How to draw the rational formula

Dear Support team,





Please let me know the drawing procedure for the rational formula on MarvinSketch.





Please see the enclosed example that drawn by Adobe Illustrator. I cannot draw well the ketone moiety in the ester group on Marvin.





The bond tool cannot be drawn between the ester carbon and oxygen written as text captions. Do you connect the chemical bond between an atom label and a text caption? If cannot, how do you draw the fatty acid group in the example? I appreciate your step-by-step procedure.





Best regards,


Hiro

As the example rational structure I uploaded cannot be displayed on my post, so I re-uploaded the structure as GIF file.





Hiro

here is a flash movie and the resulting mrv file

Hi saettel,


how to see the flash movie?





Firefox 3.0.4 on Ubuntu 8.0.4





Regards, Hans-Ulrich

I uploaded the corresponding html file...

Hi saettel,


now I see it. The problem is the size, see screenshot.


Regards, Hans-Ulrich

Hi Saettel,





Thank you so much for the Flush movie for the procedure.





My aim is expression the chemical structure without using aliphatic chain. My associates who are cell biologists prefer the rational formula expression, not the structural formula.





As you know, drawing expression by rational formula is more compact and easy understanding than the drawing by structural formula expression. Especially for the comparison among calboxylic acid, corresponding ester and amide, the rational expression is better for “beginners” as well as comparison among the various biological lipids.





Best regards,


Hiro

saettel wrote:

here is a flash movie and the resulting mrv file

Hi,


the funny thing is if I open the file it looks fine but when I calculate the formula and mass it is not correct (see attached pictures).





The text output is:


Mass = 88.1051


Exact mass = 88.052429500


Formula = C4H8O2


Isotope formula = C4H8O2


Dot-disconnected formula = C4H8O2


Composition = C (54.53%), H (9.15%), O (36.32%)


Isotope composition = C (54.53%), H (9.15%), O (36.32%)


Atom count = 14





Something is wrong...


Tobias

Hi Tobias,


Thanks for the bug report. Indeed, MarvinView displays only the first digit of the index by the bracket in keton.mrv. It is a drawing issue in MarvinView.


We will debug it.

Hi Tobias,





The problem is that MarvinView incorrectly displays the right border of the textbox, therefore it hides the last digit of the number. We will repair this bug.





Best regards,





Akos

Dear Hashima-san,





The solution for the original problem is as follows:





1. Draw the structure without abbreviation, so on the left side draw a 22-carbon-long chain.


2. Select this chain, then right-click, and select "Group"


3. Type: CH3(CH2)21, then click OK


4. Move the mouse over the chain, until the group is shown, then right-click, and select "Contract Group"





I attach a video as well.





Best regards,





Akos