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View additional product information for Vector NTI™ Express Workgroup Upgrade - FAQs (A14448)
89 product FAQs found
You can apply your Vector NTI Advance Static License by opening the license manager. Navigating to Start -->All Programs -->Invitrogen-->Vector NTI Advance --> License Manager. Next, navigate to the “Applications Tab” and click on the “Static” button. Once in the Static window, please fill in all contact details and copy and paste your license number starting with “VLKEY” into the license number field. The key field will be left blank. Select “Apply”.
Your software is succesfully licensed if the Applications Tab says “personal static” next to all modules excluding Vector Expression and Pathblazer (modules are discontinued). There will also be a green check mark in the bottom right corner of the Vector NTI program window indicating the software is licensed. Sometimes it may be necessary to close and reopen the software for the license to take effect.
If you have any questions, email bioinfosupport@lifetech.com.
This error occurs when the instxml.exe file fails to launch automatically. Find the instxml.exe file in the C:\Program Files\Vector NTI Advance folder. Double-clicking on this file will allow manual installation of the instxml file and hence allow Vector NTI to be installed. If you do not find the above file, download it from the Microsoft site:
http://www.microsoft.com/downloads/details.aspx?FamilyID=3144b72b-b4f2-46da-b4b6-c5d7485f2b42&displaylang=en
Scroll down and click on the msxml.msi link to download the file.
You will have to uncheck UAC (User Account Controller) to run the installer. The UAC is a security feature of Microsoft Windows Vista and Windows 7 Operating Systems. The UAC is designed to prevent malware from compromising the operating system but can also interfere with the installation of some application software.To disable the UAC to allow installation of Vector NTI program, follow these steps:
Go to Control Panel > User Accounts > Turn UAC on or off, uncheck UAC to help protect your computer
Restart your computer when prompted. Then try to install Vector NTI program
For more details please read the installation manual. You can download the installation manual by going to:
https://www.thermofisher.com/content/dam/LifeTech/migration/files/cloning/pdfs.par.35770.file.dat/12605019%20vnti%2011.5.2%20release%20notes.pdf
Yes. Please email your name, full contact details, your non-profit/academic institution, and the Hardware ID of the computer that you registered to bioinfosupport@lifetech.com, with “Help with free v10 license” in the Subject line. We will respond by email with your License Number and Registration Key. Please note that these requests may take up to 5 business days to process.
Yes. You can export all your DNA and RNA molecules as GenBank or FASTA files using a number of simple methods; see the v10 User Manual for details. Likewise, protein sequences can be exported as GenPept, Swiss-Prot, or FASTA format. These file formats are the de facto standards for sharing sequence information, and can be read by many commercial and free sequence analysis software applications, and can also be read as text files, using standard text editors.
Yes, simply email your contact information details to bioinfotrial@invitrogen.com to get a free, 30-day Trial License; or request one by going to the following link: https://www.thermofisher.com/us/en/home/life-science/cloning/vector-nti-software.html and clicking on the download a trial link for the correct version of the software.
Version 11 is fully backward-compatible with data stored in v10 (and in v9 and v8). Full details of how to upgrade from v10 to v11 are in the v11 Installation and Licensing Guide. Briefly:
•First, back up your existing v10 Local Database to a secure location.
•Uninstall v10 using the Add/Remove Programs functionality in your Windows Control Panel.
•Download and install v11 from our Downloads Page, or install v11 from the Vector NTI Advance 11 CD.
•During installation, you will be able to point the v11 software to the saved copy of your Local Database, and all of your existing data will be imported into the redesigned v11 Local Database automatically.
Technical Support for Academic Licenses is available by email. Simply send your question to bioinfosupport@lifetech.com.
Simply log on to Thermo Fisher Scientific website and search for the new Academic License, Cat. No. 12605099. Unfortunately, we no longer offer the 3-year Vector NTI Advance Academic License, Cat. No. 12605103.
The LMU-36 error indicates that the license number you entered does not exist.
Please make sure that you entered your license number and key code (for academic customers only) correctly.
*It is easiest to just copy the entire license number and key code from your license center on the web and paste them into the appropriate boxes in the license manager.
Please contact us at bioinfosupport@lifetech.com. Please include your license number or order number information.
It is also possible that your system clock has changed. This can be particularlly problematic when the clock is off by several hours or days. Correct your computer's clock and reapply the license number in the license manager.
Errors encountered when installing the Vector NTI program are related to the specific computer's setup. Check to see that you are logged in as the administrator. In addition, some virus software programs may also be preventing installation of VNTI database files (you may need to temporarily disable).
If you are running Windows XP SP2, check for additional suggestions by searching the FAQs for “windows SP2”
Vector NTI Advance 7.1 software is compatible with Mac OS 10.3 (Panther) and earlier versions of Mac software. Vector NTI Advance 10.3.1 PC has been tested and passed on a Windows XP SP2 partition created by Boot Camp on a MacIntel. With the difficulty that an Apple-recommended shop had in translating our software onto OS X 10.4 system, and the growing set of alternatives for running native Windows apps on MacIntels, we have decided to focus on Windows development and on testing and supporting these new hardware/software combinations. This way, Mac users can take advantage of all the newest Vector NTI Advance functionality.
