Bob Hanson sent (2004.05.19 at 9.53a [-0500gmt]) : > > >timothy driscoll wrote: > > >>it would be very useful to have a way to access different >>sub-categories of hydrogen bonds, though: >> >>select hbonds interchain select hbonds sidechain select hbonds >>mainchain >> >> >>but I think the default should be to color all hbonds white, >>inheriting the CPK color for hydrogen. and there should be no >>code-level distinction between protein and nucleic hydrogen bonds - >>one can easily build selections to tweak those apart. IMO of >>course :-) KIS (keep it simple). > >and then there's intrachain sidechain-mainchain, interchain >sidechain-mainchain.... It's a clever scheme they've come up with. I >was having some fun displaying proteins with just the hydrogen bonds >indicated. It is quite interesting how much information is there >just with this clever little offset business. I think you would find >sidechain/mainchain/interchain/intrachain issues very confusing to >anyone but the experts, and they will happily color them specially >anyway if they feel it's important. > hi,
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. 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. also, what happens (I haven't tested) if there is an hbond between residue 5A and 8B? 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? or when hbonds are between protein and non-proteins? the last case seems to me to be very important. 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. Miguel, how muddy are the waters now? I probably need to think some more about how to explain this. regards, tim -- Timothy Driscoll molvisions - see, grasp, learn. <http://www.molvisions.com/> usa:north carolina:wake forest ------------------------------------------------------- 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%62&alloc_ida84&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
