![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#7189 closed defect (fixed)
Coulombic: No module named 'chimerax.atom_search_lib'
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface/Binding Analysis | Version: | |
| Keywords: | Cc: | ||
| 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.dev202203030220 (2022-03-03 02:20:09 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.4.dev202203030220 (2022-03-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/egelmanlab01/Documents/milano/base_plate/cryosparc_P101_J258_002_volume_map_sharp_WIN480.mrc
Opened cryosparc_P101_J258_002_volume_map_sharp_WIN480.mrc as #1, grid size
480,480,480, pixel 1.08, shown at level 0.239, step 2, values float32
> open
> /Users/egelmanlab01/Documents/milano/base_plate/cryosparc_P101_J257_005_volume_map_sharp.mrc
Opened cryosparc_P101_J257_005_volume_map_sharp.mrc as #2, grid size
768,768,768, pixel 1.08, shown at step 1, values float32
> volume #2 region 0,0,0,767,767,767 step 4
[Repeated 1 time(s)]
> volume #2 change image level -0.055,0 level 0.2541,0.8 level 0.9056,1
> volume #2 step 1
> hide #!1 models
> volume #2 color darkgrey
> volume #2 level 0.2
> volume #2 level 0.25
> hide #!1 models
> view #1 clip false
No displayed objects specified.
> view #1 clip false
No displayed objects specified.
> select add #2
3 models selected
> view #1 clip false
No displayed objects specified.
> view #1 clip false
No displayed objects specified.
> close #1
> view clip false
> select clear
> ui tool show "Side View"
> open
> /Users/egelmanlab01/Documents/milano/ravi2/A0A482MFZ0_unrelaxed_rank_1_model_3.pdb
Chain information for A0A482MFZ0_unrelaxed_rank_1_model_3.pdb #1
---
Chain | Description
A | No description available
> view clip false
Drag select of 188 residues
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,559.18,0,1,0,156.44,0,0,1,218.9
> view matrix models #1,1,0,0,553.46,0,1,0,436.74,0,0,1,647.38
> view matrix models #1,1,0,0,463.1,0,1,0,440.93,0,0,1,667.14
> view matrix models
> #1,-0.61549,-0.34053,-0.71078,461.01,0.10383,0.85895,-0.50142,443.37,0.78127,-0.38242,-0.49332,675.9
> view matrix models
> #1,-0.61549,-0.34053,-0.71078,425.15,0.10383,0.85895,-0.50142,460.83,0.78127,-0.38242,-0.49332,678.91
> view matrix models
> #1,-0.61549,-0.34053,-0.71078,404.38,0.10383,0.85895,-0.50142,433.12,0.78127,-0.38242,-0.49332,733.02
> view matrix models
> #1,-0.61549,-0.34053,-0.71078,427.26,0.10383,0.85895,-0.50142,379.36,0.78127,-0.38242,-0.49332,637.45
> view matrix models
> #1,-0.61549,-0.34053,-0.71078,425.72,0.10383,0.85895,-0.50142,357.8,0.78127,-0.38242,-0.49332,598.88
> view matrix models
> #1,-0.61549,-0.34053,-0.71078,409.5,0.10383,0.85895,-0.50142,376.58,0.78127,-0.38242,-0.49332,602.12
> view matrix models
> #1,-0.61549,-0.34053,-0.71078,406.31,0.10383,0.85895,-0.50142,362.67,0.78127,-0.38242,-0.49332,568.2
> view matrix models
> #1,-0.61549,-0.34053,-0.71078,397.94,0.10383,0.85895,-0.50142,362.32,0.78127,-0.38242,-0.49332,552.56
