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ChemDraw Opening Multiple Applications on Mac

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Hello Everyone, I have had this problem with ChemDraw for a few years now and now that I am stuck working at home on a laptop (COVID), I need to address it. When I open ChemDraw it will open fine and I can start woring in it. However, it will then start to attempt to open multiple other ChemDraw applicaitons (literally the same program). They will just keep bouncing in my 'Task Bar' while I am working in the window I orignally opened. I will regululary have three different ChemDraw 'applications' showing up in my task bar (see image below). I just ignored it for a long time, but now it is consuming a large amount of CPUs and dragging down my laptop. Can someone help me!

OS: 10.15.4

CD: 18.0.0.223

Thanks for any help in advance!


Using ChemScript to export to .eps

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Dear Community,

I'm looking for a simple solution that allows a quick export to export the active document example.cdxml to example.eps within the same directory.

File -> Save As is quite a time-consuming option as it will require navigation to the document's folder. Don't know why it won't show the working directory as a default directory...?

I thought that it should be possible to create a Python ChemScript to automatically export the currently active document to example.eps and save the file to the exact same folder. Could anybody kindly help me to realize this?

Thanks!

Salt Stripping SMILES with uneven number of salts

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I have automated code that processes a CRO compound collection database file containing SMILES. The code is written in C# and I am using the ChemScript RemoveSaltsAndSolvents method. Commonly the CRO file includes SMILES which represent the chemical structure of what would be shipped, i.e. the SMILES includes salt information. For most structures, there is one part of the SMILES which represents the base chemical structure for the compound and another part of the SMILES which represents the salt with the two parts separated by a period, assuming the compound is stored with a salt. However, for some compounds, the compound/salt ratio is not one-to-one and the SMILES representation may repeat either the compound and/or the salt part of the SMILES. One example SMILES I am currently working with is:

[N+]1()=C2C=C(C=CC2=CC2C=CC(N)=CC1=2)N.[N+]1()=C2C=C(C=CC2=CC2C=CC(N)=CC1=2)N.S(=O)(=O)([O-])[O-]

In this example there are two copies of the compound structure and one copy of the salt structure. The problem I have encountered is that when I attempt to salt strip this SMILES string using RemoveSaltsAndSolvents, I get an AccessViolationException in my C# code. It is inconsistent, but sometimes my code can handle the exception and sometimes my code crashes my application. I will continue debugging to determine why my code does not always properly handle the exception. However, I was wondering if I am doing something wrong with the salt stripping or if this is just a bug. My current code reads in the SMILES from a file and then uses the RemoveSaltsAndSolvents method of a SaltTable instance, populated with my desired salts, to attempt the salt stripping. Has anyone encountered this scenario themselves? Is there any advice on anything I can do to the SMILES prior to attempting the RemoveSaltsAndSolvents?

I am currently using version 19.0 of ChemScript.

Thank for any help you may be able to provide.

Why does Chem3D minimize nitrogen dioxide (radical) so badly?

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I build from text `O-N+O`, I delete the hydrogen atom added automatically on N, then I click Ctrl+M. Both the bond length and the angle differ from what I see in the top right image here: https://en.wikipedia.org/wiki/Nitrogen_dioxide

ChemDraw 19.1 won't start - error 0xc000007b

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Hello,

I came across a strange issue with the office suite. All my software is on different disk than the operating system.

Installation of ChemOffice was not a problem, exept that ChemDraw always failed to start with error 0xc000007b afterwards but all other applications (Chem3D/ChemFinder) worked fine.

As error 0xc000007b is such generic every attemped to fix the problem failed.

However, when I gave it another shot and just kept the standard path the installer provides, all apps are working.

This seems quite odd to me and it sounds like there must be some kind of file permission error when changing the standard path.

Is this a known issue?

Cheers

Chemdraw 19.1 Problems

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Chemdraw 19.1 has introduced two bugs that I do not recall in 19.0. I did not expect so many problems in a 0.1 update!

First, when I save an edited file created in 19.0 or earlier, it often defaults to file formats that I have never heard of before "Cambridgesoft Chemdraw XML" for .cdxml files and then warns that they cannot be opened. Saving as any .cdxml seems problematic now. Similarly, when I edit .cdx files, I get "Cambridgesoft Chemdraw Exchange" and data loss warnings. This is very annoying and confusing. what happened?

Second, align bottom and align top do not work as expected anymore for text boxes. Superscript and subscript were always handled poorly, but now even boxes containing lowercase letters that extend below the line will align to the outside of the box instead of to the baseline of the bottom text line. Help! How do I align text easily now!