In order to use Vector NTI on Apple Mac OS 10.5 systems, you need to use Bootcamp to run Windows XP and Vector NTI v10 or v11 software for Microsoft Windows.
There are a few things to check for:
(1) att sites must be appropriately labeled as a Miscellaneous Recombination feature type (as in attR1 or attR2);
(2) the ccdB CDS must be annotated on the vector (as “ccdB”) and
(3) the vector must be circular.
If the molecule is still not recognized as a Gateway clone, compare the sequence of the att sites with the sequences of a similar att site which is recognized as a Gateway vector. If there are a few point mutations, edit the att sequence on the vector which is not recognized to match a vector which is recognized. Proceed with the Gateway cloning in Vector NTI program.
The single nucleotide differences are non-essential nucleotides in the att sites, but older versions of Vector NTI program have strict requirements to recognize Gateway cloning vectors.
This error indicates that you have not entered your license and key code correctly.
Be sure that you copy and paste the entire license and key strings into the appropriate boxes in the static license.
Your License number will begin with the letters VLKEY.
This error can also occur if the date and time on the computer are incorrect when the license and key are applied. Make sure that the date and time on the computer are set correctly.
If the error still persists, try rebooting your computer.
This error means that a Registration Key is not available for all requested products. The typical scenario is that you apply a license number that unlocks Vector NTI program and some modules (ContigExpress module, Bioannotator module, Align X module), but perhaps not GenomeBench, or other products such as Xpression of Pathblazer (which have been discontinued).
The LMS-42 error indicates that you have run out of seats for your license.
For version 9 or higher: If you are moving a license from one computer to another, please unregister the software from the original computer before applying the license to the new computer. You can do this by simply typing 'unregister' in the license number line of your License Manager then clicking 'apply'.
This will free up the license from the old computer.
If this is not possible because the old computer has already been disposed of, please contact our bioinformatics support group at bioinfosupport@lifetech.com.
If you need to purchase more licenses please contact us at bioinfosales@lifetech.com.
Please toggle the database choices to “Enzymes”, then go to the pull-down menu: Table | New | Enzyme. Then, fill in all of the information in each tab. Once you save the new enzyme, you will be able to use it in all of the operations pertaining to restriction enzymes.
Pressing the green E button in the top left corner of the ContigExpress Menu will activate editing mode.
The best thing to do is to clean the registry and proceed with the installation once more. Please follow the steps listed to clean the registry:
Go to Start > Run, then type regedit and hit OK.
Go to HKEY_CURRENT_USER
Open the "Software" folder.
Open the "Informax" folder
Highlight the "Vector NTI 10" folder
Delete.
Repeat the process with HKEY_LOCAL_MACHINE.
Open the "Software" folder.
Open the "Informax" folder.
Highlight the "Vector NTI 10" folder
Delete.
Now, re-install Vector NTI.
NCBI made changes to their servers which prevents Vector NTI Advance from connecting with the BLAST Servers. We are looking into possible remedies for this issue. In the meantime BLAST searches will need to be performed at NCBI's website.
The Vector NTI system information application collects data about Vector NTI software and the system on which Vector NTI software is installed and consolidates this information into one file. The system information file is helpful in the diagnosis and resolution of system-related Vector NTI problems. To access this file, follow these steps:
(1) Find the file “vntisysinfo.exe” in C:\Program Files\Invitrogen\VNTI Suite 11 and double click on it to run. (C:\Program Files\Invitrogen\Vector NTI Suite 10\ for older version)
(2) It will open the Vector NTI System Information window. Click on Info > Collect. Select “All” and click on “Proceed”. It may take 1-2 minutes to collect the info.
(3) Once it is done, you should see the “OpenGLVisual Test” window. Click either on “Yes, I can see the cube” or “No, I don't see a cube”.
(4) Now you should see all the collected information.
(5) Click on the Edit > Copy All.
(6) Open a text editor (note pad) and paste the information.
(1) Open the Matrix Editor from Start | Programs | Invitrogen | Vector NTI Suite 11 | Utilities | Matrix Editor. This will open an empty Matrix Editor window.
(2) Click on the “Load Matrix” button to open the matrices folder. Select the matrix you wish to edit or review and click on “Open”.
(3) Select the Score Matrix tab.
(4) To edit a cell, highlight a value and enter the new value.
(5) Click on “Save Matrix” to save the changes. Please note, the Save Matrix button is enabled only after you modify the name in the “Name” text box.
Somehow, the number '4' key was assigned as a system-wide shortcut for that application. You may check this as follows:
(1) Navigate (from Start | Programs |) and select the application.
(2) Right click on it, and select “Properties”.
(3) Check the 'Shortcut key' field value.
(4) If you find an association with '4', remove it.
AlignX program uses the Clustal W algorithm. Clustal W determines the scoring matrix to be used from its distance calculations on the compared sequences. In AlignX program, however, the user is allowed to specify the particular scoring matrix to be used for the multiple sequence alignment. There are about 20 different scoring matrices that the user can choose from via the “Load from File” button in Alignment Setup.
Residues in an alignment are colored according to the following coloring scheme in AlignX program:
Black on window default color—non-similar residues.
