Bob wrote: >>Q: Is there a literature reference I should read on this? If so, send it. >> > What would you like to understand that you don't now?
Don't know >>Q: Under what circumstances do you get bonding with residue -3 or -4? Can >>you give me an example pdb file so that I can see this? >> >> > The implication here is simply that you have a > > O (n) -- N(n-4) (offset -4; green) > > An example is 1qnf.pdb, DNA lyase, where O(asn 144) is hydrogen bonded > to NH(ser 140) > You won't find many of these, but "the circumstances" are just "because > that's what it does" OK ... so it is not related to any special type of structure. >>Q: These are for proteins. Shouldn't there be another color (or set of >>colors) for nucleotide chains? What color should nucleotide hbonds be? >> >> > Chime delivers these as yellow, which is appropriate, because they are > BETWEEN chains, thus have no significant "offset." It doesn't seem right to me that hbonds between chains are the same color as hbonds within a chain (like beta-sheets). It also seems to me that sidechain hbonds should be different from mainchain hbonds. >>Q: I always feel the need to play with colors ... Are these rgb values >> good? > > I think so. OK 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
