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    0 0

    Hello everybody. I am having a problem rendering the structures of molecules like buckminsterfullerene and hemocyanin. Here is the screenshot: http://www.tiikoni.com/tis/view/?id=3caae41

    I also have a false display of the double bonds in allenes (C=C=C) (instead of the double bonds being perpendicular to each other, they are parallel).

    How can I change that?

    With best regards,

    Philipp Macher


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    There is a known issue connecting to Columbus if the client PC running the clients is utilizing Java 8 - see forum post here:

    http://forums.cambridgesoft.com/messageview.aspx?catid=55&threadid=3188&enterthread=y

    However it has recently come to light that there is also a separate java compatibility issue which might also cause problems when attempting to connect to Columbus via the OMERO clients.

    SSL ciphers are not supported by Java 7u85:

    http://blog.openmicroscopy.org/tech-issues/2015/07/21/java-issue/

    It is necessary to patch the etc/grid/templates.xml file as per the note above but Glencoe have also added a fix for Columbus users in the latest OMERO clients available here:

    Windows:

    https://perkinelmer.box.com/s/7wya1smajvn0c3v61f9nurg6oqhvtdjj

    Mac:

    https://perkinelmer.box.com/s/ougp1zc9fy9y4xbcj5k5gyisgp7x4sgn

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

    - PerkinElmer Technical Support


    0 0

    As per the document “Graphical Representation Standards for Chemical Structure Diagrams”, (IUPAC, Pure and Applied Chemistry 80, 277–410)
    section GR-6, there exisits a shorthand that indicates all resonance forms of a delocalised system by a curve or circle.

    I'm wondering if there is a method or an implimentation for draying such curved delocalised bonds within Chemdraw 15.1 (or earlier). In particular I'm interested in complex curves and non-closed curves, for example, such as those that might be used in to depict bridged bicylics molecules or the allyl radical. (The middle and right-most figures in the image. From the above guidelines, section GR-6.1, p 380.)


    I'm currently using straight, dashed bonds in my structures, but the IUPAC guidelines state that they should be solid. If a nice, clean method doesn't exist I'd like to make a feature request for this, as it is IUPAC recommended for structures. Any sort of help would be much appreciated.


    0 0
  • 08/06/16--06:59: Columbus 2.7.1 Upgrade
  • Can we upgrade directly from v2.6 to v2.7.1, or do we need to upgrade through v2.7?

    Thanks,
    Chris


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    I'm currently using IE8 on my (company) PC, I don't have the possibility to upgrade to higher IE versions.

    I have a chemical database on Filemaker Pro, which normally uses the CS ChemDraw ActiveX control plugin from Internet Explorer. Even though the plugin is installed, I repeatedly get the following message when I try to look at a structure embedded in Filemaker Pro:

    "You currently use Microsoft Internet Explorer 8.

    This page will use CS ChemDraw ActiveX control, but isn't installed on your computer.

    Do you want to install it now?"

    In the past, the chemical structures appeared correctly.

    Is it possible for instance that a security patch prevents FM Pro from accessing a third application plugin?


    0 0
  • 08/06/16--06:59: Release of Columbus 2.7.1
  • Highlights of Columbus 2.7.1 release include the following (full details are available at the bottom of this message as well as in the release notes):

    • Support for additional HCS readers and other imaging modalities including our Vectra Quantitative Pathology Imaging system
    • Performance and security enhancements
    • Search/filter enhancements
    • Minor bug fixes
    If you have not received a notification via email with a link to your personalized PerkinElmer Download Center, please reach out to us. Thanks.

    Details of new features and bug fixes:

    -Added ability to import Celigo datasets (COL-1466)

    -Added ability to import Ensight/Kaleido 1.2 datasets (COL-1467)

    -Added ability to import Vectra datasets (COL-1589)

    -Added ability to import MetaSystems datasets (COL-1468)

    -Added ability to import Zeiss datasets (COL-1469)

    -Added ability to import Biotek datasets (COL-1496)

    -Added ability to filter tables showing published status of screens and plates (COL-1276)

    -Improved metadata capture for Arrayscan datasets (COL-1610)

    -Improved metadata support for Columbus exported and transferred datasets, flat-field correction and orientation matrix information is maintained (COL-1424, COL-1503, COL-1504)

    -Improved user interface, removed inconsistencies (COl-1227, COL-1312, COL-1407)

    -Improved default memory settings, increased maximum Java VM heap space to avoid out of memory errors (COL-1507)

    -Improved publishing of assay definition layouts, concentration values and unit strings are now in separate columns in the csv-text file download to be easily consumed by the High-Content-Profiler (COL-1637)

    -Security enhancements for user authentication and file uploads (COL-1634, COL-1594)

    -Fixed problem when importing timeseries Cell Voyager 7000 datasets where images where created out of sequence (COL-19)

