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double atoms in the figure

Feb 28, 2012 at 2:16 PM

Hello,
I am new to the chem4word feature. After adding a chemical to a document, it seems it has double the atoms(only some) this is quite iterating. 
Some double atoms are near the one that are numbered, some like a carbonyl there are two oxygens there.

 If I new how to upload the figure so someone could advise me I would.
Thanks

Developer
Feb 29, 2012 at 2:57 AM

Hi,

We need some more information about this issue.

Is this issue is occuring only when you are importing a chemical to document from  Load From "OPSIN" or even when you mark the term as chemistry by right click context menu also?

Could you please provide us some of the sample chemical names for which double atom problem occurs. This will help us to help us to figure out what is causing problem and fix the problem by next release.

Regards,
MRC Customer Support Team

 

 

 

Developer
Feb 29, 2012 at 7:11 AM
Edited Feb 29, 2012 at 7:49 AM

Hi,

We have reproduced the issue which you are facing. After some investigation we came to know that, it is not that displaying the double atoms. In that, one is the real atom and the other one (one that is small in size, looks like a subscript) is a label set for that particular atom.

If have gone through Chemistry Word add-in user guide you might also have across the functionality of setting labels to the atoms in the molecule, in 2D editor mode. So, when you import chemical to document and if its corresponding cml has some default label set like label “c” is set for atom “C”, it will also get displayed in the 2D picture imported to document.

If you want to get rid of/remove this label just follow steps given below:

1)      Select an imported chemical click on Edit tab in Chemistry category and select Edit 2D.

2)      Now, you are able see a 2D Editor window with imported chemical 2D structure.            
Select\Click on an atom for a label is set. Now you will round shaped action menu bar.

3)      In round shaped action menu bar, just find remove label and click on it ( remove button would look like a1\F (a backward slash over “a1” as subscript of “F”)

I am also sharing the screenshot of 2D Editor Window with how to delete the alredy set label to an atom at the link https://skydrive.live.com/redir.aspx?cid=9d47a79dec6d64e2&resid=9D47A79DEC6D64E2!111&parid=root

I hope this would help you to overcome the problem you are facing. Please let us know if you have any further queries.

Regards,
MRC Customer Support Team

 

 

Mar 4, 2012 at 10:00 PM
Thanks,
I am still not sure where do I turnoff this agitating default. Importing many molecules to my paper and than go one by one to remove the labels is obviously not the ideal way to go.
Thanks again for the thorough e-mail.
Eyal

On Tue, Feb 28, 2012 at 11:11 PM, MadhusudhanGS <notifications@codeplex.com> wrote:

From: MadhusudhanGS

Hi,

We have reproduced the issue which you are facing. After some investigation we came to know that, it is not that displaying the double atoms. In that, one is the real atom and the other one (one that is small in size, looks like a subscript) is a label set for that particular atom.

If have gone through Chemistry Word add-in user guide you might also have across the functionality of setting labels to the atoms in the molecule, in 2D editor mode. So, when you import chemical to document and if its corresponding cml has some default label set like label “c” is set for atom “C”, it will also get displayed in the 2D picture imported to document.

If you want get rid of this label just following steps below:

1) Select an imported chemical click on Edit tab in Chemistry category and select Edit 2D.

2) Now, you are able see a 2D Editor window with imported chemical 2D structure.
Select\Click on an atom for a label is set. Now you will round shaped action menu bar.

3) In round shaped action menu bar, just find remove label and click on it ( remove button would look like a1\F (a backward slash over “a1” as subscript of “F”)

I am also sharing the screenshot of 2D Editor Window with how to delete the alredy set label to an atom at the link https://skydrive.live.com/redir.aspx?cid=9d47a79dec6d64e2&resid=9D47A79DEC6D64E2!111&parid=root

I hope this would help you to overcome the problem you are facing. Please let us know if you have any further queries.

