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FAQ: Frequently Asked Questions
Common questions
Q: Licensing issue for major version upgrade...?! What do I do?
A: Please select 'Upgrade a license from an older Workbench' in the 'License Manager' when starting up the new version of the Workbench.
Read more: http://www.clcbio.com/index.php?id=141&manual=Upgrade_license.html.
Q: How do I install plug-ins or upgrade my license on Windows Vista?
A: To do this, you need to open the Workbench with administrator rights: Right-click the CLC Workbench icon and click "Run as administrator". Then install the plug-in as described in the help. When you restart the Workbench after having installed the plug-in, you need to open it with administrator rights again: Right click the CLC Workbench icon and press "Run as administrator".
Q: Can I rearrange the layout of a sequence or alignment for publishing?
A: You can change the layout using the Side Panel and the zoom functionality.
If you need more detailed control over e.g. how annotation labels are placed etc, you can export the data in a vector graphics format. Click Export Graphics and select the .svg format.
SVG is a vector graphics format which means that all the elements in the view can be edited and moved individually. Open the exported graphics in a vector graphics editor (if you don't have one installed, try the free Inkscape). Now you can re-arrange all the elements as you like.
Q: When I print from the Workbench I don't get what I see on the screen, the output is either too big or too small.
A: The images sent from the Workbench have a resolution of 600dpi. If the settings for your printer specify a different image quality, the image will be scaled. To print the image in the proper size, you need to access the properties of your printer after pressing Print from the Workbench. Set the printing resolution to 600dpi, and the image should be printed in the right size. For details on how to set the printing resolution of your printer, consult your operating system manual or printer manual.
Q: How do I right-click on a Mac with one-button mouse?
A: The right-click is meant for users with a two-button mouse. For Mac users with a one-button mouse: press the Ctrl key while clicking with the mouse. This is equivalent to "right-clicking".
Q: Do you have to paste sequences manually?
A: In all CLC's workbenches it is possible to import and search e.g. NCBI for sequences. You can also import sequences in different formats, e.g. Fasta, Text Newick, GenBank, SwissProt, Embl, Pir and Vector Nti - click here to get a full list of the supported formats. The last option is to copy paste the sequences manually.
Q: Do you have to scroll to see a whole DNA sequence?
A: Our workbenches have several ways of changing the way a sequence is displayed. For example: "Wrap", "Zoom out", "Fit width"... The zoom tools are found in the upper right corner of the workbench.
Q: How do I locate my error logs?
A: On Mac OS X:
Library -> Application Support -> CLC bio -> Workbench -> log
On Windows 2000 and XP::
C:\ -> Documents and Settings -> %username% -> Application Data -> CLC bio -> Workbench -> log
On Windows Vista and Windows 7:
C:\ -> Users -> %username% -> AppData -> Roaming -> CLC bio -> Workbench -> log
Q: Can I share my data across CLC's programs?
A: Sharing data with Free Workbenches:
The Workbenches are fully integrated across platforms. That means data can be exchanged seamlessly between all workbenches, and viewed and handled according to the features available in the current workbench.
The exchange of data is of course platform independent, so mixed environments with Mac, Windows, and Linux computers is handled without any problems!
In a CLC Free Workbench, data can be shared by exporting a collection of files in zip format from within the Workbench and sending this file to another user.
Sharing data with Commercial Workbenches:
You can easily share data by adding a location on a shared network drive. Simply click the "Add Location" button at the top of the Navigation Area and select a folder shared network drive. You will now have direct access to this folder from within the workbench.
Q: Is it possible to wrap sequences and alignments?
A: Yes - both functions are available in the "View Preference" side panel, where you can also toggle a vertical space every 10 residues.
Q: Can I change a sequence name?
A: In the Navigation Area, sequence names can be changed by clicking the sequence and pressing the F2 key. In the views (sequence view, alignment view etc), the name can be changed by right-clicking the name and select Rename Sequence.
Q: Where can I locate my user settings file?
A: You have to look for a file called usersettings.xml which you can find by looking the way we have listed below.
On Mac OS X:
Library -> Application Support -> CLC bio -> Workbench -> Settings -> %workbench name% -> %version number%
On Windows 2000 and XP:
C:\ -> Documents and Settings -> %username% -> Application Data -> CLC bio -> Workbench -> Settings -> %workbench name% -> %version number%
On Windows Vista:
C:\ -> Users -> %username% -> AppData -> Roaming -> CLC bio -> Workbench -> Settings -> %workbench name% -> %version number%
Q: I can't get a license - the program is unable to connect to your server?
A: Many universities and large organizations use proxy servers, which means you have to know these proxy settings in order to get things working - you may have to contact your local network support in order to get it set up properly.
In some cases it could be a local firewall or security package that is prohibiting the program to establish a connection to our server. Make sure to check that CLC's software is not being blocked by such tools.
If you're in doubt how to get the license registration process going - once you have established the connection - you may want to take a look in our license registration manual, which you can read by clicking here (500K PDF-file).
