Quick Reference Guide

Transcription

1 Quick Reference Guide MDL CrossFire by MDL Information Systems GmbH, Frankfurt am Main, Germany Beilstein Database: Copyright , Beilstein-Institut zur Förderung der Chemischen Wissenschaften licensed to Beilstein Chemiedaten und Software GmbH and MDL Information Systems GmbH. Gmelin Database: Copyright , Gesellschaft Deutscher Chemiker, licensed to MDL Information Systems GmbH; , Gmelin Institut fuer Anorganische Chemie und Grenzgebiete der Max-Planck-Gesellschaft zur Förderung der Wissenschaften. All rights reserved.

2 1. Starting MDL CrossFire Database Selection Search Options Search Using the Text Search Using the Easy Data Search (EDS) Using the Fact Editor Field Name Field Value Operators Special Hot Keys (Fact Editor) Using the Structure Editor Drawing/Editing Atoms Drawing/Editing Bonds Drawing Rings Template Files Functional Groups Setting Atom Attributes (individual attributes) Structure Query Options (global attributes) Creating User-defined Generic Groups Creating User-defined Atom Lists Generics: Tips & Tricks Reaction Attributes Further Reaction Attributes (optional) Special Hot Keys (Structure Editor) Running structure or reaction searches Combined search Results Query Result AutoSearch Combined Search Display Hits Main Screen Tree View Function of Buttons Print and Export Printing Export and Report One Click Reporting Reference Reporting Default Settings Getting Help

3 1. Starting MDL CrossFire To start Commander from whichever platform you are using: double click the icon on your desktop or select in the Windows start menu Programs: MDL CrossFire Commander V6 Text Search Fact Search Structure Window From the Commander click the Button or select from Menu Application: CrossFire Fill in the login-box as required. Click the checkbox if you want your user ID and your password to be saved. You will not be asked for them again after clicking the box. (Do not do this if you are using a networked installation of CrossFire or if you share a computer with others.) 3

4 1.1 Database Selection Select Database: These Listboxes select the Databases you will be searching in. You may select one or more databases by using the checkboxes. In the case of only one database being checked, the currently active database is displayed bold. The abbreviation informs you about which version of the database is available. 1.2 Search Options Text Search: Type in keywords, one or more, to be searched. Example: diabetes Structure Editor: Draw and search for a structure as a molecular species or as component of a reaction. Fact Search: Enter a Factual Query in the Text field, e.g. bp>100 or au=maier Use the Fact Editor (Table), or the Easy Data Search (EDS) predefined forms to conduct a search for specific facts. 2. Search 2.1 Using the Text Search Select the level of your search: The level determines the indexes which will be browsed with the text you enter in the query field. 4

5 Type your Keywords into the field, you can enter one or more words: Examples: Malaria or Antimalaria, Aldol Condensation, Cancer Treatment, Effect of Melatonin on sleep disorder. We recommend to limit the search term to 5-6 words maximum. Submit the query by carriage return or F7 or press Start Search. If more than one word is typed an AutoSearch search will be performed. If you have selected in bibliographic fields only the Basic Index Citations will be searched. The result will be a list of references. If you have selected All Text Fields you will be prompted to determine the context you want to apply for your search. Choose Substances, Reactions or Citations to determine the context you want to be searched. The number of occurrences is shown for each word in the column of the context for each word separately. Choose the context you want by clicking the header. Important Notes for the use of the Text Search: CrossFire reads the input with right truncation If more than one word is entered into the text search field the operators near, proximity, and and are used in AutoSearch (see Section 3.2) Click the Options button to change the default settings: - For more sophisticated searches Boolean operators can be used. 5

6 If a query-like text is introduced, for the example bp=100 the user will be prompted: If Yes is chosen Commander translates the input into the Fact Editor Field. Please press Start Search again to submit your Query. If No is chosen Commander will execute the entered text as a text search. 2.2 Using the Easy Data Search (EDS) The upper box of the EDS is for expert searching using the Commander s operators and field names: The lower box enables you to use predefined forms to start a factual search. Double Click or select and click Open to enter data: 6

