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    Jobs which have been successfully submitted to the cluster job manager may be canceled at any time via the cluster job status page.

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    Jobs which have been successfully submitted to the cluster job manager may be canceled at any time via the cluster job status page. However, its not possible to cancel a job during the job submission phase via the Columbus user interface. If a job has stalled during submission it will not prevent subsequent jobs from running, nevertheless the job can be cleaned up via the psql command line interface of the columbus_webapp database.

    1) connect the the columbus server via ssh
    2) switch to the columbus user account

    $ su - columbus

    3) connect to the columbus_webapp database

    $ psql columbus_webapp

    4)Jobs can be selectively removed from the job status page using either their unique job ID, or by their status.

    - to clean up a job based on the job status ID (example uses ID 100):

    columbus_webapp=> delete from cluster_jobstatus where id=100;

    - to clean up ALL jobs with a status listed as 'Submitting':

    columbus_webapp=> delete from cluster_jobstatus where state='SU';

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    In ColumbusPlus the Remote Reference is a requirement for the Cluster system to access a corresponding measurement's images and perform the analysis. You will find Remote Reference under the Measurement Info tab in the Browse view. If the Remote Reference is missing a Cluster analysis will fail. If your system has been in use and data imported prior to being upgraded to ColumbusPlus you will find that any existing measurement data will not have a Remote Reference. To set the Remote Reference manually using measurement data available in Columbus:

    Export to the shared file system

    - Switch to the Export View

    - Select Export Options - Method - Export to Disk (*)

    - Export Folder - the path to the shared file system used by the Columbus Cluste

    - Image Data - tick checkbox and select SinglePlane TI

    - Start Export

    If you are uncertain of the Export Folder path refer to the import_path parameter in the /etc/columbus/*.config file

    For purposes of this example the Export Folder is


    To export to this path the acapella user requires write access. This would normally be the case if the shared file system is owned by columbus (acapella user typically being in the same group) but if you see a warning to the effect:

    Selected directory /columbus_cluster/data/image1 does not exist.

    Check and potentially change the permissions to allow acapella to write, if writable you will see:

    Selected directory /columbus_cluster/data/images OK.

    Once exported by default the folder created will bear the name of the Screen appended with the Screen ID within []

    For purposes of this example Reference Screen is the name of the Screen and the Screen ID in Columbus is [3152]. Therefore the first folder created is Reference Screen[3152] then a plate and finally the measurement folders containing the images. The full path in this example being:

    /columbus_cluster/data/images/Reference Screen[3152]/Plate[3202]/2008-06-12T123202+0100[3252]/2008-06-12T123202+0100[3252]

    Confirming the above path on the Columbus Server

    - Log into the Columbus server using ssh

    - Navigate to the top level folder in the Export Folder path i.e the measurement level

    - Get the path, for instance using the above pwd command

    - Switch to the Browse view in Columbus interface

    - Edit the Remote Reference adding the path such as above but append ‘file://‘ to the beginning.

    When adding the remote reference be mindful of any escape characters, for instance spaces in the path. Our screen started with 'Reference Data' in which case \ would need to preceeding any spaces ‘Reference\ Data'. If a special character has not been accounted for you will typically see the following error on attempting cluster analysis:
    1. Error Message: tcgetattr: Inappropriate ioctl for device Connection to gcc1 closed.
    Ammended path for this example:

    file:///columbus_cluster/data/images/Reference\ Screen[3152]/Plate[3202]/2008-06-12T123202+0100[3252]/2008-06-12T123202+0100[3252]
    1. (*) If you are only exporting a single measurement as oppose to a large Screen and do not need to preserve the folder hieracy the exported subfolders can be simplify by choosing: Screen or Screen+Plate or the default Screen+Plate+Measurement in Generate Subfolders. You will find this under the left drop down arrow at the bottom of the Select Export Options section.