Regards,
MRC Customer Support Team

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--
Eyal Saiet

Developer
Mar 5, 2012 at 5:32 AM

Hi,

Please download and  refer the Chemistry Word Add-in user guide , especially How to Edit 2-D Structures section, which also has a subsection called Set Label/Remove Label that will clearly gives you idea about how to remove a label for an atom.

The default label is coming from the cml file/data that will get downloaded from OPSIN when you search and import a chemical from it. So, it is not that application is adding the label to an atom on its own. Application will display the 2D structure for the cml data it gets from the OPSIN. And you said that default labels are coming for carbonyl components.

The application is also comes up with around 600 odd cml files for different chemical components. So, just use right context menu to mark the term as chemistry, this won’t have such problems as I have tested for few of carbonyl components (those cml files don’t have built labels as such). And I would prefer you to use OPSIN when you don’t get a proper chemical component from right click menu.

For more details on how to use context menu to mark as chemistry term and other related things  please refer the User guide, which has all the steps explained.


Regards,
MRC Customer Support Team

Mar 12, 2012 at 1:33 AM
Thanks for the help.
Does ctrl-z anf ctrl-y work with chem4word?
Eyal

On Sun, Mar 4, 2012 at 9:32 PM, MadhusudhanGS <notifications@codeplex.com> wrote:

From: MadhusudhanGS

Hi,

Please download and refer the Chemistry Word Add-in user guide , especially How to Edit 2-D Structures section, which also has a subsection called Set Label/Remove Label that will clearly gives you idea about how to remove a label for an atom.

The default label is coming from the cml file/data that will get downloaded from OPSIN when you search and import a chemical from it. So, it is not that application is adding the label to an atom on its own. Application will display the 2D structure for the cml data it gets from the OPSIN. And you said that default labels are coming for carbonyl components.

The application is also comes up with around 600 odd cml files for different chemical components. So, just use right context menu to mark the term as chemistry, this won’t have such problems as I have tested for few of carbonyl components (those cml files don’t have built labels as such). And I would prefer you to use OPSIN when you don’t get a proper chemical component from right click menu.

For more details on how to use context menu to mark as chemistry term and other related things please refer the User guide, which has all the steps explained.


Regards,
MRC Customer Support Team

Read the full discussion online.

To add a post to this discussion, reply to this email (chem4word@discussions.codeplex.com)

To start a new discussion for this project, email chem4word@discussions.codeplex.com

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--
Eyal Saiet

Mar 12, 2012 at 1:45 AM
Hello,
I went back and tried to add new labels.
I clicked on the molecule figure and selected edit 2D. Than I added a label to one of the atoms. When I was done I hit ok, but got the message(attached)
After I pressed ok on the message, the view, edit and view CML are all disabled..
What do you think the problem is?
Thanks
Eyal

On Sun, Mar 4, 2012 at 2:00 PM, Eyal Saiet <ejsaiet@alaska.edu> wrote:
Thanks,
I am still not sure where do I turnoff this agitating default. Importing many molecules to my paper and than go one by one to remove the labels is obviously not the ideal way to go.
Thanks again for the thorough e-mail.
Eyal


On Tue, Feb 28, 2012 at 11:11 PM, MadhusudhanGS <notifications@codeplex.com> wrote:

From: MadhusudhanGS

Hi,

We have reproduced the issue which you are facing. After some investigation we came to know that, it is not that displaying the double atoms. In that, one is the real atom and the other one (one that is small in size, looks like a subscript) is a label set for that particular atom.

If have gone through Chemistry Word add-in user guide you might also have across the functionality of setting labels to the atoms in the molecule, in 2D editor mode. So, when you import chemical to document and if its corresponding cml has some default label set like label “c” is set for atom “C”, it will also get displayed in the 2D picture imported to document.

If you want get rid of this label just following steps below:

1) Select an imported chemical click on Edit tab in Chemistry category and select Edit 2D.

2) Now, you are able see a 2D Editor window with imported chemical 2D structure.
Select\Click on an atom for a label is set. Now you will round shaped action menu bar.

