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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.
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.
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 File 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.
Does Clone Manager work with Windows Vista?
Clone Manager 9 (June 2007) fully supports the Windows Vista operating system. If you are using Clone Manager 8, you can download a free update (version 8.04) that modifies text and map drawing routines to improve text appearance when used with ClearType technology (enabled by default in Windows Vista).
The Get Molecule button in the Retrieve from Entrez function seems to have stopped working. How can I get molecule data into Clone Manager?
Recent changes in the Entrez web page formatting at the NCBI may be interfering with Clone Manager's ability to capture molecule data from the GenBank file shown in the built-in Clone Manager browser window. The following work-around will let you continue to import molecule data into Clone Manager.
Use the Retrieve from Entrez function as usual to find your molecule file. With the file shown on the screen in GenBank format, click the Send To control drop down arrow in the Entrez Display bar and select Text. When the plain text of the GenBank file data appears on the screen, click the Get Molecule toolbar button in the browser window toolbar to load the molecule data into Clone Manager.
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 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.
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.
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.
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?
Recent 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 (CMSuite 8.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.
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.
I'm having trouble connecting to the REBASE FTP update site since I upgraded to Service Pack 2 for Windows XP. What can I do?
If you recently upgraded to XP Service Pack 2 and you are no longer able to connect to the REBASE FTP update site, you can try to change the FTP access configuration setting in the Clone Manager program. Click Enzyme Lists, then click the REBASE Update toolbar button or select the Update tab (version 8). Click the FTP Access Configuration button (lower right) and then check the box for Firewall Passive Mode. Try to update your enzyme list again using the FTP option. If you are still not successful, you may want to consider selecting the alternate option (getting the REBASE file from the web or having it sent to you automatically by email). Click the Help button on the Update screen for detailed instructions.
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 or click on the Wipe All Sites toolbar button (version 8) to remove all primer sites. Save the file again so the deleted sites will be permanently removed.
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.
How can I get a GenBank file from NCBI?
You can use the built-in web browser interface and your internet connection to get a sequence file from NCBI. Click File, Retrieve from Entrez. In the search bar, leave the control set to Nucleotide if you are looking for a DNA molecule. In the Search For box, enter the locus name, accession number or descriptive information. Click the Go button. When the results are listed, find the file you want and click on the accession number link to view the contents of this file. If the molecule data is in standard GenBank format, you can click the Get Molecule button on the browser window toolbar to import the molecule for immediate use.
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 Manger. (Note: complex features consisting of joins and orders not currently supported.)
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 Manger program.
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.
When I double-click on a Clone Manager file (*.cm5) in Explorer, the Clone Manager program doesn't automatically start and load this molecule. What do I need to do to get this working?
You need to check the file association for the Sci Ed Molecule (*.cm5) file type. In Explorer, click Tools, Folder Options, and select the File Types tab. Scroll down to the cm5 extension (Sci Ed Molecule file type). Click the Advanced button, select (highlight) Open, click the Edit button and then check the two entries described below.
For Clone Manager version 8 or 9:
Step 1: For the field Application Used to Perform Action, make sure the entry matches one of the following samples (substitute 8 for 9 if you are using Clone Manager 8):
"C:\Program Files\SciEd9\CMSuite9.exe" /dde or
"C:\Program Files\SciEd9\Clone9.exe" /dde
Step 2: A checkmark should appear in the checkbox Use DDE and the DDE Message should be [open("%1")]
Step 3: In the lower area of the same dialog box, for the field Application, make sure the entry matches the following sample:
CMSuite9 or
Clone9
For Clone Manager 7 Editions:
Step 1: For the field Application Used to Perform Action, make sure the entry matches one of the following samples:
"C:\Program Files\SciEd7\SECentral.exe" /dde or
C:\PROGRA~1\SciEd7\SECENTR~1.EXE /dde
Step 2: A checkmark should appear in the checkbox Use DDE and the DDE Message should be [open("%1")]
Step 3: In the lower area of the same dialog box, for the field Application, make sure the entry matches the following sample:
SECent~1
If you did not install in the default directory, Program Files\SciEd9, SciEd8, or SciEd7 should be replaced by your installation directory. Older versions of the program installed in the directory C:\SECentral. If you are using Windows 98, you can check file associations using the View menu, Folder Options.