The minimal sequence is shown here: load molecule.pdb, mol-object load grasp-map.phi, map-object
ramp_new ramp-name, map-object show surface, mol-object set surface_color, ramp-name, mol-object -- For example: load molb.pdb load molb.phi, e_pot ramp_new e_lvl, e_pot show surface, molb set surface_color, e_lvl, molb -- You can also give ramp_new explicit range and RGB color information ramp_new e_lvl, e_pot, [-10,0,10], [ [0,1,0], [1,1,1], [1,0,0] ] For now, I think you are fixed at having exactly three colors, but that restriction will go away in a future version. Think of ramp objects as gadgets which take scalar information, such as the level in a 3D map object, and can convert it into an interpolated color range. You can change the level by CTRL-clicking on the color bar and move the object by CTRL-clicking on the border. Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.sourceforge.net] On Behalf Of Seth Harris > Sent: Saturday, June 07, 2003 3:13 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] color by grasp phi map potential? > > Well, this question is probably directed straight to Warren unless > someone's found it in the code or I've missed an obvious button. > > Main question: > > I wrote out a GRASP potential map and read it in to PyMOL with no > complaints. How do I then go about applying it to a surface (i.e. > coloring the surface with it)? Activating the color ramp gadget you > mentioned? > > > Subsidiary questions/comments: > > I really like the roving feature...very nice! I was getting a lot of > intra-residue dashed lines showing up. I was wondering if there > was a minimum distance threshold for calculation of polar interaction > or a different mechanism for filtering out polar interactions within > a residue itself. > Aah, I think I just figured it, at least why it's happening...I often > create new objects which are duplicates of a given chain and once > these are created, whether displayed or not, the polar interaction > dashes show up presumably being calculated between the original > molecule and the duplicate object underlying it. Perhaps those > interactions could somehow be hidden when one or the other object is > hidden, leaving the "primary" polar interactions only? Meanwhile, > something to look out for when roving detail is on if your Arg's and > others look a little cobwebbed with dashes. Also in flipping roving > on and off sometimes I can't get the polar interaction dashes to come > back even though all other representations (sticks, nb_spheres) seem > to. > > Another comment on roving, when roving detail mode is turned off it > didn't restore the chain colorings and features I had displayed > before I went a-rovin'. I guess one might want it to remain in the > roving display and perhaps it's not trivial to have a "restore > pre-roving features without moving the display back to a stored scene > which does come very close to the desired functionality. Excellent! > > Anyway, it's awesome. I hope to try building with it sometime soon, > data depending... > Thanks, > Seth > -- > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Seth F. Harris, PhD > Agard Laboratory > University of California, San Francisco > Mission Bay Genentech Hall > 600 16th St. Suite S416 > San Francisco, CA 94143-2240 > 415.502.2930 > > > ------------------------------------------------------- > This SF.net email is sponsored by: Etnus, makers of TotalView, The best > thread debugger on the planet. Designed with thread debugging features > you've never dreamed of, try TotalView 6 free at www.etnus.com. > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
