Re: [Jmol-users] DNA rendering

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

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. Here one may run into 
difficulties with
    non-canonical base pairs if the analysis is to be done automatically.
    An alternative would be that the user defines the ladder bases .
    I am aware of one program that generates ladders of this type
    (Prepi) and here one has both options.
    Moreover, this type of ladder representation with 'end-to-end' rungs
    does not work for more complex structures with
    base triads or base tetrads, for example.
    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.
   
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 require
    any base pairing analysis and can be applied to all possible structures.
 
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.

Regards.

js

Miguel wrote:

>>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, I will have to look again.
>>    
>>
>
>I am a little confused ... I thought that point would get connected to the
>corresponding point on the other side.
>
>If we draw the line to the N1/3 then there will be a gap in the middle and
>our ladder will be 'unzipped' ... is that what you want?
>
>  
>
>>>Q: Is there a new command, or is it a variant of 'cartoon'?
>>>      
>>>
>>Hmm, I thought a new command, but I am not sure what the pros and cons
>>are, not sure it matters on my end. Thinking... The rendering will be
>>different only wrt the bases, not the backbone... unless you want to
>>make the backbone flat, for example... then it would really be a new
>>command I think.
>>    
>>
>
>OK. At this point it probably does not matter one way or the other.
>
>
>
>Miguel
>
>
>
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-- 
Dr. Juergen Suehnel
Biocomputing Group
Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
[formerly Institute of Molecular Biotechnology (IMB)]
Jena Centre for Bioinformatics
Beutenbergstr. 11
D-07745 Jena/Germany	

fon: +49 (0)3641 65 6200
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e-mail: jsu...@fl...
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