> volume #2 level 0.3
> volume #2 level 0.23
> view matrix models
> #1,-0.61549,-0.34053,-0.71078,399.83,0.10383,0.85895,-0.50142,361.38,0.78127,-0.38242,-0.49332,549.29
> view matrix models
> #1,-0.61549,-0.34053,-0.71078,397.63,0.10383,0.85895,-0.50142,362.02,0.78127,-0.38242,-0.49332,535.24
> view matrix models
> #1,-0.61549,-0.34053,-0.71078,408.04,0.10383,0.85895,-0.50142,406.69,0.78127,-0.38242,-0.49332,532.83
> view matrix models
> #1,-0.65542,-0.32475,-0.68188,407.76,0.10217,0.85642,-0.50608,406.7,0.74833,-0.40136,-0.52813,532.89
> view matrix models
> #1,-0.65542,-0.32475,-0.68188,400.87,0.10217,0.85642,-0.50608,417.78,0.74833,-0.40136,-0.52813,523.87
> view matrix models
> #1,-0.82484,-0.24563,-0.50922,399.49,0.1196,0.8045,-0.58178,418.24,0.55257,-0.54078,-0.63421,523.97
> view matrix models
> #1,-0.82484,-0.24563,-0.50922,409.35,0.1196,0.8045,-0.58178,418.12,0.55257,-0.54078,-0.63421,526.31
> view matrix models
> #1,-0.64897,-0.29482,-0.70137,410.73,0.11949,0.87093,-0.47666,417.57,0.75137,-0.39315,-0.52998,526.2
> view matrix models
> #1,-0.68931,-0.30008,-0.65939,410.47,0.19457,0.80006,-0.56749,418.34,0.69785,-0.51948,-0.4931,526.26
> view matrix models
> #1,-0.68931,-0.30008,-0.65939,416.02,0.19457,0.80006,-0.56749,416.6,0.69785,-0.51948,-0.4931,525.81
> view matrix models
> #1,-0.68931,-0.30008,-0.65939,413.7,0.19457,0.80006,-0.56749,416.61,0.69785,-0.51948,-0.4931,523.42
> view matrix models
> #1,-0.68931,-0.30008,-0.65939,411.83,0.19457,0.80006,-0.56749,416.07,0.69785,-0.51948,-0.4931,520.16
> view matrix models
> #1,-0.68931,-0.30008,-0.65939,409.4,0.19457,0.80006,-0.56749,409.83,0.69785,-0.51948,-0.4931,515.24
> view matrix models
> #1,-0.5733,-0.36494,-0.73358,410.23,0.19404,0.80939,-0.55429,409.76,0.79604,-0.46012,-0.39321,515.06
> volume zone #2 nearAtoms sel & #1 range 6.48
> volume zone #2 nearAtoms sel & #1 range 15
> view matrix models
> #1,-0.79105,-0.42527,-0.43976,408.68,-0.079921,0.78453,-0.61491,409.1,0.60651,-0.45128,-0.65459,515.27
> view matrix models
> #1,-0.79105,-0.42527,-0.43976,404.56,-0.079921,0.78453,-0.61491,417.74,0.60651,-0.45128,-0.65459,507.62
> view matrix models
> #1,-0.79105,-0.42527,-0.43976,410.74,-0.079921,0.78453,-0.61491,415.36,0.60651,-0.45128,-0.65459,506.42
> volume zone #2 nearAtoms sel & #1 range 15
> view matrix models
> #1,0.95396,-0.014325,0.2996,412.97,0.18509,0.8141,-0.55044,415.96,-0.23601,0.58055,0.77927,495.77
> view matrix models
> #1,0.95396,-0.014325,0.2996,413.08,0.18509,0.8141,-0.55044,415.82,-0.23601,0.58055,0.77927,489.77
> view matrix models
> #1,0.79652,0.5931,-0.11739,412.19,-0.49407,0.5266,-0.6918,414.83,-0.34849,0.60904,0.71248,489.53
> view matrix models
> #1,-0.073465,0.97343,-0.2169,408.48,-0.9955,-0.084613,-0.042558,412.73,-0.059779,0.21279,0.97527,490.78
> view matrix models
> #1,-0.073465,0.97343,-0.2169,411.36,-0.9955,-0.084613,-0.042558,430.62,-0.059779,0.21279,0.97527,483.97
