Hi Josh, I think the way to go is find an existing PDB DNA model and simply align it to your RNA by say matching the P backbone atoms. For example if the RNA is chain A of model #1 and the double stranded DNA is model #2 with chains A and B use a command like match #2:3-15.A@P #1:1-13.A@P I would not recommend using the Chimera RNA command which only builds very crude models with center-liine paths specified. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html Tom On Sep 23, 2013, at 12:09 AM, Joshua Carter wrote:

Hi,

I'm working on a project in chimera that involves modeling the binding of a RNA-guided protein complex to a double stranded piece of DNA. What I need to do is be able to is either match a DNA pdb to the existing RNA pdb I have or build one using the rna command in chimera. I know there is a path command, is there any way I could specify that to build along a pdb I have already? Or am I just barking up the wrong tree entirely?

Thanks, Josh _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users