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    Connect to Columbus via SSH. Issue the following command: $ rpm -qa | grep -i columbus-2 example output: [root@BigRed ~]# rpm -qa | grep -i columbus-2 Columbus- The Columbus version installed in this case is 2.8.3 RAH

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    Connect to the Columbus server via SSH. Issue the following command: $ rpm -qa | grep -E 'Columbus|Acapella' Example output: [root@BigRed ~]# rpm -qa | grep -E 'Columbus|Acapella' Acapella-server- Columbus-nginx-1.0.8-2.rhel6.x86_64 Columbus-omero- Columbus-webservice- Columbus- Columbus-db- Acapella-columbus-webapp- Columbus-downloads- Columbus-webapp- Acapella- RAH

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    I cannot get my Chemdraw excel plugin to work, although it had been functioning previously. I have worked through both enabling the add-in, as well as checking the ChemDrawExcelAddIn17.ExcelAddIn registry values.

    Neither has helped

    Can you offer any additional solutions?

    Windows 10 64 bit

    Microsoft office 32 bit

    Chemdraw professional 17.1

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    A delay in the writing of the results file ( to the shared file system can cause one or more of the following errors leading to a failure of batch analysis:

    Timeout: File is not a valid zip file

    URL is not a file:

    In vesions of ColumbusPlus up to 2.8.2 the following file on the server can be modified to increase the amount of time before reading the file:


    Change line 173 from

    submit_results_to_columbus.apply_async((job, cluster_conf_dir),



    submit_results_to_columbus.apply_async((job, cluster_conf_dir),


    This example increases the countdown time to 30 seconds, though it may need to be increased further. After changing restart Columbus for changes to take effect

    $ /etc/init.d/columbus restart

    In versions above 2.8.2 (i.e soon to be released 2.9.0) the strategy to check the results is changed further. It features as timeout on line 50 of aforementioned file, however in light of new strategy it is highly unlikely this value need to be changed but is shown here for reference.

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    Normally the Remote Reference is populated automatically after import to ColumbusPlus. However if the transfer service that transfers the data from the local storage (/OMERO/OMERO/s3-upload) to the shared file system is delayed it can lead to the Remote Reference being missing.

    Typically no errors appear in the Colunbus Interface but can be found on the server in the file:


    A typical example might include:

    (No more files to transfer but measurement.done file did not appear after 600 seconds)

    It is possible to increase the 600 second transfer timeout. In the file:


    Line 183 keep_retry_time = 600 # seconds

    Increase the timeout to allow the transfer service more time to start copying files.

    After editing the file restart Columbus for changes to take effect:

    $ /etc/init.d/columbus restart

    In versions above 2.8.2 (i.e soon to be released 2.9.0) the strategy to transfer data is changed to avoid this.

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    In ColumbusPlus the Remote Reference is a requirement for the Cluster system to access a measurement's corresponding images and perform a batch analysis. You will find Remote Reference under the Measurement Info tab in the Browse view. If the Remote Reference is missing a Cluster analysis will fail. Essentially it is a URL being the path to the images on the shared file system.

    There are a number of reasons why the Remote Reference might be missing, these include:

    Data imported before the Cluster was available. This can be made good and is covered here:

    Data import repeated as a result of missing data. For example data imported was started but stopped before completion. The import was then repeated to patch in missing data however the Remote Reference is missing. This behaviour is improved in Columbus versions above 2.8.2.

    Data was transferred from Harmony to Columbus. This behaviour is improved in Columbus versions above 2.8.2.

    Data was imported to ColumbusPlus, the Custer system was available but still the Remote Reference is missing. This further scenario and reasons why are covered here:

    In all of the above the data can be exported to the shared file system and the Remote Reference made good manually as is covered here:

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  • 10/23/18--12:48: Local Import with Columbus
  • A local import though Columbus accesses data through the server's Linux file system. Whereas a client import uses the Helper to transfer data from the source to the server via the client.

    A local Import can offer a distinct advange especially in the case of data accessed via a network share. Essentially it involves fewer network hops getting the data to the server, thus quicker and less to go awry. There is also no requirement for the client to remain connected via the Helper or otherwise after local import has been initiated.

    The image data to be imported must be available through the Server's Linux file system. Essentially you can either copy the file/s to the server or more practically you can mount the network share to the server. Perhaps one of the more common shares would be a Windows share to the Linux system, in which case please see the following technical note which you might find useful:

    The "columbus" user account on the server must have read access to this share in order to perform the local import and read the files, please bear this in mind when setting up the mount. After setup on the Linux system:

    - Log into the Columbus web interface and go to the Import view

    - The Helper needs to be installed and a connection file downloaded as is typical but this is merely to access the Import view

    - Select the Import Type

    - Remove any current Source Folder path starting client://

    - Enter the Soure Folder path

    Essentially this is the path to the files on the server starting with a forward slash /

    You can also use the path starting Local:// or local:// (this was a requirement in legacy versions of Columbus). A caveat for using a local import is that it is not possible to browse the server's file system through the Columbus web interface. Whist this sounds like a bit of a hurdle providing you know the name of the mount point and have the mapped drive available for reference you can easily derive the path to the files. Essentially it would start with /, the name of the mount point, followed by the path to the files on the file share. For instance if the mount point is called fileshare and the data is available in the directory path /data/dataset/ the full path would be /fileshare/data/dataset/

    - Choose Import Mode (default Normal)

    - Select a Naming Preference

    - Start the import

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    ChemDraw Mac freezes (stops responding) when trying to save an existing ChemDraw file (edit).

    The exisiting FAQ fix does notwork retrospectively so work is lost. It also only works once (OSX10.14 so is a persistent fault that effectively disables ChemDraw. Problem seems to be machine specific - iMac late 2012 has the fault. MacBookPro 2017 works OK.

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    I am trying to estimate end-to-end distance (R) of molecule in Chem3D ver.16.

    I selected two farthest atoms, and then went to Structure -> Measurements -> Display distance measurement.

    Is this a right way to estimate R of my molecule??

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    Hello support team,

    When I copy and paste a scheme from Chemdraw 16 to PowerPoint 365 (Windows 10) it doesn't get scaled to full page.

    P.S: I just noticed this problem was already discussed and answered in the forum:


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    A week ago I updated to ChemDraw 18. Since then i have not been able to paste a structure from ChemDraw into Word without issue. A properly formatted structure in ChemDraw will end up with all atom labels having the stacked alignment. Note - this is not just for labels in the middle of a chain, rather, labels at the end also take on a stacked alignment. Even subscripts will line up vertically rather - a different behavior than a "Stacked Vertically" text alignment option applied within ChemDraw.

    Copies of the docx, cdx, and a pdf are included at the following link:

    So far I have uninstalled ChemOffice, restarted, and reinstalled. No luck.

    Any ideas?

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    Take the following question as an example: I would like to export (e.g. WriteFlex) an image with a stencil overlay. How do I combine an image and stencil to a single image item? #require AcapellaUserInterface a1_0002(|image) a1_0002_objects(image | objects) UI::C_ImageView( "", ["channel1"], image_color=["gray"], stencil_labels=["overlay1"], stencil_color=["colorset@rainbow"], stencil_style=["body"], UI=UI | UI ) UI::C_ImageViewSetFrame(image, objects.body, UI=UI | UI) UI::C_ImageViewGetImage(0, UI=UI | visualimage=Visual.image) ======================================= With older versions (Acapella 4.x) replace ["string"] with vec("string") RH

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    Hi, I'd really like to know how to prevent ChemDraw from automatically numbering the carbon atoms in molecules brought in using the Name to Structure function. It's particularly annoying because when I delete the numbers and then move or edit the molecule in any way, the numbers reappear!

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    I have Asus zen max pro set in which I am not able to install the google chrome. I thought that it may be the devices issue that is why I contracted Asus laptop battery replacement but there I got to know that my device is absolutely fine then what is the exact issue and kindly tell me the valid solution regarding this issue.

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    Hello all,

    Recently we launched ELN 12.1.10 and at the moment we have an error that we hope to have a quick fix for.

    The error:

    "Sorry, while accepting previous revisions, This method or property is not available because the document is locked for editing."

    Any help would be appreciated!

    Thank you


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    The following command will list the packages that are installed with Columbus: $ rpm -qa | grep -E 'Columbus|Acapella' The output for Columbus 2.8.2 would look like: $ rpm -qa | grep -E 'Columbus|Acapella' Columbus-nginx-1.0.8-2.rhel6.x86_64 Acapella-server- Columbus-db- Acapella-columbus-webapp- Columbus-downloads- Columbus-omero- Columbus-webservice- Columbus- Acapella- Columbus-webapp- RAH

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