocyanine derivatives Alternating silicon and hetero atom chains Greatly enhanced dictionary of trivial annelated ring systems ADVANTAGES OF AUTONOM 2 0 AUTONOM delivers IUPAC compatible names in seconds AUTONOM creates names based on algorithms AUTONOM will not name a structure incorrectly It gives a warning if the structure cannot be named
6. trademarks etc in this publication does not imply even in the absence of a specific statement that such names are exempt from the relevant protective laws and regulations and are therefore free for general use Furthermore the CrossFire system is subject to the licence agreement and the terms and conditions for the Beilstein data and database system Manual Version 2 September 1996 for Beilstein Commander Version 2 1 and CrossFire Server Version 3 1 Table of Contents 1 THE COMMA N DE SE 2 1 1 SYSTEM REQUIREMENTS RECOMMENDED iii 3 1 2 WINDOWS SERRES E E AS 4 A NO 4 1 2 2 TYPE OF SE E 5 Re Ee LE EE 6 1 2 4 The CrossFire Host AddressS coooomooncocecocacccccaninacicenaraccnaranonarinesacinrns 7 1 2 5 ed EE 7 1 2 6 CrossFire Root NECIO eek 8 1 2 7 TCP IP Communications ROQUE ss nat aan iaa 9 1 2 8 Type of COMMUNICATIONS en RSR ias 9 1 2 9 Type of Communication Port SGeitmge 10 1 2 10 Open VMS Alpha Server nono nonononononnnnnnnonononnnnnnnnnnnnnnnos 11 1 2 11 Program Ela AA 11 1 2 12 Installation Parameters Summary 12 1 2 13 Installation Process Indicator 13 SA A O 14 1 3 MACINTOSH SETUP asta aaa een a nn Ei 15 1 4 WORKING WITH THE BEILSTEIN COMMANDER cccoccccconccccnnnaccnononancncnnancnonancccnnanines 16 1 4 1 The Application Function Bar sangen tante 17 2 CROSSFIRE PLUSREACTIONS zu2uuuuu00000unnnannun0n aunununnunnnunnunnnunnnnnnnnnnnn mann
7. with CrossFire plusReactions as reaction substructures You can define the role of a structure or substructure in the reaction and search using reaction attributes such as reaction centers bond fate and atom atom mapping Hyperlinks allow navigation to Substances and to Literature references Citations These are now stored in a separate domain of the database This facilitates citation searching and a citation orientated display You can now display in one document all of the compounds and reactions that have been abstracted from the original reference Hyperlinks again are provided to Substances and Reactions 21 Hyperlinks These allow seamless navigation between substances reactions and citations Thus for example when you are viewing a reaction one mouse click on the hyperlink calls up the substance record for one of the reaction partners Similarly when viewing some properties simply click on the citation hyperlink to call up the citation record showing all the compounds and reactions abstracted from that reference Display Context You can carry out structure searches on the whole database or on subsets factual searches and combined searches The Display Context of the search which is automatically set at search time a search for reactions will result in a display in reaction context can be subsequently changed for either single compounds lists of compounds or reactions or citations or for the whole hit set By usi
8. 3 4 Enter Reg No This Goto option allows you to find a particular entry in the database Enter the registry number in the edit field 5 3 5 First Used Item This Goto option finds the first entry in the file or database 5 3 6 Last Used Item This Goto option finds the last entry in the file or database 63 5 4 The View Menu The view menu has the following options Cols 2 Molecule View 5 4 1 Rows Use this option to set the number of rows displayed in the Browser 5 4 2 Cols Use this option to set the number of columns displayed in the Browser 5 4 3 Molecule View The molecule view dialog box allows you to define how you would like the molecules to be displayed See section on molecule view for more information 64 5 5 The Help Menu 5 5 1 Contents Use this command to display the Help opening screen From the opening screen you can jump to step by step instructions for using the Display and various types of reference information Once you open Help you can click the Contents button whenever you want to return to the opening screen 65 Q Appendices 6 Appendices 6 1 Appendix A Other Applications From Beilstein Information 6 1 1 Application Current Facts Current Facts in Chemistry is a collection of the latest information on organic and medicinal chemistry delivered four times a year on CD ROM With Current Facts every quarter investigators have access to the most re
9. 4 7 1 Contents command Use this command to display the Help opening screen From the opening screen you can jump to step by step instructions for using the Beilstein Commander and various types of reference information Once you open Help you can click the Contents button whenever you want to return to the opening screen 4 7 2 Using Help command Use this command for instructions about using Help 4 7 3 About command Use this command to display the copyright notice and version number of your copy of the Beilstein Commander 4 7 4 Context Help command Use the Context Help command to obtain help on some portion of the Beilstein Commander When you choose the Toolbar s Context Help button the mouse pointer will change to an arrow and question mark Then click somewhere in the Beilstein Commander window such as another Toolbar button The Help topic will be shown for the item you clicked Shortcut Li Keys SHIFT F1 98 E The Browser 5 The Browser The Browser is used either when examining BSD files of factual queries structure queries or templates or when viewing the History hitsets or structures in a database Browse BS9501 874546 of 6546266 RN 919054 of 7004207 File Edit Goto View Help The Browser has a menu bar and a configurable number of cells for viewing the entries in the files or lists 60 5 1 The File Menu The file menu has the following options 5 1 1 Load This option is active
10. 5 7 Save ES ARA bete 51 4 6 QUERY MENU COMMANDS tint tietun tint t kenar tina tkne nanena nanna urnen nunnana 52 4 6 1 Structure Query Options iii 52 4 6 2 Structure Search RESIICHONSS Lan mien een A 53 4 6 3 Stereo Gal EE 55 4 6 4 Taulomer Search rias reed 55 40 5 Databases ae ee ee Re ee T 55 4 6 6 Display CONIOXE EE 56 4 7 HELP MENU COMMAND Scania rear ehe 58 ALA COMENIS command aaa A aan 58 Fe AISI A en net eaten 58 AT ADO ECO NM Ae None 58 4 7 4 Context Help command 58 5 THE BROWSER atinada 60 5 1 THE FILE MENU 0d eier 61 LEO DEE 61 EE ee 61 LEP DE D LE A ANN 61 O hehehe RTC RE 61 5 2 THE EDIT MENU o A a ee der 62 ZT O OU O 62 Bi REENEN a EE 63 ES USE MOE a diem ennemie 63 De Last USC Mana 63 DEMO METANO asia Nat EE EA A A strate 63 B70 4 EMer ACO INO OTRO PORN BP O O EDO 63 53 9 First Used ME ii A 63 OO ASS COME td AAA aa ene AAA 63 5 4 THE VIEW MENU engeren 64 LD ee et 64 J42 CO a en en ee ne E 64 SAS MOIECUIE VIEW Se E 64 5 5 THE HELP MENU ses ta oe 65 D GON CNS tata da alada 65 PREISEN aaron 66 6 1 APPENDIX A OTHER APPLICATIONS FROM BEILSTEIN INFORMATION 67 6 1 1 Application UN leas 67 6 1 2 Application ere 67 6 1 3 Application AUTONOMA ner ee ans tase 69 8 17 24 ADDICAION Sandra a Tales a a E 70 6 2 APPENDIX B CROSSFIRE CLIENT SCRIPT COMMANDS ere 73 6 3 APPENDIX C BSD ROSDAL MDL SKETCH FORMAT CONVERSION 75 6 3 1 Conversion of MDL Sketch format to BSD 75 6 3 2
11. administrator 10 1 2 10 OpenVMS Alpha Server OpenVMS Alpha Server The CrossFire server is able to run on an IBM RS6000 under 41 or on a DEC Alpha machine under OpenYMS If the CrossFire server is running on a DEC Alpha machine under Opern MS then the Beilstein Commander needs an adaption and you should click YES Please ask pour system administrator for more details lt Back Cancel The CrossFire server is also available for DEC Alpha machines running under OpenVMS 6 2 or higher If you have CrossFire installed on A DEC Alpha you should select YES Please ask your system administrator for details 1 2 11 Program Group Selection Select Program Folder x Setup will add program icons to the Program Folder listed below You may type a new folder name or select one from the existing Folders list Click Next to continue Program Folders Existing Folders nes ompuServe CS Chem ffice Hauptgruppe RoboHELP 95 a lt Back Cancel Please enter or select a name of the Program Group where you would like to have the Beilstein Commander icon installed on your desktop The default value is Beilstein 11 1 2 12 Installation Parameters Summary Start Copying Files Before the installation starts Setup will give you an overview of all parameters entered so far At this point you can to go back and change some settings If you click on Next the installation w