> view matrix models
> #1,0.84976,0.17839,0.49607,414.39,0.099468,0.86984,-0.4832,433.03,-0.5177,0.45995,0.72141,482.56
> view matrix models
> #1,0.84976,0.17839,0.49607,415.4,0.099468,0.86984,-0.4832,443.15,-0.5177,0.45995,0.72141,493.43
Drag select of 2 residues
> select /A:81
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models
> #1,-0.93504,-0.331,-0.12705,412.93,0.20812,-0.80253,0.55914,444.86,-0.28704,0.49638,0.81928,493.78
> view matrix models
> #1,-0.93504,-0.331,-0.12705,416.99,0.20812,-0.80253,0.55914,428.17,-0.28704,0.49638,0.81928,494.88
> view matrix models
> #1,-0.7503,-0.30727,-0.58535,419.09,0.06814,-0.91665,0.39384,428.59,-0.65758,0.25562,0.7087,494.7
> volume #2 level 0.2
> view matrix models
> #1,-0.7503,-0.30727,-0.58535,412.65,0.06814,-0.91665,0.39384,417.4,-0.65758,0.25562,0.7087,487.04
> view matrix models
> #1,-0.8359,-0.52282,-0.16712,411.58,0.36148,-0.75349,0.54916,417.4,-0.41304,0.39863,0.81884,487.08
> view matrix models
> #1,-0.8359,-0.52282,-0.16712,412.93,0.36148,-0.75349,0.54916,420.86,-0.41304,0.39863,0.81884,487.8
> view matrix models
> #1,-0.8485,-0.33514,-0.40955,413.16,0.085335,-0.85043,0.51912,420.3,-0.52227,0.40553,0.75019,487.64
> volume zone #2 nearAtoms sel & #1 range 20
> select clear
> volume zone #2 nearAtoms sel & #1 range 20
no atoms specified for zone
> volume zone #2 nearAtoms sel & #1 range 20
no atoms specified for zone
> select add #1
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> volume zone #2 nearAtoms sel & #1 range 20
> view matrix models
> #1,-0.8485,-0.33514,-0.40955,443.91,0.085335,-0.85043,0.51912,393.5,-0.52227,0.40553,0.75019,505.84
> view matrix models
> #1,-0.8485,-0.33514,-0.40955,424.15,0.085335,-0.85043,0.51912,412.38,-0.52227,0.40553,0.75019,541.42
> open
> /Users/egelmanlab01/Documents/milano/ravi2/A0A482MF80_unrelaxed_rank_1_model_3.pdb
Chain information for A0A482MF80_unrelaxed_rank_1_model_3.pdb #3
---
Chain | Description
A | No description available
> view clip false
Drag select of 83 residues
> view matrix models #3,1,0,0,162.42,0,1,0,493.41,0,0,1,479.71
> hide #3 models
> open
> /Users/egelmanlab01/Documents/milano/ravi2/A0A482MFQ0_unrelaxed_rank_1_model_3.pdb
Chain information for A0A482MFQ0_unrelaxed_rank_1_model_3.pdb #4
---
Chain | Description
A | No description available
> view clip false
Drag select of 24 residues
> view matrix models #4,1,0,0,436.52,0,1,0,322.61,0,0,1,540.84
> view matrix models
> #4,-0.38792,-0.47171,-0.79184,441.53,-0.75866,-0.32446,0.56495,319.1,-0.52341,0.81989,-0.232,548.58
> view matrix models
> #4,-0.38792,-0.47171,-0.79184,465.55,-0.75866,-0.32446,0.56495,365.57,-0.52341,0.81989,-0.232,522.58
> view matrix models
> #4,-0.38792,-0.47171,-0.79184,414.36,-0.75866,-0.32446,0.56495,416.21,-0.52341,0.81989,-0.232,526.32
> view matrix models
> #4,-0.38792,-0.47171,-0.79184,415.28,-0.75866,-0.32446,0.56495,412.05,-0.52341,0.81989,-0.232,522.16
