PyMOL>load ./selSi.pdb,obj ObjectMolReadPDBStr: read MODEL 1 ObjectMolReadPDBStr: read MODEL 2 ObjectMolReadPDBStr: read MODEL 3 ObjectMolReadPDBStr: read MODEL 4 ObjectMolReadPDBStr: read MODEL 5 ObjectMolReadPDBStr: read MODEL 6 ObjectMolReadPDBStr: read MODEL 7 ObjectMolReadPDBStr: read MODEL 8 ObjectMolReadPDBStr: read MODEL 9 ObjectMolReadPDBStr: read MODEL 10 ObjectMolReadPDBStr: read MODEL 11 ObjectMolReadPDBStr: read MODEL 12 ObjectMolReadPDBStr: read MODEL 13 ObjectMolReadPDBStr: read MODEL 14 ObjectMolReadPDBStr: read MODEL 15 ObjectMolReadPDBStr: read MODEL 16 ObjectMolReadPDBStr: read MODEL 17 ObjectMolReadPDBStr: read MODEL 18 ObjectMolReadPDBStr: read MODEL 19 ObjectMolReadPDBStr: read MODEL 20 CmdLoad: "./selSi.pdb" loaded as "obj". PyMOL>hide everything, all PyMOL>dss PyMOL>show cartoon, all PyMOL>set bg_rgb, [1,1,1] Setting: bg_rgb set to [ 1.00000, 1.00000, 1.00000 ]. PyMOL>color red, ss h PyMOL>color cyan,ss s Executive: Colored 19 atoms. PyMOL>color gray,ss ""+l Executive: Colored 752 atoms. PyMOL>set cartoon_highlight_color,yellow Setting: cartoon_highlight_color set to yellow. PyMOL>orient PyMOL>set ray_trace_mode, 3 Setting: ray_trace_mode set to 3. PyMOL>set antialias, 2 Setting: antialias set to 2. PyMOL>ray 600,600 Ray: render time: 0.96 sec. = 3749.6 frames/hour (0.96 sec. accum.). PyMOL>png molecule.png ScenePNG: wrote 600x600 pixel image to file "molecule.png". PyMOL>set stereo,1 Setting: stereo set to on. PyMOL>set all_states,1 Setting: all_states set to on. PyMOL>stereo walleye Setting: stereo_mode set to 3. PyMOL>select bb,n. c+ca+n Selector: selection "bb" defined with 150 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 150 atoms. PyMOL>set line_width,0.5 Setting: line_width set to 0.50000. PyMOL>set bg_rgb, [1,1,1] Setting: bg_rgb set to [ 1.00000, 1.00000, 1.00000 ]. PyMOL>zoom complete=1 PyMOL>set ray_trace_mode, 0 Setting: ray_trace_mode set to 0. PyMOL>ray 1200,600 Ray: render time: 4.15 sec. = 868.4 frames/hour (5.11 sec. accum.). PyMOL>png stereo.png ScenePNG: wrote 1200x600 pixel image to file "stereo.png". PyMOL>run /data/PSVS/PSVS-v1.4-dev/strcalc//average3d.py PyMOL>from average3d import avgStates Traceback (most recent call last): File "/farm/software/pymol-1.1r1-x64/modules/pymol/parser.py", line 455, in parse exec(layer.com2+"\n",self.pymol_names,self.pymol_names) File "", line 1, in ? ImportError: No module named average3d PyMOL>set all_states,1 Setting: all_states set to on. PyMOL>set stereo,0 Setting: stereo set to off. PyMOL>hide everything, all PyMOL>avgStates('obj','name CA',1,0,'yesfit_ALL','yes',1,0,0) -------------------------------------------------------------------------------- Averaging 20 states [1, 20] of object "obj and name CA" (20 total states) to get new single-state object "yesfit_ALL"... -------------------------------------------------------------------------------- -> proceeding WITH FITTING to reference state... intrafit_rmsds = [-1.0, 2.2982349395751953, 1.695713996887207, 2.1666631698608398, 1.955872654914856, 1.8875679969787598, 2.5647664070129395, 2.9223370552062988, 