12. be carried out for full structures generic structures and Markush structures The structure editor allows two types of stereochemistry to be defined for molecules Firstly the absolute configuration of asymmetric or chiral centers can be defined by using bond types of steric up or steric down or steric unknown Direct input of R S configuration according to the Cahn Ingold Prelog conventions in not possible Secondly configuration of double bonds can be specified by using the bond type of double stereo When this descriptor is used the absolute input configuration will be searched for in the database Direct input or E Z or Syn Anti descriptors is currently not possible Absolute Stereo Search When this level is used the exact configuration will be searched for Only compounds which have the identical absolute configuration as the query structure will be found as hits Relative Stereo Search The same as for Absolute but also retrieves the mirror image and the racemate of the query Thus structures will be retrieved with all stereocenters as defined in the query and also those with all their stereocenters of opposite configuration to the definition in the query This way compounds and their enantiomers can be retrieved However no diastereoisomers will be retrieved Racemic Stereo Search Retrieves only the racemate of the query 4 6 4 Tautomer Searching A compound which exhibits prototropic tautomerism is one which
13. for the following e History e Hitsets e Structures e Fact Queries e Databases Use this option to load the selected entry into the active application 5 1 2 Save This option is only active for customer files or databases Use it to save the structure in the Beilstein Commander in the selected place in the customer database 5 1 3 Delete This option is only active for customer databases Use it to delete the selected entry from the customer database 5 1 4 Exit Exit the Browser and return to the calling application 61 5 2 The Edit Menu The edit menu has the following option 5 2 1 Copy Copies the selected entry to the clipboard 62 5 3 The Goto Menu The Goto menu has the following options First User Item Last User Item Enter ItemNo Enter RegNo First used Item Last used Item 5 3 1 First User Item This option is only active for customer files or databases Use this Goto function to find the first item in your own section of a customer database 5 3 2 Last User Item This option is only active for customer files or databases Use this Goto function to find the first item in your own section of a customer database First Gap This Goto option finds the first gap in a file or customer database where you will be able to store a structure 5 3 3 Enter Item No This Goto option allows you to find a particular entry in the database Enter the sequential number in the edit field 5
14. menu options 4 1 5 2 3 4 command Use the numbers and filenames listed at the bottom of the File menu to open the last four documents you closed Choose the number that corresponds with the document you want to open 4 1 6 History Select this option to call up the Browser to display the session History You can load previous queries into the Commander by using the Load option in the Browser file menu 4 1 7 Hitsets This option starts the Browser which displays the temporary session hitsets and any hitsets that you have permanently saved You can load the query into the Commander by using the Load option in the File menu of the Browser 4 1 8 Print command Use this command to print a document This command presents a Print dialog box where you may specify printing either the actual query or a range from the session queries the number of copies the destination printer and other printer setup options Shortcuts 37 Toolbar Keys CTRL P Macintosh 3 P Command P 4 1 9 Exit Quit command Use this command to end your Commander session You can also use the Close command on the application Control menu The Commander prompts you to save any queries or hitlists with unsaved changes Shortcuts Mouse Double click the application s Control menu button Keys ALT F4 Macintosh SS Q Command Q 38 4 2 Edit menu commands The Edit menu has the following options Windows version is shown Ctrl Z Ctrl X
15. not supported and is ignored Link nodes will be ignored Resolve link node using R groups Amino acid symbols are not supported and are translated into G groups Atom aliases are ignored Unsaturated atoms are not supported Atom value is not supported Ring bond count is not supported DEL RN O INT No of R group in Atom is not supported 9 Singlet diradical is not supported 10 Aromatic bonds are not supported 11 Bond stereo care is not supported 12 Mappings more than 1 is not supported 13 Mappings no partner is not supported 14 Atom exact change is not supported 75 6 3 2 Conversion Rosdal to MDL Sketch format All attributes can be converted with the following exceptions 1 Predefined atom list M 2 Atom symbols Ku Ha or Rf 3 Shortcuts or predefined generic group symbols 4 AC when the definition is due to a H atom bond being broken 76 Index TT 7 Index De E een E AAA E NE A E OEE 37 A About command u a Rte teks Sua eu Re ARE A ib ee ened he 58 Absolute Stereo Search 55 Appendix B CrossFire Client Script Commande 74 Application ee ON 70 Application Current Pacts vecino ii ii ara 68 APPLICATION FUNCTION BAR 17 18 Application Menu Commande 41 Application M O E taninos at an USE 68 Application Nope aper Ee A tias 41 Applications MA Rs Ann ARRET ARE Men ARR MR A RER Ann 71 E een AAT 46 Automatic Context Selection 44 B Beilstein Structure Bdt f sets nina en an
16. of the Structure Editor can be found in the Structure Editor Help or relevant manual section Button 42 4 4 4 Task Browse Database Pressing the button starts the browser which allows you to browse through the selected database The database can be browsed and structures copied to the Commander Button 9 4 4 5 Task Update Database This option will only be available and enabled when a customer database has been selected in the database combo box Selecting this option starts the browser in update mode The database can be browsed and structures present in the Commander can either be added as new records to the database or they can overwrite existing records Button El 4 4 6 Task Delete Database Record This option will only be available and enabled when a customer database has been selected in the database combo box Selecting this option starts the browser in delete mode The database can be browsed and the selected structure can be deleted Button be 4 4 7 Task Start or Name All searches must be started from the Commander A query must have been formulated and be present in either the structure panel or the fact panel or both After starting a dialog box displays the status of the search and the Search button changes to a Stop button to stop the search When the search is completed a dialog box displays the hit list number and number of hits and asks if the hit list should be displayed or not If Autono
17. parameters Connections to the CrossFire Server EN TCP IP Address or Host Name Path to the CrossFire Server fire bin CrossFire Root Directory fire TCP IP Communication Product Ms WINDOWS SOCKET Rexec C Telnet Login Script Logout Script Note 4 change will terminate an existing session T Open MS Alpha Server M Capture Session Cancel Help Enter the connection parameters in this dialog box for connection to the CrossFire server The entries will normally have been correctly input by the network supervisor If you change any entry you might loose the connection to the server and CrossFire will not run The following must be input TCP IP address or host name Here you can enter a numeric address e g 111 111 111 001 or a symbolic name e g test com Path to the CrossFire server Please ask your system administrator for more details If you have a default installation on the server then the entry should be xfire bin for an RS6000 AIX and xfbin for a DEC Alpha server OpenVMS The entry for the DEC Alpha 48 server will be set automatically if the box labeled OpenVMS Alpha Server is checked CrossFire root directory Please ask your system administrator for more details If you have a default installation on the server then the entry should be xfire for an RS6000 AIX and for a DEC Alpha machine OpenVMS TCP IP communications product The Beil
18. time seconds Within the script you may use the following place holders to represent fields from the Login to Server and Options Connections dialog boxes User ID from the Login dialog box Password from the Login dialog box C Command to start the CrossFire Server This command is constructed from the CrossFire program path and the 73 SAA database root path in the Options Connections dialog box Example 1 typical procedure wait login send U sends a line feed wait pass P wait send C Example 2 a firewallin between wait gt gt is the Firewall prompt send c 123 456 789 101 this is the connect command for accessing an external server wait login send U U is for userid sends a line feed wait pass P P is for password wait send C C is for the XFIRE server command 74 6 3 Appendix C BSD Rosdal MDL Sketch format conversion 6 3 1 Conversion of MDL Sketch format to BSD Since in the native CrossFire structure editor the basic philosophy is that the default setting for free sites is none this will also be assumed for structures coming from ISIS draw Thus to set maximum free sites on particular atoms this must be explicitly done from within ISIS Draw To set free site on all atoms this is most easily done using the Structure Query Options in the Commander All attributes can be converted with the following exceptions R logic is
