copy/paste from symyx draw

Hi there,

 

I encountered the problem when copy structure from symyx draw and tried to paste into Marvin Sketch. I knew it worked before I updated to the new version 5.11.14.

My symyx draw is 4.0 and the structure can be pasted into word, excel, so that means the structure was copied into clipboard. I can also copy a smiles text and paste into MarvinSketch window, so I guess the symyx format is not compatible with the 5.11.14,

 

Could you take a look at it?

Thanks

Hongzhou

Hi Hongzhou,



Yes, we are aware of this bug in 5.11.4; therefore we fixed it in version 5.11.5 that you can download it from our webpage:

http://www.chemaxon.com/download/marvin/ />

Best Regards,

Efi

Thanks Efi for your quick response. I will download the new version soon.

One more question, I donwloaded 5.11.15 and checked the release notes. Seems likes symyx draw fix is the only change. Is that possible you can tell me which jar file was updated since we put the whole project into TFS and I don't want to add another 100 MB just for this update.

Thanks

Hongzhou

Dear Hongzhou,

Unfortunately, we cannot give you additional jars. Please install the new 5.11.5.

Thank you for your understanding,

Efi

That's ok, I can figure it out.

One thing related, with new version, when I copy the structure from symyx Draw and paste into MarvinSketch,

the size of structure is smaller and bond width is bigger. therefore it makes it harder if I want to couple a ring to the existing structure and bond width will be different and looks not pretty. I have symyx 4.0.

Thanks

Hongzhou

We will looka t it. First I can only advise you to put down the structure, select it, and then press clean. It should only rearrange the molecules, and resize the bonds of the selection. However we are on to find the root of the problem, and repair it.

I could reproduce your issue. The problem is that we standardize the sizes on import. At this time the best I can advise you to speak with the responsible developers about this feature request. I will forward your request to them.

Thanks for looking into it.

Hi,

During copy-paste we import the structures from .skc, where we have an automatic standardization. Therefore the imported structures will be resized but! the relative sizes are the same. So if you copy and paste first from Marvin and then back, you will have the relative bond sizes as you've expected. I hope this helps.

Regards,
Domi

Hi Domi, I think you misintepreate my issue. When I copy from Symyx draw and paste into Marvin, the pasted structure should have Marvin's default bond length and width after your automatic standardization. After all, once molecule is in marvin, it should look like marvin structure.

This is how it works on our systems... Yould you specify what OS and Java version you  use?

I am with WinXP SP3, Java 1.6.0.20, Symyx Draw 4.0, Marvin 5.11.5. I attached a screenshot, where you can see that the small ring was pasted into Marvin. If you want to couple with another ring, more likely it will cause structure error if you don't clean up first.

Hi Hongzhou,

This issue fixed in Marvin 5.12, only in case when the length of the bonds are the same in Symyx Draw.

Regards,
Mate