at 3.48p EDT on 2003 December 12 Friday Miguel Howard said: > > okay, I like the idea of a straight line better. maybe something > > porportional to the width of the cartoon helix? > > Now that I have had a chance to think about it, I am thinking about > changing my position on this. > > The purpose of this 'cartoon' representation is to give a general overview > of the structure. It is a visualization program, not a calculations > program. > > Therefore, I am beginning to think that Jan's initial position may be the > best option. > > So I am thinking the following: > > If the end of a helix/sheet joins another helix/sheet then that end of the > helix/sheet will be defined by the mid-point between the two alpha carbons > at the two ends of the helices/sheets. > > If the end of a helix/sheet joins joins a nothing/turn, then that end of > the helix/sheet will be calculated as the projection of the mid-point onto > the true center axis of the helix/sheet. (We can have a separate > discussion about the 'true center axis' of a helix or sheet.) > > What do you think? >
the end result troubles me a little. if I understand you correctly, two adjacent helices would be shown essentially as one "bent" representation? this concerns me because it implies (visually) a bent helix, and it isn't - it's two different helices. the backbone must pass though some sort of transition to get from one helix to another, even if that transition is only a few atoms (say carbonyl of one residue to amine of the next). it is important to visually acknowledge that transition, in my opinion. otherwise, students may assume that the regular hydrogen bonding pattern of the helix (n to n+4) extends through the "bent" region. which, if you look at the perpendicular helices in 1kyz, is obviously not possible. thoughts? :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest ------------------------------------------------------- This SF.net email is sponsored by: IBM Linux Tutorials. Become an expert in LINUX or just sharpen your skills. Sign up for IBM's Free Linux Tutorials. Learn everything from the bash shell to sys admin. Click now! http://ads.osdn.com/?ad_id=1278&alloc_id=3371&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
