Several Difficulties with bolding bonds for rotamers

In trying to draw rotamers, I've come across several limitations in Marvinsketch compared to Chemdraw.

1) Group rotation in 3d is used enough that it should have a toolbar button, like it does in Chemdraw. As far as I can tell, in Marvinsketch I have to go through several menus (Edit > Transformation > Rotate in 3D > Group Rotation) to do what I can do with one click in Chemdraw.

2) Once I've drawn a quaterphenyl with the aid of the Group Rotation function, I want to shade/bold some of the bonds to get a nice suggestion of depth and orientation. In Chemdraw, I just select the bold, straight bond or the bold wedge bond, and click on whichever bonds I want to change. In Marvinsketch, (a) it's not obvious how I can draw a bolded wedge bond. It's not an option from the toolbar, and if I draw a normal single bond, select it, and go to Bond > Type in the menu, the "Single Up" option, which looks like what I want, is grayed out. (b) it's very hard to click on the bonds that are shortened by the perspective caused by Group Rotation. The "hotspot" over which I hover to select the perspective-shortened bonds on the phenyl rings is extremely small and located somewhere not intuitive. I've attached a screenshot with an asterisk next to one of the hard-to-click-on bonds.

3) (off-topic) I just noticed that when I tried to select, copy, and paste the red asterisk, instead of creating a duplicate red asterisk, my cursor changes to an A.

I've attached a screenshot of what I drew in Chemdraw, and my attempt to draw the same thing in MarvinSketch.

Dear Sibo,

let me reply in order of your questions.

1. You can personalize the graphical user interface to better suit your needs or style so you can add a "Group rotation" button to any of the toolbars. For more information  https://docs.chemaxon.com/display/marvinsketch/Advanced+Changes

2. In MarvinSketch you can  make bold the double bond and the single bond at disposition, the single up and down bonds are considered bold bond per se.

You are right it is a little bit difficult to select bonds which are shorter then the default. You can select these bond more easily using i.e. the rectangular/lasso selection tool.

3. Could you send us the ChemDraw file please. It might be a bug or an intentional behavior (if the asterisk stands for Any atom)

Please find attached your structure in .mrv file.

Should you need any further information, please do not hesitate to contact us.

Best regards,

Nikolett Mihala

Nikolett,

Thanks for your replies and work on MarvinSketch. I still have issues with applying the Single Up bond style--after selecting a single bond, the "Single Up" style is grayed out. I've attached a screenshot showing this behavior.

As for selecting shortened bonds, clicking and dragging around the bonds works, but it's not as convenient as just clicking on the bond, especially when multiple bonds need to be styled. Hopefully future versions of MarvinSketch can address this.

For the issue with copy and pasting the asterisks, I attached it in the first post.

Thanks again for all the work on this promising software!

Dear Sibo,

the wedge bond are disabled, because when you rotate the phenyl group(s) in 3D, the canvas automatically will change to 3D mode, where wedge bonds can not be interpreted. Here you can use bold bond or draw the wedge bonds in 2D before making the Group rotation action.

The red asterisk here is placed  as text. MarvinSketch if the entire textbox is selected by a selection tool tries to add chemical meaning to it so the asterisk becomes any atom. If you select the content of the textbox by the "Insert Text" tool from the Tool toolbar it will be copied as text, however the eventual formatting will be lost.

I hope this is useful to you.

Best regards,

Nikolett Mihala

Love the Group rotation tool! Thanks for implementing it! Now you just need a clever icon for the button so it doesn't take up so much room in the toolbar.

Thank you for the nice feedback.

Best regards,

Efi