In former versions of Jmol, the cartoon for nucleic acids had "sidechain" sticks coming out from the midpoint between phosphorus atoms towards the base. 11.0.RC3 (likely started before this) draws the sticks from the phosphorus itself. I have no objection to that, but the wrong phosphorus is being associated, which belongs to the neighbour residue.
For ex., on 140d.pdb, base in [G]20:B in linked to phosphorus in [C]21:B As a consequence: 3'-terminal P is associated to two bases 5'-terminal P is associated to no bases (and, if the 5'-residue has no P as in 140d, the residue is colored red instead of orange). The 5'-terminal base is not drawn as cartoon. This seems general, it happens in other molecules such as 255d.pdb, 5tra.pdb, 2zna.pdb To see it better, use select all; cartoon on; spacefill off; select _P; spacefill 50%; select all ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
