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 Executive: Colored 31 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 756 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: 0.80 sec. = 4516.0 frames/hour (0.80 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 144 atoms. PyMOL>hide everything,all PyMOL>show lines,bb PyMOL>color blue,bb Executive: Colored 144 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: 1.61 sec. = 2242.6 frames/hour (2.40 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, 4.0042223930358887, 3.7992887496948242, 5.2255210876464844, 4.2224512100219727, 5.6249451637268066, 5.596437931060791, 6.1109800338745117, 6.1569371223449707, 5.968597412109375, 6.8422636985778809, 5.0402531623840332, 6.6654577255249023, 4.5058450698852539, 6.2352724075317383, 6.3009052276611328, 6.9405031204223633, 6.5237832069396973, 5.4230566024780273, 6.3203592300415039] -> atom index_map = [None, 2, 21, 40, 51, 65, 75, 97, 116, 126, 150, 169, 183, 198, 217, 227, 237, 259, 269, 291, 301, 308, 324, 343, 357, 372, 387, 402, 424, 434, 449, 466, 483, 505, 524, 548, 565, 580, 601, 620, 642, 649, 669, 693, 704, 715, 732, 754, 773] "obj and name CA" index = 1 rmsd = 2.818 "obj and name CA" index = 2 rmsd = 2.530 "obj and name CA" index = 3 rmsd = 3.054 "obj and name CA" index = 4 rmsd = 3.388 "obj and name CA" index = 5 rmsd = 2.938 "obj and name CA" index = 6 rmsd = 2.070 "obj and name CA" index = 7 rmsd = 2.431 "obj and name CA" index = 8 rmsd = 2.584 "obj and name CA" index = 9 rmsd = 1.693 "obj and name CA" index = 10 rmsd = 1.590 "obj and name CA" index = 11 rmsd = 2.357 "obj and name CA" index = 12 rmsd = 1.873 "obj and name CA" index = 13 rmsd = 1.199 "obj and name CA" index = 14 rmsd = 2.078 "obj and name CA" index = 15 rmsd = 2.313 "obj and name CA" index = 16 rmsd = 1.690 "obj and name CA" index = 17 rmsd = 2.183 "obj and name CA" index = 18 rmsd = 2.969 "obj and name CA" index = 19 rmsd = 2.597 "obj and name CA" index = 20 rmsd = 2.613 "obj and name CA" index = 21 rmsd = 2.051 "obj and name CA" index = 22 rmsd = 1.742 "obj and name CA" index = 23 rmsd = 2.390 "obj and name CA" index = 24 rmsd = 2.916 "obj and name CA" index = 25 rmsd = 2.640 "obj and name CA" index = 26 rmsd = 1.598 "obj and name CA" index = 27 rmsd = 1.886 "obj and name CA" index = 28 rmsd = 2.151 "obj and name CA" index = 29 rmsd = 1.365 "obj and name CA" index = 30 rmsd = 1.135 "obj and name CA" index = 31 rmsd = 1.752 "obj and name CA" index = 32 rmsd = 1.455 "obj and name CA" index = 33 rmsd = 1.189 "obj and name CA" index = 34 rmsd = 1.785 "obj and name CA" index = 35 rmsd = 1.853 "obj and name CA" index = 36 rmsd = 1.721 "obj and name CA" index = 37 rmsd = 2.268 "obj and name CA" index = 38 rmsd = 2.636 "obj and name CA" index = 39 rmsd = 2.303 "obj and name CA" index = 40 rmsd = 3.275 "obj and name CA" index = 41 rmsd = 3.281 "obj and name CA" index = 42 rmsd = 3.678 "obj and name CA" index = 43 rmsd = 3.852 "obj and name CA" index = 44 rmsd = 4.564 "obj and name CA" index = 45 rmsd = 6.632 "obj and name CA" index = 46 rmsd = 8.394 "obj and name CA" index = 47 rmsd = 10.896 "obj and name CA" index = 48 rmsd = 12.938 PyMOL>cartoon putty, yesfit_ALL and name CA PyMOL>show cartoon, yesfit_ALL and name CA PyMOL>color red, ss h Executive: Colored 93 atoms. PyMOL>color cyan,ss s PyMOL>color gray,ss ""+l Executive: Colored 1529 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: 1.24 sec. = 2905.3 frames/hour (3.64 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit