Angel wrote: >>> Hi. Starting to do a page with DNA models. >>> A little idiosyncrasy of Jmol versus Chime: >>> some H bonds are calculated differently; see atached image >>> I'm not sure anything can be done, but just in case, you should know. I've seen Chime drawing similar things sometimes, guess it's based on distance between atoms. >> >> Hmmm ... that clearly looks like a Jmol bug. >> >> What .pdb model are you using? >> > I'm using 1d66-pwz.pdb > from > http://molvis.sdsc.edu/dna/1d66-pwz.pdb > or > http://www2.uah.es/biomodel/pruebas/jmol/dna_jmol/1d66-pwz.pdb
1D66 seems to be a favorite of many people. In addition, I have no credentials as a biochemist :-) Therefore, it is with some reluctance/trepidation/self-conscious-fear that I feel compelled to say ... 1D66.pdb is messed up. The base for [C]28 is in the wrong orientation. That is why Jmol is not forming the hbonds as you would expect. And the hbonds in RasMol/Chime are also incorrect. I have attached a screen shot from RasMol2.6b2 that demonstrates the problem. I used RasMol instead of Jmol to demonstrate that this is not an error in coordinate calculations within Jmol. The disoriented creature is [C]28 ... its forlorn partner is [G]11 ... go see for yourself. This occurs in both 1D66.pdb as well as 1D66-pwz.pdb. Please advise. Miguel
<<attachment: rasmol1d66.gif>>
