id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8567 Clipper missing rish.23@… Tristan Croll "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Attempted to download and use ISOLDE v1.4 but got an error message about missing ""toolshed"". Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TthRuvB_models/7PBU_TRuvA_HJ.pdb"" format pdb Chain information for 7PBU_TRuvA_HJ.pdb #1 --- Chain | Description A B C D F J L | No description available E G | No description available H | No description available I K | No description available > open ""/Volumes/ANTHONY16GB/Fu Lab/Ruv/PDB and > Maps/TRuvA_HJ/TRuvA_HJ_3.9A_density_zflip.mrc"" Opened TRuvA_HJ_3.9A_density_zflip.mrc as #2, grid size 256,256,256, pixel 0.95, shown at level 0.163, step 1, values float32 > ui tool show ""Hide Dust"" > surface dust #2 size 5.7 > color #2 #fffc79 models transparency 0 > color #2 #fffc7914 models > color #2 #fffc7925 models > hide atoms > show cartoons > select #2 /I,J,H,F Nothing selected > select #1 /I,J,H,F 6929 atoms, 7021 bonds, 415 residues, 1 model selected > select #1 /L,J,H,F 8525 atoms, 8593 bonds, 531 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1 10718 atoms, 10952 bonds, 600 residues, 1 model selected > volume #2 level 0.2222 > ui tool show ""Fit in Map"" > fitmap #1 inMap #2 Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density_zflip.mrc (#2) using 10718 atoms average map value = 0.161, steps = 68 shifted from previous position = 5.71 rotated from previous position = 1.06 degrees atoms outside contour = 7070, contour level = 0.22215 Position of 7PBU_TRuvA_HJ.pdb (#1) relative to TRuvA_HJ_3.9A_density_zflip.mrc (#2) coordinates: Matrix rotation and translation 0.99984069 0.01737190 -0.00410044 -1.60914243 -0.01739070 0.99983821 -0.00459471 2.75611463 0.00401995 0.00466529 0.99998104 -6.76348379 Axis 0.25108532 -0.22018475 -0.94258943 Axis point 224.79770913 172.22372745 0.00000000 Rotation angle (degrees) 1.05659080 Shift along axis 5.36430191 Average map value = 0.161 for 10718 atoms, 7070 outside contour > fitmap #1 inMap #2 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density_zflip.mrc (#2) using 10718 atoms average map value = 0.161, steps = 28 shifted from previous position = 0.00758 rotated from previous position = 0.0151 degrees atoms outside contour = 7077, contour level = 0.22215 > open ""/Volumes/ANTHONY16GB/Fu Lab/Ruv/PDB and > Maps/TRuvA_HJ/TRuvA_HJ_3.9A_density.mrc"" Opened TRuvA_HJ_3.9A_density.mrc as #3, grid size 256,256,256, pixel 0.95, shown at level 0.163, step 1, values float32 > ui tool show ""Hide Dust"" > surface dust #3 size 5.7 > hide #!2 models > color #3 #ffffb230 models [Repeated 1 time(s)] > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 10718 atoms average map value = 0.1247, steps = 96 shifted from previous position = 4.98 rotated from previous position = 0.873 degrees atoms outside contour = 6935, contour level = 0.16283 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.47116,0.8819,-0.01625,74.248,0.88052,0.47135,0.050158,-49.919,0.051894,0.0093246,-0.99861,259.79 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.47116,0.8819,-0.01625,75.07,0.88052,0.47135,0.050158,-49.631,0.051894,0.0093246,-0.99861,237.69 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.38654,0.91024,0.14852,-55.096,0.90564,-0.40506,0.12546,43.042,0.17436,0.086013,-0.98092,211.11 > view matrix models > #1,-0.025079,0.9992,0.031016,0.21374,0.9628,0.015792,0.26975,-34.515,0.26905,0.036627,-0.96243,203.05 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 10718 atoms average map value = 0.2473, steps = 504 shifted from previous position = 11.4 rotated from previous position = 16 degrees atoms outside contour = 5329, contour level = 0.16283 > view matrix models > #1,-0.17511,0.90728,0.38232,-12.211,0.94556,0.046781,0.32206,-42.428,0.27431,0.41791,-0.86609,144.48 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.17511,0.90728,0.38232,-5.1236,0.94556,0.046781,0.32206,-43.533,0.27431,0.41791,-0.86609,137.87 > view matrix models > #1,-0.17511,0.90728,0.38232,-4.0558,0.94556,0.046781,0.32206,-46.188,0.27431,0.41791,-0.86609,129.68 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 10718 atoms average map value = 0.1719, steps = 92 shifted from previous position = 7.8 rotated from previous position = 10.9 degrees atoms outside contour = 5911, contour level = 0.16283 > view matrix models > #1,-0.17511,0.90728,0.38232,-6.5168,0.94556,0.046781,0.32206,-45.563,0.27431,0.41791,-0.86609,129.76 > undo > view matrix models > #1,-0.17511,0.90728,0.38232,-6.278,0.94556,0.046781,0.32206,-49.955,0.27431,0.41791,-0.86609,128.24 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 10718 atoms average map value = 0.1759, steps = 96 shifted from previous position = 4.13 rotated from previous position = 10.6 degrees atoms outside contour = 5911, contour level = 0.16283 > view matrix models > #1,-0.17511,0.90728,0.38232,-10.709,0.94556,0.046781,0.32206,-50.115,0.27431,0.41791,-0.86609,127.45 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 10718 atoms average map value = 0.2413, steps = 184 shifted from previous position = 8.68 rotated from previous position = 15.6 degrees atoms outside contour = 5131, contour level = 0.16283 > view matrix models > #1,-0.17511,0.90728,0.38232,-7.3089,0.94556,0.046781,0.32206,-49.727,0.27431,0.41791,-0.86609,122.55 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 10718 atoms average map value = 0.1793, steps = 116 shifted from previous position = 4.7 rotated from previous position = 10.4 degrees atoms outside contour = 5725, contour level = 0.16283 > ui mousemode right translate > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.17511,0.90728,0.38232,-5.7184,0.94556,0.046781,0.32206,-49.416,0.27431,0.41791,-0.86609,115.33 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 10718 atoms average map value = 0.1793, steps = 100 shifted from previous position = 7.4 rotated from previous position = 0.0211 degrees atoms outside contour = 5734, contour level = 0.16283 > save ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/7pbu_half.pdb"" relModel #3 > hide #!2 models > volume #3 level 0.2963 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 10718 atoms average map value = 0.1793, steps = 44 shifted from previous position = 0.0219 rotated from previous position = 0.0402 degrees atoms outside contour = 7615, contour level = 0.29631 > volume #3 level 0.3408 > view matrix models > #1,-0.17511,0.90728,0.38232,-8.0805,0.94556,0.046781,0.32206,-48.572,0.27431,0.41791,-0.86609,117.74 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.89408,-0.016708,-0.4476,300.29,-0.19647,0.91267,0.35838,-1.3946,0.40252,0.40836,-0.81928,95.812 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 10718 atoms average map value = 0.1805, steps = 80 shifted from previous position = 4.63 rotated from previous position = 5.79 degrees atoms outside contour = 7937, contour level = 0.3408 > volume #3 level 0.237 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 10718 atoms average map value = 0.1805, steps = 48 shifted from previous position = 0.0207 rotated from previous position = 0.0228 degrees atoms outside contour = 6668, contour level = 0.23698 > view matrix models > #1,0.63279,-0.57775,-0.51553,157.5,-0.73892,-0.25156,-0.62507,335.15,0.23145,0.77648,-0.5861,47.825 > view matrix models > #1,0.55946,-0.5951,-0.57694,177.09,-0.82066,-0.30008,-0.48628,338.41,0.11625,0.74553,-0.65626,76.238 > view matrix models > #1,0.69737,-0.56709,-0.43828,138.34,-0.6048,-0.1375,-0.78441,317.96,0.38456,0.8121,-0.43887,4.9447 > view matrix models > #1,0.71309,-0.23763,-0.65958,117.16,-0.70107,-0.24585,-0.66937,333.67,-0.0030973,0.93973,-0.34191,34.517 > view matrix models > #1,0.71832,-0.23694,-0.65412,115.72,-0.69571,-0.24723,-0.67444,333.61,-0.0019178,0.93954,-0.34243,34.426 > view matrix models > #1,0.63414,-0.65638,-0.40869,155.97,-0.76276,-0.44441,-0.46979,346.91,0.12674,0.60964,-0.78248,105.98 > view matrix models > #1,0.55268,-0.68897,-0.4689,178.6,-0.82587,-0.37735,-0.41897,341.94,0.11172,0.61881,-0.77755,106.45 > view matrix models > #1,0.49272,-0.80828,-0.32235,187.03,-0.84308,-0.35167,-0.40688,339.81,0.21551,0.47224,-0.85472,118.65 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 10718 atoms average map value = 0.152, steps = 88 shifted from previous position = 3.64 rotated from previous position = 5.52 degrees atoms outside contour = 7474, contour level = 0.23698 > view matrix models > #1,0.41564,-0.8979,-0.14502,191.14,-0.87498,-0.3512,-0.33327,336.52,0.24832,0.26541,-0.93161,149.44 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 10718 atoms average map value = 0.1577, steps = 120 shifted from previous position = 3.92 rotated from previous position = 5.84 degrees atoms outside contour = 7300, contour level = 0.23698 > view matrix models > #1,0.5002,-0.82185,-0.27268,181.63,-0.84327,-0.39081,-0.369,340.9,0.1967,0.41452,-0.88853,132.43 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 10718 atoms average map value = 0.1577, steps = 160 shifted from previous position = 1.87 rotated from previous position = 9.93 degrees atoms outside contour = 7300, contour level = 0.23698 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.5002,-0.82185,-0.27268,184.77,-0.84327,-0.39081,-0.369,345.02,0.1967,0.41452,-0.88853,128.05 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 10718 atoms average map value = 0.1586, steps = 172 shifted from previous position = 5.27 rotated from previous position = 11.9 degrees atoms outside contour = 7371, contour level = 0.23698 > view matrix models > #1,0.5002,-0.82185,-0.27268,187.23,-0.84327,-0.39081,-0.369,344.24,0.1967,0.41452,-0.88853,124.88 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.1294,-0.82549,-0.54939,271.75,-0.86168,0.18055,-0.47424,278.68,0.49067,0.53476,-0.68794,43.546 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 10718 atoms average map value = 0.1797, steps = 156 shifted from previous position = 2.9 rotated from previous position = 13.8 degrees atoms outside contour = 6683, contour level = 0.23698 > view matrix models > #1,0.17206,-0.84826,-0.50085,263.21,-0.87254,0.10476,-0.47717,291.13,0.45724,0.51912,-0.72212,54.463 > undo > view matrix models > #1,0.17199,-0.78919,-0.58958,264.38,-0.87294,0.15525,-0.46246,282.68,0.4565,0.59421,-0.66221,37.922 > select #1 /I,G,E 1629 atoms, 1754 bonds, 51 residues, 1 model selected > delete atoms sel > delete bonds sel > delete atoms #1,3 > delete bonds #1,3 Undo failed, probably because structures have been modified. > open ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/7pbu_half.pdb"" Chain information for 7pbu_half.pdb #1 --- Chain | Description A B C D | No description available E G | No description available I K | No description available > hide atoms > show cartoons > select #1 /I,G,E,K 2170 atoms, 2336 bonds, 68 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1 8548 atoms, 8616 bonds, 532 residues, 1 model selected > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 8548 atoms average map value = 0.1663, steps = 48 shifted from previous position = 0.197 rotated from previous position = 0.9 degrees atoms outside contour = 5637, contour level = 0.23698 > view matrix models > #1,0.99359,-0.045286,0.10353,-4.9038,0.067958,0.97146,-0.22727,19.375,-0.090286,0.23285,0.96831,-13.237 > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 8548 atoms average map value = 0.1692, steps = 72 shifted from previous position = 1.48 rotated from previous position = 2.77 degrees atoms outside contour = 5433, contour level = 0.23698 > hide #!3 models > show #!2 models > view matrix models > #1,0.97746,0.17275,-0.12136,-4.8517,0.19918,-0.94517,0.25882,180.95,-0.069995,-0.27716,-0.95827,253.21 > view matrix models > #1,0.91814,0.314,-0.2417,-1.5115,0.36948,-0.8988,0.23588,156.8,-0.14317,-0.30587,-0.94125,263.87 > view matrix models > #1,0.075471,0.9221,-0.37951,44.473,0.99673,-0.08082,0.0018419,6.2546,-0.028974,-0.37841,-0.92518,256.74 > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 8548 atoms average map value = 0.161, steps = 76 shifted from previous position = 3 rotated from previous position = 5.78 degrees atoms outside contour = 5781, contour level = 0.23698 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.075471,0.9221,-0.37951,45.027,0.99673,-0.08082,0.0018419,7.5695,-0.028974,-0.37841,-0.92518,280.63 > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 8548 atoms average map value = 0.1762, steps = 436 shifted from previous position = 9.66 rotated from previous position = 6.86 degrees atoms outside contour = 5684, contour level = 0.23698 > view matrix models > #1,0.075471,0.9221,-0.37951,48.371,0.99673,-0.08082,0.0018419,8.0011,-0.028974,-0.37841,-0.92518,288.03 > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 8548 atoms average map value = 0.1855, steps = 164 shifted from previous position = 7.88 rotated from previous position = 12.7 degrees atoms outside contour = 5535, contour level = 0.23698 > view matrix models > #1,0.075471,0.9221,-0.37951,50.13,0.99673,-0.08082,0.0018419,9.4657,-0.028974,-0.37841,-0.92518,303.51 > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 8548 atoms average map value = 0.1653, steps = 108 shifted from previous position = 9.44 rotated from previous position = 8.03 degrees atoms outside contour = 6078, contour level = 0.23698 > volume gaussian #2 sDev 4 Opened TRuvA_HJ_3.9A_density_zflip.mrc gaussian as #4, grid size 256,256,256, pixel 0.95, shown at step 1, values float32 > volume #4 color #b2ffff34 > volume #4 color #b2ffff33 > fitmap sel inMap #4 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density_zflip.mrc gaussian (#4) using 8548 atoms average map value = 0.1674, steps = 76 shifted from previous position = 5.08 rotated from previous position = 8.72 degrees atoms outside contour = 2008, contour level = 0.12843 > view matrix models > #1,0.075471,0.9221,-0.37951,49.103,0.99673,-0.08082,0.0018419,10.094,-0.028974,-0.37841,-0.92518,309.54 > fitmap sel inMap #4 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density_zflip.mrc gaussian (#4) using 8548 atoms average map value = 0.1674, steps = 96 shifted from previous position = 6.15 rotated from previous position = 0.00569 degrees atoms outside contour = 2008, contour level = 0.12843 > volume gaussian #3 sDev 4 Opened TRuvA_HJ_3.9A_density.mrc gaussian as #5, grid size 256,256,256, pixel 0.95, shown at step 1, values float32 > close #4 > volume #5 color #b2b2ff2e > volume #5 color #b2b2ff3a > volume #5 color #b2b2ff3b > view matrix models > #1,0.075471,0.9221,-0.37951,49.502,0.99673,-0.08082,0.0018419,8.4824,-0.028974,-0.37841,-0.92518,289.53 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.32616,0.74328,-0.58408,151.57,-0.44488,-0.66586,-0.59892,348.09,-0.83409,0.064501,0.54785,116.83 > view matrix models > #1,-0.44444,0.84493,-0.29761,111.27,-0.87159,-0.33114,0.36149,217.48,0.20688,0.42006,0.8836,-105.45 > fitmap sel inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 8548 atoms average map value = 0.164, steps = 116 shifted from previous position = 15.3 rotated from previous position = 11.8 degrees atoms outside contour = 2129, contour level = 0.12843 > view matrix models > #1,-0.42424,0.8629,-0.27464,102.63,-0.86784,-0.30081,0.39543,207.49,0.2586,0.4061,0.87648,-108.95 > view matrix models > #1,-0.7969,0.56426,-0.21578,181.35,-0.60312,-0.72267,0.33762,240.95,0.034573,0.39919,0.91621,-85.966 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.7969,0.56426,-0.21578,181.59,-0.60312,-0.72267,0.33762,243.07,0.034573,0.39919,0.91621,-90.839 > fitmap sel inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 8548 atoms average map value = 0.164, steps = 140 shifted from previous position = 5.91 rotated from previous position = 28 degrees atoms outside contour = 2129, contour level = 0.12843 > fitmap sel inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 8548 atoms average map value = 0.164, steps = 24 shifted from previous position = 0.00383 rotated from previous position = 0.00312 degrees atoms outside contour = 2130, contour level = 0.12843 > view matrix models > #1,-0.7969,0.56426,-0.21578,181.62,-0.60312,-0.72267,0.33762,243.12,0.034573,0.39919,0.91621,-93.075 > view matrix models > #1,-0.7969,0.56426,-0.21578,182.25,-0.60312,-0.72267,0.33762,241.6,0.034573,0.39919,0.91621,-94.62 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.77849,0.60131,-0.17997,168.97,-0.6276,-0.7417,0.23663,263.6,0.0088058,0.29716,0.95479,-83.259 > view matrix models > #1,-0.95544,0.29101,-0.049374,214.06,-0.29405,-0.92388,0.24489,244.84,0.02565,0.2485,0.96829,-80.799 > view matrix models > #1,-0.90243,0.20619,-0.3783,271.82,-0.25363,-0.96402,0.079574,271.75,-0.34828,0.16776,0.92226,-14.111 > view matrix models > #1,-0.93491,0.25441,-0.24743,248.28,-0.29423,-0.94549,0.13959,264.76,-0.19842,0.20331,0.9588,-44.184 > view matrix models > #1,-0.93147,0.17645,-0.31816,270.06,-0.28508,-0.89732,0.33696,225.21,-0.22604,0.40458,0.88613,-57.065 > fitmap sel inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 8548 atoms average map value = 0.164, steps = 132 shifted from previous position = 4.39 rotated from previous position = 25.2 degrees atoms outside contour = 2129, contour level = 0.12843 > view matrix models > #1,-0.99502,0.092683,-0.036707,243.11,-0.097689,-0.97992,0.17383,240.1,-0.019859,0.17655,0.98409,-67.565 > fitmap sel inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 8548 atoms average map value = 0.164, steps = 112 shifted from previous position = 1.58 rotated from previous position = 20.9 degrees atoms outside contour = 2130, contour level = 0.12843 > view matrix models > #1,-0.82289,-0.39397,0.40944,215.82,0.3253,-0.91746,-0.22901,242.65,0.46587,-0.055262,0.88312,-81.427 > view matrix models > #1,-0.95339,-0.19901,0.2268,235.31,0.2086,-0.97782,0.018881,225.65,0.21801,0.065311,0.97376,-81.044 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.95339,-0.19901,0.2268,237.28,0.2086,-0.97782,0.018881,227.84,0.21801,0.065311,0.97376,-84.856 > view matrix models > #1,-0.95339,-0.19901,0.2268,239.43,0.2086,-0.97782,0.018881,228.79,0.21801,0.065311,0.97376,-88.449 > view matrix models > #1,-0.95339,-0.19901,0.2268,238.49,0.2086,-0.97782,0.018881,227.72,0.21801,0.065311,0.97376,-89.255 > open ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/7pbu_half.pdb"" Chain information for 7pbu_half.pdb #4 --- Chain | Description A B C D | No description available E G | No description available I K | No description available > hide #1 models > select subtract #1 Nothing selected > hide #4 atoms > show #4 cartoons > fitmap #4 inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 10718 atoms average map value = 0.1547, steps = 132 shifted from previous position = 6.99 rotated from previous position = 19.3 degrees atoms outside contour = 3238, contour level = 0.12843 > volume gaussian #3 sDev 3 Opened TRuvA_HJ_3.9A_density.mrc gaussian as #6, grid size 256,256,256, pixel 0.95, shown at step 1, values float32 > close #2 > volume #6 color #ffb2ff2f > volume #6 color #ffb2ff2e > hide #!5 models > fitmap #4 inMap #6 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#6) using 10718 atoms average map value = 0.1637, steps = 60 shifted from previous position = 0.291 rotated from previous position = 0.23 degrees atoms outside contour = 3475, contour level = 0.1331 > volume gaussian #3 sDev 2 Opened TRuvA_HJ_3.9A_density.mrc gaussian as #2, grid size 256,256,256, pixel 0.95, shown at step 1, values float32 > volume #2 color #ffb2b24a [Repeated 1 time(s)] > hide #!6 models > fitmap #4 inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 10718 atoms average map value = 0.1762, steps = 72 shifted from previous position = 1.56 rotated from previous position = 0.44 degrees atoms outside contour = 3985, contour level = 0.13699 > select add #4 10718 atoms, 10952 bonds, 600 residues, 1 model selected > view matrix models #4,1,0,0,1.4444,0,1,0,-0.97577,0,0,1,-5.2919 > fitmap #4 inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 10718 atoms average map value = 0.1762, steps = 92 shifted from previous position = 5.56 rotated from previous position = 0.466 degrees atoms outside contour = 3991, contour level = 0.13699 > view matrix models #4,1,0,0,1.4573,0,1,0,-1.0136,0,0,1,-5.6328 > view matrix models #4,1,0,0,1.9172,0,1,0,-1.1061,0,0,1,-10.108 > view matrix models #4,1,0,0,3.496,0,1,0,0.68787,0,0,1,-11.626 > view matrix models #4,1,0,0,3.4726,0,1,0,0.5065,0,0,1,-12.77 > fitmap #4 inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 10718 atoms average map value = 0.1762, steps = 136 shifted from previous position = 7.89 