Fwd: Re: [Jmol-users] DNA rendering

[<jsu...@fl...>]

----- Forwarded message from jsu...@im... -----
    Date: Sun, 18 Sep 2005 17:20:26 +0200
    From: J=FCrgen S=FChnel <jsu...@im...>
Reply-To: J=FCrgen S=FChnel <jsu...@im...>
 Subject: Re: [Jmol-users] DNA rendering
      To: Miguel <mi...@jm...>

Quoting Miguel <mi...@jm...>:

>
>> 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 acid first.
> [snip]
>>     So, teh conclusion is that this representation does not work for all
>> structures
>>     and that even for regular  double helix structures one may run into
>> difficulties
>>     if it comes to non-canonical base pairs.
>
> So this problem is more difficult than I (naively) thought :-(
>

Right.

>> 2. A way to overcome this problem is to represent single bases as tubes
>> along the
>>     major axis of the bases, see example 2. This approach does not requi=
re
>>     any base pairing analysis and can be applied to all possible
>> structures.
>
> OK, so I assume that this is what Frieda was recommending.
>
>> 3. The current cartoon representation has already a ladder-like
>> appearance (for regular structures).
>>      In my view it is better than the rendering type described in 2.
>>      For other purposes, however, it would be useful to have a more
>> realistic
>>      but still cartoon-like representation with sugar boxes added,
>>      see example 3.
>
> I see some white pentagons near the backbone. I assume that those are the
> sugars.
>

Right.

> 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.
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*).
RNA has the O2'H group linked to C2', whereas in DNA there is a C2'H
group without O2'. This is not relevant for the cartoon-like rendering,
however.

js

>
>
> Miguel
>
>
>
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