19. Conversion Rosdal to MDL Sketch format 76 1 INDEX aria ar Na 78 VI E The Commander 1 The Commander The Beilstein Commander provides the user interface for Beilstein s suite of products Since the different products for example CrossFire and Autonom have different interface requirements the Commander configures itself accordingly When using CrossFire the Commander is configured with a Structure and Reaction editor a Fact editor and the Display Hits module These are all linked together through the Commander to give one coherent interface unit The Commander provides the means to access the CrossFire and your own customer databases allowing searches to be carried out results displayed and the database to be browsed thus giving you the ability to navigate seamlessly through the world of organic chemistry 1 1 System Requirements recommended IBM PC or compatible Macintosh Platform 486 PC compatible or 68040 class computer or Pentium PC PowerPC chip class computer Memory 12 Mbyte not including 16 Mbyte not including OS requirements OS requirements Storage 15 Mbyte hard disk storage 15 Mbyte hard disk storage Operating System MS Windows 3 1x Mac OS 7 5 Release 2 MS Windows NT or MS Windows 95 Connectivity MS Winsocket 1 1 Mac TCP compliant Protocol TCP IP connection to server TCP IP connection to server Novell LAN Workplace 4 0 4 1 or TCP IP extension products that are Winsocket 1 1 compliant
20. The Beilstein Commander Beilstei BEILSTEIN INFORMATION BEILSTEIN INFORMATION Distributed by Beilstein Informationssysteme GmbH Varrentrappstrasse 40 42 D 60486 Frankfurt Germany Tel 49 69 7917 410 Fax 49 69 7917 321 BEILSTEIN INFORMATION Help Desk CustomerService Beilstein Informationssysteme GmbH Varrentrappstrasse 40 42 D 60486 Frankfurt Germany Tel 49 69 7917 258 Fax 49 69 7917 321 In the US Tel 800 275 6094 Fax 888 BEILSTEIN Beilstein CrossFire Copyright by Beilstein Informationssysteme GmbH Frankfurt Beilstein Data Copyright by Beilstein Chemiedaten und Software GmbH Beilstein Institut f r Literatur der organischen Chemie Frankfurt Gmelin Data Copyright by Gmelin Institut f r Anorganische Chemie und Grenzgebiete der Max Planck Gesellschaft zur F rderung der Wissenschaften This work is subject to copyright All rights are reserved whether the whole or part of the material is concerned specifically the rights of translation reprinting reuse of illustrations recitation broadcasting reproduction on microfilm or in other ways and storage in data banks Duplication of this publication or parts thereof is only permitted under the provisions of the German Copyright Law of September 9 1965 in its version of June 24 1985 and a copyright fee must always be paid Violations fall under the prosecution act of the German Copyright Law The use of registered names
21. a dd ere es eet Seet ee or sh 63 Enter Reg Novia Ee i 63 Exact Searches A EN O EA 53 SE eebe A TAN 61 Exit Quit commande 38 F Fact eeh 27 LE Ee EE 17 26 30 Ke CEV 20 Fl MACANO a 35 PMA A a Olek AS AS da ani a e a 15 A o de o BR REE 75 First Gap ae re ne AMT ne eege eege ege ALES 63 First Used ltem 2 eege ie e ad aa 63 First Ser AA A Ac en en A aE el a a A nr Re EE 63 FOTMAL CONVERSION Eed 76 H H lp menu commands oct iia ee dass 58 Kr TEE 37 MISES RNA Me pee dl dE tallo ld acto De tes Aer ll er E e dl eno Auer 37 Ee ee E o lc a rs 7 EK EE 22 I Implic t Fre amp Sites anne an a a it An 52 Implicit Ring Closures EE 53 Installation Parameters Summara ss 13 Installation process Indicator ses 14 L East Used Hem rta nr cdo PR Un EH 63 LastUstce let esu Sege ee PES e dis 63 Modes odo ee nd del o dee se a qe ed eebe do ER 61 ES Split nn cok RM sath ask Sob ies Ft EL Pe a 49 Logout e EEN 50 M Macint sh EE 29 Macintosh Studio 16 Molecul Vale Wena seer t ta a 45 64 Multicomponent Compounds seen 53 79 N Negativo Chalt n AA din Neue 54 Ni dias 35 Non Beilstein Structure Editor seen 28 Number Of AOS surintendant dd ee id 54 Number of Components 2 023 2 2 Aaa 54 Number OF R die ls u uuln een mn A ren mot dee ee ee 54 Number of Ring Closures tii idilio 54 O Open command il lies 35 OpenVMS Alpha Server Aaen Eeer 11 50 Options menu c
22. ai ege 28 buttons na sn EE nd 17 C Capture Sessions 50 CHAT SES its artnet teawasduhscuasdedeavtoageciuiodsa caus otensswoododeaybadeveustedes svebedepseene ste nt sic 53 Citations uan ner An A Sn E An en nd stat RS dt ia 21 COTS each EEE e RER Ee AR SRE EE Sea ea ER HE Dane ak uaa rach tee aes EEE 64 Combined Queries Oper tot 4 2 3 3 gedd Ze Seege eene 26 32 Commander 22 2 ta A SU A SH ets den ne Pen E e des a 1 2 commander interface ironia iniciara dla liarla 17 Communications Product tie net sentant braceros ica docs 9 eu EE 48 UE EE 65 Contents command Munster Mn Us treat Ms te ed nd ege sie 58 Context Help Command nina bre ride dat oc dons rnb ads dns AD seit 58 Conversion RAR a En MEN UT A OS 76 VE EEN 62 ew commadd Eege ee eege EE teen AE ete iii Ee ste tes 39 GrossPire mirad A en tes ea beac a cies 25 26 GCrossFir Metiu OPIO nn ane rl Nan ku eA RA Nei erin is 33 34 CrossFire PIUSREACHONS eege e SES SERA a as eld 19 20 CrossFire Toot director Eeer 49 CA rear ERINNERN ENTER 39 D Database Browse Button ia 27 Database RECO dt A LA E ete mind en eee te LO 27 Database Selection Box EES 21 Databases tele een ungenau delata deidad 55 Delete teste iia 61 78 Destination Path Tr Re RC a re ende hen CP 6 IR 27 Display Contexte AA AA A artnet lan 22 Display Tu E E 56 Display Context BOX rer trees A A nis urines Teese 27 E Edit menu comm nds ease ege neg esta en NEE dee EE 39 EnterHemiNO ss L
23. alled in the above example Windows95 Choose Next to proceed with the installation or Cancel to exit the setup 1 2 2 Type of Installation Type of installation Select type of installation you need Workstation All program files will be installed on the harddisk of your computer Network All program files will be installed on the network of your computer System Parameter ma Set or modify your setup disk for the use with CrossFire lt will not install the Beilstein Commander lt Back Cancel Choose Workstation to install the Commander on a single PC Choose Network to install the Commander program files on a network server together with a setup for user workstations This setup is a modified version of the disk setup if a user launches this setup he only needs to enter a path for his local working directory and a name for the program group All other settings will be taken from the network installation The modified setup will only copy some system files into the local Windows installation of the user It will not copy any Beilstein Commander files to the user directory Choose System Parameter if you want to define system settings for use with the CrossFire server and to modify the first setup diskette After this has been completed Setup will exit without installing the Beilstein Commander You can now distribute the set of installation diskettes among other users of th
24. an 20 2 1 SYSTEM DESIEN EE 21 2 2 SEARCHING A Add 23 3 THE EROSSEIREIINTERF GE 2 unse 25 3 1 THE TASK FUNCTION BAR 27 3 2 STRUCTURE REACTION PANEL ses aan ne 28 3 21 ONUCIUFe KEELT 28 Ord FACTS PANEL cuado atari 30 3 3 1 Facts e e 30 3 4 SUBSET SELECTION e ns rate a iaa 31 3 5 COMBINED QUERIES OPERATOR cccooccccccnnccccnonononcnnanonononcnononnnncnnnnacanonancn cnn anananns 32 4 THE CROSSFIRE MENU OPTIONS 222 00000000000un0n2 anuuuununnnunnununnunnnnnunnnnnn 33 A1 EIEEIMENU COMMANDS acto GEES en ca ae 35 EM NEW orna E dE 35 4 1 2 Open EE 35 4 1 3 SAVE COMMNMANO e a anda ada ada dada dada 36 Reeder GE 37 AT Ds L command EE 37 ANS aa 37 ATP IAN OS EE 37 4 1 6 PAC COMMANC EE 37 419 EXE QUE ele EE 38 4 2 EDIT MENU COMMANDS EE 39 4 2 1 Undo Can t Undo command EE 39 4 22 CUT COMMAN DEER 39 4 23 COPY COMMANDO EE 39 4 24 Paste command EE 40 4 3 APPLICATION MENU COMMANDS sia a 41 4 3 1 Application No Ree e BEE 41 4 4 TASK MENU COMMANDS redemande still 42 LA Task DIEDIAYV peier nes 42 AA Tas FACE EON OM cacas dono 42 4 43 Task SVUCTUTE ele 42 4 4 4 Task Browse Database 43 4 4 5 Task Update Database 43 4 4 6 Task Delete Database Record 43 4 4 7 Task Start or NAMGC linia ee 43 4 5 OPTIONS MENU COMMANDS nan 44 4 5 1 Structure and Fact ee 44 4 5 2 Automatic Context SCICCHON EE 44 4 5 3 Startup Task Options menu 45 2 94 MOSCHEE VIEW tarro aiii 45 4 5 5 de 48 Eo a VE s ttings ON ENTRE AE 51 4
