Molecules in Avogadro

I think you want to consider “named selections.” You can then mark the ligand as a named selection, and do whatever you want with the interactions. You can also access the list of named selections through the API.

Tim was working on some docking features at one point, but I don’t know his status on that.

We’d definitely be happy to help with that. If you don’t think a named selection would work, we should figure out another approach that wrks for you.

Cheers,
-Geoff

On Feb 4, 2010, at 4:50 PM, Skaidrius wrote:

I will try to be specific. :slight_smile:

What I actually need, is to implement a functionality allowing to visualise
inter-atom interactions between ligand and receptor (for example, I select any
atom of ligand, and neighbor receptor atoms, depending on their interaction
energy, changes their colour). So, here it comes a need to be able to have more
than one structure in the same work area.

I am looking for a platform for that. One pretendent is Avogadro. As I imagine,
I can create a plugin, by which I will be able to implement such visualisations.

Feel free to correct me, if I am wrong, as I am quite new here.

I’ve done something similar in my somewhat abandoned randomDock extension:

http://github.com/dlonie/avogadro-RandomDock

I didn’t know about named selections, though – I’ll have to look into
that if I revive the project. But yes, it is absolutely possible to
work with multiple molecules in the same workspace (I called them
"scenes" in my code, but what’s in a name? :wink: ). What you propose
sounds very possible, and might even be easiest through the python
interface.

Dave

On Thu, Feb 4, 2010 at 5:58 PM, Geoffrey Hutchison
geoff.hutchison@gmail.com wrote:

I think you want to consider “named selections.” You can then mark the ligand as a named selection, and do whatever you want with the interactions. You can also access the list of named selections through the API.

Tim was working on some docking features at one point, but I don’t know his status on that.

We’d definitely be happy to help with that. If you don’t think a named selection would work, we should figure out another approach that wrks for you.

Cheers,
-Geoff

On Feb 4, 2010, at 4:50 PM, Skaidrius wrote:

I will try to be specific. :slight_smile:

What I actually need, is to implement a functionality allowing to visualise
inter-atom interactions between ligand and receptor (for example, I select any
atom of ligand, and neighbor receptor atoms, depending on their interaction
energy, changes their colour). So, here it comes a need to be able to have more
than one structure in the same work area.

I am looking for a platform for that. One pretendent is Avogadro. As I imagine,
I can create a plugin, by which I will be able to implement such visualisations.

Feel free to correct me, if I am wrong, as I am quite new here.


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Your question about the project tree is a good one. It’s certainly possible to “teach” it to reflect multiple molecular fragments in the “universe.” This would be a good feature to allow users to select multiple fragments at once.

I will add this to the feature request list.

Thanks and best regards,
-Geoff

On Feb 11, 2010, at 4:15 AM, Skaidrius wrote:

Thank you, I will try to check named selection.

I expected initially, that project tree should be capable to reflect all molecules in the scene, but it
shows only one. Are you planning to “teach” the project tree to reflect all
molecules?

Thanks,
Sk.