Help

Hi:

I need some help with two problems.

1. How to draw straight horizontal/vertical line or arrow;

2. How to make MarvinSketch to show in a node of a ring two elements one above the other and not side by side; for example, I do not want NH represented as NH, but as N and than H under N (no superscript or subscript).

Many thanks and regards.

Bojan

Hello,

Please enable the Grid and Guidelines from the View menu. That will help. For the other, can you please send an example what you are trying to achieve? Thanks

kniesz wrote:

Hello, Please enable the Grid and Guidelines from the View menu. That will help. For the other, can you please send an example what you are trying to achieve? Thanks

Thank you, grid of course.

As to the other question, see attachment. With YES is marked what I want, and with NO is marked what I get and I do not want.

Bojan

please try and start rotating the molecule. you will notice the change of the relative coordinates. 

I do not understand what do you mean by rotating the molecule. I tried it this way: I selected the entire molecule, than Edit/Transform/Rotate in 2D. The molecule did rotate, but the position of NH node remained same all the time.

Select the molecule and press space until the spur wheel appears. You can then simply rotate the molecule with the mouse. Attached a screenshot on what I mean, and with the desired location of the H atom. 

Sorry, but no luck with me. I tried your instructions but NH remains in the very same position all the time. Attached you may see the original structure (in black) and the same structure rotated in two different directions. What am I doing wrong; is there any option to be set in MarvinSketch.

Bojan

The optimal location is automatically calculated. What could work for you is moving the N atom slightly up, that changes the relative position of H. 

Thank you for your kind effort, but no luck with your instructions. There is no way to put N over H, only side by side, like NH.

Bojan

Hello Bojan,

Not sure why it does not work for you, as this is just a simple atom movement. Anyway, I am attaching a before / after screenshot showing the result. Only the position of the N atom has been slightly changed (cannot even recognise, really).

Fine, thank you. That means I am certainly doing something wrong. Therefore, please explain how to move only one (i.e. N) atom.

Bojan

kniesz wrote:

Hello Bojan, Not sure why it does not work for you, as this is just a simple atom movement. Anyway, I am attaching a before / after screenshot showing the result. Only the position of the N atom has been slightly changed (cannot even recognise, really).

Further to my previous post, please tell me also, how did you enter NH group. I did it as Alias (have entered N and H) and afterward  put this Alias group into the position.

Regards,

B.

Hi Bojan,

Thank you for the additional information.

Marvin Sketch handles Alias labels as a whole, and rotates these accordingly. That is why rotating and moving this item did not work, as you expected.

You can draw NH by selecting the N atom tool from the list of the atoms on the toolbar and left-clicking the right place, or with active Selection tool, hovering over the atom, you would like to change, then pressing the "N" keyboard button.

(You do not need to enter the H, because Marvin Sketch can calculate the implicit Hydrogens automatically.
For this, please make sure, that the "On Hetero" option is selected via View > Implicit Hydrogens menu.)

After these, the position of the H is still automatically generated, but rotating the structure, or moving the atom, as Krisztian described before, should do the trick.

Best regards,
Eszter 

eszabo wrote:

Hi Bojan, Thank you for the additional information. Marvin Sketch handles Alias labels as a whole, and rotates these accordingly. That is why rotating and moving this item did not work, as you expected. You can draw NH by selecting the N atom tool from the list of the atoms on the toolbar and left-clicking the right place, or with active Selection tool, hovering over the atom, you would like to change, then pressing the "N" keyboard button. (You do not need to enter the H, because Marvin Sketch can calculate the implicit Hydrogens automatically. For this, please make sure, that the "On Hetero" option is selected via View > Implicit Hydrogens menu.) After these, the position of the H is still automatically generated, but rotating the structure, or moving the atom, as Krisztian described before, should do the trick. Best regards, Eszter

Thank you very much Eszter. I really appreciate your help that proved I had a wrong approach. Now, everything is OK.

Thanks again and best regards,

Hi Eszter,

Again me, asking for a bit of help. I attached two files, test1 and test2. Each of the files has a certain feature marked with a red ellipse. What am I asking you is to teach me how to enter each of said features in the structure. In test1, I entered NH2 .H3PO4 as alias. In test 2, I entered small square as Draw/Rectangle. Were the steps I took correct or are any other ways to obtain said results.

Thank you and best regards.

Bojan

Hello Bojan,

 

May I ask what you want to achieve here? Only simple drawing or you would like to send these into further calculation-query?

If you delighted with the results that way, I think the alias is fine. If you want it i other format, please let me know what would you expect to see and I am happy to give you a hand how to do it.

Best regards,

Efi

Hello Efi,

No, no further calculations is provided for, only a simple representation and as a result, a png or svg image. As far as I understand you, alias is fine for such a use.

Thank you and kind regards.