Thank you. Interestingly… These alter commands do work on the DNA in my original working .pse file, the file that contains all of the structures. They do work on the “save molecule” as a cif file that I shared with you, if I open it into PyMOL by itself. They also work if I open the chain F.cif into my original working .pse file. This will fix the new chain F but not the old chain F.
Something about saving the chain out as a cif file and bringing it back in alters something besides just the atom naming. > On Mar 22, 2019, at 1:43 PM, Thomas Holder <thomas.hol...@schrodinger.com> > wrote: > > Hi Adam, > > The atom naming is nonstandard. If you fix that, the cartoon will be complete. > > alter name P01, name="P" > alter name O01, name="O5'" > alter name O02, name="OP1" > alter name O03, name="OP2" > unbond name OP1, name O3'+O5' > unbond name OP2, name O3'+O5' > > PyMOL doesn't yet write bonds to mmCIF (it's on our TODO list, unfortunately > the mmCIF spec doesn't make this straight forward). You could save to MMTF > instead, it stores all bonds. > > Cheers, > Thomas > > >> On Mar 22, 2019, at 5:42 PM, h. adam steinberg <h.adam.steinb...@gmail.com> >> wrote: >> >> 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> >> >>> 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 > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc.
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