Blue on cyan—consensus residues derived from a block of similar residues at a given position.
Black on green—consensus residues derived from the occurrence of greater than 50% of a single residue at a given position.
Red on yellow—consensus residues derived from a completely conserved residue at a given position.
Green on window default color—residue weakly similar to consensus residue at a given position.
To modify alignment display colors, open the Alignment Display Setup dialog box. Click on Change the colors for the specific project using the drop-down menus, observing the modifications in the preview box. Click OK to save color changes in the alignment project. The changes will be applied to the alignment next time you open the project.
Follow these steps to export oligo sequences from Vector NTI software to an excel spreadsheet.
In the Database Explorer:
(1) Select the Oligo Database from the pull down menu
(2) Make sure to display the column with the actual oligo sequence
Right-click on the column header in the database explorer, and choose “Columns”, then display “Sequence”.
(3) Use the “Camera” tool to copy all or selected entries to an Excel spreadsheet.
Launch a molecule in the Vector NTI molecule viewer and select the region of the molecule that you wish to amplify. Then, click on the “Analyses” pull-down menu and you will see various primer design options for PCR amplification.
Yes, DLS supports Vector NTI software running on PC and Mac operating systems. For more information on supported platforms, please consult the DLS installation guide located at: https://tools.thermofisher.com/content/sfs/manuals/VectorNTI_DLS_man.pdf
Make sure all users have minimum read and write permissions to the following folders:
Vector NTI v. 11
C:\Vector NTI Database
C:\Program Files\Vector NTI Suite 11
Vector NTI v. 10
C:\Vector NTI Database
C:\Program Files\Vector NTI Suite 10
The Vector NTI version 11 manual can be downloaded from:
http://tools.thermofisher.com/content/sfs/manuals/VectorNTI_UserManual.pdf
For Vector NTI Express go to:
For Vector NTI Express Designer go to:
Yes, Vector NTI software supports IUPAC ambiguous code symbols. Please see and refer to the following ambiguous codes and their meanings.
Bases
W ---> A or T
R ---> A or G
K ---> G or T
Y ---> C or T
S ---> C or G
M ---> A or C
B ---> C or G or T
H ---> A or C or T
D ---> A or G or T
V ---> A or C or G
N ---> A or C or G or T
Amino acids
B ---> N or D
Z ---> Q or E
X ---> Any amino acid
Please follow the steps below to document your oligo anlaysis:
(1) After completing the oligo analysis, click on “Save Results.”
(2) A “Save Oligo Analysis Results To” dialog box pops up.
(3) You will see the default File name: OligoAn.log
(4) Click on “Save”.
(5) Open the saved file with a text editor.
(6) From there, you can copy and paste into a word document. You may have to change the font to Courier to get a better view.
DB_lock is common when Vector NTI Advance program closes inappropriately. To fix this problem, locate then delete the file called 'DB_lock' from your database folder. By default, the database is the C:\VNTI Database. If you created a separate database and are unsure which database is being used, the best thing to do is to do a search for the db_lock file on your hard drive (search hidden folders, as well), then delete this file. You may have to restart your computer. The message may also happen if Vector NTI program is pointing to a location where a database does not exist.
If you are unable to find the db_lock file as above, you will need to delete the appropriate file in the registry. We highly recommend that you complete the following steps with the help of your IT personnel.
(1) Start > Run and type regedit. Click on OK. This action will Open the Registry Editor.
(2) Open HKEY_CURRENT_USER\Software\Informax,Inc\Vector NTI 10\Vector NTI\directories.
(3) Check the path to your database in the 'maindir' and correct it. It should be either “C:\Vector NTI Database\” installation
(4) If you see other paths then you will need to change it to the actual location of your database. For example if your database is located in the folder 'MySeq' in the 'D' drive. Then your database path in the registry should be changed to D:\MySeq\Vector NTI Database\
Follow these steps to make the reverse complement of a DNA sequence on a PC computer.
For the PC:
(1) Open a DNA sequence.
(2) Highlight the entire sequence in the sequence pane (or type ctrl + A).
(3) Right-click on the highlighted sequence and choose Reverse Selection to Complementary.
(4) To save the reverse complement, click the Save icon or choose File > Save.
To change the starting coordinate of your DNA sequence, follow these steps:
(1) Open a circular DNA.
(2) Choose Edit > Molecule Operations > Change Starting Coordinate
(3) The Change Starting Coordinate dialog box appears, allowing you to designate the current sequence position that you want to define as the new starting coordinate.
(4) Enter the “New start” position. For example, if you want 10th base position to be 1st base position (starting coordinate), then enter 10 in the box.
(5) Click on OK to accept the new start position.
This could be due to the missing/misplacement of help files (*.HLP) in the default location (C:\Program Files\Vector NTI Suite 10\*.HLP). When this happens you should see the following message:
Cannot find theC:\Program Files\Vector NTI Suite 10\*.HLP.
The prompt “Do you want to try to find this file yourself?” will display. Click on Yes.
Navigate and find the file “*.HLP”.
The file could be either VectorNTIExplorer.HLP or Vector NTI 10.HLP. Click on OK.
