Coordinate behaviour by placing template on canvas

Hi,

This intent of this query is just  to get a small clarification. I would be pleased if someone could clarify this.

When the behaviour of coodinates is set to clean 3D under "insert -> template library" option. Is that the behaviour of all coordinates present on marvinsketch canvas should change when ever a template is choosen from template library?

Thanks in advance,

Yogitha

Hi,

Yes, exactly. So regardless the corrdinates displayed in the Template Library, when you select a template and move your mouse over the canvas, the structure of the template should already be 3D cleaned.

Best regards,

Akos

Hi,

Thank you for the reply.

Best regards,

Yogitha

akospapp wrote:

Hi, Yes, exactly. So regardless the corrdinates displayed in the Template Library, when you select a template and move your mouse over the canvas, the structure of the template should already be 3D cleaned. Best regards, Akos

Hi,

Thanks for the valuable reply. One short question. If suppose a structure/ molecule is already placed on marvin sketch canvas and now the template options are set to 3D clean. How do the structure on canvas behave when a template selected from template library is placed on the canvas? Is that the structure on canvas should also be 3D cleaned?

Thanks in advance.

Regards,

Yogitha

Hi,

No. Why should it be 3D cleaned?

Best regards,

Akos

akospapp wrote:

Hi, No. Why should it be 3D cleaned? Best regards, Akos

Hi,

After placing the template structure, draw a structure on the same marvin canvas. The structure attains 3D clean,. This is because the template structure is placed on the canvas.

Best regards,

Yogitha

Yogitha.P wrote:

akospapp wrote: Hi, No. Why should it be 3D cleaned? Best regards, Akos Hi, After placing the template structure, draw a structure on the same marvin canvas. The structure attains 3D clean,. This is because the template structure is placed on the canvas. Best regards, Yogitha

Hi,

No it does not attain 3D clean. But there is 3D click drawing feature in Marvin that adds the next methyl group in the next optimal tetrahedral direction. Try this out:

1. Switch off the 3D cleaning in the Template Library

2. Draw something, e.g. a cyclohexane

3. Ctrl+3 (but be sure that the cleaning method is set to Fine Build)

4. Select the single bond tool (or hit 1 on the keyboard)

5. Click on a carbon atom of the ring (or if you drew something else, click on a carbon atom having at least one implicit hydrogen)

It seems to be 3D cleaned.

Best regards,

Akos

Hi,

Thanks much for the reply. I understand that it is because of 3D click drawing feature. I tried the following and observed 3D clean active. Is this because of 3D click drawing feature?

The following below is the flow.

1. Draw a simple structure eg: propane

2. Now set the template option to 3D clean and place something eg: Napthalene from template. Template semd 3D cleaned.

3. Switch off the 3D cleaning in the Template Library and add a single bond to propane at  position 2 (C2).

4. The structure (propane) appears to be 3D cleaned.

Thanks & Best regards,

Yogitha

Hi,

Did you try the steps I wrote? See what happens when you call the 3D clean (Ctrl+3) after drawing?

Also, please make counter-test for your test example, e.g. use a different tool, like the chain drawing tool. Then apply 3D clean. You will see it is different.

Best regards,

Akos

akospapp wrote:

Hi, Did you try the steps I wrote? See what happens when you call the 3D clean (Ctrl+3) after drawing? Also, please make counter-test for your test example, e.g. use a different tool, like the chain drawing tool. Then apply 3D clean. You will see it is different. Best regards, Akos

Hi,

Thanks much for the reply. Yes it is different.  It's working.

Best regards,

Yogitha