3) In round shaped action menu bar, just find remove label and click on it ( remove button would look like a1\F (a backward slash over “a1” as subscript of “F”)

I am also sharing the screenshot of 2D Editor Window with how to delete the alredy set label to an atom at the link https://skydrive.live.com/redir.aspx?cid=9d47a79dec6d64e2&resid=9D47A79DEC6D64E2!111&parid=root

I hope this would help you to overcome the problem you are facing. Please let us know if you have any further queries.

Regards,
MRC Customer Support Team

Read the full discussion online.

To add a post to this discussion, reply to this email (chem4word@discussions.codeplex.com)

To start a new discussion for this project, email chem4word@discussions.codeplex.com

You are receiving this email because you subscribed to this discussion on CodePlex. You can unsubscribe on CodePlex.com.

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--
Eyal Saiet




--
Eyal Saiet

Developer
Mar 12, 2012 at 4:20 AM
Edited Mar 12, 2012 at 4:52 AM

Hi,

Ctrl+z and Ctrl+y doesn't work as excepted, in chemistry add-in for word. However, Ctrl+z still works but you need to hit Ctrl+z several times . This behavior doesn't really work as we expect in word.

And adding  new labels to atoms in 2D editor is working fine. As I have tried the same for few of the molecules, it is till fine.

I couldn't see any attachments attached as you specified in the last relpy. Could you just share me the message you had got some how or mail it to me @ v-magumb@microsoft.com . I will take a look at the message and will let you know the updates on the same.

Regards,
MSR Customer Support Team

 

 

Mar 12, 2012 at 6:59 AM
Hello,
Do you have an opinion about my problem bellow?
Eyal
On Sun, Mar 11, 2012 at 5:45 PM, Eyal Saiet <ejsaiet@alaska.edu> wrote:
Hello,
I went back and tried to add new labels.
I clicked on the molecule figure and selected edit 2D. Than I added a label to one of the atoms. When I was done I hit ok, but got the message(attached)
After I pressed ok on the message, the view, edit and view CML are all disabled..
What do you think the problem is?
Thanks
Eyal




On Sun, Mar 4, 2012 at 2:00 PM, Eyal Saiet <ejsaiet@alaska.edu> wrote:
Thanks,
I am still not sure where do I turnoff this agitating default. Importing many molecules to my paper and than go one by one to remove the labels is obviously not the ideal way to go.
Thanks again for the thorough e-mail.
Eyal


On Tue, Feb 28, 2012 at 11:11 PM, MadhusudhanGS <notifications@codeplex.com> wrote:

From: MadhusudhanGS

Hi,

We have reproduced the issue which you are facing. After some investigation we came to know that, it is not that displaying the double atoms. In that, one is the real atom and the other one (one that is small in size, looks like a subscript) is a label set for that particular atom.

If have gone through Chemistry Word add-in user guide you might also have across the functionality of setting labels to the atoms in the molecule, in 2D editor mode. So, when you import chemical to document and if its corresponding cml has some default label set like label “c” is set for atom “C”, it will also get displayed in the 2D picture imported to document.

If you want get rid of this label just following steps below:

1) Select an imported chemical click on Edit tab in Chemistry category and select Edit 2D.

2) Now, you are able see a 2D Editor window with imported chemical 2D structure.
Select\Click on an atom for a label is set. Now you will round shaped action menu bar.

3) In round shaped action menu bar, just find remove label and click on it ( remove button would look like a1\F (a backward slash over “a1” as subscript of “F”)

I am also sharing the screenshot of 2D Editor Window with how to delete the alredy set label to an atom at the link https://skydrive.live.com/redir.aspx?cid=9d47a79dec6d64e2&resid=9D47A79DEC6D64E2!111&parid=root

I hope this would help you to overcome the problem you are facing. Please let us know if you have any further queries.

Regards,
MRC Customer Support Team

Read the full discussion online.

To add a post to this discussion, reply to this email (chem4word@discussions.codeplex.com)

To start a new discussion for this project, email chem4word@discussions.codeplex.com

You are receiving this email because you subscribed to this discussion on CodePlex. You can unsubscribe on CodePlex.com.

