Re: [PyMOL] fix cartoon backbone

[h. a. s. <h.a...@gm...>]

I’ve altered the chain names and I’ve altered the residue numbers, sorted, and rebuilt but I’m still not getting a complete cartoon.

I see in obj02 there is an “A” in front of my “D” chain 16-33, and a “B” in front of my “D” chain 34-46, similar for obj03. I’m assuming that is now the issue. Is there some type of alter command for that part? 



> On Mar 21, 2019, at 1:41 AM, Kevin Jude <kj...@st...> wrote:
> 
> The DNA in 1CGP is made up of two annealed half sites, so there are four chain assignments for the two strands. If you want to display it as intact DNA, after adding the linking phosphate you can use the alter command to make the chains continuous. HTH.
> 
> --
> Kevin Jude, PhD
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431 <tel:%28650%29%20723-6431>
> On Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg <h.a...@gm... <mailto:h.a...@gm...>> wrote:
> Hi All,
> 
> I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. After I fixed those two breaks (add in the correct atoms and join them) how do I get the cartoon of the DNA to be complete? PyMOL still creates the cartoon with the breaks.
> 
> Thanks!
> 
> Adam
> 
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