[Chimera-users] Average structure

[George Tzotzos]

Hi everybody,

I’m analysing the Principal Components of an Amber trajectory. I have generated a number of representative pdb files which are concatenated for each PC.

Question: Is there a way to generate an average structure in Chimera from the concatenated PDB files? 

I know this can be done using MD movie but this solution requires that I generate a new topology file for my complex (the original topology file contains ligands and water molecules). 

Thank you in advance for any suggestions

Regards

George