> 1. Is there a way to have smoothed loops for only a portion of a > structure? > I would like to show the details of one portion of my molecule, while > keeping the rest of the molecule as cartoonish and simplistic as possible. > The "smooth loops" toggle under the cartoon menu changes the smoothing for > the entire molecule.
No. Unfortunately loop smoothing is a global property of the object. The best you can do is to excise the loop into one object (use "create") and the rest of the protein (plus one residue on each end) into another: # working example load $PYMOL_PATH/test/dat/1tii.pdb, prot create loop, prot//A/74-81/ create rest, prot and not A/75-80/ delete prot set cartoon_smooth_loops, 0, loop set cartoon_smooth_loops, 1, rest hide show cartoon > 2. When displaying helices as cylinders, is there a way to alter where > the > loop reconnects to the cylinder? Without smoothing, the loops terminate > just short of the cylinder, leaving a rather ugly gap. Apparently, > Ribbons > used to have a way of altering this, but obviously I would like to do all > of > this in Pymol! Hmm. Well, you can fix it manually, but you need to enable the ribbon in order for you mouse click to register properly... show cartoon show ribbon edit_mode set cartoon_cylindrical_helices,1 Now, ctrl-left-click-and-drag on the ribbon of the wayward C-alpha atom in order to place it back on the cylinder. (Click "unpick" first to make sure no atom is currently picked). hide ribbon I'll see what we can do about this in the future... Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020