25. arch button sets the query options to exclude all multicomponent charged or radical compounds 4 6 2 Structure Search Restrictions The Extended Options allow the following global restrictions can be set for the search 93 Extented Query Options Number Of Atoms F g 5 2 4 Number Of Components F BE Number Of Ring Closures F 8 F Positive Charge F g 5 r Y Negative Charge Lt 2 r Y Total Charge Balance F Y Number of Radicals F 4 F Y Minimum and maximum values can be independently set using the micro scrolls Use the reset button to go back to the system default values no restrictions Number of Atoms The total number of atoms to be found in the retrieved structure Number of Components The total number of components to be found in the retrieved structure Salts and addition compounds Number of Ring Closures The total number of rings to be found in the retrieved structure Defined as the smallest number of ring bonds which must be broken in order to convert the structure into an acyclic structure Positive Charge The total number of positive charges to be found in the retrieved structure Negative Charge The total number of negative charges to be found in the retrieved structure Total Charge Balance The total charge balance to be found in the retrieved structure Number of Radicals The total number of radicals to be found in the retrieved structure 54 4 6 3 Stereo Searching This can
26. ation it will be the suggested entry Please ask your system administrator for more details If you will leave this entry empty then you have to enter this information within the Commander under Options Connections Path lt Back Cancel Enter the path to the CrossFire server The suggested entry corresponds to a standard installation Please ask your system administrator for more details You can skip this and enter the information later in the Communications dialog box which is in the options menu of the Commander 1 2 6 CrossFire Root Directory Connections to the Crossfire Server EN CrossFire Root Directory Please enter the CrossFire root directory which is the path on the server where all temporary files and CrossFire system directories will be located For a standard installation it will be the suggested entry Please ask your system administrator for more details If you will leave this entry empty then you have to enter this information within the Commander under Options Connections Directory es Ze Enter the CrossFire root directory The suggested entry corresponds to a standard installation Please ask your system administrator for more details You can skip this and enter the information later in the Communications dialog box which is in the options menu of the Commander 1 2 7 TCP IP Communications Product TCP IP Communications Product Please select the desired TCP IP comm
27. cent twelve months of organic chemistry as reported in 100 top journals Literature structures reactions preparations physical and chemical properties including toxicological and environmental data keywords citations authors and CODENs Scientists needing access to the most recent advances in their field find in Current Facts an indispensable tool for daily research Using Current Facts you can search for structures substructures stereoisomers and tautomers of compounds presently under investigation Substructure query types can include bond and stereo chemical descriptors atom types generic groups e g acyclics hetero cycles etc The fact editor is a sophisticated data navigator that allows posing elaborate queries with remarkable ease Boolean operators and or not enable the scientist to combine queries and to manipulate lists of hitsets Current Facts displays structures and as many data fields as the user wishes to see Hypertext links let you jump directly to the record of the highlighted compound You can use this to navigate along synthesis paths 6 1 2 Application Molterm MOLTERM is an ASCII terminal emulation program with an integrated structure and fact editor running under Microsoft Windows Having a mouse supported structure editor allows construction of detailed full and substructure searches and translation into the structure commands of STN DIALOG and DARC Since MOLTERM is a Windows program it can excha
28. create a new document in the Beilstein Commander You can open an existing document with the Open command Shortcuts Toolbar Keys CTRL N Macintosh 38 N Command N 4 1 2 Open command Use this option to load previously stored queries into the Commander When you choose this option the File Open dialog box will be displayed where you can select the file you want to open You can create new documents with the New command Shortcuts Toolbar Keys CTRL O Macintosh 3 O Command O 35 1 Choose Open from the file menu to display the File Open dialog box This box allows selection of the drive path and file to be opened 2 Select a file If you know which query you want to load enter the number in the INO field and click OK If you would like to examine the contents of the file click the browse button to start the Browser 3 Browse through the contents either using the slider or the page keys to view the file You can start browsing at a particular query by entering its number in the INO field 4 Double click a query or choose Load Entry from the file menu to transfer the query to the Commander 4 1 3 Save command Use this command to save the active document to its current name and directory When you save a document for the first time the Beilstein Commander displays the Save As dialog box so you can name your document If you want to change the name and directory of an existing document before you save it c
29. e system If they run the setup again from the modified diskettes they will not see the System Parameter option and they will not be prompted for any CrossFire system parameter settings Remember to use a backup copy of the installation diskettes before you choose this option 1 2 3 The Destination Path Choose Destination Location Click the Browse button to select or enter the complete path of the directory in which the program and associated files should be installed Make sure that you have write access for the directory The button Disk Space allows you to select a drive 1 2 4 The CrossFire Host Address Connections to the Crossfire Server EN TCP IP Address or Host Name Please enter the TCP IP address of the host where the CrossFire Server is located Please ask your system administrator for more details If you will leave this entry empty then you have to enter this information within the Commander under Options Connections Address 1 1 1 1 ao Enter the TCP IP address of the host where the CrossFire server is located Please ask your system administrator for more details You can skip this and enter the information later in the Communications dialog box which is in the options menu of the Commander 1 2 5 CrossFire Server Path Connections to the Crossfire Server Path to the CrossFire Server Please enter the path to the CrossFire Server software For a standard install
30. ent query implies the context Substances Hits will be Substances shortcut use the display as context selection box This box contains a list of the available display contexts Choose between substance reaction 96 citation By default the display context is the same as the query context Thus a hitlist retrieved from a substance query molecule or property will be displayed as a list of molecules and their properties You can change the display context either before you start the search or you can convert a hit list and display it in a different context For example you can take a list of reactions and display these records as a list of citations The display context can also be changed on the fly for individual records This is achieved by means of hyperlinks There are now three distinct types of hyperlinks Substance using the Beilstein Registry Number Reaction using the Reaction Identification Number and Citation using the citation Identification Number Irrespective of how you are displaying information these links permit instant access to information about other substances reactions or citations 57 4 7 Help menu commands The Help menu offers the following commands which provide you assistance with this application Contents Offers you a table of contents of topics in the help system Using Help Provides general instructions on using help About Displays the version number of this application