    -Fixed problem with email validations on user profile page (COL-952)

    -Fixed problem when importing ScanR datasets with similar channel names which caused an import failure (COL-1285)

    -Fixed version number of SOAP web-service to match Columbus version (COL-1382)

    -Fixed problem with printing an image analysis sequence including a "Filter Image" building block (COL-1425)

    -Fixed problem where images from Columbus when displayed Spotfire did not have the same channel coloring (COL-1456)

    -Fixed problem with automatic log file cleanup, where old PostgreSQL log files have not been removed (COL- 1491)

    -Fixed problem importing analysis scripts with too long file names (COL-1578)

    -Fixed problem where well result tables in the secondary analysis page and error logs could not be downloaded (COL-1629)


    0 0
  • 08/06/16--06:59: Error Connecting
  • Had no issues connecting previously, but now a lengthy error message is the only result when trying to connect. "Sorry, an error occurred while opening a client connection: while setting up connection to central database: an error occurred while executing the SQL "Open": A network-related or instance-specific error occurred while establishing a connection to SQL server. The server was not found or was not accessible. Verify that the instance name is correct and that SQL server is configured to allow remote connections. (provider: SQL Network Interfaces, error: 26 - Error Locating Server/Instance Specified)" Our IT dept cannot seem to fix this. The desktop that serves as the SQL server is operating seemingly normally. I was able to log into the SQL server application just fine from the local server desktop. What can the issue be?

    0 0

    I'm wondering why when you start up E-Notebook you cannot immediately go into offline mode. Or perhaps this is just the case with our setup? If there is some kind of connection error, we cannot even access our offline notebook to input data for when the connection is restored. Why is the button greyed out after selecting the SQL config file and only "Connect" is clickable?

    0 0

    In the Chemical Symbols, we have + and - and others but no "d+" and "d-" (here d = lowercase delta). That would be a good addition to the menu, e.g. when drawing mechanisms of reaction with transition states.


    0 0

    これまでCBVU12を使用しておりましたが、この度バージョンアップを計画しています。

    ①CBVU12のアンインストール

    ②CBOU13のインストール

    を行いましたが、CBVU12で参照できていたcambridgesoftのサイト:

    http://www.cambridgesoft.com/support/DesktopSupport/Documentation/ChemDrawPlugin/UserDocs/basics.aspx

    にアクセスすると、下記メッセージが表示されてしまいます(pluginが使用できない)。

    「You currently use Microsoft Internet Explorer 9.
    This Page will use CS ChemDraw ActiveX Control,
    but it isn't installed on your computer.
    Do you want to install it now?」

    CBOU14にインストールし直しても同様です。

    推定される原因・調査/対処方法など、知見がありましたご教授頂けないでしょうか。

    (なお、

    C:\Program Files\CambridgeSoft\ChemOffice2012\ChemDraw\READMECP.htm は

    正常に表示できています。)

    よろしくお願いします。


    0 0

    If, after upgrading Columbus you have trouble connecting or transferring data from Harmony to Columbus and receive the following error:

    ERROR: 8/8/2016 9:31 AM Transfer to Columbus Cannot create Columbus job.

    Error code: 5003, error text: 'The request failed because the authentication token was invalid.'

    it is likely that the Columbus account needs resetting in Harmony. Simply re-entering the Columbus user credentials via Harmony is usually sufficient but on occasions it is necessary to use the following workflow to create a new authentication token:


    1) In Harmony select 'Settings' ...'User Accounts' ...'Manage Columbus Account'
    2) Leave the Columbus URL the same but temporarily change the user account and password to something completely different, i.e. use the details of a different columbus user account or enter incorrect details...then select 'OK'.
    3) Select 'Manage Columbus Account' again
    4) now enter the correct user account and password for your columbus account ...select 'OK'

    The act of re-entering the password in this way will reset the authentication token and should resolve the problem.

    RH


    0 0

    I'm currently unable to save an analysis file from the Image Analysis tab to a database folder in my own account. I'm getting the following error:

    Columbus could not handle the request:
    OMERO/Ice exception: omero::SecurityViolation

    /OMERO/PerkinElmerCTG/Acapella-4.0.2/AcapellaResources/AcapellaColumbusWebapp/ProcLib/columbus/util_treeview.proc(371) [Columbus::nav_AALSaveAnalysisAs]: 
    /OMERO/PerkinElmerCTG/Acapella-4.0.2/AcapellaResources/AcapellaColumbusWebapp/ProcLib/columbus/nav_analysis.proc(365) [columbus::SetAnalysis]: OMERO/Ice exception: omero::SecurityViolation 
     

    I'm able to download the .aas file and run batch analysis; the analysis runs but after the last well, the results don't save to the database, which makes me think there might be a write restriction on a particular directory.

    Please let me know if you have any suggestions/workarounds.

