![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Last modified 3 years ago
#8567 assigned defect
Clipper missing
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Tool Shed | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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
<https://github.com/pypa/pip/issues/10151>
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
<https://github.com/pypa/pip/issues/10151>
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
<https://github.com/pypa/pip/issues/10151>
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
<https://github.com/pypa/pip/issues/10151>
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
<https://github.com/pypa/pip/issues/10151>
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
<https://github.com/pypa/pip/issues/10151>
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 "<frozen importlib._bootstrap>", line 1030, in _gcd_import
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 850, in exec_module
File "<frozen importlib._bootstrap>", 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 <module>
__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 "<frozen importlib._bootstrap>", line 1030, in _gcd_import
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 850, in exec_module
File "<frozen importlib._bootstrap>", 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 <module>
__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 <lambda>
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
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Tool Shed |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Clipper missing |
comment:2 by , 3 years ago
This is very confusing - it looks like the Toolshed has installed ISOLDE without automatically installing Clipper first. Clipper is declared as a dependency in the bundle_info.xml and to my knowledge this has always worked correctly in the past... Clipper 0.18.0 for MacOS is on the Toolshed, so you could always install it manually in the same way you installed ISOLDE (I should also mention that there are newer Clipper/ISOLDE versions available both for ChimeraX 1.5 and the 1.6 daily builds, so it might be worth updating). That should take care of your immediate problem, but I'm still concerned about how this happened in the first place.
Note:
See TracTickets
for help on using tickets.
Reported by Anthony Rish