Hi, I am using Xplor-NIH for structure determination of nucleic acids. I have used anneal scripts and refinement scripts to produce two separate RNA structures. What I would like to do is to use Xplor to model RNA-RNA interactions between these two RNA structures.
But before I ask you how to produce a script to incorporate RNA-RNA interactions, I would like to know how to generate water or produce a water box to surround an RNA structure. I have also read in the manual that you can further refine your structure using a water refinement protocol. Will this protocol generate water molecules around an RNA structure and then start the refinement step. I am a beginner to Xplor so I would really appreciate any help you can provide.. Usman
