> On Aug 17, 2005, at 9:08 AM, Miguel wrote: >> color <object> monomer was also broken. >> >> Frieda ... note that I think that you may want to be using 'color >> <object> >> monomer' instead of 'color <object> group' > > I saw posts on color <object> group when I searched, but did not quite > understand them. Since the "color group" command was not working, I > could not check out "color <object> group" to see how it works.
By <object> I mean 'atom', 'cartoon' ... If you do not specify an object it defaults to 'atom' So, the following are the same: color atoms group color atom group color group # Miguel does not like this I do not like saying 'color group' or 'color green' ... I prefer that people always say 'color atom orange' because I believe that it is more clear. > I > assume that <object> would be something like "protein" or ":A", and > that this would be a way of effecting "color group" without changing > the selected set, is that correct? No. color atoms cpk color trace group color cartoon monomer >> 'group' uses the position of the group (residue) relative to its chain >> as >> defined in the .pdb file. >> >> 'monomer' uses the position of the monomer relative to the polymer. > > I.e., 'monomer' sees the first monomer in a polymer as number 1, and > counts from there, instead of seeing the first one as whatever it is > numbered in the pdb file? Yes. (actually, it starts counting from 0 rather than 1 ... but it is a minor point) > I do not know whether this accounts for > "color group" in Chime resulting sometimes in chains that do not have > the full spectrum of color in them, but it would be nice if this is a > way to avoid that. Correct. That is the purpose of 'color trace monomer' Miguel ------------------------------------------------------- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
