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(showing articles 1 to 50 of 50)
(showing articles 1 to 50 of 50)

    0 0

    Image data can be imported to Columbus using the following import.script:

    https://perkinelmer.box.com/v/importscript

    Download the above script and move it to the server using a suitable application such as WinSCP

    https://winscp.net/eng/download.php

    The image data to be imported must be available on a mounted file system on the server. Essentially you can either copy the file/s to the server or you could mount a share to the server with the files on it. 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:

    https://access.redhat.com/solutions/448263

    In the command line below the path to the image files appears as Image_Data_Folder

    To check for suitable import types please refer to the "Import Type" menu, you will find this in the Import View in Columbus. In the command line below this appears as Import_Type

    The image import is executed by command line as follows:

    $ acapella -s User=Columbus_User_Name -s Password=Columbus_User_Password -s Host=Columbus_IP_Address -s ImportType=Import_Type -s DatasetFolder=Image_Data_Folder -s ScreenName=Columbus_Screen_Name import.script

    For instance in the following example an ArrayScan TIF, in the path /home/columbus/ImportTest, will be imported to screen name Test using the columbus user.

    $ acapella -s User="columbus" -s Password="columbus" -s Host="localhost" -s ImportType="ArrayScan TIF" -s DatasetFolder=/home/columbus/ImportTest -s ScreenName="Test" import.script


    0 0

    Symptoms:
    After installing the Helper Application, MacOS reports the following error when attempting to execute the Helper connection file:



    Cause:
    The MacOS security settings prevent applications downloaded from unknown developers from being executed.

    Solution:
    To avoid this message, visit 'System Preferences' -> 'Security & Privacy' -> 'General' and select “Allow applications downloaded from: Anywhere”.

    Note that the “Allow applications downloaded from: Anywhere” setting is hidden by default on later versions of MacOS, but can be activated using the following workflow:

    1. Open the Terminal app from the /Applications/Utilities/ folder and then enter the following command syntax:

    sudo spctl --master-disable

    Hit return and authenticate with an admin password

    2. Launch System Preferences -> 'Security & Privacy' -> 'General'

    3. The 'Anywhere' option under 'Allow apps downloaded from:' should now be available


    0 0

    Hi everyone,

    After updating to ChemDraw 16, I have encountered two issues with converting ChemDraw documents to .eps files for use in Latex documents.

    The bond width in the exported .eps file is almost twice that of the ChemDraw document. This looks bad when printing documents.

    When drawing cyclohexanes and pyranoses in chair conformation, the bold and wedged bonds becomes misaligned.

    I have also tried to convert the ChemDraw files to .pdf. This gives me the same problems.

    Is there anything that I can do about it? Some settings I can change?


    0 0

    My computer was recently updated to Windows 10 from Windows 7. Using ChemDraw Pro 2016, new structures added have a different size than in Windows 7. The old structures are larger than the new structures. For example, benzene.

    Window 7, ChemDraw 2016. HxW is 0.89 x 0.78 inches with scaling 74% of original.

    Windows 10, ChemDraw 2016, HxW, 0.70 x 0.62 with scaling 74% of the original.

    Note the preferences in ChemDraw Excel and in ChemDraw are the same on both computers. The only solution that I have found is if I run ChemDraw in Windows 7 compatibility mode, I get the Windows 7 structure size.

    How do I control the size of the structures being created in Excel. Note, I am not asking about resizing one structure, I want to create several hundred structures. The objective is to get ChemDraw to produce the same size structure, irrespective of the compatibility mode.

    I should also note that this is not a 4K monitor issue as I am not using a high resolution monitor.


    0 0

    hi, is it possible to convert a CAS-Nr (eg 50-00-0 for Formaldehyde) into a structure? In ChemDraw Professional 17, Structure/Convert Name to Structure draws the structure when Formaldehyde is entered, but can`t convert the CAS into the structure. thanks in advance, stefan

    0 0

    Is it possible to get ChemScript updated to support the latest Python versions? And to please compile 64-bit versions? ChemScript is currently very much behind the times and only getting more so. We want to use ChemScript, but our framework that we want to integrate it into is 64-bit Python 3.6.


    0 0

    Hi everybody!

