The pseudoatom business looks very cool. I'll have to try it out.
In the meantime, I wanted to mention that you certainly can make transparent CGOs. Here's some code that I wrote to visualize dock output in our lab. The files it reads in have lines that look like <junk> x y z r <junk> temp <junk> Where x,y,z are the coordinates, r is the radius and temp is some index that we use to look up colors. If you save this in a file, you'll have a new command, sds, that will read in such a file and show the output as spheres. Transparency defaults to 0.4, but you can change it. -michael #!/usr/bin/env python """ Use PyMOL to show DOCK spheres """ from pymol import cmd,cgo colors = {'1':[.66,.66,.66],#'grey' '2':[1,0,0],#'red', '3':[.55,0,0],#'dark red', '4':[0.65,1,1],#'blue2', '5':[.25,.88,.82],#'blue7', '6':[0.004,.55,.55],#'blue8', '7':[0.004,.55,.55],#'blue8', '8':[0,1,1],#'blue13', '9':[0,1,1],#'blue13', '11':[0.60,.98,.60],#'pale green', '12':[0.56,.93,.56],#'light green', '13':[.20,.80,.20],#'lime green', '14':[.23,.70,.44],#'green8', '15':[.23,.70,.44],#'sea green', '16':[.18,.55,.34],#'sea green', '17':[.18,.55,.34],#'green', '18':[0,.5,0],#'forest green', '19':[0,.5,0],#'forest green', '20':[.13,.55,.13],#'dark green', '21':[.13,.55,.13],#'dark green', } def graph_temp_via_cgo(name,data,transparency=0): """ Data should be [x,y,z,r,temp] where x,y,z are the coordinates, r is the radius temp is something like temperature that we use to look up colors. """ obj = [] for x,y,z,r,temp in data: #transparency = (y/200.0) obj.extend( [ cgo.ALPHA,1-transparency]) obj.extend( [ cgo.COLOR] + colors[temp]) obj.extend( [ cgo.SPHERE,x,y,z,r] ) cmd.load_cgo(obj,name,1) return name def dock_file_to_data(filename): data = [] f = file(filename) for line in f: if not line.strip(): continue if line.startswith('#'): continue junk1,x,y,z,r,junk2,temp,junk3 = line.split() x,y,z,r = map(float,(x,y,z,r)) data.append([x,y,z,r,temp]) f.close() return data def show_dock_spheres(filename,transparency=0.40): """ Reads in a DOCK sphere file and graphs the results as dock spheres. You can pass the transparency as an additional argument. """ transparency = float(transparency) data = dock_file_to_data(filename) graph_temp_via_cgo('dock_spheres',data,transparency) cmd.extend('sds',show_dock_spheres) On 4/6/07, DeLano Scientific <del...@delsci.info> wrote:
Pre 1.0: fragment methane, mysph remove hydro and mysph alter mysph, vdw=2.0 as spheres, mysph set sphere_transparency, 0.5, mysph Post 1.0: pseudoatom mysph, vdw=2.0 as spheres, mysph set sphere_transparency, 0.5, mysph Cheers, Warren ________________________________ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of jjv5 Sent: Friday, April 06, 2007 4:55 AM To: PyMOL-users@lists.sourceforge.net Subject: [PyMOL] Single transparent sphere Hi, Does anyone know of a good way to create a single transparent sphere of varying size? We've tried using a single atom and changing the vdw, but we are unable to produce a surface of a single atom. CGO objects work but cannot be made transparent. What we'd really like is a transparent CGO sphere. Any ideas? Thanks, Jim ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
-- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net