Miguel sent (2004.05.19 at 5.36p [+0200gmt]) : >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. > agreed - see my recent email to the list.
>>>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'? > sorry - I misunderstood your comment. I thought you were trying to find some cheimcal difference, but this is 'just' a visualization thing. my mistake. >>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. > no I didn't. >And under 'color hbonds type' the default color is yellow. > >Q: What are you advocating? > sorry for perpetuating confusion :-) when I visualize hbonds with 'hbonds 0.1' they are white. if I color hbonds by type, the 'default' color is yellow. I am advocating consistency between these two defaults - and I suggest white since it is 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. > and in fact, I retract my own statement here. see my recent email to the list responding to Bob's comments. my day, my life, is a work in progress. please excuse the mess. :-) 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
