Dihedral Angle

Hi

Probably a stilly question but is there a way to calculate the dihedral angle between two hydrogens in my 3D minimum enegry conformation?

Thank you,

Ben

Hi Ben,

It's rather funny than silly. I mean, what's your 3D minimum enegry conformation? :)

The dihedral angle is defined for 4 atoms, thus 2 hydrogen atoms aren't just enough. The 4 atoms should not necessarily be connected (in a successive manner), but typically they are.

Can you be more specific?

 

Thanks
Miklos 

Hi Miklos,

I mean the torsion angle between two hydrogens on adajacent carbons.  For example the minimum energy of n-butane (Attached) how do I find the angle between the indicated hydrogens using MarvinSketch?

Thank you,

Ben

Yes.  Go to View -> Open MarvinSpace.  Select Display -> Draw Type -> Ligand -> Hydrogens.  Then click on the third button in the toolbar ("measure dihedral of four atoms") and click on H-C-C-H sequentially.

If you want to set a dihedral angle to a particular value, use this page.

Thanks Bob!

Actually, mspace also provides a somewhat clumsy way to change the dihedral angle. 

After the torsional angle monitor is set up (as you described in your post) click the green circle around the monitored (measured) bond. After the first click the green circle turns to yellow and shifts left, if you click again it shift right from the original position. Let me remark that clicking the circle is not straightforward, actually, it's frustrating, so don't give up.

When the yellow circle is shifted left, then the right side of the molecule (with respect to the rotatable bond) is kept fixed and you can rotate the left side about the axis by dragging the mouse.

Suggestions to improve this feature are welcome.

Regards

Miklos

Which version of MarvinSpace has this feature?  I am using desktop MarvinSpace 5.4.0.  I can see the circle moving to the right or left, but it does not change color, and I cannot get the halves of butane to rotate independently.

It would be useful simply to be able to type the desired dihedral angle.  For example, after setting the monitor, double-clicking on the value of the angle should allow you to type a new value.

Hi Bob,

All versions, this feature has been available since mspace was first released.

I admit that the change of color of the semi circle is hardly visible. It becomes pale green but does not really change color.

To do the rotation press ctrl and the RIGHT mouse-button. Note that it works on mac touch pad with gestures, but make sure that the order is

1. ctrl 

2. right click (two fingers on pad)

3. press mouse button

We will implement the direct setting of the value.

BR

Miklos

I still can't get it to rotate.  Right now I'm using a laptop with a track pad, no mouse.

On Macs, right-click is usually either option-click or control-click.  Neither is working for me.  Doing anything on the track pad with two fingers doesn't seem to make it behave any differently from doing it with one finger.

You can use the touch pad to mimic secondary (right) click. Go to System preferences, there select Trackpad in the hardware section, and tick "Tap trackpad using two fingers for secondary click".

Then you can emulate right click with two finger tap and thus the ctrl key pressed event will be processed by mspace and the rotation should work....

Does this help?

M.

Yes, that works now.  But boy, is it unintuitive.  Wouldn't control-OPTION-click-drag be a more sensible way of implementing this feature?

After I rotate the bond, is it possible to import that structure with the rotated bond back into MarvinSketch?

Also, when I open MarvinSpace from within MarvinSketch 5.4.1.x (desktop or browser applet) or Marvin 5.5 (browser applet within iCab), the molecule background obscures the bottom of the popup menus. 

Hi Bob,

I'm glad it works finally. And I agree with you, that it is not intuitive! We will implement the new modifier keys according to your suggestion. In the meantime, we have started work on the modifiable measurement monitor as well. 

The new torsion angle can be imported back in msketch in case if mspace was launched from msketch.

The obscured menu problem sounds bad: we worked on that problem and tested it on many many platforms etc. however, iCab was not part of the test - we'll take a look at it, thank you for drawing our attention to this problem.

 

BR

Miklos

mvargyas wrote:

The new torsion angle can be imported back in msketch in case if mspace was launched from msketch.

How?  I opened MarvinSpace from MarvinSketch, but I don't see a way to transfer the rotated structure back into MarvinSketch.  The only way I can see to do it is to save the structure and then reopen it with MarvinSketch.  I'm using desktop MarvinSketch 5.4 right now.

Hm, that's odd. This problem was fixed in 5.4, but I experience a regression here: msketch exits when mspace is quit. That's a bug, we'll fix it (again!... :(  ).

Miklos