From: Luca J. <luc...@ma...> - 2005-02-17 18:16:08
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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 --------------------------------------------------------------- |