Thank you for spotting this, Angel. The problem is with the new "traceAlpha" method.
1) If you set traceAlpha off it will look better. 2) I have checked in a fix that shouldn't make this necessary. But there is a catch. The catch is simply that with "traceAlpha ON" (default for Jmol 11) the connection of the base to the backbone trace is imperfect -- they do not technically connect. Instead, the end of the stick connecting to the base is the average of the two phosphorus atom positions -- that is, the same point is used for the traceAlpha as for not traceAlpha. In effect, the stick connectors do not move, but the backbone trace does just a bit. It is all very close for general purposes, but not exact. So in some unusual cases, like your 14d0, with "set traceAlpha on" you may see a small gap between the base connector stick and the backbone trace. In all cases it is very close. I hope that will do. After all, it IS just a cartoon! 3) I also notice that the connection to the purine and pyrimidine rings are to carbon instead of nitrogen. Surely people do not want that, right? So I have added to this bug fix a switch to a nitrogen; when available, give it a check, please. I'll buid this as 11.1.3 and put it on the St. Olaf web site so you can try it today if you want to. Bob Angel Herraez wrote: >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 > > ------------------------------------------------------------------------- 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
