Hi Maria and Adam, I think it's not that complicated. You need "cartoon_ring_mode" for the residue selection. Example:
fetch 1rna, async=0 as cartoon select firstres, chain A & resi 1 set cartoon_ring_finder, 2 set cartoon_ring_mode, 2, firstres color blue color red, firstres extend 1 Hope that helps. Cheers, Thomas On 02 Aug 2016, at 12:42, harold steinberg <h.adam.steinb...@gmail.com> wrote: > I believe that you can only apply the cartoon setting to an entire obj > (object). And so you are correct in trying to duplicate the nucleotide so you > can apply one setting to it, while allowing the other setting to display the > rest of them. But that doesn’t work either since the program will only allow > one display type at a time. There may be a complex way to override it but I > do not know it. > > The way I have gotten around this in the past is to set up the entire object > the way you want it, then render it once with each setting. > > Then open both of the resulting images in photoshop or similar program. Put > them both into one file as layers. > > Then delete most of one of the files (say the top one) so only the single > nucleotide is left in the cartoon setting that you want in that layer. The > rest of the image will appear from the bottom layer. > > Then you can flatten the image and save it. It’s fast and works great. > > >> On Aug 2, 2016, at 9:41 AM, COSTA Maria <maria.co...@i2bc.paris-saclay.fr> >> wrote: >> >> Dear pymol-users, >> >> I’m still learning how to use pymol to do basic things. >> At present, I’m working with a nucleic acid molecule that is colored by >> sequence domains (each domain is a different objet). All the domains are >> displayed in the cartoon mode, with backbone as dumbbell and >> cartoon_ring_finder,0 (no nucleobases or riboses displayed). Now, I would >> like to display only the first residue of one of the domains as >> cartoon_ring_finder,2 (ring only for nucleobases) and then color it >> entirely (dumbbell + ribose stick + base ring) with a different color from >> the rest of the domain sequence. The problem is that it does not work ! >> >> I tried to copy that nucleotide into a new objet to manipulate it >> independently but all the arguments I write in the command line do not apply >> to it, nothing is changing on the screen. The only thing that works is the >> menu on the right, use the objet line corresponding to this residue, display >> it entirely as sticks and then change the color of the sticks. But that’s >> not what I need! >> >> Do you have any ideas how to display the desired nucleotide? >> >> Many thanks in advance, >> >> Maria > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
