Importing Image Data to Columbus using Command Line

July 19, 2018, 12:02 pm

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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

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Columbus Helper is reported as damaged when executed on MacOS

July 19, 2018, 12:02 pm

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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

Problems converting ChemDraw to .eps and .pdf

July 22, 2018, 1:45 pm

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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?

ChemDraw Excel structure size in Windows 10

July 23, 2018, 2:44 pm

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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.

converting CAS to Structure?

July 25, 2018, 7:44 am

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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

ChemScript Update to 64-bit Python 3.6/3.7

August 8, 2018, 2:44 am

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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.

Can't open ChemDraw files from Power Point

August 8, 2018, 2:44 am

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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

add SMARTS function to chemscript

August 9, 2018, 3:08 am

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Is it possible to add SMARTS function to Chemscript?

It will be helpful for substructure recognition.

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Volocity Measurement Parameters

August 15, 2018, 6:40 am

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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.

Columbus db fails to initialise

August 21, 2018, 6:06 pm

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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

Cyrillic symbols in ChemDraw Ultra

August 22, 2018, 6:16 pm

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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?

Pasting from ChemDraw to Powerpoint

August 22, 2018, 6:16 pm

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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?

Modify default Gaussian Interface Input Template

August 28, 2018, 8:08 am

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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

Recommended/formal procedure for creating deuterated molecules

September 6, 2018, 12:57 pm

≫ Next: Recommended/formal procedure for representing charged aromatic rings

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Hello Chemdraw users,

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

Best,

Eric

Recommended/formal procedure for representing charged aromatic rings

September 6, 2018, 12:57 pm

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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

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ChemDraw and Mojave compatibility

October 1, 2018, 3:39 am

≫ Next: ChemDraw folder in Documents (Mac)

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

ChemDraw folder in Documents (Mac)

October 1, 2018, 10:54 pm

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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?

Check the Acapella version running on the cluster

October 5, 2018, 8:17 pm

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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

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RH

ChemDraw ActiveX activation level

October 6, 2018, 8:21 pm

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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?

How do you run Batch Analysis on the Cluster

October 9, 2018, 8:55 pm

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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: