gene construction kit
Return to the Gene Construction Kit Product Page- Is there a way to pick some enzymes from the lists available in GCK and make my own list? That way I can just go to "My list" and add all when marking restriction enzyme sites in my constructs.
- I have a plasmid in which I can't 'Mark Sites' - the menu item is grayed out - what's going on?
- How do I search a construct for a known sequence of DNA from another source?
- I'm having difficulties opening Mac GCK files on a Windows system. I thought the files could be transferred between operating systems?
- I've followed your instructions for adding file extensions, and am still unable to open GCK Mac files on my Windows PC - what now?
- What about transferring GCK files from Windows to Mac systems - are any modifications required?
- I used to be able to "Mark Sites" in my construct - now when I select this feature I get an error message saying "No enzyme list files were found in the GCK Data folder". Where did they go - and how do I get them back?
- How can I identify restriction enzymes that will only cut a segment of DNA at a single location - i.e. "unique cutters"?
- I just upgraded my installation of Gene Construction Kit on a Windows machine, and when trying to launch, I get a "Error code -199" - what's going on?
- My system recently crashed and now when I try to launch GCK I get a "not able to locate a valid license file" error. What can I do?
- After installing GCK from the CD on my Windows system, I get the error message, "We are unable to locate a valid license for this software at your location" when I first try to run it. Any suggestions?
Chapter 4 in the GCK manual describes what we call "List Windows". These are the files for storing enzymes used in the "Mark Sites" and "List Sites" feature available in the Construct menu.
What you'll need to do is first create a new List window by selecting "New" from the File menu, and then choosing the "List" radio button. Name it something like "My Enzymes" - (or whatever you prefer)
Now, you can open up the enzyme list files that are included with GCK from which you want to move enzymes into your new file - just select "Open" from the File menu, look in the "GCK Data" folder, and click on the "List" radio button (this will display only those enzyme list files).
Now - the easy part .... simply highlight the enzymes you are most interested in from the GCK file by single clicking on the enzyme name, and then "Copy" and "Paste" them into your new list file. Use the Shortcut Keys - [Ctrl/Command+C ; Ctrl/Command+V] - for the copy/paste commands - as sometimes the clipboard gets confused when working in these types of windows.
Note - To speed up the process, you can select multiple enzymes at a time by holding down the Ctrl/Command key while selecting them - then simply Ctrl/Command+C; Ctrl/Command+V into your new List file.
Once you have moved all your favorite enzymes into your new list file, simply save it in the "GCK Data" folder, and it will be available in the drop down menu next time you choose to 'Mark Sites'.
Back to Top 2. I have a plasmid in which I can't 'Mark Sites' - the menu item is grayed out - what's going on:Most likely the option to 'Hide Sites' was selected (perhaps inadvertently) from the Construct -> Display menu. Once you've chosen to 'Hide Sites', GCK will not allow you to 'Mark' new sites because they would essentially be invisible to you - causing confusion (and sometimes rage)!
The fix is simply to choose Construct -> Display -> Show Sites. Now the 'Mark Sites' menu option should again be available (and any previously marked sites should appear on your construct).
The results will be the same for the other options in the Display menu: Show / Hide Regions, Frames, Sites, Introns, Primers, Comments, and Generations (if applicable for the active construct file). If the feature is set to 'Hide' then its menu option will not be available.
Back to Top 3. How do I search a construct for a known sequence of DNA from another source:Page 3-23 in the current GCK manual describes the process for "Finding a Sequence".
Begin by activating the window of the construct in question and then selecting "Find Sequence" from the Construct Menu. From here you basically have two options:
For short DNA segments, simply type in the bases you wish to search for then select 'Search'.
For larger stretches - you can use the Shortcut Keys - [Ctrl/Command+C ; Ctrl/Command+V] - for the copy/paste commands - to copy the text from the known segment, and pasting into the Search dialog.
GCK will then search the sequence starting from the cursor and will highlight the next occurrence of that sequence in the sequence listing itself.
