>>- 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.
I agree ... but that is what they call it. > 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. Understood. > just want to make sure we are all on the same page. > really it means 'color hbonds structure' as far as I can tell. Perhaps that would have been a better choice of terms ... but we are stuck with 'type' > 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. :-) Nope ... now you're on target. It would be some work to detect beta-sheet hbonds. But, frankly, I am now having second thoughts about whether or it would be worth doing. <wince and duck> Bob thinks that RasMol compatibility is better. And 'color hbonds type' is not something that you have used. Let me sleep on it. 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
