Newbie, how to draw methane with all hydrogens and all bonds

User 5c48d4e3b9

27-05-2009 13:34:33

How do I draw a methane with all four atomic bonds and all four hydrogens?


How do I draw a water molecule as lewis structure? I can never get the hydrogens to show.


For that matter, how do I draw a Hydrogen molecule? The hydrogens never seem to show without any other atoms in the canvas.


 


Thanks for your time

User 870ab5b546

28-05-2009 02:04:43

In MarvinSketch, all heavy (non-H atoms) are explicit, but H atoms may be implicit or explicit.  


From the View menu, you may choose whether to show all implicit H atoms, those on heteroatoms and terminal C atoms (default), only those on heteroatoms, or none at all.  MarvinSketch does not show the bonds to implicit H atoms.  


If you wish to see the H atoms *and* the bonds to them, you must make them explicit.  Choose Structure -> Add -> Add Explicit Hydrogens.  Or, after you draw the heavy atoms, click on the H button, click and hold on the atom to which you want to add an H atom, drag, and release.


To show the lone pairs in a structure, choose View -> Misc -> Lone Pairs.

User 5c48d4e3b9

28-05-2009 12:35:19

well, I basically tried all your suggestions but it didn't work. I was not able to draw a simple water molecule showing all bonds. However, it might have to do something with my installation since I installed on a Linux computer also and there it seems to work fine. I will uninstall, download the installer including JRE, reinstall and see what happens.


Thx for your input though.

User 5c48d4e3b9

28-05-2009 15:55:10

in the meantime I uninstalled and reinstalled from marvinbeans-5_2_02-windows_with_jre.exe


but the behaviour hasn't changed. There definitely is a difference between the Win Version and the Linux Version.


To test I drew a fatty acid with 12 carbons. In Windows I am not
able to make the hydrogens visible in a ball and stick display or any other display option. In the
linux version I go to Structure>Add>Add explicit hydrogens and
the hydrogens become visible. Definitely not so in the Windows version,
here it is impossible, even in 3D to display the hydrogens.


Any ideas?


For the record, I am using WinXP on a Dell Inspiron 6400 JRE 1.6.0_07


the linux machine has ubuntu 8.04 up to date

User 870ab5b546

28-05-2009 15:57:45

I'm a Mac user, and I avoid Windows as much as possible, so I'm afraid I can't help you anymore.  But I'm sure the good folks at ChemAxon will step up.

ChemAxon 0a9e2a55e1

29-05-2009 11:19:13

Hi!


We cannot reproduce this bug. The explicit and implicit hidrogens works fine in ball and stick mode in Vista and Xp woth java 1.6.13.


Please check if there is any message on the console when you choose Structure > Add > Add Explicit Hydrogens.


 


Best Regards,


Peter

User 5c48d4e3b9

29-05-2009 13:22:59

thanks for taking care of my problem, Peter.


No, there is no message in the console. I attach the test file and a screen shot of how it looks on my screen.


 


What I want to see is a fatty acid with all explicit hydrogens displayed. In the linux version I can do this by drawing the structure and then going to Structure>add>add explixit hydrogens. The screen shot from the linux version is attached too.


 


Side note: what would really like to do is to display the hydrogens AND the carbons AND the electron pair between them but I guess that's not possible.

ChemAxon 40e8f9506d

03-06-2009 12:27:03










DrScum wrote:

Side note: what would really like to do is to display the hydrogens AND the carbons AND the electron pair between them but I guess that's not possible.



A bit circumstantial, but you can use Alias atoms to get the carbons displayed.


Open Periodic Table (Ctrl+M), click the Advanced tab, select Alias from the bottom of the page (Custom property button group), write C into the text field below then click the atoms  in your sketch you want to have displayed.


Of course, this is not really convenient for your molecules of 10-20 carbons, but still, a workaround.


 


regards,


Annamaria

ChemAxon 990acf0dec

03-06-2009 13:20:15

Hi,


To make the carbon labels always visible, open the Preferences dialog (Edit>Preferences), and on the General tab switch on the "Always" radiobutton at the "Carbon Labels" section (bottom right).


Cheers,


Akos

User 5c48d4e3b9

03-06-2009 14:00:01

THX Acos, that was the hint I was hoping for.


Regarding my inital problem? No ideas what has happened to my windows version?


 


I guess another incentive to switch to Linux!

ChemAxon 7c2d26e5cf

05-06-2009 18:35:48

I assume that the cached user settings are different in your Windows machine. Delete HOME/chemaxon/marvin.properties that stores your personal settings (e.g.: C:\Documents and Settings\myaccount\chemaxon\marvin.properties). Probably, it helps.

User 5c48d4e3b9

05-06-2009 19:12:18

Thank you very much, that did the trick!