Quick way of adding atom labels?

You seem to be able to add atom labels by:

Selecting an atom

Going to Periodic System

Going to Advanced

Selecting Alias as the Custom Property type

Entering the label and then going to close.

Is there any faster way of doing this if I want to assign a label of my choosing to each atom in a molecule?

Also why do custom properties not show up on the list of properties when one goes to Edit properties? Is this intentional?

Hi,

You can start with selecting all the atoms you want to change, and then set the Alias label in one batch . Alternatively, you can create a template from the alias you want to frequently use: select the atom bearing the alias, and then select the Add to MyTemplates option from the context (right-click) menu.

Regarding the atomic properties: the "Custom properties" that you can set through the Advanced tab of the Periodic System dialog (like Value or SMARTS, or even the query properties, like Unsaturated) are reserved properties, and cannot be set through the general Atom Property editor, and therefore are not listed there either.

Best regards,

Akos

akospapp wrote:

Alternatively, you can create a template from the alias you want to frequently use: select the atom bearing the alias, and then select the Add to MyTemplates option from the context (right-click) menu.

Hi Akos,

That is a fairly convenient, albeit somewhat unintuitve, solution to problem. A slight downside is the the template will not just contain the label but will also contain the element information for that atom e.g. I can not use my carbon 1 locant on a pyridine without turning it into benzene.

As I am dealing with mostly carbon containing molecules this will not be a major problem.

When adding some common locants as templates I noticed that the "My Templates" bar seems to be capped at displaying 24 custom templates even if there is space for the bar to expand into. Further templates can be added but will not display on the bar. (on MarvinSketch 5.4.1.1)

Thanks for the help,

Daniel

Hi Daniel,

i'm really sorry for answering so late, i have missed this topic unfortunatelly.

There is a maximum for the displayable toolbar template buttons. It is set to 30 by default. You can set this up in the Options dialog of the Template Library dialog.

The number of the templates that is visible on the toolbar can be between 1 and 50. If you need more than that, it is possible, but will cause a problem with the Options dialog.

Regards,
Istvan

ifajth wrote:

Hi Daniel, i'm really sorry for answering so late, i have missed this topic unfortunatelly. There is a maximum for the displayable toolbar template buttons. It is set to 30 by default. You can set this up in the Options dialog of the Template Library dialog. The number of the templates that is visible on the toolbar can be between 1 and 50. If you need more than that, it is possible, but will cause a problem with the Options dialog. Regards, Istvan

Thanks Istvan, that works well. However it is not immediately obvious to me why you would not have the default be 50. The bar's behaviour appears to be identical up till the point where you hit the maximum allowed templates and it is more intuitive to have a longer bar rather than your "add to my templates" request being ignored. (an error indicating that the max template limit should be changed would be a great change) You seem to already have it set up such that if the bar is too long you get a drop down bar with the undisplayable templates so I can't immedately envisage problems with 50 templates except on very small screens.

I think we set the default limit 30 because it affects the initialization time of the application. Since these molecules have to be imported before the application can be made visible.

The absolute limit is set to 50 because of the memory consumption of the molecules on the template buttons in one hand, and in the other hand, the toolbar has a limitation since it can contain only one row (also the drop down bar has this limitation), so there is an absolute limit because of the screen size. So we set the absolute limit to 50 based on empirical tests.

Regards,
Istvan