I’m sorry, I thought she was trying to use two different cartoon modes and two different colors.
> On Aug 2, 2016, at 12:07 PM, Thomas Holder <thomas.hol...@schrodinger.com> > wrote: > > 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. H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 ------------------------------------------------------------------------------ _______________________________________________ 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
