> Hi, just wondering what happened with the DNA rendering as ladder and/
> or 'broken-rung' ladder... Below is Miguel's last post that I can
> find on this topic.
Frieda,
To date I have not done any work on rendering DNA as a ladder.
Miguel
--
Hi, just wondering what happened with the DNA rendering as ladder and/or 'broken-rung' ladder... Below is Miguel's last post that I can find on this topic.FriedaOn Sep 18, 2005, at 12:46 PM, Miguel wrote:Q: Can someone tell me which atoms make up the sugur? A detailed atom numbering scheme of the n
Quoting Miguel <[EMAIL PROTECTED]>:
So, in DNA and RNA the sugar forms five-membered rings with the main atoms
C1', C2', C3', C4', O4'.
Note that in some PDB files instead of the prime '
a star * is used (C1*, C2*, C3*, C4*, O4*).
Yes. Jmol supports this.
In fact, I think that all of the .p
>> Q: Can someone tell me which atoms make up the sugur?
>
> A detailed atom numbering scheme of the nucleic acid backbone is available
> in
> Fig 2. of http://www.imb-jena.de/ImgLibDoc/nana/IMAGE_NANA.html.
Thanks
> So, in DNA and RNA the sugar forms five-membered rings with the main atoms
> C1'
- Forwarded message from [EMAIL PROTECTED] -
Date: Sun, 18 Sep 2005 17:20:26 +0200
From: Jürgen Sühnel <[EMAIL PROTECTED]>
Reply-To: Jürgen Sühnel <[EMAIL PROTECTED]>
Subject: Re: [Jmol-users] DNA rendering
To: Miguel <[EMAIL PROTECTED]>
Quoting Miguel
On Sunday 18 September 2005 15:37, Miguel wrote:
> Q: Can someone tell me which atoms make up the sugur?
Sugar rings consist of five or six ring system, such as that of glucose, see
[1]. In DNA, two OH are replaced by two OR, where R=phosphate or base.
The sugar ring in DNA is actually a five rin
> I have a few comments on nucleic acid rendering.
> For illustrative examples look at http://www.fli-leibniz.de/js/Jmol/DNA/ .
>
> 1. Generating ladders is simple for regular structures, see example 1.
> Nevertheless, you have always to perform an analysis of base
> pairing patterns in th
On Sep 18, 2005, at 3:17 AM, Juergen Suehnel wrote:
I have a few comments on nucleic acid rendering.
For illustrative examples look at
http://www.fli-leibniz.de/js/Jmol/DNA/ .
2. A way to overcome this problem is to represent single bases as
tubes along the
major axis of the bases, se
On Sep 18, 2005, at 1:11 AM, Miguel wrote:
I am a little confused ... I thought that point would get connected to
the
corresponding point on the other side.
I was thinking that the rungs would be interrupted as you described
below.
If we draw the line to the N1/3 then there will be a
I have a few comments on nucleic acid rendering.
For illustrative examples look at http://www.fli-leibniz.de/js/Jmol/DNA/ .
1. Generating ladders is simple for regular structures, see example 1.
Nevertheless, you have always to perform an analysis of base
pairing patterns in the nucleic aci
> Would it be possible to originate the rung from the same spot where, in
> cartoon, the stick-like projection leaves the backbone?
That point is the mid-point between phosphorus atoms.
> If so, I would
> connect that point to:
>
> Adenine: N1
> Guanine: N1
> Cytosine: N3
> Thymine:N3
>
> If not,
On Sep 15, 2005, at 11:36 AM, Miguel wrote:
Frieda wrote:
Is there a rendering for DNA in Jmol that simplifies the bases into
something like rungs of a ladder?
Frieda
closest thing is the 'cartoon' rendering.
It would be very easy to implement a 'ladder' representation.
Excellent!
Q: W
> Is there a rendering for DNA in Jmol that simplifies the bases into
> something like rungs of a ladder?
> Frieda
closest thing is the 'cartoon' rendering.
It would be very easy to implement a 'ladder' representation.
Q: What are the atoms that get linked?
Q: Is there a new command, or is it
Is there a rendering for DNA in Jmol that simplifies the bases into
something like rungs of a ladder?
Frieda
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