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
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
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 th
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)
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
___