> volume zone #2 nearAtoms #4 range 20
> view matrix models
> #4,-0.38792,-0.47171,-0.79184,449.44,-0.75866,-0.32446,0.56495,367.91,-0.52341,0.81989,-0.232,545.5
> view matrix models
> #4,-0.38792,-0.47171,-0.79184,408.03,-0.75866,-0.32446,0.56495,394.46,-0.52341,0.81989,-0.232,546.97
> view matrix models
> #4,-0.38792,-0.47171,-0.79184,408.95,-0.75866,-0.32446,0.56495,404.83,-0.52341,0.81989,-0.232,529.61
> view matrix models
> #4,0.13263,-0.95229,0.27488,403.16,0.98617,0.098968,-0.13298,398.18,0.099429,0.28872,0.95224,522.96
> view matrix models
> #4,0.13263,-0.95229,0.27488,394.86,0.98617,0.098968,-0.13298,388.88,0.099429,0.28872,0.95224,546.36
> view matrix models
> #4,-0.76655,-0.56945,0.29686,401.74,-0.64212,0.6863,-0.34159,400.83,-0.0092131,-0.45246,-0.89174,543.47
> view matrix models
> #4,-0.76655,-0.56945,0.29686,402.87,-0.64212,0.6863,-0.34159,403.09,-0.0092131,-0.45246,-0.89174,538.7
> volume zone #2 nearAtoms #4 range 10
[Repeated 1 time(s)]
> view matrix models
> #4,-0.76655,-0.56945,0.29686,403.79,-0.64212,0.6863,-0.34159,406.3,-0.0092131,-0.45246,-0.89174,532.67
> volume zone #2 nearAtoms #4 range 10
> view matrix models
> #4,-0.76655,-0.56945,0.29686,401.52,-0.64212,0.6863,-0.34159,408.57,-0.0092131,-0.45246,-0.89174,531.45
> volume zone #2 nearAtoms #4 range 10
> view matrix models
> #4,-0.74612,-0.64707,-0.15687,401.27,-0.61272,0.75948,-0.21854,408.96,0.26055,-0.066941,-0.96314,530.85
> view matrix models
> #4,-0.74612,-0.64707,-0.15687,408.9,-0.61272,0.75948,-0.21854,409.63,0.26055,-0.066941,-0.96314,525.05
> volume zone #2 nearAtoms #4 range 15
> view matrix models
> #4,-0.74612,-0.64707,-0.15687,409.62,-0.61272,0.75948,-0.21854,409.29,0.26055,-0.066941,-0.96314,531.22
> volume zone #2 nearAtoms #4 range 15
> view matrix models
> #4,-0.74612,-0.64707,-0.15687,411.01,-0.61272,0.75948,-0.21854,408.91,0.26055,-0.066941,-0.96314,532.69
> volume zone #2 nearAtoms #4 range 15
> volume zone #2 nearAtoms #4 range 14
> volume zone #2 nearAtoms #4 range 14.5
> view matrix models
> #4,-0.74612,-0.64707,-0.15687,411.05,-0.61272,0.75948,-0.21854,408.31,0.26055,-0.066941,-0.96314,530.13
> volume zone #2 nearAtoms #4 range 15
> view matrix models
> #4,-0.74612,-0.64707,-0.15687,408.16,-0.61272,0.75948,-0.21854,407.36,0.26055,-0.066941,-0.96314,527.5
> view matrix models
> #4,-0.74612,-0.64707,-0.15687,405.64,-0.61272,0.75948,-0.21854,408.28,0.26055,-0.066941,-0.96314,520.99
> view matrix models
> #4,-0.44577,-0.88875,-0.10684,402.69,-0.55513,0.36811,-0.74587,405.99,0.70222,-0.27318,-0.65746,517.41
> view matrix models
> #4,-0.44577,-0.88875,-0.10684,410.68,-0.55513,0.36811,-0.74587,411.54,0.70222,-0.27318,-0.65746,510.25
> view matrix models
> #4,-0.51984,-0.85328,-0.041114,411.24,-0.61471,0.40705,-0.6756,412.05,0.59321,-0.32593,-0.73612,510.56
> view matrix models
> #4,-0.49487,-0.86514,-0.081472,411.06,-0.60795,0.41169,-0.6789,412.04,0.62089,-0.28644,-0.72969,510.63
> view matrix models
