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  • 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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    I am trying to install Columbus on CentOS 6. Everything seems fine however I am having issues with Postgresql. This is the error message that I get:

    Installing : Columbus-db-2.5.0.120577-gen.x86_64 5/162
    Non-fatal POSTIN scriptlet failure in rpm package Columbus-db-2.5.0.120577-gen.x86_64
    postmaster (pid 775) is running...
    creating postgres user columbus
    Stopping postgresql service: [ OK ]
    Starting postgresql service: [FAILED]
    Installation aborted! Could not restart postgres database!
    warning: %post(Columbus-db-2.5.0.120577-gen.x86_64) scriptlet failed, exit status 1


    AND this:


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    Hi all,

    After windows 10 anniversary upgrade, when I double click chemdraw file (*.cdx), it opens an additional blank document page on top of my structure.

    So I have to move of close that blank document to see the structure.

    if I excute the chemdraw.exe then open the structure, it works normally i mean it doesn't open additional blank page...

    I am using surface book with Windows10 Build 1607..

    any insightful help will be highly appreciated.

    Cheers!


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  • 10/03/16--12:30: 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".


    0 0
  • 10/03/16--12:30: 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".


    0 0
  • 10/06/16--12:43: Perimeter of Cells
  • The trick is to use the select region BB. You select the border and calculate the area of that border.

    Then use calculate properties to get the correct units [µm].

    Analysis Sequence "[New Analysis]"

    Analysis Sequence "[New Analysis]"

    Input Image

    Stack Processing (fixed, string) : Individual Planes (, string)

    Flatfield Correction (fixed, string) : None (, string)


    Input Image

    Input

    Stack Processing (fixed, string) : Individual Planes (, string)

    Flatfield Correction (fixed, string) : None (, string)

    Find Cells

    Channel (fixed, string) : DPC (, menu)

    Select channel for cell detection

    ROI (fixed, string) : None (, menu)

    Select population for ROI

    Method

    Method (fixed, string) : B (, menu)

    Select method for cell detection

    Common Threshold (fixed, string) : 0.4 (default, numeric)

    Controls common threshold calculation. Adjust by the tuning illustration Initial Mask.

    Area (fixed, string) : > (fixed, string) 100 (default, numeric) µm²(fixed, string)

    Minimum allowed area of cell. All objects with area less than the limit are discarded as artifacts.

    Split Factor (fixed, string) : 7.0 (default, numeric)

    The Split Factor influence on splitting of clump cells to the individual objects.

    Individual Threshold (fixed, string) : 0.4 (default, numeric)

    The parameter adjusts the object borders, i.e. the detected cells could appear larger or smaller.

    Contrast (fixed, string) : > (fixed, string) 0.1 (default, numeric)

    Defines the minimum allowed contrast of cell. All objects with contrast less than the limit are discarded as artifacts. Adjust by the tuning illustration Low Contrast Cells.

    Output Population (fixed, string) : Cells (, string)

    Name of the output population


    Find Cells

    Input

    Channel (fixed, string) : DPC (, menu)

    Select channel for cell detection

    ROI (fixed, string) : None (, menu)

    Select population for ROI

    Output

    Output Population (fixed, string) : Cells (, string)

    Name of the output population

    Select Region

    Population (fixed, string) : Cells (, menu)

    Select population

    Region (fixed, string) : Cell (, menu)

    Select region by which a new region should be created.

    Method

    Method (fixed, string) : Standard (, menu)

    Select method by which a new region should be created

    Border (fixed, string)

    Turn the border calculation ON/OFF

    Output Regions (fixed, string) : Cell (, string)

    Common prefix for region names


    Select Region

    Input

    Population (fixed, string) : Cells (, menu)

    Select population

    Region (fixed, string) : Cell (, menu)

    Select region by which a new region should be created.

    Output

    Output Regions (fixed, string) : Cell (, string)

    Common prefix for region names

    Calculate Morphology Properties

    Population (fixed, string) : Cells (, menu)

    Select population

    Region (fixed, string) : Cell Border (, menu)

    Select region which should be characterized.

    Method

    Method (fixed, string) : Standard (, menu)

    Select a method

    Area (fixed, string)

    Turn the area calculation ON/OFFUnit for area property

    Output Properties (fixed, string) : Cell Border (, string)

    Common prefix for the property names


    Calculate Morphology Properties

    Input

    Population (fixed, string) : Cells (, menu)

    Select population

    Region (fixed, string) : Cell Border (, menu)

    Select region which should be characterized.

    Output

    Output Properties (fixed, string) : Cell Border (, string)

    Common prefix for the property names

    Calculate Properties

    Population (fixed, string) : Cells (, menu)

    Select population, for which a custom defined property should be calculated.

    Method

    Method (fixed, string) : By Formula (, menu)

    Select a method

    Formula (fixed, string) : A (, string)

    Calculate a new property with formula in style 100*(A-B)/C and thereupon specify below the corresponding variables A, B etc. Please use only single characters (A, B, ..,Y).

    Variable A (fixed, string) : Cell Border Area [µm²] (, menu)

    Select a property to which the variable A should correspond to

    Output Property (fixed, string) : Perimeter [µm] (, string)

    Name of the calculated property


    Calculate Properties

    Input

    Population (fixed, string) : Cells (, menu)

    Select population, for which a custom defined property should be calculated.

    Output

    Output Property (fixed, string) : Perimeter [µm] (, string)

    Name of the calculated property

    Define Results

    Define Results

    Input

    Acapella version: 4.1.2.118496. Timestamp: 2016-10-06 10:12:51 +0200.


    0 0

    I am currently running Chemdraw on a Samsung UHD (4K or 3840 x 2160) and I've found that ChemOffice Professional 15 is almost useless on my machine. All buttons are way too small!

