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Sci-Ed Software
Software for the Molecular Biologist

Frequently Asked Questions

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Does Clone Manager work with Windows 10?

The latest version of Clone Manager 9 (version 9.5) fully supports and is fully tested on the Windows 10, Windows 8, and Windows 7 operating systems. If you are using Clone Manager 9, you can download a free incremental update to bring your software to the latest version.

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How do I use the new Clone Manager Help system?

In the latest version of Clone Manager, small context-sensitive Help buttons are no longer used. Instead, click on the main toolbar Help button (far right) to open the Help system. Click on a category in the list provided to navigate to information within that category. For more specific help questions, click the Show button in the Help window toolbar to open the search pane on the left. Type in a keyword related to the help needed and click the List topics button. Then select the topic to display and click the Display button. Click the Hide button to close the search pane.

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How can I print topics from the Clone Manager Help system?

Some users are finding they are unable to print full pages from the help files -- the end of each line is clipped off at the right side. This may affect the Clone Manager Help system files, as well as the Quick Tours or Tutorial files. These files are printed by the Help engine using the Internet Explorer print function. You may find that increasing the right margin setting will help. To change the right margin, open Internet Explorer and click Settings, Print, Page Setup. You can try changing the Right Margin setting from 0.75" to 1.5".

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What happened to my Work Boxes?

The current version of Clone Manager (ver 9.5) now uses the updated Windows File, Open and File, Save dialog boxes. This adds a navigation pane and search box, but eliminates the custom buttons for Work Boxes and Add Work Box. If you previously used Work Boxes to store shortcuts to the locations you use most often, you can use Windows Favorites (Windows 7 or 8) or Quick Access (Windows 10) in much the same way. To store your molecule file locations:

In Windows 7 or 8, using File Explorer, navigate to the folder you want to select so that it appears as the last item in the address bar near the top of the window. Without changing this selected location, use the mouse to scroll the navigation pane (at the left) until you can see the Favorites group. Right-click on Favorites and select the option Add Current Location to Favorites.

In Windows 10, navigate to a folder that you want to show up in Quick Access and right-click on the folder and select Pin to Quick Access. You can do this in File Explorer on in the Clone Manager File, Open or File, Save dialog boxes.

With your folder names stored in Favorites or Quick Access, your preferred locations are still easy to access when opening or saving files in Clone Manager.

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How can I paste a molecule into the new version of Clone Manager?

If you are accustomed to using the Paste Molecule button in the old File, Open dialog box in Clone Manager to load a molecule directly from the clipboard, you can use File, Import from Clipboard to accomplish the same task.

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My GenBank file has features with the Regulatory key. How can I read these into Clone Manager?

Clone Manager ver 9.5 has a new list of feature keys supported in GenBank/EMBL file formats and new support for mandatory qualifiers. Modify your list of feature keys that should be imported when you open a file in standard GenBank or EMBL format. Click File, Preferences, then click the Import Features tab. Click the Add button to include a new feature key in the designated features list. When the dialog box appears, select the Regulatory key from the list. Then select the Draw as Type to tell the program how to display this feature in Clone Manager.

If you select Region as the Draw as Type for Regulatory features, you will be able to see the features on your map and on the features table. You can later change small regulatory features to Labels or less important ones to Info Only if your map becomes cluttered. To change the drawing style for an individual feature, select the feature on the Features tab and click the Edit toolbar button.

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The function Browse Entrez and Search can no longer get to the Entrez web site. What can I do to update the URL so Clone Manager can find this site?

The Clone Manager function Browse Entrez and Search accesses the Entrez web site using a URL that is stored in the Clone Manager Program. This URL has changed and you will need to update the Entrez URL in Clone Manager to continue to access this site.

In Clone Manager, click File, Browse Entrez and Search (you will not be able to get to the Entrez web site at this time). In the web browser window in Clone Manager, click the toolbar button Properties -- Internet Access (last on right). You need to add 4 characters to the Entrez URL shown. Put the cursor just after the text "ncbi" and type in ".nlm" (making sure there is a dot between ncbi and nlm). Click OK to save your change. Close the web browser window and start again by clicking File, Browse Entrez and Search to reach the Entrez web site.

The complete URL should read: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide.

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When I use Clone Manager, NCBI web applications report that my browser is no longer supported. What can I do to continue to use Entrez or BLAST with Clone Manager?

