Re: [PyMOL] fix cartoon backbone

[Jared S. <jar...@co...>]

Hi Adam -

The characters between the object names and the chain IDs are the segment IDs.  You can remove them by setting them to the empty string using `alter`:

alter all, segi=""

Hope that helps.

Cheers,
Jared


On March 22, 2019 at 12:14:46 PM, h. adam steinberg (h.a...@gm...) wrote:



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

On Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg <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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