7 2.3 Using the Fact Editor Field Name Fill in the code of the field you want to search for: Type the codes directly into the field or Pick them from the data structure, which can be opened by the Select the appropriate field code by double click. button or F2-key. You can search for a special field name by using the Find button and typing the name of the desired property or attribute in the Look for... dialog box Field Value Fill in the search term(s) (e. g. values, keywords, phrases) you are looking for: You can fill in ranges or use "<" and ">" operators when looking for numerical values You can use truncation when you look for text ("*" for any number of letters, "?" for exactly one letter); you can truncate at the beginning, middle or end of the word You can see a list of field values (index of all entries in this field) by the -button or F2- key Operators Use the logical operators proximity, and, not, or to combine fact queries: Proximity means that the search terms have to appear in the same field (see manual for details) Hierarchical order of the operators: proximity > and, not > or If you want to combine fact queries in another order use parentheses The parentheses appear as a "+" in front of the operator in the fact editor table (but within the fact editor window in the commander they are shown as parentheses). o If you use the "expand"-function by clicking the -button or F2-key, make sure the cursor is placed in the field you want to expand o The F3-key opens a window where you can type in the query 7

8 2.3.5 Special Hot Keys (Fact Editor) Ctrl + X Cut Query cuts the whole fact query Ctrl + C Copy Query copies the whole fact query Shift + Del Cut Selection cuts the field selected previously Ctrl + Ins Copy Selection copies the field selected previously Ctrl + V Paste caution: pasting a whole query will delete the lines written previously Ctrl + D Delete All deletes the whole fact query Ctrl + L or Delete Line deletes the single fact query line the cursor is placed in 2.4 Using the Structure Editor Two Structure Editors are available in this version: ISIS/Draw 2.4 (default) and the MDL CrossFire Structure Editor. You can select the tool of your choice at Menu Options: Structure Editors The instructions here describe use of the MDL CrossFire Structure Editor. Press Drawing tool. or double click in the Structure Editor Window to open the Draw the structure or fragment, or the reaction or parts of a reaction you want to search for. Menu Function Bar Standard Bar T o o l b o x Windows-type Menu Atom, bond and template buttons Short-cut buttons for some features of the Menu Toolbox Keys: edit select lasso erase rotate magnify reduce Drawing/Editing Atoms Activate the edit tool and choose one of the atom buttons (Function Bar) Draw the structure with the currently active atom (and bond) Click on an already existing atom to open the atom dialog box to change it (edit mode) Atom buttons Further choice of atoms as well as generic groups: 8

9 Atoms: H, F, Cl, Br Atom lists: A (any atom), M (any metal), X (any halogen) Elements...: Opens periodic table from which you can choose any atom Generics...: Opens table of generics from which you can choose predefined atom lists, predefined generic groups, user-defined atom lists A n and user-defined generic groups G n (see below) Drawing/Editing Bonds Activate the edit tool and choose one of the bond buttons Draw the structure with the currently active bond (and atom) Click on an already existing bond to open the bond dialog box to change it (edit mode) Bond buttons: single, double, triple Further choice of bonds: Drawing steric bonds (up, down ) for stereogenic atoms Defining Z/E-isomers (double steric ) for double bonds Allowing groups of bonds (any, double/triple, steric unknown ) Selecting user-defined bonds o Stereo information will only be taken into account in a search if the Structure Query Options have been set to absolute or relative stereo search Drawing Rings Clicking one of the window -buttons pastes the corresponding ring into the structure Annelated rings: drag the square in the middle of the bond to the bond you want to fuse Spiro-fused compounds: drag the square at the atom to merge it to another atom Template Files Template files contain pre-defined molecules, substructures as well as functional groups 1. Choose from the menu File; Template... and select a template file 2. You can view the contents by using the browse button, but you cannot pick a molecule and paste it in the structure window from this menu 3. Use the template button to browse the chosen template file and select the desired (sub)structure by double click 9

10 2.4.5 Functional Groups Make sure you follow the structure conventions used in the Beilstein database (see manual); if you are not sure how to draw a functional group choose it from the template file "residue.bsd" Setting Atom Attributes (individual attributes) On clicking at an atom (edit mode) an atom dialog box appears; further atom specifications such as number of free sites, charges, radicals, exact mass, set attachment points etc. can be defined. You can allow or exclude isotopes (apart from D and T) and set or delete maximum free sites after selecting the atom(s) within the menu Query Structure Query Options (global attributes) Options which will be taken into account for the whole structure query can be set in the Structure Editor from the menu Query or in the Commander by opening the dialog box with the Options...-button (hereby you can use those options for drawings imported from other structure editors such as ISIS) These options define if stereochemistry is taken into account and if tautomers etc. are allowed Creating User-defined Generic Groups 1. Choose from the atom box : Generics..., and select a number 2. Place the G n -atom symbol in the structure you are drawing 3. Draw the desired fragments for the generic group and select those fragments 4. Press the -button and choose the number of the generic group For fragments containing more than one atom you have to set attachment points: 1. Click at that atom of the fragment by which it is to be attached to the parent structure (edit mode) 2. Press the Attachments... button in the atom dialog box 3. Click the appropriate number(s) 4. While defining a generic group the attachment points in the parent structure are displayed; otherwise they are not visible To define a frequency click at the [Gn] symbol marking the generic group (edit mode) (see manual for details) Creating User-defined Atom Lists 1. Choose from the atom menu : Generics... and select a number 2. Place the A n -atom symbol in the structure you are drawing 3. Press the -button and select the number of the atom group 4. Choose the desired atoms from the periodic table appearing on the screen 10