Back to Top 4. I'm having difficulties opening Mac GCK files on a Windows system. I thought the files could be transferred between operating systems:Yes - GCK Mac files can be opened using the Windows version of GCK, and vice versa. The file formats are really the same - the only difference is that Windows operating systems require the use of file extensions (the 3 letters after the "." at the end of files) - to determine what type of application to associate the file with.
As a result Mac GCK files will need to have the following 3 letter extensions added to their filenames - prior to moving them to the Windows machine - based upon the type of GCK document as outlined below:
GCK Construct Files (default graphic view): add ".gcc" to the filename
GCK Construct Files (default sequence view): add ".gcs" to the filename
GCK Illustration Files: add ".gci" to the filename
GCK Gel Files: add ".gel" to the filename
GCK List Files: add ".gcl" to the filename
As an alternative to manually adding file extensions to each GCK file type, we have written a Macintosh application that converts Mac GCK files to Windows versions by automatically adding the appropriate file extension. This application is available FREE via download.
Just click on the Macintosh --> Windows GCK2 File Convertor to begin the download. Using this application on a Macintosh machine, you can convert an entire folder of GCK Mac files to Windows files in no time!
We've also found that some email handlers can affect the file format when transferring files from Mac to Windows machines and vice versa. So, if your method of transfer is email, be sure to compress the files with an application such as WinZip or Stuffit, before sending.
Back to Top 5. I've followed your instructions for adding file extensions, and am still unable to open GCK Mac files on my Windows PC - what now:It could be a problem with your file naming scheme. Believe it or not - some characters found on the keyboard should not be used in naming GCK files (or any other files for that matter) as they can cause the operating system confusion. Mac users generally have the freedom to use most any character they wish in naming a file - the exception being a colon (:), and sometimes a forward slash, /, which can cause issues for POSIX paths. If you work with GCK solely on your Macintosh, and never share any of your files with a Windows user - you don't have to worry about file names and these compatibility issues.
However, if files will be shared with a Windows user, the recipient could have problems opening and working with the file if any of these "illegal" characters are used in the name:
\ (backslash), / (forward slash), : (colon), * (asterisk), ? (question mark), " (double quotes), < (left angle bracket), > (right angle bracket), | (pipe)
If you notice these, or other strange characters in the file name, try having the GCK-Mac file re-saved, avoiding the use of illegal characters, before being transferred to the Windows user. For a lot more detail about file, folder and directory more naming schemes and limitations, please visit the subjects on Wikipedia and Microsoft.
Back to Top 6. What about transferring GCK files from Windows to Mac systems - are any modifications required?Under the OSX operating system, GCK Windows files readily open using the Mac version of GCK - both by double-clicking and opening through the hierarchal menu of the application.
As with the transfer of files to a Windows machine, we've found some email handlers can affect the file format. So, if your method of transfer is email, be sure to compress the files with an application such as WinZip or Stuffit, before sending.
Back to Top 7. I used to be able to "Mark Sites" in my construct - now when I select this feature I get an error message saying "No enzyme list files were found in the GCK Data folder". Where did they go - and how do I get them back?Page 7-9 in the current GCK manual describes the "GCK Data Folder" - which holds data that is used by GCK to perform some of its tasks. For example, this is where restriction enzyme lists and codon tables are stored.
More than likely, the path - or location - that the application looks for this folder has be inadvertently changed. To restore the defaults - select "Choose GCK Data Folder...." from the File menu.
You'll want to then select the folder titled "GCK Data" - it is located in the main Gene Construction Kit application folder under both Macintosh and Windows systems. Next time you choose 'Mark Sites' - all the standard enzyme lists should now be available.
