Thanks, Bob But I'm not sure we are talking about the same details. And the problem is not limited to a particular pdb file.
> set traceAlpha off Yes, that fixes the aspect and the double-base bonding at 3' in 11.0.RC3 > 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 Sorry? What I see is - with traceAlpha ON (default), the base connects to the P atom - with traceAlpha OFF, the base connects to the midpoint between P atoms The problem is, - with traceAlpha ON, the base in residue (j) connects to the P atom in residue (j+1). This should be fixed. - with traceAlpha OFF, the base (j) connects to the midpoint between P atoms (j) and (j+1). This is OK, as it would be (j-1) and (j) Now, with your new 11.1.3 version this is solved: - with traceAlpha ON (default), the base in residue (j) connects to the midpoint between P atoms (j) and (j+1) [if j+1 is not available, to the last P (j) atom itself] **good!** - with traceAlpha OFF, the base connects to the same point [except for the last one if P(j+1) is missing, it extrapolates to some midpoint **OK, no big deal** I understand this change will be incorporated into 11.0 too. Good! I'm closing an update of my website and don't have the time to investigate into the interesting navigation mode, but I think this cartoon behaviour is bad as it is in 11.0.RC3. There is still the problem of the 5'-terminal portion being colored red instead of orange when that P atom is missing; likely due to specific models, not that important. > 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 I'm not worried by this. > 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. I'm not concerned about that (it was worse before). > 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 think this was discussed before. N makes more sense, of course. **done in 11.1.3, too** Beautiful! Thanks for all the great work, Bob ------------------------------------------------------------------------- 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