31. exists in two or more forms arrived at by a formal transfer of a hydrogen atom to or from a heteroatom from or to any other atom in the compound accompanied by a rearrangement of electrons which results in one or more of the double bonds being shifted This type of search is only valid for full structures 4 6 5 Databases Use this option to display the Databases dialog box where you can choose the database to search When using CrossFire you can choose between searching the Beilstein File and any CrossFire customer databases that you may have Only one database may be selected at a time 99 Database Information CrossFire Server Software Version 3 0 Build 6 Copyright c Beilstein Informationssysteme GmbH 1995 Current database is BS9501 with 6546266 compounds Copyright c Beilstein Chemiedaten und Software GmbH 1995 Available contexts SRC Substances Reactions Citations Current context S XPS license expires Fri Dec 31 23 59 59 1999 DBS license expires Fri Dec 31 23 59 59 1999 XPR license expires Fri Dec 31 23 59 59 1999 DBR license expires Fri Dec 31 23 59 59 1999 User bsmgh rights R AILRead None Shortcut Use the database selection box 4 6 6 Display Context This option will only be enabled when the Beilstein File has been selected in the database combo box The current database allows for data display in the contexts shown on the left Reactions Citations The curr
32. he handbook and director of the Beilstein Institute in Frankfurt am Main from 1961 until March 31st 1978 Since April 1st 1978 Reiner Luckenbach has been director of the Institute The Beilstein Institut which adopted the legal status of a trust in 1951 is engaged in close cooperation with Beilstein Informationssysteme GmbH in the rapid publication of the supplementary series of Beilstein 72 6 2 Appendix B CrossFire Client Script Commands The CrossFire Client uses two script files to establish or terminate TELNET sessions e XFLOGIN SCR e XFLOGOUT SCR Both scripts are ASCII text files with the following rules e Lines starting with one of several 4 letter keywords plus a blank are interpreted as commands All other lines are comments In a command line the characters from 6 up to excluding the line feed are a single command parameter e Keywords are case insensitive the case of command parameters is not changed The following commands are defined IIA II WAIT string Wait until the host sends string SEND string Send string to the host If a carriage return keystroke is to follow the characters sent a tilde has to be the final character of string PASS password Send a password suppressing screen output A tilde see SEND should not be appended Instead of inserting a password into the script you should consider using the P place holder DELA delay time Wait for delay
33. his entry empty then you have to enter this information within the Commander under Options Connections C Regec lt Back Cancel Enter the type of communication lf you have CrossFire installed in house then we recommend that you use REXEC services lf you are using CrossFire through Internet then we recommend Telnet lf you choose Telnet then you may have to edit script files They will be available through the Beilstein Commander under Options Communications Please refer to the appendix of the Beilstein Commander guide or to chapter 3 of this guide for a description of the script syntax Please ask your system administrator for more details You can skip this and enter the information later in the Communications dialog box which is in the options menu of the Commander 1 2 9 Type of Communication Port Settings Connections to the Crossfire Server EN Please enter the address of the Telnet port of the server The default value is 23 Please ask the system administrator for details or if you know that nothing has been changed accept the entered entry and click the Next button TPORT fg Sa Telnet and Rexec port numbers TPORT and or RPORT can be set on the server by the system administrator The default value for the TPORT is 23 and for the RPORT 512 If you see a greyed out entry you should accept the setting as is and click on the Next button For more details please contact your system
34. hoose the Save As command Shortcuts Toolbar Keys CTRL S Macintosh 38 S Command S Use this option to save queries in a file bsd First time use requires the input of a file name Thereafter when save is selected the fact query will be automatically stored in the same file under the same INO Each file can contain more than one structure Each structure is given an internal number INO starting with 1 for the first structure 1 Choose Save from the file menu to display the file save dialog box Either 2 Input the internal number INO you want to assign to this query and click OK to store the query Or 3 Click the browse button to display the file contents Either double click a cell to store the query or select a cell and choose Save Entry from the File menu options 36 To store a modified query under a different INO use Save As 4 1 4 Save As command This option is similar to the save option except that it saves the query under a new file name or under a new INO in the same file To save a document with its existing name and directory use the Save command 1 Choose Save As from the file menu to display the file save dialog box Either 2 Input the internal number INO you want to assign to this query and click OK to store the query Or 3 Click the browse button to display the file contents Either double click a cell to store the query or select a cell and choose Save Entry from the File
35. ically evaluated organic compounds in printed form The Handbook is published in series each covering the literature of a certain time period All volumes from the Fifth Supplement EV onwards are published in English Each series consists of 27 nominal volumes which may be subdivided into several subvolumes in the more recent series The individual compounds are arranged according to the Beilstein System which classifies all organic compounds according to their structures For each compound described Beilstein covers the following aspects structural formula compound name s molecular formula constitution and configuration natural occurrence isolation from natural products preparation and purification structural and energy parameters of the molecule physical properties chemical properties reactions characterization and analysis salts and addition compounds Altogether more than 350 different kinds of physical data are found in the Handbook For anyone concerned with organic chemistry the Beilstein Handbook is a unique and indispensable source of information In 1981 Beilsteins Handbuch der Organischen Chemie celebrated its centenary The first edition of Beilstein appeared in the years 1881 1883 as two subvolumes in which around 15 000 carbon compounds were described on 2 200 pages Evaluation of the literature and editorial treatment for this first edition and the two subsequent editions which ra
36. ignifying the complete database The hit set can also be selected in the Fact Editor Thus the combo box will contain a list of all permanently saved hit lists and all session hit lists displayed as follows Subset E All TEST2 411 Reactions in BS9501 001 120 Substances in B59501 003 1147 Citations in B59501 When the subset is selected it will overwrite the present if any factual query 31 3 5 Combined Queries Operator When a combined query has been input in the Commander with entries in both the Facts panel and the Structure panel the combined queries operator will be displayed as a label between the two panels The setting is always AND When one of the panels is cleared the label will not longer be displayed The fact query will always be searched for first and the resulting hitset will be used as a subset for the structure search 32 E The CrossFire Menu Options 4 The CrossFire Menu Options The Menu bar has the following options 4 1 4 2 4 3 4 4 4 5 4 6 34 File menu Edit menu Application menu Task menu Options menu Query menu 4 1 File menu commands The File menu has the following options Windows version is shown Open Ctri O Save Ctri S Save As History Hitsets Ctrl P 1 CACMDR2 TERPEN BSD 1 2 CACMDR2 STEROIDS BSD 1 3 CACMDR2 HETCYC BSD 1 4 CACMDR2 AMINACID BSD 1 Exit 4 1 1 New Use this command to
37. ill proceed 12 1 2 13 Installation Process Indicator 22 Setup Beilstein Welcome to the Beilstein Commander This setup will install the unique interface to the CrossFire system Please take a few minutes afterwards to have a look at the release notes for important information on the current release Please refer to the manuals for more detailed information on all parts of the system The Beilstein Commander is the basic hub of CrossFire and allows you to call external editors for formulating structure reaction and property queries BC Beilstein Commander Of x File Edit Application Task Options Query Help Dee cel El a 2 r Database p59602PR m Displays Substances zl i Status Idle z Copying program files cimdlsk dll At this point you will be shown several graphics containing previews of the new Beilstein Commander some dialog boxes about the progress of the installation 13 1 2 14 Finished Setup Complete X The final dialog box tells you whether the installation has succeeded or not Click Finish to finish the setup procedure After a successful installation you can start the Commander by double clicking Beilstein the icon in the Program Manager 14 1 3 Macintosh Setup Start the Beilstein Commander Installer by double clicking the icon This installer will place the Beilstein Commander software in a folder called Beilstein on your hard disk The i
