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RE: [PyMOL] Re: PyMolWiki
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From: Warren D. <wa...@de...> - 2005-02-17 17:32:25
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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 -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf Of > Luca Jovine > Sent: Thursday, February 17, 2005 8:12 AM > To: Mailing List PyMol Users > Cc: jav...@ut... > Subject: [PyMOL] Re: PyMolWiki > > Hello, > > I apologize for being late, but... how about a section about > nucleic acids? As in any other related program, they always > end up being the poor siblings of proteins (I can't believe > PyMOL's cartoon command still does not recognise the most > common 5' and 3' nucleotides!), and I'm pretty sure people > who work with them would benefit from such a section in the Wiki. > Thanks, > > 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 FAX: +1.212.860-9279 > E-Mail: luc...@ma... - luc...@ms... > W3: http://www.mssm.edu/students/jovinl02 > --------------------------------------------------------------- > > |