Best,

DJW

Table background colour

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Is there a way of changing the background colour of a table in ChemDraw?

Chemdraw 19.1- issues with "undo"

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I am having issues with the "undo" function undoing multiple steps instead of what was last done in chemdraw (both when i click actual button and when using CTRL Z). This occured a bit towards to the tailend of when I was using chemdraw 19 and I was hoping the update would fix this issue. It has become really annoying and I'd like to know how to make it stop!!


ChemDraw Export High Quality PDF or EPS

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Hello,

I am trying to export from ChemDraw 19.1.0.8 to PDF or EPS. The document contains chemical structures, text and PNGs with transparency. Unfortunately, ChemDraw does not offer PDF export (a feature that should be standard given the wide spread of PDF) and EPS export does not work properly - chemical structures are shifted relative to PNGs.

While this shift is not a lot (maybe a few mm on an A4 page), it is annoying and for me makes the file unusable.

I also tried a few workarounds:

- pasting into Illustrator CS6 and PDF export: no shift between PNG and structures, but misalignment of text (including atoms in structures). When I open the EPS in illustrator, text alignment is correct but PNGs are misaligned.

- pasting into InkScape: text alignment is OK and also structure/PNG, but PNG transparancy is a problem

- pasting into Word: no alignment issues, no transparency issues, but low quality PDF export

- ChemDraw 18 on a different machine shows the same behaviour, while ChemDraw 13 exports without the PNGs.

So as of now I do not have any feasible method to convert a CDX file to a printable (PDF) document.

Any suggestions on how to get a high quality PDF from what I see on my screen in ChemDraw?

Thanks in advance!

How do you define image analysis?

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Hi all,

Is the Harmony based image analysis best refered to as spatial analysis? or morphometric analysis? of cells. Or is there a more defined appropariate terminology that I have missed here?

Any comments are much appreciated. We are planning a new project and I want to be certain of the methodology.

Regards,

GW

ChemDraw 17.1 - Atom Number stuck to the Molecule - How to move?

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Hello all,

Grad student in organic chemistry here. I am writing up my experimental part and I have a problem concerning ChemDraw. I am displaying atom numbers every few atoms to make clear how I would like to number my molecules for NMR assignment. How can I prevent the Atom numbering label to be stuck to the Atom itself? I want to be able to move the text Box with the numbering with the keyboard as it was possible in the past to make sure the number goes where I want..

I Would be really excited for some help

Best,

J.

Gaussian 16W with Chem3d

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Hi

Am running the newest version of Chem3d (I believe 19.1.0.8) and am having issues interacting with Gaussian 16W (in particular, every time I try to do a job, I get an out of memory error and have to modify the job)

With what I have seen so far doing an internet search the problem appears to be that I have to use an earlier version of Gaussian, which I can't get (just recently bought that license for my University). I would much rather use the CHEM3d to set up Gaussian jobs as that is much easier for my undergrads to understand rather than have to teach them how to use Gaussian and Gaussview.

Thanks in advance for any answers

ChemDraw 19.1 Splash Screen

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The splash screen of ChemDraw in my Wibdows 10 64 bits stays on top of all applications, it does not get hidden when I click on another application (MS Word, Outlook). It means that for the few minutes it takes to load on my old laptop with challenged memory, I cannot do anything else as the screen is obscured by it.

Delta+ and Delta-

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In the menu, it is possible to add + and - charges for atoms. It would be nice to be able in a simple click to add "d+" and "d-" (d here is for the lowercase Greek letter delta, this forum does not allow me to set the font to Greek).

Chemical Formula higher by 2 hydrogens

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I keep getting an addition of 2 extra hydrogens (2 amu) to the molecular weight of some structures converted from SMILES strings. This seems to happen only for a subset of structures that are somewhat more complicated. I have Chemoffice 19 plug-in for Excel 365 ( windows 10). When I use ChemDraw or our internal tools the problematic structures are converted to formula and Mw correctly. I only see the error in Excel.

Leo


ChemDraw19 on Mac 10.14.6

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Either use 'sigma orbital' highlight then choose 'Curves' and select 'faded' - colour fine if bond horizontal defaults to white on any other angle. Same result achieved by taking 's orbital' and distorting shape to make ellipsoid.

Probably only a problem for those of us using ChemDraw in teaching but still frustrasting.

the fade orbitals are not coloured

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Either use 'sigma orbital' highlight then choose 'Curves' and select 'faded' - colour fine if bond horizontal defaults to white on any other angle. Same result achieved by taking 's orbital' and distorting shape to make ellipsoid. Probably only a problem for those of us using ChemDraw in teaching but still frustrasting.

