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 _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ZC2vp55wsN9oFwgr_7x8uTkJWSRtOjFf-57C6a5eaPE&s=KSnVSB_1bn5_DFbGDbFWEcHlPnycwLNU9F17YUusNjw&e=> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe<https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwMFaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=ZC2vp55wsN9oFwgr_7x8uTkJWSRtOjFf-57C6a5eaPE&s=ykQcuf-69yksat0POrChZPePpS8xtSm3KjfNVuHSY6A&e=> _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe