Tuesday, 17 June 2008

Glucocorticoid receptor (3)

Again the same molecule with a few more pictures. They were made with the "apple cutting" plugin from Lightnir. It cuts a plane through the protein. The orientation of this plane is not entered manually but chosen automatically by the viewing perspective which is a pretty cool idea in my opinion.

With pymol and this plugin you can quickly visualise a binding pocket and make pictures like this one ...

... or this one ...

... or this one.


Lightnir said...

Ok, I added changing the orientation of the plane to my TODO list on that script. Also a plane preview would be nice(using PyMols CGO). Any other wishes?


Felix said...

hi, actually I just ment to say that it is a nice thing that this plane is automatically chosen according to the viewing perspective. of course it would also be fun to see this plane but not necessary.
one thing you could do, is that you cannot only use selections but also objects for the ligand and pocket (my ligand was an object because I wanted to change it separately from the protein). but of course it is no problem either to create a selection
anyway, I think that plugin is very nice as it is

Lightnir said...

Hi! You are right about adding the object support. I wonder why I haven't thought of this earlier. I've already implemented this feature it in the new version of the plugin.
I'll probably implement the rest of my ideas on this weekend, when i have more time for it. So stay tuned.

PS. I hope with a little help of this tool we will see here binding site images more often ]:)