rotated from previous position = 0.369 degrees atoms outside contour = 3978, contour level = 0.13699 > view matrix models #4,1,0,0,2.4725,0,1,0,0.058822,0,0,1,-15.938 > fitmap #4 inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 10718 atoms average map value = 0.1762, steps = 100 shifted from previous position = 3.36 rotated from previous position = 0.528 degrees atoms outside contour = 3997, contour level = 0.13699 > hide #!2 models > show #1 models > hide #1 models > show #!2 models > hide #!2 models > show #!3 models > fitmap #4 inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 10718 atoms average map value = 0.1762, steps = 60 shifted from previous position = 0.0192 rotated from previous position = 0.25 degrees atoms outside contour = 3995, contour level = 0.13699 > view matrix models #4,1,0,0,2.5598,0,1,0,0.73703,0,0,1,-15.856 > fitmap #4 inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 10718 atoms average map value = 0.1762, steps = 68 shifted from previous position = 0.685 rotated from previous position = 0.145 degrees atoms outside contour = 3993, contour level = 0.13699 > fitmap #4 inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 10718 atoms average map value = 0.1762, steps = 48 shifted from previous position = 0.00465 rotated from previous position = 0.0686 degrees atoms outside contour = 3992, contour level = 0.13699 > show #1 models > hide #1 models > show #1 models > fitmap #1 inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 8548 atoms average map value = 0.1864, steps = 140 shifted from previous position = 8.85 rotated from previous position = 16.4 degrees atoms outside contour = 2799, contour level = 0.13699 > fitmap #1 inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 8548 atoms average map value = 0.164, steps = 100 shifted from previous position = 0.203 rotated from previous position = 13.6 degrees atoms outside contour = 2131, contour level = 0.12843 > fitmap #1 inMap #6 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#6) using 8548 atoms average map value = 0.1717, steps = 80 shifted from previous position = 0.549 rotated from previous position = 10.8 degrees atoms outside contour = 2362, contour level = 0.1331 > fitmap #1 inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 8548 atoms average map value = 0.1864, steps = 56 shifted from previous position = 0.364 rotated from previous position = 2.9 degrees atoms outside contour = 2796, contour level = 0.13699 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 8548 atoms average map value = 0.2786, steps = 80 shifted from previous position = 1.96 rotated from previous position = 1.89 degrees atoms outside contour = 4725, contour level = 0.23698 > hide #1 models > hide #!3 models > show #!5 models > fitmap #1 inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 8548 atoms average map value = 0.164, steps = 100 shifted from previous position = 1.77 rotated from previous position = 15.4 degrees atoms outside contour = 2130, contour level = 0.12843 > fitmap sel inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 10718 atoms average map value = 0.1547, steps = 68 shifted from previous position = 1.86 rotated from previous position = 0.842 degrees atoms outside contour = 3238, contour level = 0.12843 > show #!6 models > fitmap sel inMap #6 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#6) using 10718 atoms average map value = 0.1637, steps = 60 shifted from previous position = 0.296 rotated from previous position = 0.236 degrees atoms outside contour = 3476, contour level = 0.1331 > hide #!5 models > show #!2 models > fitmap sel inMap #6 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#6) using 10718 atoms average map value = 0.1637, steps = 56 shifted from previous position = 0.00181 rotated from previous position = 0.0035 degrees atoms outside contour = 3475, contour level = 0.1331 > fitmap sel inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 10718 atoms average map value = 0.1762, steps = 92 shifted from previous position = 1.57 rotated from previous position = 0.485 degrees atoms outside contour = 3984, contour level = 0.13699 > fitmap sel inMap #6 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#6) using 10718 atoms average map value = 0.1637, steps = 68 shifted from previous position = 1.57 rotated from previous position = 0.483 degrees atoms outside contour = 3475, contour level = 0.1331 > fitmap sel inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 10718 atoms average map value = 0.1547, steps = 64 shifted from previous position = 0.29 rotated from previous position = 0.232 degrees atoms outside contour = 3241, contour level = 0.12843 > hide #4 models > hide #!6 models > show #4 models > show #!6 models > hide #!6 models > show #!5 models > hide #!2 models > view matrix models #4,1,0,0,3.0114,0,1,0,2.4463,0,0,1,-16.54 > view matrix models #4,1,0,0,2.8519,0,1,0,2.1565,0,0,1,-17.344 > fitmap sel inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 10718 atoms average map value = 0.1547, steps = 64 shifted from previous position = 2.08 rotated from previous position = 0.00751 degrees atoms outside contour = 3238, contour level = 0.12843 > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc (#3) using 10718 atoms average map value = 0.2473, steps = 68 shifted from previous position = 5.12 rotated from previous position = 0.57 degrees atoms outside contour = 6502, contour level = 0.23698 > fitmap sel inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 10718 atoms average map value = 0.1547, steps = 84 shifted from previous position = 5.12 rotated from previous position = 0.569 degrees atoms outside contour = 3237, contour level = 0.12843 Populating font family aliases took 304 ms. Replace uses of missing font family "".AppleSystemUIFont"" with one that exists to avoid this cost. > save ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/7pbu_half_guassian5.pdb"" models #4 relModel #5 > open ""/Volumes/ANTHONY16GB/Fu Lab/Ruv/PDB and > Maps/TRuvA_HJ/7PBU_TRuvA_HJ.pdb"" Chain information for 7PBU_TRuvA_HJ.pdb #7 --- Chain | Description A B C D F J L | No description available E G | No description available H | No description available I K | No description available > hide sel atoms > show sel cartoons > select subtract #4 Nothing selected > hide #4,7 atoms > show #4,7 cartoons > hide #4 models > fitmap #7 inMap #5 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 19243 atoms average map value = 0.1152, steps = 72 shifted from previous position = 2.68 rotated from previous position = 0.884 degrees atoms outside contour = 11288, contour level = 0.12843 > hide #!6 models > fitmap #7 inMap #6 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc gaussian (#6) using 19243 atoms average map value = 0.1203, steps = 48 shifted from previous position = 1.07 rotated from previous position = 0.258 degrees atoms outside contour = 11310, contour level = 0.1331 > fitmap #7 inMap #2 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 19243 atoms average map value = 0.1265, steps = 48 shifted from previous position = 1.2 rotated from previous position = 0.409 degrees atoms outside contour = 11169, contour level = 0.13699 > fitmap #7 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc (#3) using 19243 atoms average map value = 0.1533, steps = 56 shifted from previous position = 0.133 rotated from previous position = 0.151 degrees atoms outside contour = 14018, contour level = 0.23698 > save ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/7pbu_full.pdb"" models #7 relModel #3 > hide #7 models > show #7 models > show #!3 models > hide #!5 models > select add #7 19243 atoms, 19545 bonds, 1131 residues, 1 model selected > view matrix models #7,1,0,0,0.17831,0,1,0,0.11228,0,0,1,-1.451 > fitmap #7 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc (#3) using 19243 atoms average map value = 0.1533, steps = 48 shifted from previous position = 1.46 rotated from previous position = 0.0328 degrees atoms outside contour = 14017, contour level = 0.23698 > select #7 /I,K,J,L 5356 atoms, 5472 bonds, 300 residues, 1 model selected > select #7 /I,K,E,G 2170 atoms, 2336 bonds, 68 residues, 1 model selected > delete atoms sel > delete bonds sel > select add #7 17073 atoms, 17209 bonds, 1063 residues, 1 model selected > fitmap #7 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc (#3) using 17073 atoms average map value = 0.1501, steps = 48 shifted from previous position = 0.0406 rotated from previous position = 0.239 degrees atoms outside contour = 12633, contour level = 0.23698 > view matrix models #7,1,0,0,3.5852,0,1,0,2.3264,0,0,1,-3.2958 > fitmap #7 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc (#3) using 17073 atoms average map value = 0.1222, steps = 104 shifted from previous position = 4.31 rotated from previous position = 6.5 degrees atoms outside contour = 13403, contour level = 0.23698 > fitmap #7 inMap #5 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 17073 atoms average map value = 0.1106, steps = 84 shifted from previous position = 3.83 rotated from previous position = 11.7 degrees atoms outside contour = 10861, contour level = 0.12843 > fitmap #7 inMap #6 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc gaussian (#6) using 17073 atoms average map value = 0.1148, steps = 56 shifted from previous position = 1.68 rotated from previous position = 4.28 degrees atoms outside contour = 10688, contour level = 0.1331 > fitmap #7 inMap #2 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 17073 atoms average map value = 0.1204, steps = 108 shifted from previous position = 1.61 rotated from previous position = 3.24 degrees atoms outside contour = 10387, contour level = 0.13699 > fitmap #7 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc (#3) using 17073 atoms average map value = 0.1502, steps = 60 shifted from previous position = 0.254 rotated from previous position = 1.91 degrees atoms outside contour = 12622, contour level = 0.23698 > view matrix models #7,1,0,0,2.5098,0,1,0,3.751,0,0,1,-4.5831 > fitmap #7 inMap #5 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 17073 atoms average map value = 0.1106, steps = 76 shifted from previous position = 2.9 rotated from previous position = 9.41 degrees atoms outside contour = 10862, contour level = 0.12843 > show #!5 models > hide #!3 models > view matrix models #7,1,0,0,3.7001,0,1,0,3.6016,0,0,1,-5.2363 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.99939,0.011132,0.033153,-1.7639,-0.012078,0.99952,0.028465,1.4696,-0.032821,-0.028848,0.99904,2.1961 > view matrix models > #7,0.96141,0.25592,0.10099,-34.72,-0.26459,0.96066,0.084446,29.013,-0.075402,-0.10791,0.9913,17.573 > fitmap #7 inMap #5 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 17073 atoms average map value = 0.1106, steps = 112 shifted from previous position = 1.34 rotated from previous position = 16.9 degrees atoms outside contour = 10858, contour level = 0.12843 > ui mousemode right ""translate selected models"" > fitmap #7 inMap #6 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc gaussian (#6) using 17073 atoms average map value = 0.1148, steps = 56 shifted from previous position = 1.68 rotated from previous position = 4.27 degrees atoms outside contour = 10687, contour level = 0.1331 > fitmap #7 inMap #2 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 17073 atoms average map value = 0.1204, steps = 76 shifted from previous position = 1.63 rotated from previous position = 3.25 degrees atoms outside contour = 10382, contour level = 0.13699 > fitmap #7 inMap #3 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc (#3) using 17073 atoms average map value = 0.1502, steps = 72 shifted from previous position = 0.24 rotated from previous position = 1.89 degrees atoms outside contour = 12629, contour level = 0.23698 > save ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/7pbu_full_No_DNA.pdb"" relModel #3 > save ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/7pbu_full_No_DNA.pdb"" models #7 relModel #3 > select up 36339 atoms, 36777 bonds, 2195 residues, 11 models selected > select up 36339 atoms, 36777 bonds, 2195 residues, 11 models selected > select down 17073 atoms, 17209 bonds, 1063 residues, 1 model selected > show #!2 models > hide #7 models > hide #!5 models > volume #2 level 0.156 > volume #2 level 0.1682 > show #7 models > fitmap #7 inMap #2 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 17073 atoms average map value = 0.1204, steps = 60 shifted from previous position = 0.259 rotated from previous position = 1.91 degrees atoms outside contour = 12136, contour level = 0.16817 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.89084,0.43905,0.11677,-50.104,-0.44282,0.89658,0.0071978,67.845,-0.10154,-0.058122,0.99313,14.536 > fitmap #7 inMap #2 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 17073 atoms average map value = 0.1204, steps = 92 shifted from previous position = 0.26 rotated from previous position = 11.7 degrees atoms outside contour = 12132, contour level = 0.16817 > view matrix models > #7,0.81015,0.58321,-0.059402,-34.37,-0.5785,0.81175,0.080036,84.404,0.094897,-0.030477,0.99502,-12.317 > fitmap #7 inMap #2 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 17073 atoms average map value = 0.1204, steps = 140 shifted from previous position = 0.241 rotated from previous position = 14.6 degrees atoms outside contour = 12134, contour level = 0.16817 > view matrix models > #7,0.72359,0.68977,0.025178,-47.793,-0.68971,0.72116,0.065065,110.1,0.026723,-0.064446,0.99756,-0.63667 > fitmap #7 inMap #2 moveWholeMolecules false Fit molecule 7PBU_TRuvA_HJ.pdb (#7) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 17073 atoms average map value = 0.1204, steps = 112 shifted from previous position = 0.0827 rotated from previous position = 9.29 degrees atoms outside contour = 12132, contour level = 0.16817 > show #1 models > hide #7 models > fitmap #1 inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 8548 atoms average map value = 0.1864, steps = 120 shifted from previous position = 0.212 rotated from previous position = 13.6 degrees atoms outside contour = 3931, contour level = 0.16817 > select add #1 25621 atoms, 25825 bonds, 1595 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.95339,-0.19901,0.2268,239.49,0.2086,-0.97782,0.018881,227.39,0.21801,0.065311,0.97376,-94.822,#7,0.72359,0.68977,0.025178,-46.793,-0.68971,0.72116,0.065065,109.77,0.026723,-0.064446,0.99756,-6.2041 > view matrix models > #1,-0.95339,-0.19901,0.2268,239.89,0.2086,-0.97782,0.018881,226.99,0.21801,0.065311,0.97376,-94.396,#7,0.72359,0.68977,0.025178,-46.387,-0.68971,0.72116,0.065065,109.37,0.026723,-0.064446,0.99756,-5.7776 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.94506,-0.21128,0.24945,236.64,0.242,-0.96518,0.099344,207,0.21978,0.15426,0.96328,-105.37,#7,0.71417,0.69825,0.049108,-49.157,-0.69639,0.70168,0.15066,102.11,0.070738,-0.14179,0.98737,-0.67178 > view matrix models > #1,-0.92403,-0.28007,0.26026,241.63,0.31367,-0.94454,0.097255,194.71,0.21859,0.1715,0.96063,-107.19,#7,0.66207,0.74668,0.064276,-50.562,-0.74511,0.64662,0.16338,112.64,0.080431,-0.15606,0.98447,0.20976 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.92403,-0.28007,0.26026,241.13,0.31367,-0.94454,0.097255,195.01,0.21859,0.1715,0.96063,-107.34,#7,0.66207,0.74668,0.064276,-51.057,-0.74511,0.64662,0.16338,112.94,0.080431,-0.15606,0.98447,0.055792 > fitmap #1 inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 8548 atoms average map value = 0.1864, steps = 92 shifted from previous position = 5.47 rotated from previous position = 7.96 degrees atoms outside contour = 3934, contour level = 0.16817 > select #1 /B :93-133 670 atoms, 672 bonds, 41 residues, 1 model selected > fitmap #1 inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 8548 atoms average map value = 0.1864, steps = 48 shifted from previous position = 0.00573 rotated from previous position = 0.0648 degrees atoms outside contour = 3931, contour level = 0.16817 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.95789,-0.075931,0.27692,213.85,0.10309,-0.99105,0.084857,232.89,0.268,0.10983,0.95714,-104.78 > undo > select add #1 8548 atoms, 8616 bonds, 532 residues, 1 model selected > select subtract #1 Nothing selected > select add #1 8548 atoms, 8616 bonds, 532 residues, 1 model selected > select #1 /B :93-133 670 atoms, 672 bonds, 41 residues, 1 model selected > ui mousemode right ""translate selected atoms"" > fitmap #1 inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 8548 atoms average map value = 0.1863, steps = 84 shifted from previous position = 0.349 rotated from previous position = 3.03 degrees atoms outside contour = 3847, contour level = 0.16817 > fitmap sel inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 670 atoms average map value = 0.2083, steps = 168 shifted from previous position = 8.95 rotated from previous position = 68.1 degrees atoms outside contour = 233, contour level = 0.16817 > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 670 atoms average map value = 0.2356, steps = 116 shifted from previous position = 2.71 rotated from previous position = 41.3 degrees atoms outside contour = 368, contour level = 0.23698 > volume #2 level 0.1872 > select #1 /B :93-106 217 atoms, 217 bonds, 14 residues, 1 model selected > select #1 /B :93-104 187 atoms, 187 bonds, 12 residues, 1 model selected > select #1 /B :93-105' 202 atoms, 202 bonds, 13 residues, 1 model selected > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 202 atoms average map value = 0.3192, steps = 104 shifted from previous position = 2.78 rotated from previous position = 37.4 degrees atoms outside contour = 83, contour level = 0.23698 > show #!3 models > hide #!2 models > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 202 atoms average map value = 0.3525, steps = 100 shifted from previous position = 2.64 rotated from previous position = 24.2 degrees atoms outside contour = 79, contour level = 0.23698 > volume #3 level 0.3286 > hide #!3 models > show #!2 models > select #1 /B :117-133 301 atoms, 301 bonds, 17 residues, 1 model selected > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 301 atoms average map value = 0.2649, steps = 124 shifted from previous position = 0.937 rotated from previous position = 20.1 degrees atoms outside contour = 201, contour level = 0.3286 > show #!3 models > hide #!2 models > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 301 atoms average map value = 0.2649, steps = 120 shifted from previous position = 3.18 rotated from previous position = 0.00787 degrees atoms outside contour = 201, contour level = 0.3286 > volume #3 level 0.3897 > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 301 atoms average map value = 0.2649, steps = 140 shifted from previous position = 3.36 rotated from previous position = 0.0137 degrees atoms outside contour = 230, contour level = 0.38968 > hide #!3 models > show #!2 models > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 301 atoms average map value = 0.2649, steps = 120 shifted from previous position = 2.84e-05 rotated from previous position = 0.000289 degrees atoms outside contour = 230, contour level = 0.38968 > fitmap sel inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 301 atoms average map value = 0.2016, steps = 52 shifted from previous position = 0.583 rotated from previous position = 9.43 degrees atoms outside contour = 122, contour level = 0.18723 > fitmap sel inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 301 atoms average map value = 0.2016, steps = 88 shifted from previous position = 6.01 rotated from previous position = 0.0696 degrees atoms outside contour = 121, contour level = 0.18723 > volume #6 level 0.148 > hide #!6 models > volume #2 level 0.2756 > select #1 /B :105-117 189 atoms, 189 bonds, 13 residues, 1 model selected > undo > select #1 /B :105-116 182 atoms, 182 bonds, 12 residues, 1 model selected > select #1 /B :106-116 167 atoms, 167 bonds, 11 residues, 1 model selected > select #1 /B :81-93 190 atoms, 190 bonds, 13 residues, 1 model selected > volume #2 level 0.2305 > select #1 /B :94-105 185 atoms, 185 bonds, 12 residues, 1 model selected > fitmap sel inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 185 atoms average map value = 0.2279, steps = 148 shifted from previous position = 3.22 rotated from previous position = 88.9 degrees atoms outside contour = 89, contour level = 0.23054 > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 185 atoms average map value = 0.3273, steps = 156 shifted from previous position = 2.58 rotated from previous position = 15.1 degrees atoms