Well, thank you very much Blaine! That worked great!
> On Mar 22, 2020, at 10:01 AM, Mooers, Blaine H.M. (HSC)
> <blaine-moo...@ouhsc.edu> wrote:
>
> Hi Adam,
>
> On my first attempt with Jared's commands, I pasted both for loops at the top
> PyMOL prompt with a semicolon between the commands.
> This failed because I created a Python syntax error.
>
> When I issued Jared's commands one at a time, they worked.
>
> Alternatively, rewrite Jared's for loops as list comprehensions.
> Now you can paste the two list comprehensions separated by a semicolon at the
> PyMOL prompt.
>
> [cmd.bond(f"/5fur//E/{i}/O3'", f"/5fur//E/{i+1}/P") for i in range(1, 80)];
> [cmd.bond(f"/5fur//F/{i}/O3'", f"/5fur//F/{i+1}/P") for i in range(81, 160)]
>
> This worked for me. I am using PyMOL 2.3.4, the incentive product, but it
> should work for older versions, even PyMOL 0.99.
>
> You can issue many commands on one line if they are separated by semicolons.
> There are some restrictions and limitations.
> For more details, https://github.com/MooersLab/EasyPyMOL and
> https://www.ncbi.nlm.nih.gov/pubmed/27488983
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
> ________________________________________
> From: h. adam steinberg [h.adam.steinb...@gmail.com]
> Sent: Sunday, March 22, 2020 8:16 AM
> To: Jared Sampson
> Cc: pymol-users
> Subject: [EXTERNAL] Re: [PyMOL] broken DNA cartoon
>
> 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<mailto: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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