Hydrogens not showing in MarvinSpace

MarvinSpace doesn't show hydrogens for some reason. I've been looking everywhere and i just can't find a solution.

EDIT: found it, took me 3 hours but found it.

Nevermind, found it. Can't believe it took me 3 hours to do so...

Hi Daniel,

I am sorry for the inconvenience caused.

Please find a screenshot attached. You can find this option  under

Display/Ligand/DrawType/Hydrogens.

Display/Macromolecule/DrawType/Hydrogens.

Display/Water/DrawType/Hydrogens.

See also in MSpace/Help under Menu opitons.

Display/Macromolecule/DrawType/Hydrogens.

 

Do you have suggestion what would be the best place for these options?

Thanks,

Miklos

 

p.s. For the request of Hans-Ulrich Wagner, the original dopamine example has been removed. A new example about limonene has been inserted.

Wow, thanks for replying anyway. Yes, i think it'd be much easier if everything in the Marvin Suite had the same standard menu layout, where it may apply. Just as a way to standardise your menus so users can find things more easily and quickly.

That said, i love your software and think it's easily the best out there (recent convert from, clunkier, costlier, chem software). Keep up the amazing work.

Thank you very much! We are gona consider your advice.

Regards:
Balázs 

Hi MarvinSpace developers,

in our student courses we are often producing molecules in MarvinSketch and visualizing these in MarvinSpace. And to see the hydrogens we must always show these options "Display/Ligand/DrawType/Hydrogens". Do do this once is acceptable. But it must be done every time after closing/opening MarvinSpace. MarvinSpace does not remember this option.

But as I know MarvinSpace has still no file to save those options. It's an old topic of me I am looking for such a storage. When do we get it ? 

Another possibility here would be to set the default to display the hydrogens.

Best regards, Hans-Ulrich

Dear Hans-Ulrich,

thanks very much for your comment. We are aware that storing user settings in a config file would be a very useful feature to MarvinSpace. It is already in our backlog for a long time.
Let's discuss separately in email, how could we give a higher priority to this request.

Thank you,

Miklos 

Hello,

we have the same Problem. We use MarvinSpace to display conformations of small molecules and we also need hydrogens displayed.

So we need to set Display / Draw Type / Ligand / Hydrogens again and again when we start MarvinSpace.

We also regularely change the Background-colour into "white" and quality into "High".

Is there a possibility in the meantime that we can store these settings in a configfile and - if yes - where do we find this configfile?

I have fond a description of MarvinSpace Parameters and Events
https://www.chemaxon.com/marvin/help/developer/space-par.html

for exapmple:
Ligand.Hydrogens=true
Ligand.Quality="High"
Background.Color="#FFFFFF"

Can you tell me, how to use this settings as defaults?

Thanks in advance
Udo

Hi Udo,

In MarvinSpace 6.2, there will be a button on the toolbar for easily enable/disable hydrogen visualization.
This setting (along with some others, like draw and color types for molecules) is saved to a config file.

I will check how we could save more properties (like the ones you mentioned).

Regards,
Andras

Hi Udo,

I found out, that you can do that with the current version of MarvinSpace.

If you create a text file with this content:

MarvinSpace Log File

Quality High

Background.Color #ffffff

Ligand.Hydrogens true

 

You can load it, by using File/Process Exisiting Log File...

Regards,

Andras

Hi Andras, That means that with our current deployed version 6.1.2 we don't have a chance to set the defaults as standard e.g. by automatically process the log files, right? We have to open this file manually for 6.1.2, correct? Thx Edith

Yes. Unfortunately, it is correct. András solved it in version 6.3.

Best Regards,

Efi