Re: [PyMOL] [EXTERNAL] broken DNA cartoon
Thank you Blaine! Now I know why, and how to manually fix this. > On Mar 20, 2020, at 10:52 PM, Mooers, Blaine H.M. (HSC) > wrote: > > The O3' to P bond lengths are 2.2 Angstroms when they should 1.6 Angstroms. > This is outside the bond length range that PyMOL accepts so the bond is > absent when you display the model as line or stick model. > This is why the cartoon is missing or broken. > 5FUR is a 8.5 Angstrom cryo EM structure. > Perhaps the associated paper explains this discrepancy. > > 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: Friday, March 20, 2020 8:57 PM > To: pymol-users > Subject: [EXTERNAL] [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 Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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
> 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
>
> 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
>>
>>
>> ___
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>> Unsubscribe:
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Re: [PyMOL] [EXTERNAL] Re: broken DNA cartoon
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
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
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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Re: [PyMOL] [EXTERNAL] Re: broken DNA cartoon
Well, thank you very much Blaine! That worked great!
> On Mar 22, 2020, at 10:01 AM, Mooers, Blaine H.M. (HSC)
> 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
> 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
>
> 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
>
>
> ___
> 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
>
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