Please follow these steps to add a hyperlink to a sequence file.
(1) In the Database Menu of the Local Vector NTI database, open the Column Fields Manager.
(2) Click the button for a “New” record (the file card with the yellow star).
(3) Change the “Type” from 'String' to 'List of URLs' and give the category a name, such as 'Web Links'.
(4) Click OK.
(5) Close the User Field Definitions window.
(6) Highlight the molecule that you wish to add a hyperlink to, right-click and choose Edit.
(7) Click on the User Fields tab.
(8) Click on 'Web Links' to select it and click on the 'Change Value' button.
(9) In the 'Role' field, enter the name of the link, or some relevant description.
(10) In the 'URL' field, enter the address; for example: http://www.thermofisher.com.
(11) Click Add
(12) Click OK.
(13) The hyperlink will now be available under the User Field folder in the Text Pane when that molecule is opened.
Tm values are calculated by two methods; the method used is dictated by the length of the primer. If the primer is short (in the 35 bases or less range), the Thermal Tm calculation (nearest neighbor method) will be used. For primers longer than 35 bases, a %GC Tm is used (%GC method). More information about the algorithms can be found in Appendix E the Vector NTI Advance manual.
To fix internal identification errors, try the following:
(1) Try to find the file name “xxxList.vdb”. It should be in C:\Vector NTI Database\Tables\. For example, 'xxx' is 'Mol' for DNA sequences.
(2) Change its name to “xxxListCopy.vdb”. For DNA sequences change 'MolList.vdb' to 'MolListCopy.vdb'.
(3) If the above does not solve the problem, then change the folder name 'Tables' to 'TablesCopy'.
Yes, it is possible. Vector NTI shared databases use portable data format and file naming conventions to ensure that both Macintosh operating system and Windows operating system users of Vector NTI software can access common databases.
There are several operations that users can perform on a Shared Database. These include:
() Copying data to/from the local database.
() Various database management operations such as creating and deleting subset, etc.
() Database searches.
Please note, if you deposit molecules to the shared database, and a colleague wishes to use them, he or she must first copy sequence(s) to their local database. Others cannot work on the file copy that resides in the shared database
(1) Keep all the sequences in a .txt file (note pad). For example, follow Fasta format convention (the sequence should start with > and file name and second line should be your sequence. Arrange all of your sequences in a concatenated format.
(2) Open the Vector NTI Explorer window.
(3) Drag and drop the file right on the window OR Go to “Table” > Import > Molecule from Text File.
(4) You may accept the MAIN folder or create new subset to import your data into the database.
For example, arrange all of your sequences in the following format.
>sequence 1
aaacgatgac...
>sequence 2
gggggcgaatgac...
>sequence 3
tttttttcgaatgac...
In order to open your DNA sequence, first do the database clean up (Vector NTI Explorer > Database menu > Database Clean Up).
If database clean up does not solve the problem, follow these steps:
(1) From the Vector NTI Explorer window, select the Enzymes database.
(2) Click on “Table” or “Enzyme” and then select Import > Enzymes from Archive.
(3) Navigate to C:\Vector NTI Database and select the file DBINIT.EA4. Click OK.
(4) If you get an alert message “..already exists in the database”, select appropriate option from: Overwrite/Overwrite All, or Skip/Skip All, or Rename/Rename All.
The shared database must be set up from a computer that has a static license with a Workgroup license. Before you start creating a shared database, find a place on your network where the database will be located. The location should be accessible from the computers of all potential users of the shared database. Users should be able to connect to this location or mount the corresponding network drive and have read/write/delete permissions for all files in the database directory and its subdirectories.
(1) To arrange the network directory for a new shared database, start the Vector NTI program and choose the Local/Shared Data Exchange option from the Database menu. The 'Connect To Shared Database' dialog window appears.
(2) Press the “Create New Database” button. Vector NTI software displays the standard “File Save” dialog box where you may select a location for the shared database definition file (dbdef). Select the empty directory you prepared earlier and press 'Save'. The database definition file is then created in that directory.
(3) Enter a name for the new database in the “Database Properties and Users” window and press OK. Vector NTI software writes the data you entered into the database definition file and creates the files and directories required for storing the database data. The database you just created has no registered users at first. Users become registered when they log on to the shared database.
(4) Your shared database is now set up and ready to use. Users can access the shared database by selecting 'Local/Shared Data Exchange' and pressing the “Find Database” button. Users will need to find and select the dbdef file in the dialog box. By pressing the 'Save Connection As...' button, users can save the link to one or more shared databases that will be available in the drop-down menu. Clicking on 'Connect' connects users to the shared database. Once connected, users can drag files between their local database and the shared database.
Please be aware that only one user can connect to the shared database at a time. Therefore, it is recommended that users remain connected to the shared database only while they are removing or entering molecules.
You cannot create a shared database using dynamically licensed Vector NTI software. However, if you have a static license or a temporary static license then you will be able to create a shared database. Once a shared database is created then, the DLS-licensed client computers can connect to the shared database.
To display the feature name above the sequence, follow these steps:
(1) Open a sequence.
(2) Open the Feature Map folder from the Text pane.
(3) Find the feature that you want to display in the sequence pane.
