MarvinSpace doesn't show lone pairs?

I'm trying to get MarvinSpace (5.2.3_1) to show lone pairs on a single water molecule, but they don't show up.  I've tried this on Mac OS 10.5, Windows Vista, and Windows XP (running on a VMWare Fusion virtual machine). I click on the "lone pairs" button and nothing happens.

Also, why is 3D rotation so slow in MarvinView?  I need a combination of the lone pairs & bond order display from MarvinView with the smooth graphics display of MarvinSpace - right now it seems like I can't get both features at the same time.

 

--Mike Sierk

Dear Mike,

 

We are aware of a problem with showing lone pairs in marvin, however this bug is not fixed yet. We will notify you in this topic when progress is made on this problem.

Also, why is 3D rotation so slow in MarvinView? 
I need a combination of the lone pairs & bond order display from
MarvinView with the smooth graphics display of MarvinSpace - right now
it seems like I can't get both features at the same time.

For small structures with a couple of dozen of displayed atoms marvin view performs well on a moderate computer. What structure size caused the performance problems with your setup?

Regards,

Gabor

 

 

I'm not talking about large molecules - just H2O or HCN.  It doesn't feel like a (graphics) cpu problem, as if it's slow rendering the new orientation - it's more like when the mouse tracking speed is set very slow, and you have to swipe your mouse multiple times to get the pointer from one side of the screen to the other.  As a rough approximation, in rotation mode I move the mouse from the top to the bottom of the screen, and the molecule only rotates about 5 degrees (compared to ~180 degrees in MSpace).

Dear Mike,

 

Thank You for the clarifications. In MarvinView 2D rotation mode (where the axis of rotation is perpendicular to the plane of the screen) you must "draw" a circle using the mouse:

Drawing a circle fit to the window rotates 360 degrees. Smaller circles rotates less, bigger (by dragging the pointer out the window) more. 

In 3D rotation mode in marvin view (press F7) a linear drag over the window produces 180 degrees rotation around the appropriate axis (which is paralell to the plane of the screen in this case).

Could you check if your mview behaves like this?

 

regards,

Gabor

Gabor,

Yes, MView behaves as you describe.  The issue for me is that the 3D rotation is too slow - as I said, if you compare the rotation in MView with that in MSpace, the former takes multiple passes (e.g. all the way from the top of the screen to the bottom of the screen 3 or more times) with the "linear drag" in order to rotate the molecule 180 deg., while the latter rotates the molecule 180 degrees when the mouse moves from the top of the window to the middle of the window.  It's like being in too low of a gear on a bicycle (when I am in MView), if that analogy helps.

The reason this is a problem is that I want to use it for General Chemistry students to view different molecules in a lab on molecular geometry.  If the interface is too slow/awkward, they will get frustrated.  This is also why I need to be able to display lone pairs in MSpace.

Another problem I just noticed is that if I am in MView with hydrogens displayed, and click on "Open Marvin Space", the hydrogens are not automatically displayed in MSpace - I have to click on the Display->Hydrogens button to have them show up.

Thanks,

Mike 

Dear Mike,

 

Apologies for the late answer. Thanks again for the further clarification. It seems that when displaying small structures using large windows the rotation speed is inconvenient. I noted it in our bug tracker however currently could not estimate the scheduling of the fix.

It is a good idea to inherit hydoregene/lone pair display setting from mview when opening a mspace window - we will implement it. I will notify you when it is done.

Regards,

Gabor

Thanks, Gabor.

Hi -- I came across this discussion thread looking for the same solution as the original poster, and for the same reasons. Looking for a way in a Gen Chem class to be able to help them grasp what makes a molecule polar or non-polar. It's great that you can draw lone pairs in MarvinSketch, but I'd really like them to show up when I open the molecule in MarvinSpace and that does not seem to be happening, nor can I find a way to explicitly request MarvinSpace to show lone pairs.  Thanks!

Hi Douglas,

Yes, visualization of lone pairs is not the default setup in MarvinSpace.

One can set it under the Menu/Display/Draw type/Ligand/Lone Pairs. For the protein Menu/Display/Draw type/Macro Molecule/Lone Pairs.

Best Regards,

Miklos

Thank you Miklos. I had found those menu options, but I'm still not seeing lone pairs after selecting those. Is there a way to reload the structure or otherwise refresh it with those options in place? Or some other step I need to do to get the lone pairs to show up?  Thank you!

Lone pairs should be explicitely in the structures. MarvinSpace can visualize lone pairs, which are specifically present in the file. MSpace can't add explicit lone pairs to a structure automatically.

Hi Miklos,

[I thought I had posted this response but am not seeing it -- please forgive if this is somehow a duplicate!]

So what I'm doing is using your Marvin Sketch demo page (http://www.chemaxon.com/marvin/sketch/index.php) to create a molecule WITH lone pairs. I'm then using the Open MarvinSpace option under the View menu, but no seeing any lone pairs. Turning on the lone pair viewing as you've described does not change that.  Do I need to *explicitly* add lone pairs inside MarvinSketch, vs. just making them visible?  If so, I do not see an option for doing that. How is that done?  Thank you again,

Doug

Hi Doug,

yes, first you need to *explicitly* add lone pairs in MarvinSketch. Then, you can use Ctrl+3 to clean the molecule in 3D. You can even rotate it with F7 key.

Then, switch to MarvinSpace Ctrl+Shift+M. And finally, add hydrogens and lone pairs as it was described in my previous post.

Please find my screenshot attached.

I hope this helps. Let me know if you still have problems with it. We may need to investigate further details browser and java version, etc.

Best Regards,

Miklos

So this may be my problem -- the only way I'm seeing to display lone pairs in Marvin Sketch is via View menu > Advanced > Lone Pairs.  But I'm guessing maybe that is implicit?  How do you add explicit lone pairs in Marvin Sketch?  I'm just not seeing anything about Lone Pairs anywhere else on any menus or tool bar options. Thank you!

Thank you for all of your help. I've found how to add EXPLICIT Lone Pairs -- not very intuitive from my perspective, but it works and I have them now in MarvinSpace. Thank you!

I'm finding it awkward to accurately place explicit lone pairs in MarvinSketch so that they show nicely in MarvinSpace. I love the placement of the implicit lone pairs, but of course they won't display in 3d. Do you have any tips for placing lone pairs accurately so that they show up well when pivoting, for example, a MarvinSpace model of NH3 ?  If not, I'll keep plodding at placing them by hand, but if there's a keyboard shortcut or other technique for lining them up nicely I'd love to know about it. They don't seem to automatically attach to any atoms and just have to be placed near the appropriate atom, but that seems difficult once we get to the 3d space of MarvinSpace. Thank you.

Hi Doug,

We are sorry, but there is not an easy workaround for your problems in the current version of Marvin.
This feature (LP visualization) is under development at ChemAxon now and we will inform you if any changes are made.

Best regards,
Laszlo