ChemScript help

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Is there a place where more complete documentation exists for ChemScript? help(ChemScript19.StringVetor), for example, gives no detailed descriptions as to what anything does. Right now I'm trying to solve what I thought would be a simple probelm of writing a number below each structure in a chemdraw file. Anybody with experience or advice would be appreciated.

Celery service not starting properly after installing Columbus 2.9.1 on RHEL 6.10

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After installing Columbus 2.9.1 on RHEL 6.10 the Celery service is not starting correctly.

In this case, it does not display any message on /etc/init.d/columbus start however when you do /etc/init.d/columbus status it will throw a warning.

The sympton is that Columbus login page won't let you login with a message like: "not able to login, contact your administrator"

The most likely root cause is that columbus_webapp database is missing some relations or that /var/run/celery directory has incorrect permissions. Expected permissions should look like:

$ ls -al /var/run/celery
[root@RHEL6 ~]# ls -al /var/run/celery/ total 32
drwxr-xr-x. 2 columbus root 4096 Oct 5 19:25 .
drwxr-xr-x. 33 root root 4096 Oct 1 10:17 ..
-rw-r--r--. 1 columbus columbus 89 Oct 5 19:22 celerybeat-schedule.bak
-rw-r--r--. 1 columbus columbus 2874 Oct 5 19:25 celerybeat-schedule.dat
-rw-r--r--. 1 columbus columbus 89 Oct 5 19:25 celerybeat-schedule.dir
-rw-r--r--. 1 columbus columbus 5 Oct 1 10:17 image-service.pid
-rw-r--r--. 1 columbus columbus 5 Oct 1 10:17 long-tasks.pid
-rw-r--r--. 1 columbus columbus 5 Oct 1 10:17 periodic-tasks.pid

Solution consists of removing the db and reinstalling the columbus-webapp rpm:

$ su - columbus
$ sudo /etc/init.d/columbus stop
$ dropdb columbus_webapp
$ sudo rpm -e --nodeps Columbus-webapp
$ sudo yum install Columbus-webapp
$ sudo /etc/init.d/columbus start

After this Celery should be Ok and login process should work as expected.

Regards,
Arturo

Need help understanding "Select Populations" Methods

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Hello!

I have a quick question about Columbus' "Select Populations -- Linear Classifier" method. I am trying to quantify co-localizations of puncta [IHC of cortex] and also compare those co-localizations to puncta that only carry one type of marker. We are thinking of applying the following workflow before training the linear classifier:

1) "Calculate Image" method to add two different channels [Channel A and Channel B] together to get a composite image we'll call CompImage.

2) "Find Spots" of CompImage.

3) "Calculate Morphology Properties" of CompImage.

4) "Calculate Intensity Properties" of Channel A and then Channel B.

5) "Select Population -- Linear Classifer" of CompImage, where we ask it to identify puncta that shows up only in ChannelA, only in ChannelB, and then overlapping puncta. We train by toggling between the Channel views [right-side menu] and train visually.

My question is: If we train the linear classifer on CompImage, would that be able to differentiate between the different channels that went into creating the CompImage? i.e. If I denote that the population that I am training the Linear Classifier on is CompImage, but I only select puncta that show up in Channel A or Channel B [by using the right-side menu], will the Linear Classifer know that I've done that?

Or maybe a better question is: if I add channels together, does the Linear Classifier know to differentiate between the two different channels?

Thank you very much,

~Justine

why the structure isn't correct when I did MM2 optimization in chem3d?

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hi

I have a question with MM2 optimization function of chem3d.

I draw molecule and do MM2 optimization but the structure doesn't correspond with the structure that I expect. (The structure I expect is equal to the result that calculate with dft.)

why does it happen? what is the problem?

ChemDraw Software Error

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I have music and sound problems on ChemDraw and am looking for solutions, so far I have not found the answer.


Big Sur

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Is ChemDraw compatible with the latest Mac OS update Big Sur?

Calculations interface

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I installed Chem3d v 20.0 (windows 10) and already have GAMESS 2019 installed in the default directory (\users\public\gamess-64\). When I installed Chem3d, I checked to
see that the gamess-us interface was checked for install. I also checked the preferences that
"Always display claculation interface menuitems..." was checked.

The problem is that under the Calculations tab, only Diherdal driver, extended huckel, and MM2 are showing. Please point me in the direction to get Chem3d to show the GAMESS interface.

Thanks

How to import optimized geometry from GAMESS?