(4) Click on View and then select “Display Setup”, or simply click on the “Display Setup” button. You will now see the various options in the “Molecule Display Setup” window.
(5) Click on “Fmap Setup” in order to open the “Feature Map Setup” window.
(6) Click on “Add”, select the feature you want to display on the sequence, and click on OK.
(7) Click on OK to close the “Molecule Display Setup”.
The selected feature name should now be displayed right above the sequence.
To change the features displayed in the Graphics pane, follow these stesps:
(1) Open the sequence.
(2) Select the Text pane (top left).
(3) Click on View and select “Link Panes”; All of the features will disappear from the Graphics pane.
(4) Open the Feature Map folder in the text pane; all the features should be listed in separate folders.
(5) Open the folders for the features you wish to display. For example, if you want to display only CDS, open the CDS folder.
(6) If you want to display / hide selected features, then open/close the corresponding folder.
When you select the backed up database folder, please make sure you double click on it in order to open it.
This feature is available in Vector NTI version 10 software and later.
In Vector NTI Molecule Viewer, you may choose to display your translated sequences in the DNA window in either the standard one letter code or the three letter code.
To do this:
Select the region you would like to translate and click the translate direct button in the Active Pane toolbar.
If you would like to change the code from the three letter code to the one letter code:
From the View menu you can choose Display Set-up > Sequence Set-up button
Select the radio dial button which corresponds to either 1 letter AA code or 3 letter AA code.
In ContigExpress program:
Select the region you would like to translate in the assembled contig window.
From the View menu select Consensus Translation > Select the frame you would like to translate.
Click the Val -> V button in the toolbar.
Ensure that the file name is not too long. You may need to change the name of the file.
No. In order to merge projects, you need to open them separately and drag/drop the fragments into one.
Open two projects separately and then drag/drop the fragments into one project to merge two ContigExpress projects.
Below is the standard procedure for using the vector trimming function:
(1) Choose your vector sequences for trimming from the database.
(2) Go to Tools > Send to > Polylinker to ContigExpress. Confirm that no odd Microsoft Windows characters are in file name. Send the reverse complement sequence as well. The name of the reverse complement sequence should be changed so it does not overwrite the previous one.
(3) Select the fragments to trim and go to Edit > Trim Selected Fragments for Vector Contamination. Check the sequence from the 'Polylinker' list and also highlight it. Click on 'Add Restriction Enzymes' and 'Add Cloning Insertion Point' (e.g., at HindIII site) then click “OK”.
(4) Push the Calculate! Button. The resulting red bases indicate potential trims. Clicking the OK button performs the trims.
To remove older versions of Vector NTI software from your computer, we first recommend that you backup your database with the Database menu > database backup.
Try to uninstall old version through Control Panel > Add/Remove Program (standard way).
Make hidden files visible (Tools > Folder options > View > Files and Folders).
Find a folder called “{AC0D7292-6F88-B2E6-076A3FC4352F}” and delete it.
Next, delete all registry information. In order to perform this task you must have admin privileges.
(1) From Start > Run, enter regedit and hit OK.
(2) Navigate to the HKEY_CURRENT_USER
(3) Look in software for folders called “Informax” or “Informax Inc.” and delete them.
(4) Next, look for HKEY_LOCAL_MACHINE and under 'Software' look for folder called “Informax” or “Informax Inc.” and delete them.
Older versions of Vector NTI software should now be removed.
The reason that the user-defined primers are not accepted usually depends on one or more of the following settings being too restrictive:
'Primer tab': Product length, Length of analysis, or Primer length; also the 'Uniqueness tab' may be restrictive.
Sometimes the settings under the “Structure and Pairs” tabs may also prevent primers from being found. Even if user-defined primers match the target sequence, they will not be listed if any of the parameters are too restrictive. An alternative is to try the “Find PCR primers” tool, where user-defined primers may be browsed.
To arrange the restriction enzyme list in aphabetical order, right-click on the graphics pane and choose the option DISPLAY SETUPs, and then click on RMAP setup. The next box will give you two sorting options: by 'Enzyme name' or by 'Number of Recognition sites'). Select the 'Enzyme Name' option to arrange them in the alphabetical order.
To view the fragment sequence, follow these steps:
Locate the folder where Vector NTI X program was installed. The default name is “c:\program files\Invitrogen\Vector NTI Advance X”
Find the VNTI protocol.exe and run it by double-clicking on it.
The registry information will be restored and the links should now be functional.
The 'Web Analysis' tools may not be installed under the default installation settings. Please reinstall the software and make sure to select the “Full Installation” option.
If you are carrying out a Custom Installation, please check the 'Web Connectivity' box.
To change the backbone color of a sequence, follow these steps:
(1) Click on the “Edit Picture” icon (or click on the graphics and from the pull-down menu, go to Edit > Edit Picture.
(2) Select the backbone. You will see two little black lines surrounding the edge.
(3) Right click on “Properties” and change fill color and line color.
(4) Right click again but this time chose “Redefine Axis Style by Example”.
(5) From the pull-down menu, go to View > Display Set up and save the Profile name.
