Tim wrote: >>It doesn't seem right to me that hbonds between chains are the same >>color as hbonds within a chain (like beta-sheets). >> > why not?
When you say: color hbonds type You get special colors for hbonds that are part of alpha-helices and part of turns. I assume that is because those hbonds are responsible (in large part) for creating/stabilizing those structures. It seems to me that the same thing should apply to beta sheets. And that the hbonds that are part of beta-sheets should be colored specially. But instead, 'color hbonds type' colors beta sheet hbonds the same color as other random hbonds. >>It also seems to me that sidechain hbonds should be different from >>mainchain hbonds. >> > it's kind of like saying covalent bonds are different - they are, but we > generally treat them as a group anyway. Q: Why do we have this special command 'color hbonds type'? > 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 That is a subject for another day. > but I think the default should be to color all hbonds white, inheriting > the CPK color for hydrogen. You realize that this is a change from the RasMol/Chime behavior. And under 'color hbonds type' the default color is yellow. Q: What are you advocating? > and there should be no code-level > distinction between protein and nucleic hydrogen bonds - one can easily > build selections to tweak those apart. 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
