Miguel wrote:
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.
hey, don't say that to a chemist! :)
also, what happens (I haven't tested) if there is an hbond between residue 5A and 8B?
Not sure exactly what you mean here.
A and B are two chains, so this will be yellow.
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.
really? What IS used for the calculation?
it would be colored magenta, if I'm not mistaken,
I'm pretty sure they would be yellow. Actually, I don't think rasmol shows inter-chain H bonds.
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.
really? How can that be? I'm sure that's what the "offset count" is.
Miguel, how DO you calculate the offsets, then? (Maybe I just don't know what "GroupIDs" and "Residue numbers" are.
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?
I think so. This is a pretty minor aspect of the overall display. Really quite subtle compared to ribbons and such.
Bob Hanson
Miguel
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Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr
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