(6) Open a new molecule and apply the new Profile to it and then save
A black screen means that a file called “MOLPROF.INI” got corrupted and it needs to be replaced. The file is located inside the Vector NTI Database folder. You will need to replace the file with another from a Vector NTI installation. You may also request this file from bioinfosupport@lifetech.com or uninstall and reinstall the software
To retain you display profile settings when upgrading to the lastest version, follow the steps below:
Backup your database with the Database menu > database backup. Copy the following setting files into your backup directory before you upgrade.
The default path for the files is C:\VNTI Database\ *.ini
The files that will be backuped are ConnProf.ini, Defaults.ini, Gelprof.ini, Molprof.ini, ProProf.ini, and Nmprof.ini
Vector NTI progam is installed by “Administrator”. When a “User” logs into the computer, they must have permissions to the Vector NTI Database folder, typically located at C:\Vector NTI Database. The problem will be resolved by correcting the permissions. For more information, please consult the Vector NTI Installation Guide.
For Vector NTI software to recognize the BaculoDirect DNA as a destination vector, you will need to change the properties of the BaculoDirect Linear DNA from linear to circular:
1. Go to the Exploring Local Vector NTI Database
2. Right-click on BaculoDirect Linear DNA
3. Go to “Edit”
4. Change its properties from linear to circular and save back to the dabase.
Vector NTI software will now recognize the attR sites on this circularized vector.
To obtain the license numbers for the nextwork copies of Vector NTI software, follow the steps listed below.
(1) Go to our web site to download DLS (Dynamic License Software): http://media.invitrogen.com.edgesuite.net/downloads/vector/setup.exe. To find DLS versions for various server platforms, go to: https://www.thermofisher.com/us/en/home/life-science/cloning/vector-nti-software/vector-nti-advance-software/vector-nti-advance-downloads/vector-nti-advance-archive.html
2. Once the DLS software is installed, please send the Hardware ID and your contact information to bioinfosupport@lifetech.com
3. Using the hardware ID, we will generate keys for you for the correct number of users.
The following are possible reasons for this.
(1) The computer that hosts the Dynamic License Server software is not available. If this computer is turned off or the network connection to it is experiencing problems, then the user will not be able to get a license. You can check this by copy/pasting the DLS URL into a web browser. (The form of the URL will be similar to the following: 'http://ServerName or IP Address/dls/vntidls.cgi')
If you can connect to the server text will be displayed with the DLS version number. If the version number is not displayed, please check with your IT department because it indicates that the server is not up and running.
(2) Because the DLS system uses “floating” licenses, it is possible that all licenses are currently in use by other Vector NTI users. To check if licenses are available, open the license manager and select > Dynamic License Settings > Test Connection, a dialog box will appear that tests the connection to the DLS server and lists the licenses available at that time. If licenses are not available because they are in use by others you can wait for a license to become available.
(3) In order to obtain a license you must also have 'user access' or a 'seat' for the program. If you have a 'seat' for Vector NTI software, then you will be able to use the DLS licensing software. If you do not have a 'seat', then you will be unable to use the program, even if a license is available. When a user starts the program, they get a 'seat' and a license for that program (subject to availability); when they close the program, they release the license but not the 'seat'. Therefore, it is possible that a computer that no longer exists or a Vector NTI user that is no longer in your environment could be occupying a 'seat' unnecessarily. In this case, it is necessary to remove that computer from the list of computers occupying a 'seat' for the program.
In order to clear the seats, go to the DLS Admin page located at http://ServerName of IP address/dls/vntidlsadmin.cgi and enter your Administrator password.
Go to Users > Allowed > Click on the product name (e.g. Vector NTI)
Select the computer name and click on the “Deny Selected Users” button
Be aware that if you start using Vector NTI software from a different computer, it may be necessary to remove your old computer from the list of computers occupying a 'seat' for the program.
(4) Incorrect 'URL of DLS' in the 'License Manager' program can also cause this problem. The URL tells your computer where to look for an available license and 'seat'; if this URL is incorrect, you will not be able to get a license or seat. The form of the URL will be similar to the following: 'http://ServerName or IP adress/dls/vntidls.cgi'. Be aware that if the server name or IP address changes (DHCP, for example), the client computers will need to update the URL to reflect that change.
(5) DLS software 'keys' have not been updated to reflect a newer version of the program. If a user upgrades the client Vector NTI software, new keys must be requested from Thermo Fisher Scientific and applied to the Dynamic License Server before the new version will be licensed properly. Note: upgrade to a newer version requires purchase of license update.
(6) Your computer has been denied (intentionally or inadvertently). The DLS software administrator can put certain computers on a 'Denied' list to prevent unauthorized access of the DLS. If your computer is on this list, you will not be able to get a license for the program.
This requires that the customer have support contract with us. Please follow the steps below to transfer a Dynamic License Server to a new computer.
(1) Download the DLS software from our website for your platform of choice from the following link:
http://media.invitrogen.com.edgesuite.net/downloads/vector/setup.exe
(2) Once installed, please fill out the Reinstall Request form found on our website at:
https://www.thermofisher.com/us/en/home/life-science/cloning/vector-nti-software/vector-nti-advance-software/support/re-install-request-form.html
Note: the Hardware ID is obtained from the license manager (Admin Page) of the DLS software
(3) We will then send you the license keys for the number of licenses and seats you have purchased
With the DLS license, if the server goes down the client/server connection is broken the clients cannot obtain a dynamic license and, therefore, can only run in demo mode. Once the server connection is back up and they can again obtain their dynamic license.