Please note: Images and attachments will be removed from emails. Any posts to this discussion will also be available online at CodePlex.com




--
Eyal Saiet




--
Eyal Saiet




--
Eyal Saiet

Developer
Mar 12, 2012 at 7:25 AM

Hi,

Adding labels to atoms in 2D editor and saving the same is working fine. I am not facing any such problem as you are.

Please share the error message you are getting with the email id as  I already specified in my last post.

Regards,
MSR Customer Support Team

Mar 12, 2012 at 7:49 AM

Hello,
I went back and tried to add new labels.
I clicked on the molecule figure and selected edit 2D. Than I added a label to one of the atoms. When I was done I hit ok, but got the message(attached)
After I pressed ok on the message, the view, edit and view CML are all disabled..
What do you think the problem is?
Thanks
Eyal

On Sun, Mar 4, 2012 at 2:00 PM, Eyal Saiet <ejsaiet@alaska.edu> wrote:
Thanks,
I am still not sure where do I turnoff this agitating default. Importing many molecules to my paper and than go one by one to remove the labels is obviously not the ideal way to go.
Thanks again for the thorough e-mail.
Eyal


On Tue, Feb 28, 2012 at 11:11 PM, MadhusudhanGS <notifications@codeplex.com> wrote:

From: MadhusudhanGS

Hi,

We have reproduced the issue which you are facing. After some investigation we came to know that, it is not that displaying the double atoms. In that, one is the real atom and the other one (one that is small in size, looks like a subscript) is a label set for that particular atom.

If have gone through Chemistry Word add-in user guide you might also have across the functionality of setting labels to the atoms in the molecule, in 2D editor mode. So, when you import chemical to document and if its corresponding cml has some default label set like label “c” is set for atom “C”, it will also get displayed in the 2D picture imported to document.

If you want get rid of this label just following steps below:

1) Select an imported chemical click on Edit tab in Chemistry category and select Edit 2D.

2) Now, you are able see a 2D Editor window with imported chemical 2D structure.
Select\Click on an atom for a label is set. Now you will round shaped action menu bar.

3) In round shaped action menu bar, just find remove label and click on it ( remove button would look like a1\F (a backward slash over “a1” as subscript of “F”)

I am also sharing the screenshot of 2D Editor Window with how to delete the alredy set label to an atom at the link https://skydrive.live.com/redir.aspx?cid=9d47a79dec6d64e2&resid=9D47A79DEC6D64E2!111&parid=root

I hope this would help you to overcome the problem you are facing. Please let us know if you have any further queries.

Regards,
MRC Customer Support Team

Read the full discussion online.

To add a post to this discussion, reply to this email (chem4word@discussions.codeplex.com)

To start a new discussion for this project, email chem4word@discussions.codeplex.com

You are receiving this email because you subscribed to this discussion on CodePlex. You can unsubscribe on CodePlex.com.

Please note: Images and attachments will be removed from emails. Any posts to this discussion will also be available online at CodePlex.com




--
Eyal Saiet




--
Eyal Saiet




--
Eyal Saiet




--
Eyal Saiet

Developer
Mar 12, 2012 at 8:44 AM
Edited Mar 12, 2012 at 8:46 AM

Hi,

Please send an error message screenshot to my mail id: v-magumb@microsoft.com. I couldn't any see any hyperlinks in your last post,where I can click and get the error message you attached.


Regards,
MSR Customer Support Team

Developer
Mar 12, 2012 at 10:38 AM

Hi,

I have tried several times to reproduce the issue you are encountering but I am not able to reproduce this issue on my machine. Adding labels to atoms is still working fine for most of chemicals I have tried.

Is it possible for you to share the complete steps to reproduce this issue in order by taking a sample chemical as an example?

And I would like to ask you one more question , is this problem encountering all the time when you try to add label to a atom for all the chemical you going to try?

Regards,
MSR Customer Support Team