Problem Implicit Hydrogens

Hi, now I have a curious problem here and we cannot find the reason:

As shown in the attached screenshot, it is not possible to set "Implcit Hydrogens" to "On All" or to "On Hetero and Terminal". Why are these two options light grey ? Even setting sketchImplicitH=all in the file ./chemaxon/marvin.properties doesn't help.

And it's only on my machine here (Linux Kubuntu). On all other machines, PCs or notebooks, there are no problems with setting "Implicit Hydrogens".

What's wrong ?

Best regards, Hans-Ulrich

Dear HUWagner!

   Could you please send us your marvin.properties file for testing, with your customization.xml and shorcuts.xml to our support e-mail address? (They are located in your chemaxon folder (under user home), under the used Marvin version number.)

Regards:
Balázs 

After the discussion with the user it turned out, he had a specific setting, that do not allow to paint carbon lables. The application can not paint implicit hydrogens to invisible atom labels, which led to forbid the two mentioned Imlicit Hydrogen options.

If you have a  similar problem you can take a look at your settings in Edit > Preferences dialog, on the Structure tab, and check, wether your Carbon Labels are hidden, or not.

Dear Balázs,

thank you for the really fast help.

And now we understand, the special folder .chemaxon/5.x.y is only installed after changing personal configuration settings.

Best regards, Hans-Ulrich

 

Hi,

Same here, even with the newest verison 14.10.13.0. Was there ever asolution to the problem? If I use spacefill or ball'n'stick no option is available any more. I dont recall having a problem with this previously.

Thanks,

 

Bernhard

 

Dear Bernhard,

   We do not paint implicit Hydrogens in ball and stick (or in spacefill) mode, but you can add expliit hydrogens with Structure > Add > Explicit Hydrogens menu. You still have to allow carbon label visibility (Edit > Preferences > Structure tab) to paint implicit Hydrogens on carbon labels.

Regards:
Balázs 

 

Well, the situation was:

ball'n'stick & spacefill: no option for implicit hydrogens at all

others: "On hetero" (and "Off") only (others greyed out)

 

Complete uninstall (incl removing all configuration files - except licence) and reinstall fixed the problem.

 

Thanks,

 

Bernhard

Dear Bernhard,

   I think, in ball and stick & spacefill mode you still don't have implicit Hydrogens since we do not support that. However if you will forbid painting carbon labels in the future, you will loose the ability (until this is forbidden) to select the other two options. Since you have removed all the configuration files, I can't tell, if we had any bugs, or the application was running as it is supposed to. I am glad to hear, that you found a way to solve your problem. I hope, we can give you more help next time.

Regards:
Balázs 

After some time the problem with the implicit hydrogens reappeared. So, again the menu items for these were not possible to select. I managed to point the problem to the marvin.properties file. After deletion of the file I get all the menu item options for implicit hydrogens back. I have attached the file which may help the developers and/or allows you tell me which option I have to change to get the implicit hydrogens menus back.

Thanks,

Bernhard

Dear Bernhard,

In your marvin.properties file, there is a line:

sketchCarbonVisibility=off

which disables the two implicit hydrogen options "On All" and "On Hetero and Terminal" as well.

To get back these menu items go to Edit > Preferences dialog, and at the "Carbon Labels" section on the Structure tab select anything, but "Never".

Regards,
István