To flip or invert a sequence in AlignX program, follow these steps:
From AlignX program, save the desired molecule to the database by selecting File > Save As (possible file extensions are “.txt”, “.gb”, “.gp”).
Open the molecule in Vector NTI software or ContigExpress software and follow the directions for making the reverse complement of the molecule as described in online help accessed from Vector NTI software or ContigExpress software or the Vector NTI Advance User's Manual.
In Vector NTI program:
(1) Open the molecule you want to make a reverse compliment of
(2) Go to the File Menu
(3) Select “Make a Reverse Compliment”
(4) Save this file to your database as prompted.
In ContigExpress program:
(1) Open the molecule you want to make a reverse compliment of
(2) Right click on the molecule of interest
(3) Select “Make a Reverse Compliment”
(4) Right click on the new molecule
(5) Select “Align Selected Molecule”
Add the reverse compliment file to an active AlignX project by selecting Project > Add Files.
Locate the newly created reverse copy/reverse complement file
Click Open, adding the reverse copy/reverse complement to the project.
It is very important to confirm that your sequences have not be pre-edited (usually performed at your Sequencing Core Facility). If they have been pre-edited, please have your core facility personnel provide the raw, unedited fragments. All necessary editing (e.g.: Fragment Trimming or Vector Contamination Trimming) can be performed in ContigExpress software.
The files may be in bin-hex format, which is frequently the case with files coming off a Macintosh operating system. Unfortunately, at this time ContigExpress software does not read the bin-hexed format. Please go to this website and download StuffIt at "http://www.stuffit.com/expander/". Once you have StuffIt installed, highlight the file, right-click, and select “Open with” then select “StuffIt”. It will uncompress the file. The resulting file can be opened in ContigExpress program, for example by drag and drop into CE.
Alternatively, you may want to look into the exact settings for saving and exporting abi files from the Macintosh operating system to avoid this problem.
Exporting the contig sequence is accomplished from the ContigExpress Project window. Locate the name of the contig in the list on the right-hand side of the Project window. Highlight the name of the contig and select Project > Export Item and select your desired file type. A quicker alternative uses Drag-Drop from the ContigExpress Project window into the Exploring Local Vector NTI Database window. Drag the name of the contig sequence from the ContigExpress Project window and drop it into your Database.
It is possible change the Author Name so that your name is correctly listed as the author of new molecules. From within the Exploring Local Vector NTI Database window, select View > Author Information from the pull-down menu. You may provide your name and contact information in this window.
To change Authorship of existing molecules, right click on the molecule(s), choose Set System Attributes and change author information in the next window.If your name is not showing as an option, go to View on the menu, and choose Author Info to add yourself as the author. Use System Attributes again to change the author name.
Our scripts are written in SXM, which is a Lisp dialect.
No, but you can “drag and drop” molecules from the database into Multiple Sequence Alignment, or highlight the molecules in the database and choose Align from the right-click menu or choose Align from the Align pull-down menu.
The PCR Primer Rating is calculated from the values assigned in the Primer/Oligo Quality Specifics Dialog box where “importance factors” are assigned to various primer/oligo parameters. These importance factors range from 1 (less weight) to 10 (more weight). Primer ratings should only be compared within a single analysis. The higher the total rating, the closer the primer comes to the specified parameters.
Choosing “Analyze > Restriction Fragments” will produce the fragment information. This information can be printed with the text pane by choosing Print, or it can be copied to the clipboard with the Camera icon, then pasted into another application.
The offspring molecule must contain sequences originally from its parents for it to be a descendant. If any sequences are changed in the descendant, then the lineage is broken.
Select the object (molecule) by highlighting, then right-click on it. From the right click menu, choose Edit. From the Edit window, choose the User Fields tab, select your user field to be changed, then choose Change Value.
Performing any of the actions listed above will change a hardware identification number that the program uses. When this happens, you will need to have the static or dynamic license reset.
Please fill out the “Reinstall Request Form” located at https://www.thermofisher.com/us/en/home/life-science/cloning/vector-nti-software/vector-nti-advance-software/support/re-install-request-form.html. The form asks you for the hardware ID. If you still have access to your old computer that had the software, you can get the hardware ID number on static copies by going to the Help Menu > License Manager > Applications > Static (PC). The Hardware ID for the DLS server is located in the Administration page.
In Version 10 and 11 of Vector NTI Advance program, the %GC of an oligo is part of the Oligo Analyses menu on the Analyses drop-down menu. Open the Vector NTI Explorer window and select the Oligos database. Select the oligo which you wish to see the %GC (without opening the file). Click Analyses > Oligo Analyses > Thermodynamic Properties, then click the “Analyze” button for the %GC.
Once you have aligned your sequences in AlignX program, right click in the alignment pane and choose the CAMERA option (control - apple for Mac). You will be given the option of either TEXT or META file. META file takes a snapshot of the alignment pane, but it only covers what you see on the screen (this is the only option in Vector NTI Express and Express Designer). If you wish to capture the entire aligment, use the TEXT option as described below (In Vector NTI Advance).
