Hide some carbons and something else...

Hello

I'd like to know is there option to hide carbons in cyclic forms? Or selected carbons. I'd like to have just visuality of triangle (cyclopropane) instead of three carbons with bonds on each other so nothing can be seen...

What's more - is there option to change bonds beetwen some molecules? E.g. I'd like to write down AlCl4 instead of
     Cl
Cl-Al-Cl
     Cl

I know it can exist as alias but it can't occur alone, on the other hand writing as text unables me attaching electrons flow arrows.

Any advice? Thank you!

Dear lutek14,

Carbon lables can be set in Edit<Preferences<Structure dialog box. You can use radio botton to select "Always", "Never" and "At straight angels and at implicit H atoms" (which is the default setting) options. See:https://docs.chemaxon.com/display/marvinsketch/Displaying+the+label+of+carbon+atoms

For tetrachloroaluminate you can create an abbreviated  group:

1. Draw the structure.

2. Click the Group button in the Tools toolbar
then select the structure.  Upon releasing the mouse
button, the "Create group" dialog window pops up (this dialog window may
be opened from the Structure > Group submenu as well or use the CTRL+G shortkey.

3. Type AlCl4 in the name textbox. 

4. Select the group, and choose Contract group from the contextual menu (right click).

5. AlCl₄^- will be displayed.

For more information on abbreviated group see: https://docs.chemaxon.com/display/marvinsketch/Abbreviated+%28superatom%29+groups

Alternatively, (if you do not need the structural/chemical information) you can use it as text.

To insert a text :

1. Choose the "Insert text " icon from the Tools toolbar.

2. Click on that position where you want the text to be display.

3. Type AlCl4-.

4. Format the text.

For more detailed description see: https://docs.chemaxon.com/display/marvinsketch/Graphical+objects

Regards,

Nikolett Mihala

Dear Lutek14,

   I have attached a molecule image, if you wanted to reach this, you can do it with setting the carbon label visibility off. (Edit -> Preferences -> Structure tab) Could you tell me which version of Marvin do you use? I am surprised, that you have said, that you could not attach any electron flow arrows to the abbreviation. I have attached a picture about it.

Regards:
Balázs 

Hello

Thank you for Your answers!

Carbon lables can be set in Edit<Preferences<Structure dialog box. You can use radio botton to select "Always", "Never" and "At straight angels and at implicit H atoms" (which is the default setting) options. See:https://docs.chemaxon.com/display/marvinsketch/Displaying+the+label+of+carbon+atoms

I know this option, however I was asking about possiblity to have one's carbons shown, others not. For example having in one file reaction between benzene and CH3CH2CH2Cl I wish benzen wouldn't have shown carbons, but 1-chloro-propane have it.

For tetrachloroaluminate you can create an abbreviated  group:

1. Draw the structure.

2. Click the Group button in the Tools toolbar then select the structure.  Upon releasing the mouse button, the "Create group" dialog window pops up (this dialog window may be opened from the Structure > Group submenu as well or use the CTRL+G shortkey.

3. Type AlCl4 in the name textbox.  

4. Select the group, and choose Contract group from the contextual menu (right click).

5. AlCl₄^- will be displayed.

For more information on abbreviated group see: https://docs.chemaxon.com/display/marvinsketch/Abbreviated+%28superatom%29+groups

Thanks. But when I try to use electron flow arrow it doesn't start on Al or Cl but number 4 :( I'd like to have ability to choose in such a written the movement of electrons (e.g. chlorine attacks benzyl carbocation with two electrons and in the same time two electrons are moved from bond Al-Cl onto this chlorine) I can't do it in AlCl4-, it's requied to be in structural form so it is complicated a little bit.

bzaicsek

Have you written this AlCl4(-) as a text? I can't attach electron flow to the text. Maybe it's contraced group, but then it's the problem I've written above - can't put electron flow on certain atom, it starts from number 4

Dear Lutek14,

   Thank you for reporting this bug (the arrow starts from the last character of the label), we have made a fix for this, which (hopefully) will be in our next release. However you can still manipulate the starting point of the arrow, if you set an attachment point to an atom. Then Sketch tries to allocate the atom in the name of the abbrevgroup, and attaches bonds and arrows there. (I have attached two images to this post. One is made with MarvinSketch (and it contains a source) the other is a screenshot, because attachment points does not saved to images.)

Regards:
Balázs 

For carbon labels that are only shown in special cases I can only advise you an uncomfortable solution this time. You can set Aliases to the special carbons. It is in Periodic Table > Advanced tab. There you can click to Alias button, and write an Alias string (like CH2) to the text bar, than, if you close the Periodic Table window, you can add this name to any atom, you click on. I hope, it helps.

Oh!

Thank you a lot :)

I wish you change in next release of MarvinSketch showing carbons (it might be somehow like this: user selects structure -> right click -> option "Hide/Show carbons" and voila!) That's the only thing which is requied for me to call this application as a perfect one!

Great support !

I've one more question (I wish it was the last one :) )

Why does Marvin converts stereo bonds (first picture) in molecule to normal one (second picture) when i click CMD+2? Earlier in Structure Checker it's named "Wedge Error Checker"

I need show geometric structure as well, but programme unable me. I'm quite perfectionist - I align and merge eveyrthing so it's perfectly in one line, and this is quite problematic...

Dear Lutek14,

Hey

I am using the newest version for OS X

Sorry for the late reply,

I was still unable to reproduce your case, tried to redraw, what you've drawn, and pressed cmd+2, but for me the wedge bonds did not disappear. Cleaning in 3D does remove wedge bonds, but I think this was not the case here. 

If the problem still remains - could you provide the molecule file for me, which produces this issue ? 

Regards,

Tamas Fazekas-Vigh

Dear Lutek14!

   I have tried to redraw your structure. Can you reproduce the problem with this molecule? Also: have you choosen the clean option of the checker window?

Regards:
Balázs