[Chimera-users] Building DNA along A PBD Using RNA command

[Tom Goddard]

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 at P #1:1-13.A at 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
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