Re: [PyMOL] fix cartoon backbone

[h. adam steinberg]

Thank you, that certainly brought the chains together, but sill no completed cartoon even after a rebuild. Attached is chain F, can you see anything wrong with this file that won’t let it display a complete chain? It must be with how I joined the missing atoms? I also notice that every time I open this object in PyMOL I get odd bonding happening. Even when I unbond those odd connections and resave the file, it puts them right back in when I reopen the file. I could simply fake the connection using photoshop, but I’m trying to learn to do it correctly! :) I appreciate your help!

chain F.cif
Description: Binary data

On Mar 22, 2019, at 11:31 AM, Jared Sampson <jared.samp...@columbia.edu> wrote: 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.adam.steinb...@gmail.com) wrote: On Mar 21, 2019, at 1:41 AM, Kevin Jude <kj...@stanford.edu> 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.adam.steinb...@gmail.com> 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 _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe _______________________________________________  PyMOL-users mailing list  Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net  Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

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