Saving molecule in particular 3D orientation?

If a molecule is 'Cleaned in 3D' in MarvinSketch and then rotated into a particular 3D orientation (F7), can that orientation/perspective be saved for future use?

I've tried saving a molecule in a particular orientation using various file formats, but when I reload the files, the orientation is always different to the original.

Hi, 

This 3D rotation is a bit missleading we're thinking about changing it in the future.

Ppressing F7 changes the view only, but leaves the molecule itself intact. The view is not saved into the file, therefore rotating the molecule causes no change in the file.

You can select the structure (crtl +a) and select  right click > Transformation > Rotate in 3D > Free 3D rotation then the structure is rotated and the orientation will be saved to the file.

I suggest not to use F7 together with free 3D rotation as the result in the file may be different from what you may expect.

Best regards,

Peter

Thanks Peter! The Free 3D rotation worked exactly as you outlined and can be retrieved afterwards.

Please don't get rid of the F7/Rotate in 3D option! It's a very useful way of allowing students to move from Newman-like projection to Sawhorse projection and back again.

While the Free 3D rotation does the same thing, when all of the molecule is highlighted in green (along with the superimposed blue axes), it's a good deal harder to see what's going on. Perhaps this could be looked at in future?

Also, a shortcut to Free 3D Rotation (e.g. a function key or icon) would be very useful!

[edit] Figured this out for myself by adding a new shortcut key mapping onto F8 using the Edit->Customize menu.

[edit2] OK, so I can map Free 3D Rotation onto F8 on the desktop application, but when I transfer customization.xml to configuration.xml, the Java app doesn't repond to F8. How do I fix this?

I don't suppose there is any way of changing a dihdredal angle when in 3D mode?

 

 

Thank you for your feedback.The free 3D rotation feedback is a bit messy indeed. We'll check it out.

To rotate a dihedral select a part of the structure then go to right click > Transformation > Rotate in 3D > Around arbitrary axis then you can select the rotation axis.

Peter, thank you once again for your advice!!

 

Regarding the keymap issue, can you offer a solution to that?

i.e. how do I assign F8 shortcut to 'Free 3D Rotation'  to MarvinSketch Java app server side like I can with MarvinBeans desktop application?

Configuring shortcuts is not possible in the Applet in our current release.

I don't really see the reason for this, it seems like we just missed it several years ago and nobody missed it since.

I'll ask around whether it's possible to allow the customization of shortcuts in the Applet and get back to you when I know something.

Peter

 

gezapeti wrote:

Configuring shortcuts is not possible in the Applet in our current release. I don't really see the reason for this, it seems like we just missed it several years ago and nobody missed it since. I'll ask around whether it's possible to allow the customization of shortcuts in the Applet and get back to you when I know something. Peter

Thank Peter.  The feedback and help on this forum is a great credit to you all. 

I've got good news:

It's possible to customize shortcuts using the "shortcuts" parameter and defining the url to the shortcuts.xml.

I should have known this, I'm sorry.

Peter