11 Generics: Tips & Tricks You can always edit and delete structures within a G n -group or add further structures To see the definitions of the pre-defined generic groups listed in the table use the help button and select "pre-defined generic groups" The pre-defined generic groups except G and G* can only have one bond to the parent structure whereas user-defined generic groups and atom lists can have more than one bond Reaction Attributes First draw the molecules in the structure edit mode, then switch to reaction edit mode by using the button or choose from the menu Editmode: Reaction. The function bar changes to allow reaction role setting and the select mode is activated. Select a molecule and press the / buttons to define its role as reactant or product You can define one or more reactants and one or more products You can also define only reactant(s) or product(s), so-called "half-reactions" Further Reaction Attributes (optional) Mapping: links corresponding atoms in the reactant(s) and product(s) respectively by drawing a dashed line between them in the same way a chemical bond usually is drawn Reaction centre: defines that a reaction must take place (or must not take place) at a particular atom Bond change: defines if and how a particular bond is altered during the reaction Those reaction attributes are set in the edit mode by clicking at the atom or bond (reaction mode) Use the Use the -button to delete product and reactant definitions -button to delete all the mappings Change the structure of the molecules taking part in the reaction by switching to the structure edit mode with the button or selecting Editmode: Structure from the menu. 11

12 Special Hot Keys (Structure Editor) Ctrl + D delete all N reset average bond length to standard Ctrl + E copy all F fit structure into whole window Ctrl + A select all C centre structure within the window S switch to structure edit mode + scale up structure R switch to reaction edit mode scale down structure Shift + Click (edit mode): replaces an existing atom or bond by the one currently active Shift + Drag (select mode): copies the selected structure Running structure or reaction searches Go back to Commander by clicking on NB. Searches can only be started from the Commander. Press F7 or use the Start Search button. 2.5 Combined search MDL CrossFire Commander V6 enables simultaneous searching of the Beilstein and Gmelin databases. Click the checkbox of each Database to select or deselect it. If more than one Database is selected the EDS forms are not active as they are specific for each individual database. Therefore a multiple search can only be carried out with a structure and/or text as a query. The results from each database will be displayed in parallel, in separate windows on a single screen, since different fields are connected with the content of each database. 3. Results Depending on the search option you used, Commander displays the result as described below. You always find a Button or that enables you to rework your query when the result is insufficient. 12

13 3.1 Query Result The result of the search is displayed: Number of items found Hitset number 3.2 AutoSearch If AutoSearch is enabled Commander will refine the structure or the text entered as the query. AutoSearch can be enabled/disabled in the Menu Query. AutoSearch can be stopped after Commander found the first Hit. If this option is not selected Commander will use all possible variations of the query. The result is displayed, including information on the variation of the query 13

14 Hitset number Select box Number of hits Query used in the search Use the check boxes to select one or more hitsets for display. 3.3 Combined Search The result of a search in multiple Databases (combined search) is displayed in the same fashion. Use the check boxes to select the Hitsets for display. 4. Display Hits From the display of the query result click or to open Display Hits. 14

15 Main Display Tree View 4.1 Main Screen The main screen starts on default with the Short Display of the results. Depending on the query the hits are automatically displayed as Structures BRN Molecular Formula Note: If these are displayed in red: Biological Data are available! 15

16 Reactions Citations Double click the item you want to see or select it and click for details. 16

17 4.2 Tree View On the left side of the screen the tree view provides fast navigation through saved Hitsets and Session Hitsets. Select the Hitset you want to see and the main screen switches to Short Display. Click on to drill down to details, ultimately to field level. Click on these details to display them in the main screen. The Tree View can be used to change the context of a Hitset from the original to Citations, Reactions or Substances. Do a right click onto the Hitset and select Convert... Choose the extent of the conversion and the context, which you want to put the hitset in (here converting a hitset in Citation Context to Substances or Reactions) 17