    Since yesterday I cannot open ChemDraw 16.0 files from Power Point by double-clicking, but I can copy/paste perfectly fine. I didn't install or changed anything.

    Does anybody know how to fix this? Thanks in advance!

    Lara


    0 0

    Is it possible to add SMARTS function to Chemscript?

    It will be helpful for substructure recognition.


    0 0

    Does anyone know (or know where I can find out) how volocity calculates the following parameters from an object within an ROI from the measurement tab:

    1. Bounds

    2. Skeletal Length

    3. Longest Axis

    4. Polarity

    I have been able to find the relevant information otherwise in the manual but it includes 'bounds' and 'skeletal length' without further descripction.


    0 0

    There are a number of reasons why the db component may not intialise so the Blitz-0.log is the first place to look for clues as to why.

    In this post we are interested in a specific root cause - a corruption in the Lucene Index.

    On the Columbus server the log is located here:

    /var/log/columbus/db/Blitz-0.log

    Search the log for entries relating to 'Lucene'.

    If you see an error entry in the log which reads:

    Caused by: org.hibernate.search.SearchException: Unable to open Lucene IndexReader
    at org.hibernate.search.reader.SharingBufferReaderProvider.createReader(SharingBufferReaderProvider.java:96)
    at org.hibernate.search.reader.SharingBufferReaderProvider.initialize(SharingBufferReaderProvider.java:73)
    at org.hibernate.search.reader.ReaderProviderFactory.createReaderProvider(ReaderProviderFactory.java:64)
    at org.hibernate.search.impl.SearchFactoryImpl.(SearchFactoryImpl.java:130)
    at org.hibernate.search.event.ContextHolder.getOrBuildSearchFactory(ContextHolder.java:30)
    at org.hibernate.search.event.FullTextIndexEventListener.initialize(FullTextIndexEventListener.java:79)
    at org.hibernate.event.EventListeners$1.processListener(EventListeners.java:198)
    at org.hibernate.event.EventListeners.processListeners(EventListeners.java:181)
    at org.hibernate.event.EventListeners.initializeListeners(EventListeners.java:194)
    ... 76 more
    Caused by: java.io.IOException: read past EOF
    at org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:151)
    at org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:38)
    at org.apache.lucene.store.IndexInput.readVInt(IndexInput.java:78)
    at org.apache.lucene.index.FieldInfos.read(FieldInfos.java:311)
    at org.apache.lucene.index.FieldInfos.(FieldInfos.java:60)
    at org.apache.lucene.index.SegmentReader.initialize(SegmentReader.java:341)
    at org.apache.lucene.index.SegmentReader.get(SegmentReader.java:306)
    at org.apache.lucene.index.SegmentReader.get(SegmentReader.java:228)
    at org.apache.lucene.index.MultiSegmentReader.(MultiSegmentReader.java:55)
    at org.apache.lucene.index.ReadOnlyMultiSegmentReader.(ReadOnlyMultiSegmentReader.java:27)
    at org.apache.lucene.index.DirectoryIndexReader$1.doBody(DirectoryIndexReader.java:102)
    at org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:653)
    at org.apache.lucene.index.DirectoryIndexReader.open(DirectoryIndexReader.java:115)
    at org.apache.lucene.index.IndexReader.open(IndexReader.java:316)
    at org.apache.lucene.index.IndexReader.open(IndexReader.java:237)
    at org.hibernate.search.reader.SharingBufferReaderProvider.readerFactory(SharingBufferReaderProvider.java:146)
    at org.hibernate.search.reader.SharingBufferReaderProvider$PerDirectoryLatestReader.(SharingBufferReaderProvider.java:220)
    at org.hibernate.search.reader.SharingBufferReaderProvider.createReader(SharingBufferReaderProvider.java:91)

    The likelihood is that there is a corruption in the Lucene Index.

    To resolve the issue it is necessary to replace the existing /OMERO/OMERO4_4/FullText directory so that a new Index can be created.

    Stop the Columbus services:

    $ sudo /etc/init.d/columbus stop

    Change the name and make a backup of the existing/original FullText directory using the 'mv' command:

    $ mv /OMERO/OMERO4_4/FullText OMERO/OMERO4_4/FullText.bak

    Restart the Columbus services:

    $ sudo /etc/init.d/columbus start

    Check the status to make sure all services are up.