outside contour = 117, contour level = 0.38968 > show #!3 models > hide #!2 models > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 185 atoms average map value = 0.3149, steps = 84 shifted from previous position = 3.05 rotated from previous position = 30.5 degrees atoms outside contour = 108, contour level = 0.38968 > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 185 atoms average map value = 0.3273, steps = 132 shifted from previous position = 2.46 rotated from previous position = 30.5 degrees atoms outside contour = 116, contour level = 0.38968 > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 185 atoms average map value = 0.315, steps = 76 shifted from previous position = 2.31 rotated from previous position = 30.5 degrees atoms outside contour = 108, contour level = 0.38968 > select #1 /B :95-116 341 atoms, 342 bonds, 22 residues, 1 model selected > select #1 /B :105-116 182 atoms, 182 bonds, 12 residues, 1 model selected > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 182 atoms average map value = 0.3529, steps = 272 shifted from previous position = 3 rotated from previous position = 33.2 degrees atoms outside contour = 97, contour level = 0.38968 > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 182 atoms average map value = 0.2946, steps = 80 shifted from previous position = 2.44 rotated from previous position = 18.7 degrees atoms outside contour = 124, contour level = 0.38968 > hide #1 models > show #1 models > close #1 > show #4 models > close #4 > open ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/7pbu_half.pdb"" Chain information for 7pbu_half.pdb #1 --- Chain | Description A B C D | No description available E G | No description available I K | No description available > hide #1 atoms > show #1 cartoons > show #!2 models > hide #!3 models > volume #2 level 0.1214 > select #1 /I,K,E,G 2170 atoms, 2336 bonds, 68 residues, 1 model selected > delete atoms sel > delete bonds sel > fitmap #1 inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 8548 atoms average map value = 0.164, steps = 144 shifted from previous position = 10.4 rotated from previous position = 28.9 degrees atoms outside contour = 2131, contour level = 0.12843 > fitmap #1 inMap #6 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#6) using 8548 atoms average map value = 0.1717, steps = 80 shifted from previous position = 0.55 rotated from previous position = 10.8 degrees atoms outside contour = 3075, contour level = 0.14796 > fitmap #1 inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 8548 atoms average map value = 0.1864, steps = 56 shifted from previous position = 0.362 rotated from previous position = 2.86 degrees atoms outside contour = 2350, contour level = 0.12139 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 8548 atoms average map value = 0.2786, steps = 56 shifted from previous position = 1.96 rotated from previous position = 1.92 degrees atoms outside contour = 5933, contour level = 0.38968 > fitmap #1 inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 8548 atoms average map value = 0.164, steps = 96 shifted from previous position = 1.78 rotated from previous position = 15.4 degrees atoms outside contour = 2130, contour level = 0.12843 > ui mousemode right ""translate selected models"" > select add #1 8548 atoms, 8616 bonds, 532 residues, 1 model selected > view matrix models #1,1,0,0,0.97561,0,1,0,0.10588,0,0,1,-7.099 > fitmap #1 inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 8548 atoms average map value = 0.164, steps = 72 shifted from previous position = 7.16 rotated from previous position = 0.00301 degrees atoms outside contour = 2129, contour level = 0.12843 > view matrix models #1,1,0,0,1.9294,0,1,0,0.20922,0,0,1,-13.844 > show #!5 models > hide #!2 models > fitmap #1 inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 8548 atoms average map value = 0.164, steps = 72 shifted from previous position = 6.82 rotated from previous position = 0.0107 degrees atoms outside contour = 2131, contour level = 0.12843 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.98118,0.17704,-0.07708,-7.5003,-0.17592,0.98418,0.021113,20.493,0.079598,-0.0071558,0.9968,-22.093 > fitmap #1 inMap #5 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 8548 atoms average map value = 0.164, steps = 80 shifted from previous position = 0.0927 rotated from previous position = 11.2 degrees atoms outside contour = 2131, contour level = 0.12843 > view matrix models > #1,0.934,0.33537,-0.12315,-15.13,-0.34745,0.93292,-0.094577,62.191,0.083169,0.13112,0.98787,-38.159 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.934,0.33537,-0.12315,-14.652,-0.34745,0.93292,-0.094577,61.61,0.083169,0.13112,0.98787,-42.011 > hide #!5 models > show #!6 models > fitmap #1 inMap #6 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#6) using 8548 atoms average map value = 0.1717, steps = 72 shifted from previous position = 3.37 rotated from previous position = 7.67 degrees atoms outside contour = 3076, contour level = 0.14796 > hide #!6 models > show #!2 models > volume #2 level 0.1907 > fitmap #1 inMap #2 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 8548 atoms average map value = 0.1864, steps = 68 shifted from previous position = 0.362 rotated from previous position = 2.9 degrees atoms outside contour = 4759, contour level = 0.19069 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 8548 atoms average map value = 0.2786, steps = 68 shifted from previous position = 1.96 rotated from previous position = 1.92 degrees atoms outside contour = 5933, contour level = 0.38968 > hide #!2 models > show #!3 models > view matrix models > #1,0.934,0.33537,-0.12315,-14.495,-0.34745,0.93292,-0.094577,61.602,0.083169,0.13112,0.98787,-43.391 > fitmap #1 inMap #3 moveWholeMolecules false Fit molecule 7pbu_half.pdb (#1) to map TRuvA_HJ_3.9A_density.mrc (#3) using 8548 atoms average map value = 0.2787, steps = 52 shifted from previous position = 1.39 rotated from previous position = 0.049 degrees atoms outside contour = 5928, contour level = 0.38968 > show #!2 models > hide #!3 models > show #!3 models > hide #!2 models > save ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/7pbu_half_NoDNA.pdb"" models #1 relModel #3 > show #!2 models > hide #!3 models > view matrix models > #1,0.934,0.33537,-0.12315,-13.756,-0.34745,0.93292,-0.094577,61.422,0.083169,0.13112,0.98787,-43.33 > undo > select #1 /A :97-101 77 atoms, 77 bonds, 5 residues, 1 model selected > volume #2 level 0.2028 > open ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/Coot/7pbu_half_NoDNA-coot-0.pdb"" Chain information for 7pbu_half_NoDNA-coot-0.pdb #4 --- Chain | Description A B C D | No description available > hide #1 models > volume #2 level 0.1439 > select #7 /A :97-101 77 atoms, 77 bonds, 5 residues, 1 model selected > select #4 /A :97-101 77 atoms, 77 bonds, 5 residues, 1 model selected > volume #2 level 0.09541 > volume #2 level 0.1162 > hide #4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!2 models > show #4 models > volume #5 level 0.1389 > hide #!5 models > volume #6 level 0.1433 > select #4 /A :94-133 653 atoms, 655 bonds, 40 residues, 1 model selected > ui mousemode right ""translate selected atoms"" > ui mousemode right ""move picked models"" > view matrix models #4,1,0,0,-0.22534,0,1,0,0.7089,0,0,1,-1.8283 > undo > ui mousemode right ""translate selected atoms"" > fitmap sel inMap #6 moveWholeMolecules false Fit molecule 7pbu_half_NoDNA-coot-0.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#6) using 653 atoms average map value = 0.2343, steps = 196 shifted from previous position = 20.7 rotated from previous position = 106 degrees atoms outside contour = 43, contour level = 0.14331 > undo > fitmap sel inMap #2 moveWholeMolecules false Fit molecule 7pbu_half_NoDNA-coot-0.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 653 atoms average map value = 0.2578, steps = 204 shifted from previous position = 20.6 rotated from previous position = 107 degrees atoms outside contour = 48, contour level = 0.1162 > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half_NoDNA-coot-0.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc (#3) using 653 atoms average map value = 0.2375, steps = 116 shifted from previous position = 3.24 rotated from previous position = 13 degrees atoms outside contour = 498, contour level = 0.38968 > select #4 /A :94-104 170 atoms, 170 bonds, 11 residues, 1 model selected > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half_NoDNA-coot-0.pdb (#4) to map TRuvA_HJ_3.9A_density.mrc (#3) using 170 atoms average map value = 0.2867, steps = 80 shifted from previous position = 0.672 rotated from previous position = 22.5 degrees atoms outside contour = 106, contour level = 0.38968 > hide #!6 models > show #!2 models > show #!3 models > hide #!2 models > save ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/Coot/7pbu_half_NoDNA-coot-0_edit.pdb"" models #4 relModel #3 > open ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/Coot/7pbu_half_NoDNA-coot-1.pdb"" Chain information for 7pbu_half_NoDNA-coot-1.pdb #8 --- Chain | Description A B C D | No description available > select add #4 8548 atoms, 8616 bonds, 532 residues, 1 model selected > select subtract #4 Nothing selected > hide #4 models > select #4 /8 :64-133 Nothing selected > select #8 /A :64-133 1134 atoms, 1138 bonds, 70 residues, 1 model selected > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half_NoDNA-coot-1.pdb (#8) to map TRuvA_HJ_3.9A_density.mrc (#3) using 1134 atoms average map value = 0.372, steps = 44 shifted from previous position = 0.117 rotated from previous position = 0.924 degrees atoms outside contour = 656, contour level = 0.38968 > fitmap sel inMap #3 moveWholeMolecules false Fit molecule 7pbu_half_NoDNA-coot-1.pdb (#8) to map TRuvA_HJ_3.9A_density.mrc (#3) using 1134 atoms average map value = 0.372, steps = 44 shifted from previous position = 0.117 rotated from previous position = 0.924 degrees atoms outside contour = 656, contour level = 0.38968 > close #4 > close #1 > close #7 > open ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/Coot/7pbu_half_NoDNA-coot-1-A-edits-done.pdb"" Chain information for 7pbu_half_NoDNA-coot-1-A-edits-done.pdb #1 --- Chain | Description A B C D | No description available > hide #1 models > show #1 models > color #1 #00f900 transparency 0 > color #1 #8efa00 transparency 0 > color #1 #00fa92 transparency 0 > color #1 #008f00 transparency 0 > color #8 #00fdff transparency 0 > select add #8 8548 atoms, 8616 bonds, 532 residues, 1 model selected > select subtract #8 Nothing selected > hide #1 models > open ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/Coot/TRuvA-coot-1-chainB-Pymolcopy.pdb"" Chain information for TRuvA-coot-1-chainB-Pymolcopy.pdb #4 --- Chain | Description A B C D | No description available > color #4 #ff85ff transparency 0 > hide #8 models > show #!2 models > volume #2 level 0.1664 > hide #4 models > hide #!3 models > open ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/Coot/TRuvA_sub_in_chainA.pdb"" Chain information for TRuvA_sub_in_chainA.pdb #7 --- Chain | Description A | No description available B C D | No description available > hide #7 models > close #7 > open ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/Coot/ChainA_TtRuvA_sub.pdb"" Chain information for ChainA_TtRuvA_sub.pdb #7 --- Chain | Description A | No description available B C D | No description available > hide #!2 models > show #!2 models > hide #7 models > open ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/Coot/4_TRuvA_aligned.pdb"" Chain information for 4_TRuvA_aligned.pdb #9 --- Chain | Description A | No description available B C D | No description available > color #9 bychain > fitmap #9 inMap #3 moveWholeMolecules false Fit molecule 4_TRuvA_aligned.pdb (#9) to map TRuvA_HJ_3.9A_density.mrc (#3) using 5760 atoms average map value = 0.4024, steps = 56 shifted from previous position = 0.737 rotated from previous position = 1.6 degrees atoms outside contour = 3523, contour level = 0.38968 > fitmap #9 inMap #2 moveWholeMolecules false Fit molecule 4_TRuvA_aligned.pdb (#9) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 5760 atoms average map value = 0.1685, steps = 52 shifted from previous position = 0.6 rotated from previous position = 1.47 degrees atoms outside contour = 2722, contour level = 0.16644 > save ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/Coot/ChimeraX_initial_model_session.cxs"" > hide #9 models > show #9 models > open ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/Coot/4_TRuvA_aligned_real_space_refined_001-coot-2.pdb"" Summary of feedback from opening /Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and maps/TRuvAHJ/Coot/4_TRuvA_aligned_real_space_refined_001-coot-2.pdb --- warnings | Start residue of secondary structure not found: HELIX 3 3 ALA D 145 LEU D 156 1 12 Start residue of secondary structure not found: HELIX 4 4 GLU D 160 GLN D 173 1 14 Start residue of secondary structure not found: HELIX 5 5 ALA D 179 ARG D 189 1 11 Start residue of secondary structure not found: HELIX 11 11 ALA A 145 LEU A 156 1 12 Start residue of secondary structure not found: HELIX 12 12 GLU A 160 GLN A 173 1 14 7 messages similar to the above omitted Chain information for 4_TRuvA_aligned_real_space_refined_001-coot-2.pdb #10 --- Chain | Description A | No description available B | No description available C D | No description available > hide #9 models > ui mousemode right zoom > ui mousemode right translate > ui mousemode right zoom > hide #!2 models > show #8 models > hide #8 models > show #9 models > hide #9 models > close #9 > close #10 > open ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/Coot/rama_edits-coot-0.pdb"" Chain information for rama_edits-coot-0.pdb #9 --- Chain | Description A C D | No description available B | No description available > color #9 bychain > show #!3 models > open ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/coot_edits+DNA.pdb"" Chain information for coot_edits+DNA.pdb #10 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E G | No description available I K | No description available > hide #9#!10 atoms > show #9#!10 cartoons > hide #9 models > show #!2 models > fitmap #10 inMap #2 moveWholeMolecules false Fit molecule coot_edits+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 6373 atoms average map value = 0.1893, steps = 52 shifted from previous position = 0.56 rotated from previous position = 0.653 degrees atoms outside contour = 2763, contour level = 0.16644 > fitmap #10 inMap #3 moveWholeMolecules false Fit molecule coot_edits+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc (#3) using 6373 atoms average map value = 0.4117, steps = 64 shifted from previous position = 0.564 rotated from previous position = 0.689 degrees atoms outside contour = 4013, contour level = 0.38968 > fitmap #10 inMap #5 moveWholeMolecules false Fit molecule coot_edits+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 6373 atoms average map value = 0.15, steps = 92 shifted from previous position = 2.37 rotated from previous position = 8.59 degrees atoms outside contour = 2587, contour level = 0.13891 > fitmap #10 inMap #6 moveWholeMolecules false Fit molecule coot_edits+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc gaussian (#6) using 6373 atoms average map value = 0.1628, steps = 68 shifted from previous position = 0.614 rotated from previous position = 3.47 degrees atoms outside contour = 2463, contour level = 0.14331 > fitmap #10 inMap #2 moveWholeMolecules false Fit molecule coot_edits+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 6373 atoms average map value = 0.1893, steps = 80 shifted from previous position = 1.36 rotated from previous position = 4.55 degrees atoms outside contour = 2764, contour level = 0.16644 > fitmap #10 inMap #3 moveWholeMolecules false Fit molecule coot_edits+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc (#3) using 6373 atoms average map value = 0.4117, steps = 60 shifted from previous position = 0.562 rotated from previous position = 0.686 degrees atoms outside contour = 4017, contour level = 0.38968 > close #10 > open ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/refine15+DNA.pdb"" Chain information for refine15+DNA.pdb #10 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E G | No description available I K | No description available > hide #!10 atoms > show #!10 cartoons > hide #!2 models > show #9 models > hide #9 models > select #10 /I,G,K,E 2170 atoms, 2336 bonds, 68 residues, 1 model selected > fitmap sel inMap #3 moveWholeMolecules false Fit molecule refine15+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc (#3) using 2170 atoms average map value = 0.2815, steps = 116 shifted from previous position = 10.4 rotated from previous position = 12.5 degrees atoms outside contour = 1576, contour level = 0.38968 > open ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/7pbu_half.pdb"" Chain information for 7pbu_half.pdb #11 --- Chain | Description A B C D | No description available E G | No description available I K | No description available > hide sel atoms > show sel cartoons > select add #10 6373 atoms, 6609 bonds, 2 pseudobonds, 627 residues, 2 models selected > select subtract #10 Nothing selected > hide #11#!10 atoms > show #11#!10 cartoons > hide #!10 models > hide #!3 models > show #!10 models > hide #11 models > select #10 /I,G,K,E 2170 atoms, 2336 bonds, 68 residues, 1 model selected > fitmap sel inMap #3 moveWholeMolecules false Fit molecule refine15+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc (#3) using 2170 atoms average map value = 0.2815, steps = 116 shifted from previous position = 10.4 rotated from previous position = 12.5 degrees atoms outside contour = 1576, contour level = 0.38968 > show #!3 models > ui tool show ""Volume Viewer"" > volume #3 level 0.1912 > fitmap sel inMap #3 moveWholeMolecules false Fit molecule refine15+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc (#3) using 2170 atoms average map value = 0.2815, steps = 116 shifted from previous position = 10.4 rotated from previous position = 12.5 degrees atoms outside contour = 807, contour level = 0.19117 > volume #3 level 0.2828 > show #11 models > hide #11 models > fitmap sel inMap #3 moveWholeMolecules false Fit molecule refine15+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc (#3) using 2170 atoms average map value = 0.2815, steps = 116 shifted from previous position = 10.4 rotated from previous position = 12.5 degrees atoms outside contour = 1213, contour level = 0.28279 > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > ui mousemode right ""move picked models"" > ui mousemode right ""translate selected models"" > view matrix models #10,1,0,0,-0.043405,0,1,0,-0.20886,0,0,1,-0.0046715 > undo > ui mousemode right ""translate selected atoms"" > show #11 models > hide #!10 models > show #!10 models > hide sel target a > cartoon hide sel > color #11 #ff2600 transparency 0 > color #11 #ff85ff transparency 0 > color #10 #73fa79 transparency 0 > cartoon sel > hide #11 models > fitmap sel inMap #5 moveWholeMolecules false Fit molecule refine15+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 2170 atoms average map value = 0.2052, steps = 108 shifted from previous position = 14.2 rotated from previous position = 14.9 degrees atoms outside contour = 225, contour level = 0.13891 > undo [Repeated 1 time(s)] > fitmap sel inMap #3 moveWholeMolecules false Fit molecule refine15+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc (#3) using 2170 atoms average map value = 0.2759, steps = 156 shifted from previous position = 7.61 rotated from previous position = 16 degrees atoms outside contour = 1233, contour level = 0.28279 > color sel bychain > color sel hot pink > undo [Repeated 1 time(s)] > color sel hot pink > fitmap sel inMap #3 moveWholeMolecules false Fit molecule refine15+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc (#3) using 2170 atoms average map value = 0.2759, steps = 44 shifted from previous position = 0.00547 rotated from previous position = 0.00388 degrees atoms outside contour = 1236, contour level = 0.28279 > undo > color sel bychain > color #10 #00fdff transparency 0 > color sel bychain > select #10 /I :10-17, /G :25-31 Expected a keyword > select #10 /I :10-17 & /G :25-31 Nothing selected > select #10 /I :10-17 257 atoms, 279 bonds, 8 residues, 1 model selected > fitmap sel inMap #3 moveWholeMolecules false Fit molecule refine15+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc (#3) using 257 atoms average map value = 0.3389, steps = 192 shifted from