18 4.3 Function of Buttons The buttons in the Display Hits window have the following functions: Export selected data. Select from predefined Export definition or create your own (choose Settings in Drop down menu) Go to First / Previous / Next / Last hit of the selected hitset Go to Commander. You can also press F7 Switch on/off Display of structure in Main Screen Copy structure to Structure Editor (opens the Editor) Toggle on/off Short Display Click to view the search query used Define the view on the data: - Identification (Substance/Reaction/Reference and Field Availability List) - All Fields - Hit Only (Substance/ Reaction/Reference and Abstract) - Define your own View File To define your own view click on the View button and select Define. In the window which opens you will find your saved views. Select the View File and press Apply. Press Edit if you want to Edit the View File. Press Remove if you want to delete the View File. 18

19 To create a new View File press New Select the Field you want to apply in the left screen and press Copy to add it to the View File. Repeat until all the desired fields have been copied to the right hand side of the screen. 5. Print and Export 5.1 Printing Choose File:Print or [CTRL+P] or press and select the range you want to Print (Current Hit; Hit 1 X). Select your options and the layout and press OK. Commander will print the View of the Main Screen on your standard printer. If you want to print only some facts from a hit, mark the desired detail at the check box on the top right Select one or more facts and start printing as described above. 19

20 5.2 Export and Report All information in your hits can be exported to other applications such as Microsoft Word, Microsoft Excel or your preferred HTML-Browser. You can export full hitsets, a range of hits or extract information from a hit. Select the information and use the menu File:Export or the Button format for export. to define the You will be prompted for the settings of your export. Choose one of the predefined settings for Export in various formats or Settings.. to define your own. The selected export destination will be opened with the export file when finished One Click Reporting In the Full Display view, each field is equipped with a Title Bar on top that is used to select factual data (see 4.1) and to perform One-Click-Reporting : Button One-Click-Reporting Clicking on the button or a right mouse click anywhere inside the fact opens a menu: The selected fact will be added at the end of the defined report (see first row). Use the options to operate the Report function. To view the report select Open the Report Reference Reporting MDL Commander V6 offers the possibility to export reference lists in various ways: 20

21 If a hit is in Substance context the last item of the tree of the substance is Reference. Select it and a deduplicated list of all references for this hit are displayed in the Main display. You can report, export and print it in the way described earlier. If you have a hitset in citation context you find a predefined export setting (see Chapter 5.2) for export of references to Endnote, Procite or other reference managing applications. From each hitset you can export a list of all references as HTML. You will find a predefined export setting if you click the Export Button. A framed document is produced, in which you find the compounds you exported on the left side, select them by clicking on the hit number. The facts of this hit will be displayed in the right frame. On top of the frame you find a hyperlink Reference List. Clicking this link leads to a deduplicated list of all the references of the exported compounds. 6. Default Settings Commander General: Application: AutoSearch Stop AutoSearch after 1 st Hit Save Password Startup Task Expert Mode Save Settings on Exit Save History on Exit Automatic Context Selection Show Box before a multiple Database Search Show Startup Screen No Application No Application Off Structure: Structure Editor Options: Search Stereo Free Sites: hetero atoms Free Sites: all atoms Allow addl. Fragments Allow isotopes Allow charges Allow radicals Allow additional rings Define Structure and Reaction View: Mean Bond Length MDL ISIS Draw As structure Off 12 mm Atom View 21

22 Atom Symbol Without C C as Dot Atom Number Atom Attributes Number Mass Topology Charge Radical H-Count Free Sites Valency Attachement Points Attachement Number Stereo Bond Attributes Topology Stereo Site Number Reaction Attributes Atom Mapping Reaction Center New Bond Type Text Search: Text Search Options: Words are close to each other Words are in the same fact Words are in the same document Use right truncation Use left truncation In all text fields Display Hits Short View Tree View Open Hitset in Short Display View Save Settings on Exit Include Structures Include Field Availability Selected Hits only Status Bar All Enable 22

23 7. Getting Help MIMAS users should contact the MIMAS Helpdesk: Phone: Further information about MDL products and services can be obtained from MDL Information Systems GmbH: Theodor-Heuss-Allee 108 D Frankfurt Germany UK Customer Support: Phone: Fax: Ukhotline@mdl.com MDL Headquarters: Catalina Street San Leandro, CA USA Phone: (toll free) (non US) Fax: (toll free) info@mdl.com 23