    $ sudo /etc/init.d/columbus status

    If the db component syuccessfully starts then a new FullText directory should have been created in /OMERO/OMERO4_4/

    RAH


    0 0

    Hello!

    I got problems with cyrillic symbols in ChemDraw Ultra 12.02.1076. When I choose Times new roman Cyr, or Arial cyr I get something like that:"uaaoouaaouaaouaaouo?aaaaoao?aaououaouaouo?ao?a"

    How can I use cyrrillic symbol?


    0 0

    I have a mac with external monitors. If I paste from ChemDraw to Powerpoint via the external monitor, the image is 200% size (normal size structure). However, if I try to paste from the mac monitor to Powerpoint, the structure size is 100%. What am I doing wrong?


    0 0

    Is there a way to modify the default Gaussian Interface Input Template (under the Calculations -> Gaussian Interface -> Compute Properties -> General Tab).

    Currently it has the declaration "%Mem=128MB" and we would like to change it to "%Mem=256MB".

    I've seen TechNote 386 which indicates saving a copy of the config file, modifing it and then instructing Chem3D to use that, but this is more complicated that simply modifying the %Mem setting each time.

    Thanks,


    Jonathan


    0 0

    Hello Chemdraw users,

    What is the recommended method to prepare deuterated molecules, for example, benzene-d6.

    Best,

    Eric


    0 0

    Hello Chemdraw users,

    What is the recommended procedure for creating charged aromatic rings in Chemdraw by hand? I am specifically interested in representing the delocalized pi-electrons with some form of ring with the chargd positioned inside the ring.

    For example, imidazolium cation.

    Best,

    Eric


    0 0

    Now that Mac OSX 10.14 Mojave has been released do you have any comment on compatibility?


    0 0

    Hello,

    I keep my ChemDraw templates organized in a custom folder (~/Documents/Chemistry/Templates/) and this is specified in my ChemDraw preferences. However, on launch, ChemDraw creates a ~/Documents/ChemDraw folder containing a Monomers folder and user-monomers.json.

    I cannot find a way to force ChemDraw to use a custom location for this, or to prevent ChemDraw from creating its own folder on launch.

    I am using ChemDraw Pro 17.1.1.0 on macOS Mojave.

    Any ideas?


    0 0

    As is the case for a local Columbus installation it is possible to check the exact version of Acapella running on the Columbus Plus cluster share via command line.

    For a 'local' standard installation of Columbus the command would be:

    $ acapella -version

    For a Columbus Plus installation Acapella is installed both locally and on the cluster nodes, this is usually configured as a shared directory accessible by all nodes.

    In this scenario you need to specify the path to the Acapella installation on the cluster. Example shown below:

    $ /columbus_cluster/software/Acapella/Acapella-4.1.3/bin/acapella -version

    Example of expected output:

    $ /columbus_cluster/software/Acapella/Acapella-4.1.3/bin/acapella -version
    Columbus license file - Copying of this license is not allowed. Refer to your Columbus software license agreement for details!
    PerkinElmer Acapella 4.1.3.121679 64-bit on Linux, svn revision 121679, compiled on 2018-02-08

    ---------------------------------

    RH


    0 0

    I have been trying to use ChemDraw for Excel (ChemOffice 17, Microsoft Office 365-32 bit, Windows 10, Lenovo thinkpad X1) to enumerate a combichem library. When I try to load a reaction I get a dialog box that says

    "ChemDraw Excel requires a higher level of activation for ChemDraw ActiveX Control. Some features will not work with the current level of activation."

    I have done a full uninstall and reinstall--no change. I have installed on another X1 with the same software package--no change.

    I have installed on a machine running MS Office 2016 and it works fine.

    I have played with the trust settings in excel.

    PE support has been working on it, but they say that they cannot reproduce the issue on their end.

    Any ideas from anyone?


    0 0

    Select the Batch Analysis View in Columbus:

    Select at Screen, Plate or Measurement level from the Navigation Tree

    For instance Right Click>Select to select at Screen or Plate level:

    Though to select at Measurement level just click on the Measurement. It depends how much data you want to measure i.e all in the Screen, the Plate or just the individual Measurement.

