On 2004-09-22 (22:41) Miguel wrote: >>no; it really is more of a rainbow. see attached gif for an >>example. > >Hmmm ... sure looks pretty ugly to me > well, it is a useful way to trace the path of the backbone from N to C visually. I can't comment on the colors themselves. ;-)
>>>Q: Please confirm that singleton atoms (chains of length 1) get >>>colored white. >>> >>that works for me. :-) > >Well, they should be the mid-point of the color spectrum. > either way - the scheme is more for relative position of each residue in the chain. I don't really like the term 'group' for this, but not sure what describes it better. > >>If a chain has a large number of heterogeneous molecules associated >>with it, the macromolecule may not be drawn in the full 'range' of >>the spectrum. > >I don't understand this comment. Any help in interpreting it? > sometimes, waters are given very high residue numbers (I don't know why this is true). so if the protein is 1-200, but the waters run 500-750, Rasmol would use the range 1-750 to color by group. essentially, this results in a blue protein and red solvent - not very useful. so the manual recommends 'restrict not hetero' to exclude solvent from the color scheme. > >Q: Tim, how long are these chains that you want to work with. > I don't have a specific length in mind - just any chain, really. the longer the chain, the more useful the scheme IMO but exactly how long, I can't say. >Frankly, it doesn't make sense to me that it would go through a >whole 'spectrum'. It looks like to me that you end up with too many >colors and it is too hard to interpret. > >Q: What would be wrong with red -> white -> blue? It seems to me >that it would be much easier to visualize/interpret because there >would be less noise. > my only objection is that RWB might be confused with charge. would it be difficult to let the user define the start and end colors, and have Jmol interpolate the colors between? regards, tim -- Timothy Driscoll molvisions - see, grasp, learn. <http://www.molvisions.com/> usa:north carolina:wake forest ------------------------------------------------------- This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170 Project Admins to receive an Apple iPod Mini FREE for your judgement on who ports your project to Linux PPC the best. Sponsored by IBM. Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