previous position = 18.1 rotated from previous position = 0.725 degrees atoms outside contour = 124, contour level = 0.28279 > select up 541 atoms, 582 bonds, 17 residues, 1 model selected > select up 6373 atoms, 6609 bonds, 627 residues, 1 model selected > select down 541 atoms, 582 bonds, 17 residues, 1 model selected > select down 257 atoms, 279 bonds, 8 residues, 1 model selected > select #10 /I,G,K,E 2170 atoms, 2336 bonds, 68 residues, 1 model selected > fitmap sel inMap #5 moveWholeMolecules false Fit molecule refine15+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc gaussian (#5) using 2170 atoms average map value = 0.2052, steps = 116 shifted from previous position = 14.3 rotated from previous position = 19.4 degrees atoms outside contour = 225, contour level = 0.13891 > fitmap sel inMap #6 moveWholeMolecules false Fit molecule refine15+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc gaussian (#6) using 2170 atoms average map value = 0.22, steps = 60 shifted from previous position = 0.394 rotated from previous position = 1.55 degrees atoms outside contour = 297, contour level = 0.14331 > fitmap sel inMap #2 moveWholeMolecules false Fit molecule refine15+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc gaussian (#2) using 2170 atoms average map value = 0.2376, steps = 76 shifted from previous position = 2.45 rotated from previous position = 1.25 degrees atoms outside contour = 534, contour level = 0.16644 > fitmap sel inMap #3 moveWholeMolecules false Fit molecule refine15+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc (#3) using 2170 atoms average map value = 0.2815, steps = 52 shifted from previous position = 0.854 rotated from previous position = 0.304 degrees atoms outside contour = 1211, contour level = 0.28279 > undo > select #10 /K :10-17 257 atoms, 279 bonds, 8 residues, 1 model selected > select #10 /K :14-17 128 atoms, 138 bonds, 4 residues, 1 model selected > select #10 /K :9-11 96 atoms, 103 bonds, 3 residues, 1 model selected > select #10 /E :25-29 158 atoms, 168 bonds, 5 residues, 1 model selected > undo > select #10 /E :2929 Nothing selected > select #10 /E :29 30 atoms, 31 bonds, 1 residue, 1 model selected > select #10 /I :9 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /K :9 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /E :29 30 atoms, 31 bonds, 1 residue, 1 model selected > select #10 /E :28-29 62 atoms, 65 bonds, 2 residues, 1 model selected > select #10 /E :30-32 96 atoms, 101 bonds, 3 residues, 1 model selected > undo [Repeated 1 time(s)] > select #10 /K:1-4 126 atoms, 134 bonds, 4 residues, 1 model selected > select #10 /K:1-5 158 atoms, 168 bonds, 5 residues, 1 model selected > select #10 /K:1-4 126 atoms, 134 bonds, 4 residues, 1 model selected > select #10 /G :32-46 322 atoms, 349 bonds, 10 residues, 1 model selected > select #10 /G :34-46 258 atoms, 280 bonds, 8 residues, 1 model selected > select #10 /G :33 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /K :7-9 96 atoms, 101 bonds, 3 residues, 1 model selected > select #10 /K :5-7 94 atoms, 99 bonds, 3 residues, 1 model selected > select #10 /K :35-28 Nothing selected > select #10 /E :35-28 Nothing selected > select #10 /E :28-35 254 atoms, 272 bonds, 8 residues, 1 model selected > select #10 /E :32 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /E :30 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /E :28-29 62 atoms, 65 bonds, 2 residues, 1 model selected > select #10 /E :25-27 96 atoms, 102 bonds, 3 residues, 1 model selected > select #10 /E :25-28 128 atoms, 136 bonds, 4 residues, 1 model selected > select #10 /E :28 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /E :27 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /E :25 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /E :28 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /E :25-28 128 atoms, 136 bonds, 4 residues, 1 model selected > select #10 /E :25-6 Nothing selected > select #10 /E :25-26 64 atoms, 68 bonds, 2 residues, 1 model selected > select #10 /E :25-28 128 atoms, 136 bonds, 4 residues, 1 model selected > select #10 /E :27 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /E :26 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /E :25 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /E :28 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /E :17 Nothing selected > select #10 /K :17 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /K :14-17 128 atoms, 138 bonds, 4 residues, 1 model selected > select #10 /K :13 33 atoms, 35 bonds, 1 residue, 1 model selected > select #10 /K :12-13 65 atoms, 70 bonds, 2 residues, 1 model selected > select #10 /K :12 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /K :12-13 65 atoms, 70 bonds, 2 residues, 1 model selected > volume #3 level 0.2217 > select #10 /E :25-30 190 atoms, 202 bonds, 6 residues, 1 model selected > select #10 /10 Nothing selected > select #10 /K :10 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /K :13-17 161 atoms, 174 bonds, 5 residues, 1 model selected > select #10 /E32-E36 Nothing selected > select #10 /E :32-36 161 atoms, 174 bonds, 5 residues, 1 model selected > select #10 /E :34-36 97 atoms, 105 bonds, 3 residues, 1 model selected > select #10 /E :33-36 129 atoms, 140 bonds, 4 residues, 1 model selected > select #10 /E :32 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /E :33 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /E :34 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /E :34 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /E :35 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /E :34 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /E :38-41 129 atoms, 139 bonds, 4 residues, 1 model selected > select #10 /E :37 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /E :38 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /E :39-40 64 atoms, 68 bonds, 2 residues, 1 model selected > select #10 /E :40-41 65 atoms, 70 bonds, 2 residues, 1 model selected > select #10 /E :39 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /E :40 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /E :41 33 atoms, 35 bonds, 1 residue, 1 model selected > select #10 /I:1-4 126 atoms, 134 bonds, 4 residues, 1 model selected > select #10 /I:5-9 158 atoms, 167 bonds, 5 residues, 1 model selected > select #10 /I:5 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /I:5-7 94 atoms, 99 bonds, 3 residues, 1 model selected > select #10 /I:6-9 126 atoms, 133 bonds, 4 residues, 1 model selected > select #10 /I:7-9 96 atoms, 101 bonds, 3 residues, 1 model selected > select #10 /E :34-35 64 atoms, 69 bonds, 2 residues, 1 model selected > select #10 /E :9 Nothing selected > select #10 /I :9 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /I :12 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /I :11-12 64 atoms, 69 bonds, 2 residues, 1 model selected > select #10 /I :11=0-12 Expected a keyword > select #10 /I :10-12 96 atoms, 104 bonds, 3 residues, 1 model selected > select #10 /I :19 Nothing selected > select #10 /I :9 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /I :10 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /I :111 Nothing selected > select #10 /I :11 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /I :12 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /I :13 33 atoms, 35 bonds, 1 residue, 1 model selected > select #10 /I :14-17 128 atoms, 138 bonds, 4 residues, 1 model selected > undo > select #10 /I :13-17 161 atoms, 174 bonds, 5 residues, 1 model selected > select #10 /I :16-17 64 atoms, 68 bonds, 2 residues, 1 model selected > select #10 /I :17 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /I :15 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /I :12-17 193 atoms, 209 bonds, 6 residues, 1 model selected > select #10 /I :24-29 Nothing selected > select #10 /G :24-29 158 atoms, 168 bonds, 5 residues, 1 model selected > select #10 /K :12 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /I 8-12 Expected a keyword > select #10 /I :8-12 160 atoms, 172 bonds, 5 residues, 1 model selected > select #10 /I :9-12 128 atoms, 138 bonds, 4 residues, 1 model selected > select #10 /I :910-12 Nothing selected > select #10 /I :10-12 96 atoms, 104 bonds, 3 residues, 1 model selected > select #10 /I :11-12 64 atoms, 69 bonds, 2 residues, 1 model selected > select #10 /I :13-16 129 atoms, 139 bonds, 4 residues, 1 model selected > 7 Unknown command: 7 > select #10 /I :13-17 161 atoms, 174 bonds, 5 residues, 1 model selected > select #10 /I :11-12 64 atoms, 69 bonds, 2 residues, 1 model selected > select #10 /I :115-17 Nothing selected > select #10 /I :15-17 96 atoms, 103 bonds, 3 residues, 1 model selected > select #10 /I :15 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /I :16 32 atoms, 33 bonds, 1 residue, 1 model selected > select #10 /I :17 32 atoms, 34 bonds, 1 residue, 1 model selected > select #10 /I,G,E,K 2170 atoms, 2336 bonds, 68 residues, 1 model selected > fitmap sel inMap #3 moveWholeMolecules false Fit molecule refine15+DNA.pdb (#10) to map TRuvA_HJ_3.9A_density.mrc (#3) using 2170 atoms average map value = 0.209, steps = 84 shifted from previous position = 3.75 rotated from previous position = 4.49 degrees atoms outside contour = 1253, contour level = 0.22171 > select #10 /G :31 32 atoms, 33 bonds, 1 residue, 1 model selected > save ""/Users/anthonyrish/Documents/Fu Lab/Ruv/PDB and > maps/TRuvAHJ/refine15+DNA_chimeraXedits.pdb"" models #10 relModel #3 Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/fitgui.py"", line 651, in _undo position_history.undo() File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/move.py"", line 41, in undo if restore_position(ps): File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/move.py"", line 93, in restore_position atoms.coords = xyz File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 210, in set_prop raise ValueError('Values array length %d does not match objects array length %d' ValueError: Values array length 6373 does not match objects array length 0 ValueError: Values array length 6373 does not match objects array length 0 File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 210, in set_prop raise ValueError('Values array length %d does not match objects array length %d' See log for complete Python traceback. Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/fitgui.py"", line 651, in _undo position_history.undo() File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/move.py"", line 41, in undo if restore_position(ps): File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/move.py"", line 93, in restore_position atoms.coords = xyz File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 210, in set_prop raise ValueError('Values array length %d does not match objects array length %d' ValueError: Values array length 6373 does not match objects array length 0 ValueError: Values array length 6373 does not match objects array length 0 File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 210, in set_prop raise ValueError('Values array length %d does not match objects array length %d' See log for complete Python traceback. Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/fitgui.py"", line 651, in _undo position_history.undo() File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/move.py"", line 41, in undo if restore_position(ps): File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/move.py"", line 93, in restore_position atoms.coords = xyz File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 210, in set_prop raise ValueError('Values array length %d does not match objects array length %d' ValueError: Values array length 6373 does not match objects array length 0 ValueError: Values array length 6373 does not match objects array length 0 File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 210, in set_prop raise ValueError('Values array length %d does not match objects array length %d' See log for complete Python traceback. Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/fitgui.py"", line 651, in _undo position_history.undo() File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/move.py"", line 41, in undo if restore_position(ps): File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_fit/move.py"", line 93, in restore_position atoms.coords = xyz File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 210, in set_prop raise ValueError('Values array length %d does not match objects array length %d' ValueError: Values array length 6373 does not match objects array length 0 ValueError: Values array length 6373 does not match objects array length 0 File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py"", line 210, in set_prop raise ValueError('Values array length %d does not match objects array length %d' See log for complete Python traceback. > toolshed show Downloading bundle ChimeraX_ISOLDE-1.4-cp39-cp39-macosx_10_13_x86_64.whl > ui tool show Updates Errors may have occurred when running pip: pip standard error: \--- WARNING: Value for scheme.platlib does not match. Please report this to distutils: /Users/anthonyrish/Library/Application Support/ChimeraX/1.4/site- packages sysconfig: /Users/anthonyrish/Library/Python/3.9/lib/python/site-packages WARNING: Value for scheme.purelib does not match. Please report this to distutils: /Users/anthonyrish/Library/Application Support/ChimeraX/1.4/site- packages sysconfig: /Users/anthonyrish/Library/Python/3.9/lib/python/site-packages WARNING: Value for scheme.headers does not match. Please report this to distutils: /Users/anthonyrish/Library/Application Support/ChimeraX/include/python3.9/ChimeraX-ISOLDE sysconfig: /Users/anthonyrish/Library/Python/3.9/include/ChimeraX-ISOLDE WARNING: Value for scheme.scripts does not match. Please report this to distutils: /Users/anthonyrish/Library/Application Support/ChimeraX/bin sysconfig: /Users/anthonyrish/Library/Python/3.9/bin WARNING: Value for scheme.data does not match. Please report this to distutils: /Users/anthonyrish/Library/Application Support/ChimeraX sysconfig: /Users/anthonyrish/Library/Python/3.9 WARNING: Additional context: user = True home = None root = None prefix = None WARNING: Value for scheme.headers does not match. Please report this to distutils: /Users/anthonyrish/Library/Application Support/ChimeraX/include/python3.9/UNKNOWN sysconfig: /Users/anthonyrish/Library/Python/3.9/include/UNKNOWN WARNING: You are using pip version 21.3.1; however, version 23.0.1 is available. You should consider upgrading via the '/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/MacOS/ChimeraX -m pip install --upgrade pip' command. \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Collecting ChimeraX-ISOLDE==1.4 Downloading https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxisolde/releases/1.4/ChimeraX_ISOLDE-1.4-cp39-cp39-macosx_10_13_x86_64.whl (144.8 MB) Installing collected packages: ChimeraX-ISOLDE Successfully installed ChimeraX-ISOLDE-1.4 \--- Successfully installed ChimeraX-ISOLDE-1.4 Installed ChimeraX-ISOLDE (1.4) Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 490, in get_module m = importlib.import_module(self.package_name) File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py"", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File """", line 1030, in _gcd_import File """", line 1007, in _find_and_load File """", line 986, in _find_and_load_unlocked File """", line 680, in _load_unlocked File """", line 850, in exec_module File """", line 228, in _call_with_frames_removed File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/__init__.py"", line 51, in __version__ = _version() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/__init__.py"", line 49, in _version return pkg_resources.require('ChimeraX-ISOLDE')[0].version File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 891, in require needed = self.resolve(parse_requirements(requirements)) File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 777, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.18.0' distribution was not found and is required by ChimeraX-ISOLDE During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 364, in initialize api = self._get_api(session.logger) File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 509, in _get_api m = self.get_module() File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 492, in get_module raise ToolshedError(""Error importing bundle %s's module: %s"" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's module: The 'ChimeraX-Clipper~=0.18.0' distribution was not found and is required by ChimeraX-ISOLDE ChimeraX-ISOLDE (installed) [version: 1.4] [api package: chimerax.isolde] [category: General] [tool: ISOLDE [categories: General] [synopsis: Interactive Molecular Dynamics Flexible Fitting (iMDFF)]] [tool: Ramachandran Plot [categories: Validation] [synopsis: Interactive Ramachandran plot]] [command: isolde [categories: General] [synopsis: Command-line control of ISOLDE simulations]] [command: rama [categories: General] [synopsis: Live Ramachandran validation of models]] [command: rota [categories: General] [synopsis: Live rotamer validation of models]] [command: ~rama [categories: General] [synopsis: Turn off live Ramachandran validation of models]] [command: ~rota [categories: General] [synopsis: Turn off live rotamer validation of models]]: custom initialization failed > ui tool show ISOLDE Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 490, in get_module m = importlib.import_module(self.package_name) File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py"", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File """", line 1030, in _gcd_import File """", line 1007, in _find_and_load File """", line 986, in _find_and_load_unlocked File """", line 680, in _load_unlocked File """", line 850, in exec_module File """", line 228, in _call_with_frames_removed File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/__init__.py"", line 51, in __version__ = _version() File ""/Users/anthonyrish/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/__init__.py"", line 49, in _version return pkg_resources.require('ChimeraX-ISOLDE')[0].version File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 891, in require needed = self.resolve(parse_requirements(requirements)) File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/pkg_resources/__init__.py"", line 777, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.18.0' distribution was not found and is required by ChimeraX-ISOLDE During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 558, in start_tool api = self._get_api(session.logger) File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 509, in _get_api m = self.get_module() File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 492, in get_module raise ToolshedError(""Error importing bundle %s's module: %s"" % (self.name, str(e))) chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's module: The 'ChimeraX-Clipper~=0.18.0' distribution was not found and is required by ChimeraX-ISOLDE During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py"", line 1685, in run(ses, ""ui tool show %s"" % StringArg.unparse(tool_name))) File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/cmd.py"", line 219, in ui_tool_show bi.start_tool(session, name) File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 564, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: Error importing bundle ChimeraX-ISOLDE's module: The 'ChimeraX- Clipper~=0.18.0' distribution was not found and is required by ChimeraX-ISOLDE chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: Error importing bundle ChimeraX-ISOLDE's module: The 'ChimeraX- Clipper~=0.18.0' distribution was not found and is required by ChimeraX-ISOLDE File ""/Users/anthonyrish/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py"", line 564, in start_tool raise ToolshedError( See log for complete Python traceback. OpenGL version: 4.1 ATI-4.9.51 OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0) OS Loader Version: 564.40.4~66 Software: System Software Overview: System Version: macOS 13.2 (22D49) Kernel Version: Darwin 22.3.0 Time since boot: 2 days, 22 hours, 39 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5300M: Chipset Model: AMD Radeon Pro 5300M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0043 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32207P1-020 Option ROM Version: 113-D32207P1-020 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.4 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect assigned normal Tool Shed Greg Couch all ChimeraX