    Next click on the Analysis file in the Navigation Tree to select it:

    Finally and most importantly. Before starting the analysis use the 'Run Analysis on' menu to select the desired Server:


    0 0

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


    0 0

    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';


    0 0

    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

    /columbus_cluster/data/images

    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.


    0 0

    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-2.8.3.144770-gen.x86_64 The Columbus version installed in this case is 2.8.3 RAH

    0 0

    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-2.8.3.144770-1.rhel6.noarch Columbus-nginx-1.0.8-2.rhel6.x86_64 Columbus-omero-2.8.3.144770-gen.x86_64 Columbus-webservice-2.8.3.144770-1.rhel6.x86_64 Columbus-2.8.3.144770-gen.x86_64 Columbus-db-2.8.3.144770-gen.x86_64 Acapella-columbus-webapp-2.8.3.144770-1.gen.noarch Columbus-downloads-2.8.3.144770-gen.noarch Columbus-webapp-2.8.3.1266-1.rhel6.x86_64 Acapella-4.1.3.121679-1.rhel6.x86_64 RAH

    0 0

    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


    0 0

    A delay in the writing of the results file (results.zip) 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 ...results.zip

    URL is not a file: ...results.zip

    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 results.zip file:

    /usr/local/PerkinElmerCTG/Columbus2.8/webapp/columbus/cluster/tasks.py

    Change line 173 from

    submit_results_to_columbus.apply_async((job, cluster_conf_dir),

    countdown=5)

    to

    submit_results_to_columbus.apply_async((job, cluster_conf_dir),

    countdown=30)

    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.


    0 0

    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:

    /var/log/columbus/web/long-tasks.log

    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:

    /usr/local/PerkinElmerCTG/Columbus2.8/webapp/virtualenv/lib64/python2.6/site-packages/coca/transfer.py

    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.


    0 0

    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:

    http://forums.cambridgesoft.com/messageview.aspx?catid=65&threadid=3767&enterthread=y

    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:

    http://forums.cambridgesoft.com/messageview.aspx?catid=65&threadid=3773&enterthread=y

    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:

    http://forums.cambridgesoft.com/messageview.aspx?catid=65&threadid=3767&enterthread=y


    0 0
  • 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:

    https://access.redhat.com/solutions/448263

    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


    0 0

    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.


    0 0

    Hello,

    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??


    0 0

    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:

    Solution:

    http://www.cambridgesoft.com/support/DesktopSupport/KnowledgeBase/FAQ/details/Default.aspx?TechNote=3606&KBCats=2&KBTopics=9999&KBOS=9999


    0 0

    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: https://pitt.box.com/s/tmczz867u5js4hfxzpmufl9a5elcolsf

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

    Any ideas?


    0 0

    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

    0 0

    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!


    0 0

    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

    -Mike


    0 0

    rt,通过mopac计算得到的红外光谱数据,是通过什么算法转换为红外光谱的,搞不太明白,求大神帮忙


    0 0

    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-2.8.2.143357-1.rhel6.noarch Columbus-db-2.8.2.143357-gen.x86_64 Acapella-columbus-webapp-2.8.2.143357-1.gen.noarch Columbus-downloads-2.8.2.143357-gen.noarch Columbus-omero-2.8.2.143357-gen.x86_64 Columbus-webservice-2.8.2.143357-1.rhel6.x86_64 Columbus-2.8.2.143357-gen.x86_64 Acapella-4.1.3.121679-1.rhel6.x86_64 Columbus-webapp-2.8.2.1205-1.rhel6.x86_64 RAH

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    Columbus creates and utilizes 2 databases, the omero4_4 db and also the columbus_webapp db. Both are backed up by a script which runs under /etc/cron.daily and are, by default, stored in /OMERO/OMERO4_4/db_backup To view details of how to backup the omero4_4 db, click here To manually backup the columbus_webapp you must first switch to the 'columbus' user account and issue the following command: $ su columbus - $ pg_dump -v -Fc -f /OMERO/OMERO4_4/db_backup/columbus_webapp-TEST.pg_dump columbus_webapp pg_dump -v -Fc -f - the arguments used as part of the pg_dump process to create the backup /OMERO/OMERO4_4/db_backup/ - the location where you want the backup to be stored columbus_webapp-TEST.pg_dump - the name of the backup file columbus_webapp - the name of the db being backed up RAH

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    The workflow below details the process of removing the main components of a Columbus installation. Note that this will not revert the system to a vanilla installation. Those package dependencies which were provided by the operating system will remain, as will the user accounts which were generated by the Columbus installation scripts.