Back to Top 8. How can I identify restriction enzymes that will only cut a segment of DNA at a single location - i.e. "unique cutters"?Page 3-17 in the GCK Manual describes the steps for defining "unique cutters". Using either the "Mark Sites" or "List Sites" feature found under the Construct Menu, you'll simply need to select the enzymes you are interested in identifying and move them to the "Enzymes to Mark" / "Enzymes to List" box. Next, in the "Mark/List enzymes for which ..." dialog box, set the "...more than" box to "0", and the "...less than" box to "2" - essentially marking/listing all enzymes you have defined that cut only "1" time.
Furthermore, you can define whether the enzymes are found within a selected segment, exclusively within a selected segment, or exclusively outside of a selected segment.
Using this cluster of choices together with "Mark/List enzymes for which ..." cluster allows you to find exactly the right enzymes for the task you want to accomplish.
Back to Top 9. I just upgraded my installation of Gene Construction Kit on a Windows machine, and when trying to launch, I get a "Error code -199" - what's going on?The '-199' error message is usually a result of conflicting preference information - most often caused when users upgrade from an older version of GCK. The fix is to remove the existing preference folder used by the program - and force it to be recreated with the next program launch.
First, search the primary hard drive for a folder titled "GCK Preferences".
Note: Under certain Windows OS's, the folder may be "Hidden", so select to Search for Hidden files and folders under the Advanced Search options.
Typical Windows paths:
On Windows 2000, the GCK preferences is located at ...
C:\Documents and Settings\
On Windows XP, the GCK preferences is located at ...
C:\Documents and Settings\
On Windows Vista, the GCK preferences is located at ...
C:\Users\
Once located, delete the GCK Preferences folder.
Now try re-launching GCK to ensure the fix.
Back to Top 10. My system recently crashed and now when I try to launch GCK I get a "not able to locate a valid license file" error. What can I do?Try performing a "Clean Installation" using the GCK CD you were shipped.
First, we'll need to find and remove some "Preferences" files GCK stores on your local hard drive:
Search the primary hard drive for a folder titled "Textco Preferences".
Note: Under some Windows OS's, the folder may be "Hidden", so select to Search for Hidden files and folders under the Advanced Search options.
On Windows 2000, the preferences are located here...
C:\Documents and Settings\
On Windows XP, the preferences are located here...
C:\Documents and Settings\
On Windows Vista, the preferences are located here...
C:\Users\
Typical Macintosh path:
OS X installations - Home : Library: Preferences: Textco Preferences
Select all occurrences of this folder and delete them by dragging to the trash can/recycle bin - and emptying the contents.
Next, uninstall the GCK application.
Windows users - this option should be available from the Start Menu. Goto: Start --> Program Files --> Gene Construction Kit --> Uninstall GCK
Macintosh users - simply drag the entire GCK application folder to the trash, and empty the contents.
Now, reinstall GCK from the original CD.
Back to Top 11. After installing GCK from the CD on my Windows system, I get the error message, "We are unable to locate a valid license for this software at your location" when I first try to run it. Any suggestions?There are two possible problems that can lead to this error message. First, at some time previously, you (or any other user of this computer) had installed a GCK time-dated version of the software - who's "valid license" has now expired. To check this, and remove the old files, perform a search on your primary hard drive (probably "C:") for a folder titled "Textco Preferences".
Note: Under certain Windows OS's, the folder may be "Hidden", so select to Search for Hidden files and folders under the Advanced Search options.
On Windows 2000, the preferences are located here...
C:\Documents and Settings\
On Windows XP, the preferences are located here...
C:\Documents and Settings\
On Windows Vista, the preferences are located here...
C:\Users\
Once located, simply drag this folder to the Recycle Bin and empty. Then try running GCK.
The second theory seems specific to international locations. Users of certain Windows operating systems in international sites can create 'Account Names' using the language of their resident country. We have determined that if any 'non-Western' characters have been used in the creation of an account name - GCK is unable to determine where to write the preferences files, and therefore cannot "locate a valid license". The solution is to create a new account using only Western or English characters, and re-installing GCK under this user profile. The first time GCK is launched the preference files will be created and you should be off and running.
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