    Fix this problem! How hard can it be?

    ps.

    arden13 in 2014 (high dpi display)

    The problem has to do with my mouse cursor beeing nearly invisible when I try and use it on the document. It is so small that it becomes very difficult to see and trying to hover over a particular atom or bond can be a frustrating ordeal. If I'm trying to modify a terminal bond it can be the difference of a few pixels which is incredibly frustrating.

    I've tried reducing the resolution of my computer screen, but it doesn't seem to help the problem in any way. Has anyone else ran into this sort of a problem on any other High DPI displays?

    greg in 2012 (retina)!

    When can we expect an update of Chemdraw 13 for the Mac retina display? The current version looks pretty blurry

    Best solution so far (2014), but with major drawbacks: integration in word will not longer work and blurry interface!

    http://www.danantonielli.com/adobe-app-scaling-on-high-dpi-displays-fix/


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    Hi everyone,

    So I have been trying to familiarize myself with ChemOffice as I am fairly new to the applications. Anyways, I've been trying to draw out a protein of interest by building it in ChemDraw, using the amino acid templates, 1 by 1. I then export the drawing to Chem3D, and I try to use th ribbon or cartoon display modes, but they do not show (it just stays in ball&stick mode)? I even try to get Chem3D to display the names of the residues using the RES feature, but this also does not work. Is there anything I am doing wrong?

    Thanks!

    Phillip


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    Lines and ticks render in data visualizations as thin, grey lines. These are easy enough to see in the Spotfire interface, but harder to see in exported visualizations (and for reporting/paper writing purposes, inconsistent with figures made in other software). Is it possible to change the appearance of these lines?

    An alternative to is export a data table and re-create the visualization elsewhere, but this would save time!


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    I’m working on windows 10, I use Word 2013, Powerpoint 2013 and Chemdraw pro 15.1.0.144.

    Here is my problem which happens since 10-15 days.

    1) I select and copy a structure in chemdraw,

    2) I paste the structure in word or powerpoint as image or as normal chemdraw object

    3) The structure is cropped. It is like the ‘frame’ containg the image is not centered on the image.

    For information, double click on the image in word or power point give a normal access the chemdraw editing and the structure is perfectly displayed.


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    When I open some chemdraw files I get the error message, "object(s) could not be displayed and will be lost when the file is saved." I'm not sure what objects it can't display. These chemdraws files were created on a Mac, running the same version of chemdraw. Any ideas?? I don't want to open a colleagues files and have objects deleted when I resave!


    0 0

    Hello,

    I would like to ask how can I save the points (using "point tool") I make on an image and then restore them on the image after I close the program.

    The Volocity manual states that "To save a set of acquisition points, select Save Points… from the Stage menu" but I am unable to find the Stage menu or follow the directions.

    Please let me know asap.

    Thanks,

    Katerina


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    Hi, I am trying to use Columbus' "Find Texture" module by training, but I must be missing something. I setup the building block, and then click on the "Train..." button , but nothing happens when I try and then click on the image. Is there some other trick besides left-click? This just works as a pixel classifier, right? I don't necessarily need to use upstream objects or measurements, do I?

    Screenshot of workflow: https://cl.ly/3O1T170l0J1I

    Thanks for any advice.

    David


    0 0

    Hi,

    I am using Chem3D v15 and having a world of hurt trying to get it to spit out the Connolly Solvent Excluded Volume. Version 14 this seemed to work fine.

    Any suggestions?

    Kindest regards,

    Stefan.


    0 0

    I just recently installed ChemDraw 15.1 on my new Macbook running macOS Sierra and can no longer change atom labels by hovering the cursur over an atom and clicking the relevant key on the keyboard. Likewise selecting a molecule and clicking the delete key on the keyboard no longer works. In both cases I simply get an error message reading:

    The operation could not continue because the text cannot be represented by the selected font. (#-8738)

    Any help or fix would be much appreciated as I require ChemDraw on a daily basis.

    Cheers


    0 0

    I just recently installed ChemDraw 15.1 on my new Macbook running macOS Sierra and can no longer change atom labels by hovering the cursur over an atom and clicking the relevant key on the keyboard. Likewise selecting a molecule and clicking the delete key on the keyboard no longer works. In both cases I simply get an error message reading:

    The operation could not continue because the text cannot be represented by the selected font. (#-8738)

    Any help or fix would be much appreciated as I require ChemDraw on a daily basis.

    Cheers


    0 0

    If I output texture features of the cytoplasm, there is no common feature to equate it to the spots found in the same cell. Spots are output as their own population with no common, cell ID, X/Y coordinate etc to the nuclei population even though they were found using the Nuclei population. One can not then use the spot and cytoplasm texture or STAR features together for analysis.

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


    0 0

    In order to get the class identification in HCP, regardless if you start at well level data or cell level data, you must have enough wells of positive and negative controls. Single cell level data is aggregated up to well level BEFORE the feature selection, HIT classification etc is complete.


    The only way around this is to run your data as ‘non-plate object based’ data. Then you can use the control labels
    and it will apply those controls to every cell in those wells and it can be run that way. You should still still see the PCA, feature selection, HIT classification, SOM etc but you will not get the plate-based visuals because it is running as object data.


    0 0

    Issue fixed, thank you.


    0 0

    This may occur following Columbus updates due to internal software restructuring. To run the analysis sequence in a batch analysis, follow the instructions given in the error message displayed in the job status page:

    1) Load the sequence on the Image Analysis screen

    2) Click on the "Define Results" building block to run through the sequence once

    3) Save the sequence

    4) Repeat the Batch Analysis using the new sequence

    Refreshing the sequence in this way will ensure that the analysis sequence is compatible with the current version of Columbus.


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