    WARNING: This will erase ALL user data. After these steps have been performed it will only be possible to recover the data if you have an appropriate backup available.

    Removing the Columbus packages

    1) Connect to the Columbus server via PuTTY/Terminal

    2) Stop the Columbus service

    $ sudo /etc/init.d/columbus stop

    3) Delete the Columbus file repository

    $ sudo rm -rf /OMERO/OMERO4_4

    4) Access the postgres user account

    $ sudo su postgres -

    5) Delete the omero and webapp databases

    $ dropdb omero4_4

    $ dropdb columbus_webapp

    6) Exit the postgres user account

    $ exit

    7) List all installed Columbus and Acapella packages

    $ rpm -qa | grep -E 'Acapella|Columbus'

    8) Delete any Columbus/Acapella packages listed in the output of the command in step 7)

    $ sudo rpm -e --nodeps

    9) Check for any remaining packages:

    $ sudo rpm -qa | grep -E 'Acapella|Columbus'

    The output should be empty.

    10) Remove the Columbus software repository from the /etc/yum.repos.d directory (RedHat Enterprise Linux), or the /etc/zypp/repos.d directory (SuSE Linux Enterprise Server).

    The PDF copy of this technote is available for download, here:

    https://perkinelmer.box.com/s/fe4yve96zaw5gdltzjsbzk27ks8tr13y


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    These are backups of the second psql database instance, columbus_webapp. It stores all data that Columbus needs in addition to what Omero holds. For example the tables stored under the columbus_webapp include login and authentication attempts for users connecting to Columbus from a 3rd party app via the webapp, celery queue information and also contains things like the publishing status, cluster job status and the remote references for the measurements that have been forwarded to Amazon S3 during import for the cluster functionality. It’s use/relevance depends on the whether or not you are using features like publishing or cluster computing. RAH

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    Celery is a task queuing service. It's primary use is for managing image rendering and export jobs being submitted to the Columbus server via 3rd party applications e.g. Spotfire. The Celery system picks these jobs from the queue runs them asynchronously and when complete prepares a response which is then picked up by the webapp to return to a client or webpage. Celery runs as another service component, it is started and stopped via /etc/init.d/columbus which actually uses /etc/init.d/columbus-celeryd. If the celery service doesn't respond to the standard /etc/init.d/columbus script then you can call the columbus-celeryd script directly using: $ /etc/init.d/columbus-celeryd stop/start/restart/status The Celery service starts multiple worker nodes for accepting image rendering requests, the workers log information regarding those jobs to /var/log/columbus/web/columbus-images-service.log. RAH

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    Initially you should try starting/stopping the celery service using: $ /etc/init.d/columbus-celeryd (stop/start/restart/status) If the celery service is 'hung' and does not respond to either /etc/init.d/columbus stop, or $ /etc/init.d/columbus-celeryd stop then it might be necessary to kill the Celery related processes. Typically you will see more than 1 process. There's a master but depending on the activity there will be several worker processes. They all run under the columbus account e.g: $ ps f -fU columbus UID PID PPID C STIME TTY STAT TIME CMD columbus 12688 12687 0 08:01 ? S 0:01 nginx: worker process columbus 12782 1 0 08:01 ? Sl 3:11 /usr/local/PerkinElmerCTG/Columbus2.8/webapp/virtualenv/bin/python -m celery.__main__ worker --app=columbus -n c columbus 9627 12782 2 13:25 ? Sl 0:01 \_ /usr/local/PerkinElmerCTG/Columbus2.8/webapp/virtualenv/bin/python -m celery.__main__ worker --app=columbus columbus 9731 12782 0 13:25 ? Sl 0:00 \_ /usr/local/PerkinElmerCTG/Columbus2.8/webapp/virtualenv/bin/python -m celery.__main__ worker --app=columbus columbus 9751 12782 3 13:25 ? Sl 0:01 \_ /usr/local/PerkinElmerCTG/Columbus2.8/webapp/virtualenv/bin/python -m celery.__main__ worker --app=columbus You'd need to kill the master with PID 12782 but before that the slave processes must be killed, you can use pkill -P with the parent id to do so: $ sudo kill -9 -P 12782 # Now kill the master $ sudo kill -9 12782 Now if you start Celery again it should bring it back to life. If this doesn't help then there is potential for something to be broken meaning that the image rendering jobs will fail, if that is the case then check the /var/log/columbus/web/columbus-images-service.log file for errors and forward on to the PKI informatics support team for further troubleshooting advice. RAH

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    On a default Columbus+ server users have the option to submit batch analysis jobs locally or within the cluster environment.