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I want to calculate vibrational frequencies with GAMESS. This needs to be done at the optimized geometry. I can start an energy minimization, but when I follw this by a frequency run (or IR/Raman run), the calculation is performed at the original geometry, not the previously optimized gemoetry. How can I tell Chem3D to use the result of the previous optimization?

many thanks

B. Dick

Swap H and C in an alkyl chain label

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Hello,

I'm sorry if this has been answered before, but I haven't manage to find anything with a search. I'm drawing a molecule and I need to add an alkyl chain as a side label (e.g. C6H13). If said label is on the right of the molecule, all is good in the world, and the bond is attached to the C6 part of the label. If the label is on the left, however, the bond is attached to the H13 part of the label (i.e. the label is still written C6H13 instead of H13C6), which is not goo. I even have an alkoxy chain that is currently written as C6H13O instead of H13C6O. How can I swap the positions of C and H, so that the label reads correctly?

Table Template - List Items

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If I have a table template containing a column which is defined as a list and I add, edit or delete items from this list, are the changes reflected in experiments that have already been created which contain this table item? If not, how can I roll down any changes to already created items?

hemDraw professional 15 msi file ?.

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Hello,

Can anyone tell me where I can download Chem Draw Professional?

thanks

alexsunny

Character map missing

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When I select "View Character Map" from the View drop down menu, nothing happens.

The issue started after I was using chemdraw on a second monitor, then went back to just my laptop screen.

All other toolbars and maps from the drop down menu appear as usual when I select them


No page setup menu appears; alternate way to get page into landscape orientation?

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When I go to change the orientation of my page to landscape through the page setup button (orctrl+shift+p), I find that no menu opens at all (on ChemDraw 20.0), although I do get the blue circle/ring that indicates that something is loading in Windows. Does anyone know how to fix this issue, or alternative ways to get the screen into landscape view?

Problems converting ChemDraw to .eps and .pdf ?.

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Hello,

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?

thanks

alexsunny

Origin and SIgnals Notebook

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Is it possible to have origin working in signals notebook (with a button just like Excel is implemented)?

Where is my main tool bar? Chemdraw 20.0

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I just upgraded from Chemdraw 19 to 20; I have no main tool bar. the box for the main tool bar to be shown in checked in the view menu. It is not there. This used to be a much more user friendly software. What has happened?

ERROR ChemScript Mm2OptimizeGeometry does NOT iterate

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I wanted to run Mm2 optimization as in Chem3D using ChemScript on python. The following function is supposed to do so, but it only runs once. Chaging the arguments for the RMS gradient or others do not make it iterate:

m = StructureData.LoadData('cis-Chalcone')

m.Mm2OptimizeGeometry(m.Mm2OptimizeGeometry(rmsGradient = 0.1,maxIterations = 1000,timeout_ms = 0,showIteration = True)

Instead, the only way to do the iteration is with a regular loop, but does not take the RMS gradient into account. However, this can yield an inaccurate optimization.

for i in range(300):

m_opt = m.Mm2OptimizeGeometry()

Has anyone cussessfully implemented an RMS gradient iteration on ChemScript?

Thank you

chemdraw 15 in Big Sur

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I just updated my operatine system to Big Sur. My ChemDraw 15 can not be opened. Any advise on updating the ChemDraw 15? Thanks.

Multiple MM2 minimization using Chem3D

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I would like to perform MM2 energy minimization on multiple molecules individually. If I run MM2 minimization with all molecules docked in the same script the energy minimization is calculated for the conglomerate.

How can I select them and perform MM2 one by one?

Thank you


chemdraw 20.0 Not responding once predict NMR

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I am using Chemdraw 20.0 on windows 10 home edition. Whenever I use predict NMR button, the program will stop responding and I must turn it off by force. How to solve this problem? Thanks very much.

Structure to Name crashes on pasted InChI

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ChemDraw 19 crashes after pasting in InChI=1S/C3N4/c4-1-7(2-5)3-6 and then trying Structure to Name on structure. Structure to name on manually drawn structure does not crash ChemDraw 19

win10 の host ID

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違うネットワーク環境で使用する毎にhost IDが変わり、chem draw のアクチベーションが必要になってしまう。

Win10のhost ID

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違うネットワーク環境で使用すると、同じPCでもhost IDが変わりchem drawのアクチベーションが必要になってしまうが、どうしたらよいか。

Espn.com/activate

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They have listened to everyone of my problem whether they be big or small.Have you ever had the opportunity to say a simple thank you and have let the opportunity pass?Thank you for helping me put the final touches. Sometimes we forget to thank the people when a heartfelt face -to face thank you isn't possible msg is excellent way to say for thanks.

https://xfinityactivate.launchaco.com/

https://hboxsignin.launchaco.com/

https://espnactivate.launchaco.com/

Problem with Chem3D 16.0 Save copy as .pdb

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Dear Members,

I built a ssDNA polymer in ChemDraw 16.0 and using Chem3D 16.0, I ran MM2 for energy minimization. Upon saving copy as .pdb, COMPND, ATOM, HETATM, and CONECT records are used by Chem3D; all other records in a Protein Data Bank file are ignored. Kindly suggest any method to convert the native .c3xml file to .pdb file without losing any record type.

