Re: [PyMOL] broken DNA cartoon

[h. adam steinberg]

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  
> 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  
> <mailto:h.adam.steinb...@gmail.com>
> Reply: h. adam steinberg  
> <mailto:h.adam.steinb...@gmail.com>
> Date: March 20, 2020 at 9:59:45 PM
> To: pymol-users  
> <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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Re: [PyMOL] broken DNA cartoon

[Jared Sampson]

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 
Reply: h. adam steinberg 
Date: March 20, 2020 at 9:59:45 PM
To: pymol-users 
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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