1. I just installed Gene Construction Kit on a Windows machine, and when trying to launch, I get a “not enough memory” error. I have >1GB of RAM installed on this machine - what’s going on?
The 'Not enough memory' error message which you encountered seems to have occurred after a series of security updates released by Microsoft. We have generated an updated .dll file, which can be obtained here, which should get you up and running.
After downloading this ZIP file to your computer, open it and choose to 'Extract' the file titled "asintppc.dll" to your preferred location (your desktop, your documents, etc.), then close the ZIP window. Now navigate to location of the extracted file and cut and paste this new file into the 'Gene Construction Kit' folder that was generated in your 'Programs' directory when you went through the 'Install Shield' process with the program. It will inform you that "a file of this name exists in this location, do you want to overwrite it?" - to which you simply click yes.
Now, you should be able to run the GCK 2.5 application on your Windows machine without any memory issues!
2. 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 WinXP, the folder may be "Hidden", so select to Search for Hidden files and folders under the Advanced Search options.
Typical Windows path:
C:\Documents and Settings\Owner\Application Data\Textco Preferences
Typical Macintosh path:
OS 9 installations - Macintosh HardDrive: System 9 Folder: Preferences: Textco Preferences
OS X installations - ComputerName: 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.
3. 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 7-13 in the 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. Next time you choose ‘Mark Sites’ - all the standard enzyme lists should now be available.
4. 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.
Chapter 4 in the GCK manual describes what we call "List Windows". These are the files for storing enzymes used in the "Marking 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'.
5. How do I search a construct for a known sequence of DNA from another source?
Page 3-24 in the 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:
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For short DNA segments, simply type in the bases you wish to search for then select ‘Search’.
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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.
6a. 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 use 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:
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GCK Construct Files (default graphic view): add ".gcc" to the filename
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GCK Construct Files (default sequence view): add ".gcs" to the filename
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GCK Illustration Files: add ".gci" to the filename
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GCK Gel Files: add ".gel" to the filename
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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.
6b. I’ve followed your instructions above 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.
7. 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.
Under OS 9 - users may need to open the file using the menu options within GCK first, to associate the file with the Gene Construction Kit application. After working with the file, and saving changes, it can then be opened the next time by double-clicking on the icon.
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.
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.
9. In Mac OSX, when I minimize GCK windows to the dock, sometimes when restored they are ‘inactive’ - meaning I can’t select anything, and menu commands don’t seem to work. What can I do?
The problem may occur after minimizing at least two windows (any combination of GCK Construct, Illustration or Gel Windows) to the dock. Upon ‘maximizing’ or restoring the first of these minimized windows - it appears ‘inactive’ - graphics or sequence cannot be selected, and the file does not respond to GCK menu commands (Construct --> Display Sequence).
As a workaround, until a solution is available, we have found that you can restore all open windows by simply maximizing the "last" GCK window you sent to the dock, and clicking on something within it. Then when any other GCK window is brought back up from the minimized dock location, you can work with it as normal.
For example let's say you have 3 construct windows open (C-1, C-2, and C-3). Minimize all of them in numerical order 1, 2, 3. Restoring C-1 first, you'll notice that the window is 'inactive' - same result if you restore C-2 first. However, even if you send these two windows back to the dock - and then restore C-3 (the last window sent to the dock in the first step), and click in it to make it active - then any other window, C-1 or C-2, can be brought back up successfully, and you may resume working on it.
10. 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". 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.
11. When I use GCK's Deluxe Importer to search for GenBank records, it is returning a message that says "No sequences were found". I've searched and imported this same accession number from NCBI previously, what’s going on?
We are investigating recent changes made to the NCBI interface and querying protocols. It seems the NCBI site has changed the web interface for processing search queries. The current GCK query URL <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi> is being re-directed to a new search page <http://www.ncbi.nlm.nih.gov/sites/entrez>. However, the search output page has completely changed and is now incompatible with the current version of GCK. The new NCBI search output page displays a list of results from each database which causes GCK to report the 'No sequences were found' error message.
We are working on a solution to this problem. In the meantime, it seems that a viable workaround is to bring up the GenBank record in your preferred Internet browser, and save the record locally to your desktop by choosing to 'Send' the information to a 'File'. If you need more detailed instructions on how to do this using the NCBI sequence viewer, please contact us <http://www.textco.com/about_us/contact_us.html> - we can type up an example.
Once you have a file saved to your desktop, you can use GCK's Deluxe Importer to 'Open' the file, and convert the features into graphical elements. From within GCK, you just need to choose 'File --> Deluxe Import --> Open Sequences File'. If you do not see the file listed in your open file dialog, or if the file is grayed out, just choose 'All Files' from the 'Files of Type' drop-down menu.
Thank you for your patience while we work to resolve this issue!
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