38. m is the active application this option will start the Autonom program which will generate a name for the current structure Shortcut F7 Button 43 4 5 Options menu commands The Options menu offers the following commands Options Structure and Fact Editors Startup Tasks Molecule View Connections Automatic Context Selection y Save Settings On Exit v Save History On Exit 4 5 1 Structure and Fact Editors Choose this option to display the Preferred Editor dialog box Preferred Editors Structure Editors the hrer O ISIS Draw Fact Query Editors Tabular Query Editor O ID Property Editor You can select which Structure Editor and Fact Editor you would like to use 38 Macintosh Currently only the native CrossFire Structure Editor is available 4 5 2 Automatic Context Selection Switch this option on to automatically have the display context be changed to match the query For example if you search for a reaction the automatic display context will also be reaction 44 4 5 3 Startup Task Options menu Choose this option to display the Startup Task dialog where you can select your start up application and task Select Application Crossfire O EastDoc O Current Facts AutoNom O Molterm O Sandra O No Application Started Startup Tasks Structure Editor TT Fact Editor F Display Hits Setting the startup application to CrossFire means
39. n converted to a Rosdal string for display in the structure window If some attributes could not be converted a message to that effect will be displayed in a message box Please take a look at the appendix for a description of the limitations Setting Structure Query Options Since these cannot be set from within the Non Beilstein Structure Editor they must be set in the Commander Pressing the Options button causes the query option dialog box to be displayed The options 28 can then be set and when the box is closed they will be displayed as a string in the options window Macintosh With this version of the Beilstein Commander the Beilstein structure editor is the one available for Apple Macintosh users 29 3 3 Facts Panel The Facts panel has three controls the Facts Window the Subset Selection Box and the clear button Subset 3 3 1 Facts Window Double clicking the FACTS window switches to the Fact Editor All factual queries are input here as well as combined queries with other facts or hit lists including those from structures or reactions After switching back to the Commander the query string is displayed in the Facts window Pressing the clear button deletes the contents of the window 30 3 4 Subset Selection Box The subset window provides a quick means of selecting a previous hit set for further use either in combination with a structure query or for a change of context The default is Al s
40. ng combinations of searches changes of context and hyperlinks navigation through the database results not only in solutions to organic chemistry problems but by acting as a creativity enhancer it may lead to serendipitous discoveries 22 2 2 Searching With CrossFire plusReactions you can search for Structures Reactions Properties and other factual information Structures Full structures substructures generic structures stereoisomers and tautomers can be searched for You can use global query options such as Free Sites on All Atoms or set options on specific atoms and bonds only Query atom types such as X any halogen can be set as can Atom lists e g A1 C N O S Predefined generic groups e g ALK alkyl and user defined generic groups Markush structures are easily input Reactions All the features availble in structures plus reaction role reactant or product reaction center bond fate and atom atom mapping Thus you can search for half reactions of the type 2 gt A how do make this type of compound A gt what do these starting materials give or full reactions of the type A gt B general or specific transformations Properties search for numeric values and ranges strings and keywords The CrossFire database contains more than 30 million reports on chemical physical and physiological properties You can search for example for chemical name reaction conditions biological functi
41. nge files and data with other Beilstein programs via the clipboard in addition MDL s Molfile format is also supported MDL Information Systems The most important component is the fact editor Without a detailed knowledge of the field names you can prepare a complex factual search in tabular form MOLTERM then translates the table into the retrieval language of the appropriate host STN or DIALOG No other communication program is able to construct so clearly complex queries for chemical databases Beilstein Online access to factual data for organic compounds on STN and Dialog 67 In the area of organic chemistry Beilstein Online is the world s largest factual database With about 7 million heterocyclic acyclic and isocyclic compounds the Beilstein database covers the literature from 1779 to the present The contents and data structure are based on the Beilstein Handbook of Organic Chemistry The online file contains Beilstein handbook data from the Basic Series to Supplement IV covering the literature from 1779 to 1959 and structures and facts which have been abstracted from the primary literature Regular updates give you access to the latest information published in the chemical literature The file is available on the hosts STN and Dialog Beilstein Online offers a variety of search options which make this electronic information system an excellent reference tool for organic chemists and information specialists You can either
42. nstaller will automatically recognize the processor on the Macintosh and will install only the version of the Beilstein Commander appropriate for your Macintosh e g the native Power Macintosh version for a Power Macintosh and the native 68K Macintosh version for machines with a 68xxx processor If you have an older version of the Beilstein Commander already installed the installer will ask you to OK deleting old preference files You should accept this The installer will also install a folder containing a complete MacTCP installation package The Beilstein Commander needs a MacTCP compliant TCP IP communication product to get access to the CrossFire server If you dont have MacTCP on your machine then you may use the tools included with the Beilstein Commander install Please ask your system administrator or the Beilstein HelpDesk for details After the installation you need to know a few things to get CrossFire running e the TCP IP address of the server e the CrossFire directories on the server You have to enter this information within the Beilstein Commander under Options Connections Please contact your system administrator for details If your environment is using a firewall then you have to edit a script file Please take a look at the manuals for detailed information In addition you need to know your e User ld and e Password The system will ask you for that if you try to connect to the server Please ask your sys
43. nt AS ten ten aetna Te alee tans ES 21 System DES ia IA MAN NH 20 21 T Task Browse Databases cionado die nie E dote nil lents 43 Task Delete Database Record iessen 12 222222 ee ae Ee 43 Task Dis players ooo nant 42 Task Fact Editor ea ara Mai ii it nn 42 Task Start orN ames teta olaaa ma ea Na EE 43 Task Structure Edd incio 42 Task Update Databases doi 43 TASK FUNCTION BAR 17 26 27 Task menu Commande siria caian innecesarios criadas 42 KEE 55 Faute ee Ee a E Se et Aa E des Ae ae Lio A 53 TCP IP hee cbt a o aul e eee E A ERT a a 9 Rei De cite ee en LEO ORONO 7 TCP IP address 0r Host name him EE E E A E E EESE Ee 48 TCP IP communications productname nds RAA en batida cabe denies ETOS 49 A mr SR Sn Run ne Ne EEE em te rer se Pise LTE FED 10 49 The Beilstein Handbook of Organic Chemistry ss 71 The Baits Menu ita mn M Pod donee PR Pin den PR Buea nee na en 62 The Eile Menun ya mt sense lo od e eltern end ds 61 he Goto Mei Aussee ee ae 63 O A O NO 65 The View Men 2 2 E Ne En Se Ne ee rss ue 64 Total Charge Balance ht sheet eh ern nee EESE ends 54 Type Of Communication tinas did 10 A O 3 typical proc dure niee a aeo e nn ten Bene ip Dr no ee EE ONE se 75 U Undo Cant Undo command teint entente iii 39 Update Database Button 2 tee eege E Re en Ra a LO RM lan Rat Air E 27 Using Help command rd leben 58 Ww WAT OW A US 28 81