The web browser control built into Clone Manager is set to run in IE7 compatibility mode by default. You can run a small utility program (CM Embedded Browser Update), found in the downloads section of our web site, to make a simple registry setting that will change the IE compatibility mode to IE9 for Clone Manager. This will permit you to continue to use the BLAST search and NCBI Entrez system functions without concern about loss of browser support.

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Can Clone Manager read in GenBank features with joins?

The latest versions of Clone Manager (ver 9.2 or later) adds support for GenBank joins (segmented features). If you routinely retrieve GenBank files that contain joins, you will want to change your import filter at this time. (If you do not change the import filter settings, Clone Manager will read in the CDS features with joins as well as the exons for each feature, resulting in maps with apparent duplicate features.) To change your import filter, click File | Preferences | Import Features. Select the feature key Exon, click the Edit button, and change the Draw As style from Gene to Info only.

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How can I see the basepair positions for join segments?

When viewing the Features display in the molecule viewer window, you can move the mouse over the small symbol to the left of the feature name. The cursor charges to a rectangle shape and you can click with this cursor to open a popup box that shows the location (basepair positions) for the feature segments and feature qualifiers. Click outside the popup box to dismiss. When viewing the Map, click on the feature to select (yellow highlight shows extent of feature) and then click the Properties toolbar button to see the join basepair position information. Click on any enzyme site to reset the right panel to the enzyme site list.

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Can I expand my workgroup license for Clone Manager to allow more installations?

Yes, you can add seats (installations) to your existing workgroup license for Clone Manager. Increments of 4 or 8 seats can be added as your group increases in size. Please contact us for more information.

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Does my Clone Manager license expire on a specific date?

No, your Clone Manager license does not expire. You can continue to use your Clone Manager software for as long as it is useful to you. Technical support is available by email or telephone without additional cost.

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Can the Clone Manager program read molecule files prepared by Vector NTI software?

Yes, Clone Manager can read individual molecule files generated by the Vector NTI program in a GenBank-like format. In Clone Manager, use the filter settings in File | Preferences | Import Features to tell Clone Manager which feature keys to import for molecules in GenBank formats.

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The Get Molecule button in the Retrieve from Entrez function seems to have stopped working. How can I get molecule data into Clone Manager?

If you are using Clone Manager 9, you can download a software patch that will update your program to the latest version (version 9.2 or later) which includes a new Retrieve from Entrez (E-utils) module. With this new module, you can retrieve sequence files directly from the NCBI Entrez file system without using the Entrez web page interface.

If you are using earlier versions of Clone Manager, you can use the Entrez web site search function to find your molecule file. With the file shown on the screen in GenBank format, click the small arrow next to the Send link (right margin, above file header). In the dropdown menu, set the options for Complete Record, destination File, format GenBank and then click the Create File button to download and then save the file to your computer, giving the file an appropriate name and location. You can then use File, Open to bring this saved file into Clone Manager.

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I just downloaded a new Clone Manager help file and it doesn't seem to be working. What do I need to do?

Windows security updates can enable a block that will prevent the display of compiled help (*.chm) files you download from the internet. You may need to unblock this help file before use. In Windows Explorer, right-click on the Clone Manager help file you just downloaded and select Properties from the menu. Click the Unblock button (lower right) on the General page and then click Apply. If you do not see the Unblock button, you may need to log on as administrator.

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How can I export the sequence of a primer I've just designed?

With the primer open in the primer viewer window, click the toolbar button Export Primer Sequence. Select the option to export the primer sequence to a disk file or to copy the primer sequence to the Windows clipboard so that you can paste the primer sequence into another application. If your primer is a part of a primer collection, just open the Primer List and select (highlight) this primer in your collection. Click the toolbar button Export Primer Sequence and select to export to a disk file or copy to the clipboard.

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What's the quickest way to create a PCR amplified product?

In Clone Manager Professional, click Primer, Create Product to create a new DNA molecule that is the amplified product of a PCR-type reaction using two primers and a DNA molecule that you specify. Select the molecule and then select the two primers and click OK. If an amplified product can be produced, the results screen will show the product size, GC content, melting temperature and annealing temperature. You can select to use the new molecule now, save it to disk for later user or export the product sequence as a text file.

If an amplified product can not be produced using standard PCR reaction conditions, you can opt to relax these conditions and try again. If more than one product is possible, you can opt to open the Analyze Mix Wizard to view the more detailed results and then use the Create Product toolbar button in the results section to create the product of interest.

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How can I import a primer collection?

