Thank you Jared!
The commands didn’t work, but at least I now know why, and how to manually fix
this.
> On Mar 20, 2020, at 10:37 PM, Jared Sampson <jared.samp...@columbia.edu>
> wrote:
>
> 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>
> <mailto:h.adam.steinb...@gmail.com>
> Reply: h. adam steinberg <h.adam.steinb...@gmail.com>
> <mailto:h.adam.steinb...@gmail.com>
> Date: March 20, 2020 at 9:59:45 PM
> To: pymol-users <pymol-users@lists.sourceforge.net>
> <mailto: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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