    Thanks,
    Chris


    0 0

    I am using Chemdraw Prime 15 on Mac OS 10.11.6

    In previous versions I was able to repeat atom labels by clicking on an atom in one area and then double clicking on the point where I want to repeat the atom label. This no longer works in the new version.

    Is there a solution to this? I have come to rely heavily on this functionality over the years.

    I'll make another post on a different topic, but I can no longer copy and paste anythign from chemdraw to word, pages, keynote, powerpoint, etc. In the previous version I could copy and paste as PDF into the new office.

    On a positive note - THANK YOU FOR MAKING cmd-H hide the application instead of puting grid lines on the page!


    0 0

    I have recently upgraded to Chemdraw Prime 15 on Mac OS 10.11.6.

    I am now unable to copy and paste anything from Chemdraw to most applications. It seems the clipboard is just empty after copying. I used to be able to paste as PDF into Office 2015 documents. That no longer is an option. I used to be able to copy and paste back and forth with Apple Keynote - that no longer works. I used to be able to copy and paste into a new Preview document to create an image. That no longer works. Word in Office 2011 does seem to work but I don't know how long that is going to be supported at my university.

    My only work around now is to copy and paste the chemdraw into a clean new chemdraw document and save it as an image to use in other applications. The ability to copy and paste within chemdraw tells me SOMETHING is in the clipboard. This has now tripled the time it takes me to prepare presenatations. And let's not talk about editing afterwards.

    Help? I don't think everyone has this problem. Is there something interfering with my clipboard that is not compatible?


    0 0
  • 08/28/16--09:14: Log Files
  • Targeting Log Files

    Columbus:

    The Columbus log files are found under /var/log/columbus

    If the PostreSQL database fails to initialize, check the content of:
    /var/log/columbus/db/master.err

    For all other PostreSQL database issues, check the content of:
    /var/log/columbus/db/Blitz-0.log

    If the Acapella server fails to initialize, check the content of:
    /var/log/columbus/acc/acapella.log

    For all other Acapella issues, check the content of:
    /var/log/columbus/acc/acc.log

    If the Web Server is not running, check the content of:
    /var/log/columbus/web/columbus.log
    /var/log/columbus/nginx/error.log

    Tomcat:

    The Tomcat log files are found under /var/log/tomcat6

    If the Tomcat startup fails or the Columbus web service is not accessible, check the content of:
    /var/log/tomcat6/catalina.out

    If the Web Service is accessible yet clients receive an error from the CCInterface2 web service, check the content of:
    /var/log/tomcat6/CCInterface2.log

    Extracting Log Files

    Columbus:

    A useful sub-section of log files can be easily extracted via a web browser using the following URL:
    http:///help/error/all_logs.zip

    Alternatively, the full log set can be compressed and bundled into the /tmp directory on the server by issuing:
    $ zip –r /tmp/columbus_logs.zip /var/log/columbus

    The compressed columbus_logs.zip file can be exported from the Columbus servers /tmp directory using WinSCP

    Tomcat:

    The full log set can be compressed and bundled into the /tmp directory by issuing:
    $ zip –r /tmp/tomcat_logs.zip /var/log/tomcat6

    The compressed tomcat_logs.zip file can then be exported from the Columbus servers /tmp directory using WinSCP


    0 0

    I tried to uninstall ChemBioOffice 15 and reinstall it, but after uninstalling the new installation fails because aparently ChemBioOffice is still installed. But I can't find any ChemBioOffice 15 files anywhere on my computer. Maybe I uninstalled it incorrectly, but now I don't have ChemBioOffice but I also can't install it anymore.


    0 0
  • 09/12/16--10:32: ELN protocol testing
  • Does anyone have any excels models that can be used to validate the calculations in the protocols in the Electronic Lab Notebook (CambridgeSoft)? Some best practics in this area would helpful also.


    0 0

    Dear Support Team,

    After the update from Windows Version 15xx to (Redstone) 1607, Chemdraw behaves faulty on Office 2010 and upwards for me and my colleagues. When you open a word file and try to edit a Chemdraw image within this file, a error message appears that Chemdraw is faulty or not installed. When you open Chemdraw and try to edit the image again, the same error appears. Another image within the file opens correctly.

    If you open chemdraw before the word application all behaves correctly until you close chemdraw.

    Is there a fix for this ? it is a quite annoying issue. The problem occurs with Chemdraw 14 and 15.1 with all office Versions from 2010 and upwards (The versions me and my colleagues have)


    0 0
  • 09/27/16--11:24: MacOSX 10.12 Sierra
  • I know ChemDraw was released before the latest update to Mac OSX was released but developer versions have been available for ages, have you tested ChemDraw and are there any known issues?


    0 0
  • 09/27/16--11:24: Can't Open Chemdraw file
  • I keep trying to opne a .cdxml file with Chemdraw and I keep getting the message "the specified file type is not understood or not supported".


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