44. ommands ciao o dci 44 P PASE MM O A A a EINTRETEN ES e 40 Path to the CrossFire server A O 48 POPS D 11 Positive Chat geisia A bb E a mine tiennent ee 54 Print Command une nen ee niet cave ten tie Ee ei 37 Program Group S lection ciinei Ia 12 ee EE 23 Q Query menu commands iiaiai en n oen in En eE E o E E EAN EEEO T EN E EE E EO I aa EiS 52 R Racemic Stereo Search sinn nn sans an sun nn ESETE EEEE ee 55 Radical en en aa an ren e ED en ee Bere testen 53 Rea init ti EE oP A EE dE EE 21 23 Relative Stereo SEarch tint ent nt tel nu rte a tele ee dde ds 55 REXF E no anal 10 49 ROSE Die CLOT a Re A A ere ee eege set 8 UC 64 S SEH 61 Save AS COMMA duda tidad tos sn nant ida Goud este aa beis 37 EE EE 36 Save History ON Exilio iia 51 Save Settings ON BXit EE 51 EE 20 23 Separate Components NO 53 GENEE ee arms ne alta Saga EDER ren nie ee en 7 Setting Structure Query Ines 28 SEU estas tir de AURA Sn dau ege TEEN 4 SEAL e Le er ss a a a di a LL a a ren 4 27 Startup Task Options Men trs notes dea rare bite diia ci 45 A ONO 53 O A NS 55 Structure and Fact JEditors sise 44 Structure Edit a 27 structure E E EE 17 80 Structure Q ry OPS tte 52 Structure Search Restrictions idas 53 Structure W INGO We anne nn A aah ote ENE A ce tentes Attente tite At se 28 Structure Reaction Panel aiii 26 28 SAS nn tes san 23 Subset Selection BO intimiste nicole ee 26 31 SUBSTANCIAS i
45. on All of these are stored in discrete fields See the reference guide for more information 23 E The CrossFire Interface 3 The CrossFire Interface 3 1 The Task Function Bar 3 2 3 3 3 4 3 5 26 Structure Reaction Panel Facts Panel Subset Selection Box Combined Queries Operator 3 1 The Task Function Bar The TASK FUNCTION BAR features combo boxes and buttons that are configured according to the active application For a detailed explanation see the sections about the Query menu and the Task menu Database BSR40T Display As Substances BS The task function bar has the following controls Database BSR40T DI e The Database Selection Box allows you to choose between Beilstein databases and any Customer s CrossFire Structure and Reaction databases Display As Substances The Display Context Box Choose to display context from Substance Reaction or Citation This box will only be enabled when the Beilstein File has been selected in the database combo box HH The Database Browse Button Pressing the button starts the browser which allows you to browse through the selected database The database can be browsed and structures copied to the Commander The Update Database Button This button will only be visible and enabled when a customer database has been selected in the database combo box Pressing the button starts the browser in update mode The database can be browsed and structures
46. options have already been set these settings will be displayed in the dialog box Shortcut use the query options buttorl ptiens The following global options can be set for the search These override all analogous atom attributes for example setting free sites on all atoms in this dialog box overrides any free site atom attribute information set when drawing the query Use the reset button to go back to the system default values Implicit Free Sites Sets maximum free sites up to Default Off the maximum allowed valency on all atoms Implicit Ring Closures Allows or excludes ring Default On closures between atoms or Allowed groups with free sites 52 Multicomponent Allows or excludes Default On Compounds multicomponent structures Allowed Charges Allows or excludes charges Default On other than those explicitly Allowed drawn Radicals Allows or excludes radicals Default On other than those explicitly Allowed drawn Tautomers Switches the tautomer search Default Off on See section on tautomer searching for more information Separate Components When more than one isolated Default Off component is drawn in the Separate query this switch defines whether they are to be retrieved in the same component or in different components in the hit Stereo Search Choose between Off Default Off Absolute Relative and Racemic See section on stereo searching for more information The Exact Se
47. pidly followed was managed single handedly by F K Beilstein whose name was given to the Handbook and the Company F K Beilstein was born the son of German parents in St Petersburg in 1838 after studying chemistry in Heidelberg Munich and G ttingen he was named to the Chair of Chemistry at the Imperial Technology Institute in St Petersburg where he succeeded Mendeleev His plans to publish a handbook of organic 71 chemistry rapidly matured a task which was to occupy him fully for 40 years until his death in 1906 The immense success of the 1st edition of his handbook soon compelled him to publish a 2nd edition which appeared in the years 1885 1889 and extended to three volumes with 4 080 pages Between 1892 and 1906 the third edition appeared together with a supplementary series and a complete index for the 3rd edition These 8 volumes including the supplementary series contained critically reviewed material on all the carbon compounds then known in around 11 000 pages Even before work had been completed on the 3rd edition Beilstein realized that publication of a handbook of this type exceeded the working capacity of any one individual He thus handed over the work of further publication to the German Chemical Society which under the editorship of P Jacobson and B Prager started with the publication of the 4th edition in 1918 In 1933 F Richter took over the editorship followed by Hans G Boit who was publisher of t
48. plays the attachment numbers of atoms in the parent structure Bond Attributes Switch the following attributes on or off as required Topology Displays the topology if non default Stereo Displays stereo specific bond attributes if present Mean Bond Length Set the mean bond length by pressing the button to display the mean bond length dialog box Either enter the number directly or use the micro scrolls to increase decrease the current value 46 Reaction Attributes Switch the following attributes on or off as required Atom Mapping Displays the atom mapping if present Mapping Number Displays the mapping number if present New Bond Type Displays the new bond type if present Fonts Press this button to call up the font selection box Font Font Font Style Size CH EE e ma gt Ty Book Antiqua m Fett 24 F Bookman Old Style Zi Fett Kursiv 26 F Braggadocio 28 Select Sample _ Atom Symbol radicais a0 O Atom Attribute O Bond Attribute Component Attribute O Molecule Attribute L E Reactant 1 This dialog box allows you to set the fonts for molecule display You can independently set the following Atom Symbol Atom Attribute Bond Attribute Component Attribute Molecule Attribute The Sample window will reflect the changes as you make them 47 4 5 5 Connections Choose this option to display the Connections dialog where you can enter your connection
49. present in the Commander can either be added as new records to the database or it can overwrite existing records Delete Database Record This button will only be enabled when a customer database has been selected in the database combo box Pressing the button starts the browser in delete mode The database can be browsed and the selected structure can be deleted ES Fact Editor Pressing this button will start the Fact Editor QI Structure Editor Pressing this button will start the Structure Editor O Display This button will only be active if a hitset has been created Pressing this button will switch to Display Start Start This button will only be active if a fact query or structure is present Press the button to start the CrossFire application 27 3 2 Structure Reaction Panel The structure panel has three controls the Structure Window the structure query options button and a clear button Structure 3 2 1 Structure Window The structure editor can be activated by double clicking the window Pressing the clear button deletes the contents of the structure and query options windows 3 Windows The structure editor to be used will be that set in the preferences menu Beilstein Structure Editor If query options have been set on returning to the Commander the options will be displayed as a string in the structure window Non Beilstein Structure Editor On returning to the Commander the structure will have bee
50. ry for Path to the CrossFire server Please do not enable it if you are using a different server Capture Session If this checkbox is enabled CrossLink will write a capture file MB DMP into the Beilstein Commander working directory containing all communication input and output which has been exchanged between client Beilstein Commander and 50 server The content is a mixture of HEX and ASCII characters and should be used if you need help from the Beilstein HelpDesk so that our team can analyze any communication problem 4 5 6 Save settings on Exit When this option is active user defined settings will be saved and used again in the next session 4 5 7 Save History on Exit When this option is active the session history will be saved and be available again in the next session 51 4 6 Query menu commands The Query menu offers the following command s Structure Query Options Database Information Contexts 4 6 1 Structure Query Options Selecting this menu item causes the query option dialog box to be displayed Query Options Stereo Search x Implicit Ring Closures X Multicomponent Compounds O Relative x Charges Racemic IX Radicals F Tautomers Separate Components Extended Options Options can then be set Pressing OK closes the dialog box the selected options are then displayed as a string in the options window lf the options button is pressed when
