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
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
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
intelligent
orientation vector for the strand, so only a simple circular tube will
look
right.
Cheers,
Warren
Hi Warren,
Thanks for the hint! This indeed kind of fixes the problem, but could I
say that, in my humble opinion, it's probably not the best way to
approach the issue?
I think it's pretty safe to state that everyone that works on nucleic
acids gives for granted that DNA/RNA backbone cartoons are always drawn
passing through phosphate atoms. Of course this is just a convention
stemming from textbooks and Ribbons, but, nevertheless, to my eyes the
helical fragments created using the cartoon_nucleic_acid_mode look
immediately artificially narrow. This probably just means I've been
staring at nucleic acids for far too long...
Having said that, couldn't the cartoon command be modified so that it
uses the P atom for all nucleotides, except for 5' nucleotides lacking
a phosphate where it could use the O5* atom, and 3' nucleotides with a
2',3-cyclic phosphate group (such as for example PDB residue CCC) where
it could use the PC atom? I think this would give a more satisfactory
representation, in terms of what people are already used to see.
Another (more personal) reason not to particularly like the idea of
switching to C4* atoms is that it does not work well with nuccyl (at
least in its current implementation). Of course I can modify nuccyl's
accordingly, but do we really want to use a different standard for
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
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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 FAX: +1.212.860-9279
E-Mail: lucajov...@mac.com - luca.jov...@mssm.edu
W3: http://www.mssm.edu/students/jovinl02
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