Miguel sent (2004.05.19 at 7.02p [+0200gmt]) : >Tim wrote: > > >>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. > > ok, that renders most of my argument irrelevent - 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. > ok. :-) >>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. > perhaps, under spearate thread or on the rasmol list, someone can explain to me why this limitation exists. knowing RasMol, I'm sure there is a good reason - I just don't know it. >- 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? > um, no? <wince and duck> sorry to belabor the point, but 'type' is a misleading term here. these are all hydrogen bonds, so they follow the same rules (chemically) and exhibit the same behavior - they aren't really different types of hydrogen bonds. just want to make sure we are all on the same page. really it means 'color hbonds structure' as far as I can tell. I support keeping the same command as RasMol, for compatibility - but if it really is coloring by structure, I would prefer different colors for beta sheet, alpha helix, beta turn, and random coil hbonds. is this possible? if I am still misunderstanding the issue, please tell me and I'll go quietly away. :-) 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
