Tim wrote: > my apologies for jumping in late to this discussion. > > the offset scheme in the RasMol doc appears to do a good partial job - > showing helix and turn vs all other hbonds.
Agreed. > my fear is that many of the > 'biologically significant' hbonds (i.e. those with a functional role, > not just structural scaffolding) will just be yellow, with no way to > tease them apart. this includes not only beta sheet hbonds, hbonds > within a chain, hbonds between chains, hbonds between protein and > non=protein (including solvent), etc. Yes. The only *good* news (if you can call it that) is that most of these hbonds don't actually exist. All we calculate today are backbone hbonds within the same chain. > also, what happens (I haven't tested) if there is an hbond between > residue 5A and 8B? Not sure exactly what you mean here. If you are concerned that insertion codes might mess things up, then I don't think you need to worry ... I believe that Jmol will do the right thing. The groupID is not used for this calculation. > it would be colored magenta, if I'm not mistaken, > but that gives the incorrect impression that these are close to each > other in the primary sequence. and what happens when residue numbers > are not continuous? Residue numbers are not used at all. > or when hbonds are between protein and > non-proteins? the last case seems to me to be very important. Modified amino acids in the backbone should work OK. Remember, I am only talking about backbone hbonds at this point. > I wonder if building boolean selections is not a more useful way to > address the different types of hydrogen bonds. we did something like > this with the Jmol 'within' command, which now lets you expand a > selection to include the groups that contain the selected atoms. > > can one identify (iow, select) the partners in a hydrogen bond > interaction? for example, 'select donor' or 'select acceptor'? > preferably at the atomic level, since 'within' can expand out the entire > group. then we could select not only the bonds, but the bonding > partners as well, based on type. Let's talk about this later. > Miguel, how muddy are the waters now? Somewhat murky, but not too bad :-) I am going to try to restate the question that I would like to have an answer to. - Like RasMol, Jmol only supports backbone hbonds in proteins. On the nucleotide side, it only supports those *classical* nucleotide hbonds that hold the helix together, whatever they are called. - In RasMol, the script command 'color hbonds type' will make random coil hbonds, beta-sheet hbonds, and these nucleotide hbonds all the same color ... yellow. Q: Is that the desired behavior? Miguel ------------------------------------------------------- This SF.Net email is sponsored by: SourceForge.net Broadband Sign-up now for SourceForge Broadband and get the fastest 6.0/768 connection for only $19.95/mo for the first 3 months! http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
