Hi, If I am understanding your answer, you are saying to use the cartoon_ladder_color to set the color for all sticks in the object and then dictate the color of the one stick I want to change using the atom. That's what I was trying to do. The problem is that it doesn't work in "nucleic_acid_mode, 1" b/c the C3* atom dictates the color of both the ribbon as well as the stick. And if I change the color of the N1 atom, I get a gradient from the C3* color to the N1 atom. I want the entire stick to be one color (and different from the ribbon).
Nevertheless, and since my message I figured out a convulated way to do it by duplicating the object: # To color a stick with a different color from its ribbon in # nucleic_acid_mode, 1 # obj01's sticks and ribbons are red # I want resi 150 "stick" (but not ribbon) changed to blue copy obj02, obj01 show cartoon, /obj02///150/N1 set cartoon_ladder_color,blue,obj02 Obviously, not a very elegant solution especially given that pymol has the inherent ability to do the same thing without the duplication of objects. But nice to see that there is a way after all! So, in the end let's just leave it as a feature suggestion - "A command to change the color of a specific ladder stick directly (and without changing ribbon color)" -Alex --- Warren DeLano <war...@delsci.com> wrote: > Alex, > > Hmm...not exactly. you could set a uniform cartoon color > for an object > and then color the residue on a per-atom basis, or vice > versa by setting > the cartoon_ladder_color and relying on the atomic color > for the > cartoon, but there isn't a specific per-residue ladder or > cartoon color > (yet). > > Cheers, > Warren > > -- > Warren L. DeLano, Ph.D. > Principal Scientist > > . DeLano Scientific LLC > . 400 Oyster Point Blvd., Suite 213 > . South San Francisco, CA 94080 USA > . Biz:(650)-872-0942 Tech:(650)-872-0834 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:war...@delsci.com > > > > -----Original Message----- > > From: pymol-users-ad...@lists.sourceforge.net > > [mailto:pymol-users-ad...@lists.sourceforge.net] On > Behalf Of > > Alex Luso > > Sent: Wednesday, December 14, 2005 7:01 AM > > To: pymol-users@lists.sourceforge.net > > Subject: [PyMOL] Coloring "ladder" differently from > "ribbon" > > in nucleic acid representation > > > > Hi, > > > > The new nucleic acid representation options are very > welcome. > > > > One question regarding the coloring of the ladder > > "sticks": > > > > If I am in: > > cartoon_nucleic_acid_mode, 1 > > cartoon_ladder_mode, 1 > > cartoon_ring_mode, 0 > > > > Is there a way to color the stick of a specified > nucleotide > > differently from its ribbon? > > I can get a gradient color for the stick by doing > "color > > green, /object///res/N1" > > but if I try to change the color of the other atom > involved > > in the ladder "stick" (i.e. "color green, > > /object///res/C3*"), then the color of the ribbon > changes too > > (because we are in cartoon_nucleic_acid_mode,1). It's > clearly > > possible to do b/c I can change the color of all sticks > by > > doing "set cartoon_ladder_color, green" but this > command acts > > globally. > > I guess a related point is that perhaps it would be > better to > > control the color of cartoon components directly, and > > selectively, rather than through the indirect method of > color > > of atom -> maps to color of stick. > > > > Anyway, great job of integrating cartoon ribbons and > the > > various ladder and ring options for nucleic acids. They > look > > great. I am sure other options are on the way (as well > as > > actual documentation!!). > > > > -Alex > > > > BTW: the wiki is wrong in > > > http://www.pymolwiki.org/index.php/Examples_of_cartoon_ring_an > > d_cartoon_ladder_settings > > where it says that cartoon_nucleic_acid_mode,1 # > follows > > phosphates. That should read # follows C3*, as far as I > can tell. > > > > __________________________________________________ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam > protection > > around http://mail.yahoo.com > > > > > > ------------------------------------------------------- > > This SF.net email is sponsored by: Splunk Inc. Do you > grep > > through log files > > for problems? Stop! Download the new AJAX search > engine that makes > > searching your log files as easy as surfing the web. > > DOWNLOAD SPLUNK! > > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