    Its not possible to restrict users to one method or the other via the Columbus UI, but by modifying the source code its possible to remove the local analysis option, meaning users are forced to submit batch analysis jobs to the cluster.

    The following information is valid for Columbus version 2.8.2 and may differ in future versions.

    The following change must be made:

    /usr/local/PerkinElmerCTG/Acapella-4.1.3/AcapellaResources/AcapellaColumbusWebapp/ProcLib/columbus/nav_batch.proc

    line 429

    analysisServerOptions = vec(COMPUTE_ON_LOCAL_SERVER);

    change to

    analysisServerOptions = vec();

    Note, it is recommended to make a backup of the nav_batch.proc file before modifying. Any modifications will be reverted during the next Columbus update.


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    If the 'Insert Image Column' Dialog appears cropped and messed up like this:

    - Exit Spotfire

    - Right click Desktop ... Display Settings

    - Set Scale and layout to 100%

    - Sign out of Windows

    - Sign in and it should appear as normal.

    The inspiration for this Technical Note comes from:

    https://support.tibco.com/s/article/Spotfire-analyst-client-has-display-or-weird-boarder-issues-when-custom-text-size-scale-is-changed-on-a-Windows-7-desktop-machine


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    Hi,

    I have a user who is getting Activation ID/Host owner mismatch error, he has emailed support (perkinelmer@flexnetoperations.com) a number of times with no response. Which is concerning.

    Can someone help?

    Thanks,

    Fraser
    University of St Andrews


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    After a user logs in to Columbus the session is kept alive as long as the browser is running with a Columbus application in any of the tabs. More precisely this is for all the pages like navigation, image analysis, import, export etc, not for the admin pages or job status page. The session is killed if a user logs out (as long as there are no background jobs running under this session). The session is also killed 10 minutes after the user closes the browser (or the tabs) that displayed the Columbus app. When background jobs are running the session will not be terminated, the 10 minute timeout would be applied at the point the background job finishes. RAH

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    For servers where HTTPS support has been enabled for the Columbus login and webadmin pages, its possible to disable SSLv3 encryption and leave only TLSv1 support enabled. To do that users must add a line to the server section of the /usr/local/PerkinElmerCTG/Columbus/webapp/server/config/nginx.tmpl file to specifiy ONLY the supported protocols. See the last line in the excerpt below as an example.

    ~~~~~~~~~~~~~~~~~~~~~

    # https server for /login and /webadmin requests
    server {

    listen ${https_port} ssl;
    ssl_certificate ${https_certificate};
    ssl_certificate_key ${https_key};

    # turn off SSL encryption
    ssl_protocols TLSv1;

    ...

    }

    ~~~~~~~~~~~~~~~~~~~~~

    The Columbus service must be restarted after making the modifications.

    $ sudo /etc/init.d/columbus restart

    Note: Any modification will be overwritten during the next Columbus update.


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    Is there an upper limit to the size of image files imported to Columbus?

    I have been unable to successfully import TIF files > 30 MB. I am using the Import Type method 'Columbus CSV' and have had no issues importing TIF files

    ___

    Columbus could not handle the request:
    Assertion failed: status
    status: 0

    /usr/local/PerkinElmerCTG/Acapella-4.1.2/AcapellaResources/AcapellaColumbusWebapp/ProcLib/columbus/navigator.proc(260) [Columbus::nav_DisplayImage]: 
    /usr/local/PerkinElmerCTG/Acapella-4.1.2/AcapellaResources/AcapellaColumbusWebapp/ProcLib/columbus/util_imageview.proc(262) [::Assert]: Assertion failed: status
    status: 0

    ___

    A possible solution to my problem may require tiling/segmenting these large image files into smaller image files?