Marvin Help: Can Marvin do surface simulations?

Hi, 

I am a newbie to the Marvin community. I have several questions that wish could get some help from the experienced users and friends here. 

1) Can Marvin design bond length? ( e.g. I want to created a metal crystal surface by MarvinSketch, but not sure how to design a proper bond length.)

2) Can we manipulate multiple molecules in MarvinSpace separately? ( Right now,  I put two molecules in MarvinSpace. The molecules are stick together. When I try to move one molecule, the other molecule moves as well.)

3) When I put a 3D C60 molecule that generated by MarvinSketch, with some other flat aromatic molecules in the MarvinSpace, the 3D C60 molecule become a 2D molecule? How can I active its 3D version? 

4) Overall, Can Marvin do simulations about molecules adsorption on crystal surface? (i.e. C60 on silver surface)

Thanks very much, 

Jun

Hi Jun,

1, Marvin can calculate molecular geometry including bond lengths for small (organic) molecules, but I'm afraid it won't work for metals (in general, non-covalent bonds aren't handled properly).

2, In MarvinSpace one can load structures in separate cells. Before opening and loading the second, third etc molecular structure file add a new row or new column to the molecule sheet (in the Layout pull-down menu). Then click the new cell to make it the active cell, then load the structure. It'll be placed in the new cell.

Even in case if you have multiple structures in one cell you can move them independently. To do so select either of them (use the right side panel in which your structures and other components are listed): right click the label or the little yellow rectangle, then tick Selected. Then use the Move tool in the icon toolbar (yellow cross), it is placed on top of the selected structure. Press the Ctrl key and use the right button of your mouse to drag the selected structure. 

3, MSpace displays each and every structure in 3D. If not, then that's a bug. Can you send us a screen snapshot? Also, a brief list of steps how you got there might be useful (along with the structure files, if not confidential). Thank you!

4, Marvin is not (yet) a modelling tool, it's purpose is structure editing and visualisation. Some physico-chemical, geometry and topology calculations are available (in the Tools menu of MarvinSketch, but not yet in MarvinSpace), but these do not include either absorption or modelling crystal surfaces.

Hope this helps.

Regards,

Miklos

 

Hi, Miklos, 

Thanks very much for the response and answering. 

I understand more about the Marvin now. 

1) About the 3D display, I think I need to save it in the right file format: I used MarvinSketch > insert  > template library > to draw a C60 and then saved it as a PDB file, and then I used MarvinSpace to open it later on, it showed 2D structure. Now when I saved as a .cxsmiles file, it can be opened as a 3D structure.  So the PDB format make the 3D to 2D. 

2) For the manipulate different molecules independently in one cell, it seems to still have difficulty. I put 2 C60 in MarvinSpace, and followed your instruction to select one molecules, when I start to move the selected molecule, the other molecule moves as well. (I'm in Mac OS)

You're right. Marvin is still not the modeling tool, but for structure editing and visualization. If you have other good recommendations, please let me know. 

Thanks,

Jun

Hi Jun,

Apologies for my long silence.

1, Can you send me the PDB that you saved? I could not reproduce the behaviour you reported, it be helpful to look into the source lines of the PDB file.

2, I reckon the simplest and most straightforward approach towards the resolution of this marvinspace issue would be a live presentation (sg like a goto meeting). I can demonstrate this and some other features within a 5-10 minutes, if you are interested. What do you think? Would this be suitable for you?

Regards

Miklos