1.8151755332946777, 1.8867374658584595, 1.4212273359298706, 2.188685417175293, 2.1833791732788086, 2.2977232933044434, 2.5913808345794678, 1.6526403427124023, 2.0872764587402344, 2.5713958740234375, 1.928926944732666, 2.1449155807495117] -> atom index_map = [None, 2, 16, 37, 53, 70, 80, 94, 116, 128, 135, 159, 176, 195, 214, 228, 240, 247, 269, 283, 298, 317, 329, 341, 353, 367, 374, 393, 409, 420, 441, 458, 470, 487, 504, 511, 525, 535, 552, 569, 588, 602, 626, 638, 650, 666, 677, 694, 713, 732, 747] "obj and name CA" index = 1 rmsd = 3.590 "obj and name CA" index = 2 rmsd = 1.474 "obj and name CA" index = 3 rmsd = 0.878 "obj and name CA" index = 4 rmsd = 0.566 "obj and name CA" index = 5 rmsd = 0.522 "obj and name CA" index = 6 rmsd = 0.530 "obj and name CA" index = 7 rmsd = 0.793 "obj and name CA" index = 8 rmsd = 0.834 "obj and name CA" index = 9 rmsd = 0.830 "obj and name CA" index = 10 rmsd = 0.694 "obj and name CA" index = 11 rmsd = 0.635 "obj and name CA" index = 12 rmsd = 0.588 "obj and name CA" index = 13 rmsd = 0.661 "obj and name CA" index = 14 rmsd = 0.610 "obj and name CA" index = 15 rmsd = 0.938 "obj and name CA" index = 16 rmsd = 1.273 "obj and name CA" index = 17 rmsd = 1.297 "obj and name CA" index = 18 rmsd = 0.770 "obj and name CA" index = 19 rmsd = 0.724 "obj and name CA" index = 20 rmsd = 0.632 "obj and name CA" index = 21 rmsd = 0.779 "obj and name CA" index = 22 rmsd = 1.281 "obj and name CA" index = 23 rmsd = 1.543 "obj and name CA" index = 24 rmsd = 1.016 "obj and name CA" index = 25 rmsd = 0.694 "obj and name CA" index = 26 rmsd = 0.410 "obj and name CA" index = 27 rmsd = 0.461 "obj and name CA" index = 28 rmsd = 0.539 "obj and name CA" index = 29 rmsd = 0.701 "obj and name CA" index = 30 rmsd = 0.720 "obj and name CA" index = 31 rmsd = 0.727 "obj and name CA" index = 32 rmsd = 1.440 "obj and name CA" index = 33 rmsd = 1.318 "obj and name CA" index = 34 rmsd = 1.358 "obj and name CA" index = 35 rmsd = 1.038 "obj and name CA" index = 36 rmsd = 0.867 "obj and name CA" index = 37 rmsd = 0.666 "obj and name CA" index = 38 rmsd = 0.596 "obj and name CA" index = 39 rmsd = 0.547 "obj and name CA" index = 40 rmsd = 0.473 "obj and name CA" index = 41 rmsd = 0.561 "obj and name CA" index = 42 rmsd = 0.641 "obj and name CA" index = 43 rmsd = 0.662 "obj and name CA" index = 44 rmsd = 0.559 "obj and name CA" index = 45 rmsd = 0.742 "obj and name CA" index = 46 rmsd = 0.828 "obj and name CA" index = 47 rmsd = 0.941 "obj and name CA" index = 48 rmsd = 1.948 "obj and name CA" index = 49 rmsd = 3.412 "obj and name CA" index = 50 rmsd = 4.588 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h PyMOL>color cyan,ss s Executive: Colored 57 atoms. PyMOL>color gray,ss ""+l Executive: Colored 1534 atoms. PyMOL>set cartoon_highlight_color,yellow Setting: cartoon_highlight_color set to yellow. PyMOL>set bg_rgb, [1,1,1] Setting: bg_rgb set to [ 1.00000, 1.00000, 1.00000 ]. PyMOL>set ray_trace_mode, 3 Setting: ray_trace_mode set to 3. PyMOL>ray 600,600 Ray: render time: 1.40 sec. = 2576.4 frames/hour (6.50 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit