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 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: 0.78 sec. = 4637.0 frames/hour (0.78 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: 1.45 sec. = 2488.9 frames/hour (2.22 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 18 states [1, 18] of object "obj and name CA" (18 total states) to get new single-state object "yesfit_ALL"... -------------------------------------------------------------------------------- -> proceeding WITH FITTING to reference state... intrafit_rmsds = [-1.0, 5.1611309051513672, 2.1772935390472412, 3.1622927188873291, 2.7479300498962402, 2.9322366714477539, 5.7814850807189941, 3.3312489986419678, 2.2924268245697021, 5.9456295967102051, 2.7794532775878906, 2.8492867946624756, 3.8860559463500977, 5.3634476661682129, 3.8950216770172119, 4.2990841865539551, 0.99877101182937622, 1.7758971452713013] -> 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 = 2.794 "obj and name CA" index = 2 rmsd = 1.947 "obj and name CA" index = 3 rmsd = 1.960 "obj and name CA" index = 4 rmsd = 2.066 "obj and name CA" index = 5 rmsd = 1.986 "obj and name CA" index = 6 rmsd = 1.301 "obj and name CA" index = 7 rmsd = 1.401 "obj and name CA" index = 8 rmsd = 1.681 "obj and name CA" index = 9 rmsd = 1.113 "obj and name CA" index = 10 rmsd = 0.935 "obj and name CA" index = 11 rmsd = 1.619 "obj and name CA" index = 12 rmsd = 1.508 "obj and name CA" index = 13 rmsd = 0.933 "obj and name CA" index = 14 rmsd = 1.594 "obj and name CA" index = 15 rmsd = 1.985 "obj and name CA" index = 16 rmsd = 1.668 "obj and name CA" index = 17 rmsd = 1.880 "obj and name CA" index = 18 rmsd = 2.567 "obj and name CA" index = 19 rmsd = 2.538 "obj and name CA" index = 20 rmsd = 2.369 "obj and name CA" index = 21 rmsd = 2.102 "obj and name CA" index = 22 rmsd = 1.581 "obj and name CA" index = 23 rmsd = 1.928 "obj and name CA" index = 24 rmsd = 2.273 "obj and name CA" index = 25 rmsd = 2.127 "obj and name CA" index = 26 rmsd = 1.369 "obj and name CA" index = 27 rmsd = 1.617 "obj and name CA" index = 28 rmsd = 2.008 "obj and name CA" index = 29 rmsd = 1.423 "obj and name CA" index = 30 rmsd = 1.121 "obj and name CA" index = 31 rmsd = 2.039 "obj and name CA" index = 32 rmsd = 1.999 "obj and name CA" index = 33 rmsd = 1.399 "obj and name CA" index = 34 rmsd = 1.965 "obj and name CA" index = 35 rmsd = 2.595 "obj and name CA" index = 36 rmsd = 2.173 "obj and name CA" index = 37 rmsd = 2.143 "obj and name CA" index = 38 rmsd = 2.899 "obj and name CA" index = 39 rmsd = 2.833 "obj and name CA" index = 40 rmsd = 3.492 "obj and name CA" index = 41 rmsd = 3.375 "obj and name CA" index = 42 rmsd = 3.874 "obj and name CA" index = 43 rmsd = 3.483 "obj and name CA" index = 44 rmsd = 3.955 "obj and name CA" index = 45 rmsd = 5.165 "obj and name CA" index = 46 rmsd = 6.554 "obj and name CA" index = 47 rmsd = 8.867 "obj and name CA" index = 48 rmsd = 11.144 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: 1.09 sec. = 3303.6 frames/hour (3.31 sec. accum.). PyMOL>png sausage.png ScenePNG: wrote 600x600 pixel image to file "sausage.png". PyMOL>quit