Hi Adam -
That's a fun one. It appears that most of these O3' atoms are not bonded to
the P atom of the following nucleotide, which you can see if you show the DNA
chains as sticks. Creating a bond via `bond atom1, atom2` results in a normal
cartoon. Fortunately, the DNA chains are sequentially numbered, so you can do
something like:
for i in range(1, 80): cmd.bond(f"/5fur//E/{i}/O3'", f"/5fur//E/{i+1}/P")
for i in range(81, 160): cmd.bond(f"/5fur//F/{i}/O3'", f"/5fur//F/{i+1}/P")
The offending bond lengths are much longer than a typical P–O bond, which is
why PyMOL's default distance-based bonding doesn't pick it up.
Hope that helps.
Cheers,
Jared
From: h. adam steinberg <h.adam.steinb...@gmail.com>
Reply: h. adam steinberg <h.adam.steinb...@gmail.com>
Date: March 20, 2020 at 9:59:45 PM
To: pymol-users <pymol-users@lists.sourceforge.net>
Subject: [PyMOL] broken DNA cartoon
Hi All,
When I open 5FUR either from my drive or via fetch, the DNA cartoon is broken
and mostly missing (it should span from left to right). Any ideas on how to get
the cartoon to work?
Pymol version 2.3.4
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