This is a bit of a generic question to do with displaying the results of ab initio docking.
I have 200 complexes as determined by ab initio docking with HADDOCK2.4 and I’ve added all of these to PyMOL (in one window). I want to align Chain A of every complex, and then convert the bound protein (Chain B) into a collection of ‘Center of Mass’ points around this complex to visualise clusters.
I can go through the list one-by-one and achieve the first step of aligning the complex based on Chain A to a ‘model’ Chain A, but this is extremely time consuming. Is there a way to align all molecules at once? (solved, refer to edit)
The next issue is defining the Center of Mass of only Chain B of each complex and displaying this as a collection of ‘points/spheres’ - is there a way to do this, and in batch too?
I would appreciate any help and understand this might be out of the scope of this forum. This entry on the PyMOL wiki might assist anyone who’s a bit more technical than i currently am: Center of mass - PyMOLWiki
edit: The alignment was a simple solution - using a reference Chain: (A>Align>Align all to this)