The TEXT is also used to copy a smaller portion of the alignment. Note: if you have highlighted a region beforehand, the SELECTION button will be active, if you wish to see the complete alignment choose ALL. The option “Wrap sequences” specifies how many nucleotides/aminoacids go on each line (50 works well most of the time). Click OK to copy the alignment to the clipboard.
Open Microsoft Word program and choose Paste. You may need to change the page format or font size to make it fit to the width of the page. We recommend Courier 9.
To copy the alignment into Powerpoint, we recommend that you first paste it into Word program, then copy from Word program and do a “Paste Special” as a “Word document object” into Powerpoint program.
Alternatively you may print the alignment to a pdf file.
For versions 9.0 and later:
(1) Back up your data files by going to the Vector NTI database explorer and clicking on "Database | Database backup".
(2) Make sure you are connected to the Internet.
(3) Open the license manager. The License Manager is available from the “help” pull-down menu from any Vector NTI window. Go to “Applications” and “Static”. There is a box called “License #”.
(4) Please type the word "unregister" (case sensitive) and hit return. This action will ping our registration server, and release the license from the old machine. The software will then convert to "Demo" mode.
(5) Then, please install the software on the new computer and make sure you are connected to the internet (to download a new copy of your current version of Vector NTI , go to: https://www.thermofisher.com/us/en/home/life-science/cloning/vector-nti-software.html and click on the download a trial link for the correct version of the software; to download older versions, go to: https://www.thermofisher.com/us/en/home/life-science/cloning/vector-nti-software/vector-nti-advance-software/vector-nti-advance-downloads/vector-nti-advance-archive.html
(6) Copy-paste your license number in the "License #" box and hit "Apply".
(7) Open up the Vector NTI database and go to Database | Database Restore and bring your data files in.
If you cannot unregister the computer, please fill out the form here for a manual reinstallation by Technical Support: https://www.thermofisher.com/us/en/home/life-science/cloning/vector-nti-software/vector-nti-advance-software/support/re-install-request-form.html
To update your support, please contact bioinfosales@lifetech.com for a quote.
Only one Administrator login at a time is allowed. This message also appears when the administrator tries to login after a non-standard end of the previous session (by exiting the web browser without proper log-out, for instance). Either wait for the auto-logout period to expire or delete the file Vector NTIdls.sf from the DLS working directory to fix this.
DLS installation has not proceeded properly. Confirm that the filepath information for the folder created in the web server software is correct and that the FULL filepath is displayed in the Properties. Maintain proper case. Usually a careful uninstall and reinstall by the machine administrator is required, not a user with admin rights.
Re-launch the DLS installation wizard; when you get to the spot where it says: “You already have defined DLS DB folder at c:\Vector NTI_dls.” Would you like to redefine it?
Click on Yes. Once you get the dialog box that gives you the path, click on OK, and then click on Finish. This should fix the problem.
The web server software has not registered the new web server configuration. Verify that the CGI scripts directory has been added to the server configuration. Stop and re-start the web server software. Re-booting may also be necessary, depending on the system.
(1) If the Vector NTI Suite applications have a concurrent license not in use, it will indicate the application's name and “License available”.
(2) If one of your licensed applications is not listed/missing (e.g., Vector NTI software, ContigExpress software, etc.), then this means all User Access Seats have been claimed. Please contact your DLS System Administrator to free unused seats.
(3) If none of your licensed applications are listed, all seats have been claimed. Please contact your DLS System Administrator to free unused seats.
(4) If the operating system on your computer was recently reinstalled or upgraded, you might need your former User Access Seat freed-up and made available for your “new” computer to claim it.
(5) If your seat has been denied by the DLS Administrator. (Note: The DLS Administrator can also choose to remove the Denial, thereby reinstating your access to claim a User Access Seat.)
To fix the problem, copy the attached “Microsoft libraries.sit” file to your desktop. Expand/un-compress the file with StuffIt Expander or other software. A folder called “microsoft libraries” is created, and in it are four files/extensions. Copy them into the Extensions folder in your System Folder (files called Microsoft Component Library, Microsoft OLE Automation, Microsoft OLE Library, Microsoft Structured Storage).
A static license activates the product for a particular computer and only requires internet connectivity at the time of initial activation. The end-user is provided with a license that, in conjunction with the computer's Hardware ID, generates a key that unlocks the Vector NTI modules you are entitled to use. One static license seat allows for use of Vector NTI software on one machine.
With dynamic license, a server application called DLS installed in a customer's server manages concurrent or floating user licenses for client seats. Clients can run the program on any Windows operating system (Vector NTI Advance (up to Windows 7 32 bit) and Vector NTI Express or Express Designer (up to Windows 8)) or Macintosh operating system (through Mavericks, only with Vector NTI Express and Express Designer). When an application of the Suite is launched from a client, it requests a concurrent license “key” from the DLS web server for that seat. For example, in a 2 license/5 client seat configuration, 5 machines are eligible to use the license but only 2 of these 5 machines can actually be using the license at any given time.