Thanks in advance

Rename a notebook or an experiment

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I have several notebooks in Signal. However, I started to realise that I gave them rather not very informative names.

Is it possible to rename a notebook that contains several experiments? If yes – how to do this?

With kind regards,

PT


UV Winlab Print Report and Auto add to samples

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Sorry if this is the wrong topic are for the question.

I am having trouble attempting to streamline the use of UV Winlab v6.4.0 for general use in our lab. Previously, we have been using an older version where the spectrum could be taken, modified and printed quickly without much manipulation. As we transition to this new version of Winlab I am confronted by two main issues.

The first is printing each spectrum, the report function will only print the first spectrum for the method and not the last ran spectrum. To print the last run spectrum, I need to transfer the spectrum to a secondary program. The work around I have found in Winlab is to have the report settings auto print. I would like to know if there a way to print the last run spectrum directly from Winlab on command in the desired template?

The second question regards sample management, currently we can add samples or set the number of samples to a high number at the start of the day. Is there a method to have the sample increment automatically increase each time run spectrum is used?

Thank you for any assistance.

Please improve your software. Here are some sincere suggestions.

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When I use ChemDraw, your software has many problems. It gets stuck when drawing a large number of graphics. Every time I enter ChemDraw through word editing, it opens slowly, and all toolbars cannot be fixed. Every time I open the software, the whole interface is messy. Why can't the three color selectors (color, fill color and highlight color) be merged into one toolbar, All in all, the software is still slow and stuck even on my high-performance computer. It's too bad.

ChemDraw round trip editing Mac

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I’ll keep this simple. For a long time, chemdraw structures could be pasted into word and PowerPoint, clicked on, and brought back to chemdraw. The same way it works with windows. The consistent answer support always gives is a generic incompatibility with such and such version of Microsoft office. Is support actually doing anything to get this working again? The software is expensive and to work on a presentation on a pc, then open it on a Mac and click the structures to open them in chemdraw Mac and it not work is unacceptable after it finally worked for 7 or 8 Years Yes, I know there is the copy as pdf to word and paste, etc. that is extremely inconvenient when you’re making a PowerPoint presentation and want to paste a structure and then edit if necessary. It works fine on a pc. Please don’t give me a generic bs response. I have presentations that are useless since I can’t edit them in chemdraw. This is a constant problem and again, for the price of The chem office package your team should do more than blame Microsoft and actually fix it.

ChemDraw 16 Mac does neither open .cdx nor .sdf files

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Hi, my ChemDraw 16 Mac does not open .cdx or .sdf files after I followed advice from the Cambridgesoft support group to fix another issue with my ChemDraw and Catalina (freezing on saving). I followed this advice:

http://informatics.perkinelmer.com/Support/KnowledgeBase/details/Default?TechNote=3529

Any help would be appreciated.

Need help identifying this line type

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Hello folks,

I'm having to recreate a chemical struture in Chemdraw, part of it includes this 'jagged' vertical line I haven't encountered before. I've browsed all my available toolbars and haven't found anything that would generate these shapes. I'm a legal word processor, so pardon my ignorance at perhaps not knowing something that may seem basic to all of you :-). Any assistance would be highly appreciated.

how to tear off tool palette w/ Mac track pad

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Directions say to use left click. I did a search to find Mac trackpad leftclick equivalent, but it says to just click on trackpad...doesn't work

eps file - text not saved as text (only MacBook)

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Hello everone,

I write my thesis with LaTeX. To be able to use a package called chemnum to number chemical structures automatically, I need to save all my ChemDraw-files as eps-file.

The problem is that text will not be saved as text when i save the file as eps-file on my MacBook (with Windows it's no problem!!). This is necessary to replace temporary markers. If the markers are not saved as text it's not possible to replace them automatically with numbers.

Thanks already.

Version: ChemDraw 20.0 (Mac and Windows)

Cheers

Isabel




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