Error when adding explicit hydrogens to a molecule

I use Marvin 5.7.1, but this error was already present in 5.7.0.

I'm having a problem with adding explicit Hydrogens to triple bonds in a mol-file to a structure in 3D.

What I want to do is adding hydrogens to an already existing structure determined by X-Ray which doesn't have any hydrogens.

I open the mol-file with MarvinSketch, and take the option "Add Explicit Hydrogens".

All hydrogens are added correctly, except for the hydrogen at the end of a triple bond.

I have attached files, the first one (turned-3D.png) showing an example of a triple bond at the end of a molecule when first imported into MarvinSketch.

The second one (add-explicit-H.png) shows what happens if "Add Explicit Hydrogens" is activated. That angle is definitely wrong and needs to be corrected.

I then searched for a solution, first with MarvinView3D, where I couldn't find an option to add hydrogens, and then in MarvinSpace. The third file (add-explicit-H-MSpace.png) shows the same mistake with the angle.

Clean 3D would solve this problem, but then the atomar positions determined by X-Ray are gone.

I could not reproduce this bug. Could you send me the mol file please?  (It it is confidential, you can send me by email.) Thank you,

Efi Hoffmann 

I would rather not put the file I found this error with in the forum. How can I send it to you by mail? I don't know where to find your mail adress.

Just for a reproduction of the error, every structure with a triple bond and a clean 3D with the option: fine build used and then saved works. I atttached a random structure fitting that criteria, which shows the same crooked angle when adding the hydrogens with "Add Explicit Hydrogens" without using clean 3D.

Thank you for the file and reporting this bug. We are investigating it.

Efi Hoffmann

I found that the position of sprouting Hydrogens in a double bond doesn't seem to take into account the substituents. They may end up on top of existing ones. See screenshot attached.

 

jube wrote:

I use Marvin 5.7.1, but this error was already present in 5.7.0. I'm having a problem with adding explicit Hydrogens to triple bonds in a mol-file to a structure in 3D. What I want to do is adding hydrogens to an already existing structure determined by X-Ray which doesn't have any hydrogens. I open the mol-file with MarvinSketch, and take the option "Add Explicit Hydrogens". All hydrogens are added correctly, except for the hydrogen at the end of a triple bond. I have attached files, the first one (turned-3D.png) showing an example of a triple bond at the end of a molecule when first imported into MarvinSketch. The second one (add-explicit-H.png) shows what happens if "Add Explicit Hydrogens" is activated. That angle is definitely wrong and needs to be corrected. I then searched for a solution, first with MarvinView3D, where I couldn't find an option to add hydrogens, and then in MarvinSpace. The third file (add-explicit-H-MSpace.png) shows the same mistake with the angle. Clean 3D would solve this problem, but then the atomar positions determined by X-Ray are gone.

We have just fixed this part of the bug and it will work properly in 5.9 version of Marvin, however, we could not fix the  original problem yet.

Best Regards,

Efi

This problem still exists in Marvin 6.0. Do you have an estimated date for when this is going to be fixed?

 

Best Regards,

Julia

Hi Julia,

i am sorry, we did not solved that issue yet. However, I forget to mention that you can use partial clean 3D in this case. If you select only the triple bond and the explicit  hydrogen and press  CTRL-3, it will fix the position of hydrogen and will not ruin the other part of the structure.

Best Regards,

Efi

Dear Efi,

thank you very much. We will use this, until the bug is fixed.

Best Regards,

Julia

The bug is still not fixed in 6.2.0. The workaround that you described earlier doesn't work anymore as well. It changes the positions of all hydrogens.

Do you have an estimate as to when this but will be fixed?

Best Regards, Julia

Dear Julia,

We've managed to locate the bug and we've scheduled the fix into 6.3.

Best regards,

Peter

Dear Julia,

The bug is fixed and will be released in Marvin 6.3.

Best regards,
Domi