Bold-Bond-line-Symbol problem

Software: MarvinSketch 64-bit (v 5.11.5_b106, Windows 7 64-bit, or CentOS-6.3-x86-64 both with latest AMD Catalyst video driver v 13-1)
Problem: I am formatting formulas for inserting into a PowerPoint slide. Say for example trans-2-chloro-1-methylcyclohexane. I select the stucture, do Edit, Format, make the Atom Label 18 pt bold, and make the Bond Thickness 0.15. In the resulting formula the "down" bond overlaps the Cl symbol. In Windows, the "down" bond is on top of, and partially obscures, Cl. In Linux, the "down" bond is under the Cl, and Cl partially obscures the bond. This also happens with H on a  "down" bond.
Question: How do I make this type of "bold-ed" structural formula in MarvinSketch without the bond-lines overlapping the symbols?

Unfortunately, it is a bug. Thank you for reporting it. Until we fix it, you can apply a workaround in which the atoms in question was drawn by using spaces in aliases as you can see in the attached file.

Best Regards,

Efi

Thank you, Efi. That looks a lot better! Are alias' s described in the documentation somewhere?

John K.

Dear jwkeller!

You can find some information about aliases here:

http://www.chemaxon.com/marvin/help/sketch/gui/dialogs.html#advanced

and here:

http://www.chemaxon.com/marvin/help/sketch/sketch-basic.html#custom.properties

Best regards,

Tamas Fazekas-Vigh

Sorry  - I am still in the dark: On the new file "with alias's", I see a new section mrvAlias="0 0 0 0 0 0 0 \u0020Cl\u0020 etc" which I assume inserts extra space around this Cl atom in the formula. So do I edit the .mrv file manually to insert a section like that? I need a more basic explanation of what an alias is, how to add it and how to change it.

John K.

Dear John,

in order to use alias atoms, you should go to the "Advanced" tab of the Periodic Table. In the lower part of this dialog there are buttons for several Custom Properties, "Alias" is among them. When the cursor is over this button, you can read a short description about aliases (please, see the attached screenshot).
In the current case, you should press the Alias button and type Cl in the Value textbox with a space before and after it. Finally, click on the Cl symbol; now the label does not overlap with the down bond.
Repeating this procedure helps with the hydrogen atom, too. Using spaces before and after the atom symbol is important to put the atom label in the middle.

However, it is only a workaround and might not work in every case. We will fix the original bug. Thank you again for reporting it!

Best regards,

Dora