[PyMOL] Re: cartoon_nucleic_acid_mode

[Luca J. <luc...@ma...>]

On Feb 17, 2005, at 12:32, Warren DeLano wrote:

> Luca,
>
>> (I can't believe
>> PyMOL's cartoon command still does not recognise the most
>> common 5' and 3' nucleotides!),
>
> Sorry, I neglected to send you an email about this: there was a new=20
> setting
> added to the beta called "cartoon_nucleic_acid_mode"
>
> set cartoon_nucleic_acid_mode, 1
>
> If you set this to one, then PyMOL's cartoon ribbon will go through=20
> the C4*
> carbon instead of the phosphate.  The ribbons don't look as nice, but =
I
> think it addresses this issue.  However, we still don't have an=20
> intelligent
> orientation vector for the strand, so only a simple circular tube will=20=

> look
> right.
>
> Cheers,
> Warren

Hi Warren,

Thanks for the hint! This indeed kind of fixes the problem, but could I=20=

say that, in my humble opinion, it's probably not the best way to=20
approach the issue?

I think it's pretty safe to state that everyone that works on nucleic=20
acids gives for granted that DNA/RNA backbone cartoons are always drawn=20=

passing through phosphate atoms. Of course this is just a convention=20
stemming from textbooks and Ribbons, but, nevertheless, to my eyes the=20=

helical fragments created using the cartoon_nucleic_acid_mode look=20
immediately artificially narrow. This probably just means I've been=20
staring at nucleic acids for far too long...

Having said that, couldn't the cartoon command be modified so that it=20
uses the P atom for all nucleotides, except for 5' nucleotides lacking=20=

a phosphate where it could use the O5* atom, and 3' nucleotides with a=20=

2',3-cyclic phosphate group (such as for example PDB residue CCC) where=20=

it could use the PC atom? I think this would give a more satisfactory=20
representation, in terms of what people are already used to see.

Another (more personal) reason not to particularly like the idea of=20
switching to C4* atoms is that it does not work well with nuccyl (at=20
least in its current implementation). Of course I can modify nuccyl's=20
accordingly, but do we really want to use a different standard for=20
representing nucleic acid molecules, without any clear advantage?

It would also be interesting to hear the opinion of other PyMOL users!

Thanks and best regards,

Luca

---------------------------------------------------------------
Luca Jovine, Ph.D.
Brookdale Department of Molecular, Cell & Developmental Biology
Mount Sinai School of Medicine
Annenberg Building, Room 25-18
1 Gustave L. Levy Place, New York, NY 10029-6574, USA
Voice: +1.212.241-8620=A0 FAX: +1.212.860-9279
E-Mail: luc...@ma... - luc...@ms...
W3: http://www.mssm.edu/students/jovinl02
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