Hi all, I am trying to arrange two (RNA) molecules relative to each other such that a number of selected residues are getting close enough to form contacts via H-bonds. To me it seems quite difficult to use pyMol to precisely arrange molecules in space (I use the translate and rotate commands or move the molecules around free-handed). Is there an option to at least display a coordinate system? Furthermore, I have used the measurement wizard to define distances between interacting residues. I was hoping that these displayed distances would dynamically change as I change the molecules position such that I can monitor appropriate arrangement more easily, but this does not seem to happen. Is something like this possible at all in pyMOL? Or can anyone describe a reasonable pyMOL method of how to match two (RNA) molecules to interact. I know a docking program would be best, but I fear the molecules I work with are much too complicated for this.
Thanks for your help, Michael.