Q: When trying to access the 3D viewer I get an error - something needs to be installed?
A: Java3D is required for running CLC Protein Workbench and CLC Main Workbench - currently it is these two workbenches which include our 3D viewer.
When running Mac OS X 10.3 (Panther) you need to install Java3D, as it is not included as standard. Click here to go to the download site.
If you run Windows and get this error, you need to install or update DirectX. Click here to go to the download site.
Q: How do I find sequences on my computer?
A: Your files are placed in the folder that your location points to. Place the mouse cursor on the location (the top-level folder in the Navigation Area) and you will see where your files are located.
Q: How do I email a sequence to a colleague?
A: Your files are placed in the folder that your location points to. Place the mouse cursor on the location (the top-level folder in the Navigation Area) and you will see where your files are located. When you write your email, simply attach the file from this folder.
Q: Can I start the program without loading the user settings?
A: Yes, press and hold down shift while starting the program.
Q: How do I back-up my data from the CLC Workbench?
A: Your files are placed in the folder that your location points to. Place the mouse cursor on the location (the top-level folder in the Navigation Area) and you will see where your files are located. Simply create a back-up of the files and subfolders in this folder.
Q: How do I change the way a sequence looks on print?
A: The workbench uses a WYSIWYG principle: What You See Is What You Get. This means that you should use the options in the Side Panel to change how the sequence looks on the screen. When you print it, it will look exactly the same way on print as on the screen. In the print dialog, you can also use the Print Setup to specify how many pages should be used to print the sequence.
Q: Is the workbench license linked to a computer or a person?
A: The license is linked to a computer. This allows more people e.g. in a lab to do advanced analysis.
Q: When I open a view, it looks different than when I saved it. What happened?
A: When you make adjustments to the Side Panel, e.g. how annotations should be shown, which restriction sites should be shown etc, the adjustments are not saved when you save the sequence. Instead, you have to click the Settings button in the upper right corner (
) of the Side Panel and choose "Save settings". This will enable you to save the settings under a given name and next time you open a sequence, you can apply these settings. If you check "Always apply these settings", they will be applied each time you open a view of a sequence.
Q: Can i install and use a CLC Workbench on my 64 bit Mac computer?
A: Yes, you can. Please follow these steps.
- Download and install Java for Mac OS X 10.5 Update.
- Choose Java 1.6 (64bit) as the default JRE in these two steps.
- Open the Java Preferences in /Applications/Utilities/Java/Java Preferences
- In the "Java Application Runtime Settings" drag one of the 64 bit Java versions to the top of the list. (Screenshot)
- For optimum performance re-install the Workbench after choosing the 64 bit java as default.
This will allow the installer to detect that your machine is 64 bit capable and configure the workbench appropriately.
Q: How do I import the NGS CELL-generated .cas file into a workbench?
A: The import should be a breeze if you regard these points
- do not move the .cas file or the original reads and reference files after generating the .cas file.
- the .cas file has to reside in the same folder as the command line program and it has to be imported from there.
- the .cas file has to be generated by the newest version of the NGS CELL program and imported into the newest version of the genomics workbench.
Known issues
Drag'n'drop blocked by Windows Vista
When a CLC Workbench is run in Administrator mode on Windows Vista, drag'n'drop of files into the workbench may be blocked. This is because Windows Vista by default disallows drag'n'drop from an application running at a lower security level to one running at a higher level.
Printing in landscape on Windows
On Windows when running Java 1.6.0: When printing graphics in landscape mode, the output is garbled: header and footer are interchanged and the graphics is mirrored horizontally. Workaround: Upgrade to JRE 1.6.0_01 from http://www.java.com/getjava/ or download a new Workbench installer including java.
VPN network connections unsuited for first time launches of demo workbenches
An error occurs if a VPN network connection is used the first time a demo-version is launched. Problem seems to persist.
Error message when starting up the workbench (few instances on the JRE6/Windows combination): 'The JVM could not be started. The main method may have thrown an exception.'
You will need to check the .vmoptions file located in the Workbench installation directory: C:\Program files\CLC Main Workbench 3\clcmainwb3.vmoptions
By default, this file contains a single line with text such as "-Xmx1534m", instructing the JRE to allocate, in this case, 1534MB of RAM for the virtual machine. The number 1534 depends on the machine and is set to 50% of the available physical RAM by our installer. However, this may be too high on some machines, for instance if you have a lot of physical RAM. Therefore please change the contents to eg "-Xmx256m" (256MB). You will need administrator privileges to edit the file.
On Mac OS X 10.3: When printing there is no output
Workaround: Export graphics to fx pdf and print from that document or upgrade to Mac OS X 10.4.
Wrong color on annotations when exported to .eps format
If a sequence carrying annotations are exported to .eps graphics format, the annotations may appear black in the exported file. To export with the correct annotation color disable the "Use gradients" in the Side Panel of the sequence view.
It is not possible to create a new folder or file in "My Documents", "My Music", "My Pictures", and "My Videos" through the workbench.
There is a known bug in Java, which causes the above folders to be marked as read only.