51. search for structures facts bibliographic information or perform combined searches Identify substances via the e Beilstein Registry Number e CAS Registry Number e Substance name e Molecular formula e Structure diagram etc Find information on chemical data for e Preparations e Reactions e Isolation from natural product e Chemical derivatives Get physical property data such as e Optical Data e Mechanical properties e Multicomponent system data e Spectral properties e Thermodynamic properties etc Physiological behaviour offers information on e Biological function e ecological data 68 e toxicity and the e Use of a compound Get bibliographic information on e g e Author e journal title e CODENs e patents or e publication year 6 1 3 Application Autonom IF YOU CAN DRAW IT IF YOU CAN SYNTHESIZE IT AUTONOM 2 0 CAN NAME IT Chemists engaged in organic synthesis spend a significant amount of their time assigning systematic names to compounds Systematic chemical nomenclature is a set of rules proposed by IUPAC by which chemists communicate information about the compounds they have developed The IUPAC rules for assigning systematic names to chemical structures are complex and frequently lead to ambiguous names These difficulties can be overcome by algorithms which analyze the structural diagram of the compound and generate the systematic name automatically AUTONOM AUTOmatic NOMenclature
52. stein Commander Windows Version is able to work with Novell LAN Workplace 4 0 4 1 or any TCP IP product that supports Microsofts Windows Socket version 1 1 The Beilstein Commander Macintosh Version supports MacTCP or compatible TCP IP products REXEC or TELNET service The two radio buttons allow you to choose between REXEC and Telnet Please ask your system administrator for more details Usually Telnet services are used to connect to the server lf you enable Telnet then you might have to edit Login and Logout script files You can click on the appropriate buttons and you will get a dialog box which allows you to modify the default script files These are standard ASCII files located in the Windows directory or for Macintosh in the Beilstein Commander program directory They can be edited with typical ASCII editors in the Windows environment Macintosh users should not edit them with any Macintosh text editor but within the edit box of the Commander For a Telnet session you will require a Login Script and example is as follows Login Script 49 XFLOGIN SCR wait login send ZU ZU is for userid sends a line feed ZP is for password wait send ZC ZC is for the XFIRE server command Logout Script XFLOGOUT SCR send exit OpenVMS Alpha Server If this checkbox is enabled the Beilstein Commander can communicate with a DEC Alpha server running under OpenVMS It will also change the ent
53. tem administrator for this information 15 1 4 Working with the Beilstein Commander The Commander interface is configured automatically according to the application selected The buttons in the APPLICATION FUNCTION BAR and the options in the application menu will be activated according to the applications that you have installed Beilstein Commander BC File Edit Application Task Options Query Help EJ CrossFire Status Idle Once installed the unchanging features of the Commander consist of a Menu Bar Status bar and the Application Function Bar see below Depending on the application the TASK FUNCTION BAR and both the structure and facts panels are configured and displayed appropriately When the user switches from one application to another the contents of the Structure window and Facts window remain constant When the user selects a different application which causes a panel to disappear it would be made invisible but would be re displayed including contents on selection of the original application 16 1 4 1 The Application Function Bar DIAS 8 zg ba The APPLICATION FUNCTION BAR has assuming the maximum number of products the following controls A series of standard Windows interface buttons new open save print copy paste etc Buttons to select the current application you may choose from EJ CrossFire or e Autonom if it is installed Pressing the button for an application switches
54. that after starting the Commander the Login procedure for CrossFire will be automatically started 4 5 4 Molecule View Choose this option to display the Molecule View Dialog where you can set the display attributes for atoms bonds and reactions Define Structure and Reaction View Atom View r tom Attributes O Atom Symbol Number X Radical X Attachment Points Without L IX Mass IX H count X Attachment Number O CAs Dot IX Topology IX Free Sites X Stereo X Charge X Valency 2s Reaction Attributes ean bond ono LG x Atom Mapping Atom Number Bond Attributes X Topology IX Stereo Reaction Center x New Bond Type 45 Atom View Choose one of the following options Atom Symbol Includes C for carbon Without C Suppresses the display of C C as dot Displays a dot for the carbon atoms Atom Number Displays the number of the atom Atom attributes Switch the following options on or off as required Number Displays the number of the atom in the structure Mass Displays the abnormal mass if present Topology Displays topology if non default Charge Display the charge if non default Radical Displays the radicals if non default H count Displays min and max H counts if present Free Sites Displays the free sites if present Valency Displays the valency if non default Attachment Points Displays the attachment points of generic residues Attachment Number Dis
55. to the relevant Commander mode for that application but does not start a search or Autonom etc See the appendix for a description of the applications 17 E CrossFire plusReactions 2 CrossFire plusReactions CrossFire plusReactions is a complete chemical information system comprised of the Beilstein Database the CrossFire search and retrieval server software and the Beilstein Commander client The Beilstein Commander runs under Microsoft Windows or on an Apple Macintosh 2 1 System Design 2 2 Searching 20 2 1 System Design CrossFire plusReactions provides a new approach to handling chemical information The emphasis is on content not on form There are no artificial barriers between the different ways of viewing information CrossFire allows you to search and display chemical information the way you want whether it is in terms of Substances Structures and Properties Reactions or Citations and provides hyperlinks between the different data domains Reactions oom Substances The database contains over 30 million reports on properties of about 7 million organic compounds You can access the structures and their associated chemical physical physiological and bibliographic information Hyperlinks are available to reactions and literature references as well as to other referenced compounds such as precursors or components Reactions The database contains over 5 million reactions which are searchable
56. unication product The Beilstein Commander supports Novell LAN Workplace Version 4 0 4 1 or every other product which supports Microsoft Windows Socket definition version 1 1 Please ask your system administrator for more details If you will leave this entry empty then you have to enter this information within the Commander under Options Connections Novell LAN Workplace 4 0 4 1 lt Back Cancel Enter the desired TCP IP communications product The Beilstein Commander supports Novell LAN Workplace version 4 0 4 1 or other products that support the Microsoft Windows Socket TCP IP definition version 1 1 Please ask your system administrator for more details You can skip this and enter the information later in the Communications dialog box which is in the options menu of the Commander 1 2 8 Type of Communication Connections to the Crossfire Server EN Type of Communication Please select the type of communication If you have installed CrossFire inhouse we recommend to use REXEC services in this case the operating system Al Av on the server needs a list of allowed TCP IP addresses Please refer to the system manual for more details If you are using CrossFire through Internet we recommend to use TELNET If you choose Telnet then you may have to edit script files The syntax of the script files is described in the Beilstein Commander manual Please ask pour system administrator for more details If you will leave t
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