In Clone Manager Professional, you can use the Import option to create a primer collection by reading in primer data contained in a tab-delimited text file prepared in another application. Open the Primer List and click My Collections. Click the first toolbar button (Folder Options) and select Import. In the import module, select the text format file that contains your primer data. Follow the screen prompts to identify the data in each column and the first row to start importing.

Preparing data for import -- If your primer data is in an Excel worksheet, for example, you can open the worksheet in Excel and use Save As... to save your file in Text (tab delimited) format.

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I'm getting an error message when I try to access Help in the network version of Clone Manager. How can I read application Help topics?

Security updates for Windows operating systems have introduced new security features that interfere with the operation of compiled HTML help files (*.chm) accessed across a network. "Action Canceled" or "Page cannot be displayed" error messages will appear in place of help topics in the Help viewer window.

Recent versions of Clone Manager (ver 8 or 9) can access HTML Help files on local computers, in place of help files in the network program installation directory. Ask your network administrator to make the compiled help file CMSuite9.chm or Clone9.chm (CMSuite8.chm or Clone8.chm for version 8 software) available for you to copy to your home directory. (In Clone Manager, click File, Preferences, Basic to identify the location of your home directory, if needed.) Once the help file is placed in your home directory, you can start Clone Manager and use the Help buttons and Help menu items within the Clone Manager program.

You can also download a new help file from this web site, if needed. In the Downloads section, click on Clone Manager User Documents and select the appropriate help file. You may need to unblock this file after download. Please follows the instructions on the download page.

For earlier versions of Clone Manager, you can ask your network administrator to make a copy of the program help file SECentral.chm available to copy to your home directory. You can directly access this file by double-clicking on this file in Explorer and using the Contents, Index, or Search features to locate the help information needed. 

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How can I remove primer sites previously saved as part of my molecule file?

When you add primer sites to a molecule map, information about the primer site is embedded in the cm5 file, just like enzyme site information. You can remove these sites, as needed. Open the molecule file so the map is visible in the molecule viewer window. Click the Enzyme Sites/Primer sites toolbar button so primer sites are displayed on the map. To remove one primer site, click on the primer site and then use the Delete Site toolbar button to remove this site. To remove all primer sites, click the More Actions toolbar button and then select Wipe All Primer Sites to remove all primer sites. Save the file again so the deleted sites will be permanently removed.

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What should I do to get basepair numbers for enzyme sites to print on my graphic map?

With the map visible on the screen, click the Format Map toolbar button (Map Print Options in version 8), click the Sites tab, and set the checkbox Display Bp Numbers. This setting will be remembered until you change it again. Basepair numbers will appear on the printed maps, but do not appear on the small on-screen maps. When working with the screen map, hover the mouse over an enzyme site or use the list of enzyme sites at the right to identify basepair positions. Click on the column headers to sort the list by enzyme name or basepair position.

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How can I read in more/different features when importing a GenBank file?

If you are using a recent version of Clone Manager, you can identify the feature keys that should be imported when you open a file in standard GenBank or EMBL format. Just click File, Preferences, then the Import Features tab. Click the Add button to include a new feature key on the import list and select the Draw As feature type to tell the program how to display this feature in Clone Manager. (Note: complex features consisting of joins not supported in versions earlier than 9.2.)

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What's the easiest way to prepare a group of files to share with others?

You can use the multiple file conversion utility to convert a batch of files in Clone Manager format into the standard GenBank format, all in one easy step. Click File, Multiple File Conversion to get started. You can identify the files or folders of files to convert and specify the location (folder) where you want the program to save the files, and you can select the format to convert to. Files converted to the Compact GenBank format will contain essential molecule data in a format that is consistent with the standard GenBank file format and can be shared with others who do not use the Clone Manager program.

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How can I copy my sequence to the clipboard in FASTA format?

With the molecule open in the molecule viewer window, click Operations, Export Molecule Data. Set the option to FASTA in the upper section and set the option to Copy to the Clipboard in the lower section. Click OK. Your sequence data is now on the clipboard in FASTA format, ready to paste into another application. FASTA is a very simple format that is the required format for many sequence analysis programs, especially over the web.

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When I double-click on a Clone Manager file (*.cm5) in Windows, the Clone Manager program doesn't automatically start and load this molecule. What do I need to do to get this working?

In current versions of Windows, start Explorer and open a folder that contains a Clone Manager file (*.cm5). Right-click on the file and point to Open With. If Clone Manager appears on the list of programs, you can select it. Otherwise, select Look for another app on this PC and then find the Clone Manager program.  

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