> #4,-0.49487,-0.86514,-0.081472,412.39,-0.60795,0.41169,-0.6789,412.93,0.62089,-0.28644,-0.72969,510.03
> view matrix models
> #4,-0.49487,-0.86514,-0.081472,412.07,-0.60795,0.41169,-0.6789,414.49,0.62089,-0.28644,-0.72969,520.34
> view matrix models
> #4,-0.49213,-0.86915,-0.048893,412.44,-0.58269,0.37061,-0.72327,414.31,0.64675,-0.32745,-0.68883,519.78
> view matrix models
> #4,-0.49213,-0.86915,-0.048893,412.93,-0.58269,0.37061,-0.72327,414.65,0.64675,-0.32745,-0.68883,519.54
> volume zone #2 nearAtoms #4 range 15
> view matrix models
> #4,-0.49213,-0.86915,-0.048893,427.99,-0.58269,0.37061,-0.72327,389.73,0.64675,-0.32745,-0.68883,507.07
> volume #2 level 0.22
> volume #2 level 0.2
> volume #2 level 0.24
> close#3-4
Unknown command: close#3-4
> close#3-4
Unknown command: close#3-4
> close#3-4
Unknown command: close#3-4
> hide #4 models
> select add #4
299 atoms, 301 bonds, 42 residues, 1 model selected
> select subtract #4
Nothing selected
> volume #2 level 0.28
> select #1/A:28
10 atoms, 10 bonds, 1 residue, 1 model selected
> view matrix models
> #1,-0.8485,-0.33514,-0.40955,433.53,0.085335,-0.85043,0.51912,389.58,-0.52227,0.40553,0.75019,544.32
> volume #2 level 0.25
> volume #2 level 0.3
> view matrix models
> #1,-0.8485,-0.33514,-0.40955,420.52,0.085335,-0.85043,0.51912,398,-0.52227,0.40553,0.75019,521.52
> view matrix models
> #1,-0.8485,-0.33514,-0.40955,420.76,0.085335,-0.85043,0.51912,393.22,-0.52227,0.40553,0.75019,506.06
> view matrix models
> #1,-0.8485,-0.33514,-0.40955,417.83,0.085335,-0.85043,0.51912,393.87,-0.52227,0.40553,0.75019,496.62
> view matrix models
> #1,-0.8485,-0.33514,-0.40955,415.16,0.085335,-0.85043,0.51912,392.63,-0.52227,0.40553,0.75019,481.77
> volume #2 level 0.23
> select clear
> select #1/A:168
10 atoms, 10 bonds, 1 residue, 1 model selected
> view matrix models
> #1,-0.82243,-0.51519,0.24123,413.59,0.46447,-0.85297,-0.23814,396.46,0.32845,-0.083811,0.9408,485.42
> view matrix models
> #1,-0.82243,-0.51519,0.24123,387.39,0.46447,-0.85297,-0.23814,431.99,0.32845,-0.083811,0.9408,506.25
> view matrix models
> #1,-0.82243,-0.51519,0.24123,396.95,0.46447,-0.85297,-0.23814,445.27,0.32845,-0.083811,0.9408,508.35
> view matrix models
> #1,-0.70372,-0.55087,0.44869,396.76,0.48537,-0.83394,-0.26262,445.37,0.51885,0.032969,0.85423,508.94
> view matrix models
> #1,-0.70372,-0.55087,0.44869,397.33,0.48537,-0.83394,-0.26262,446.1,0.51885,0.032969,0.85423,509.67
> view matrix models
> #1,-0.72416,-0.53251,0.4382,397.24,0.47143,-0.84602,-0.24902,446.04,0.50333,0.026255,0.86369,509.6
> view matrix models
> #1,-0.71738,-0.54837,0.42973,397.34,0.49926,-0.83485,-0.23189,446.05,0.48592,0.048194,0.87268,509.45
> view matrix models
> #1,-0.9002,-0.39012,-0.1935,398.36,0.42518,-0.88344,-0.19687,445.82,-0.09414,-0.25949,0.96115,508.08
> view matrix models
> #1,-0.9002,-0.39012,-0.1935,397.33,0.42518,-0.88344,-0.19687,447.05,-0.09414,-0.25949,0.96115,501.2
> view matrix models
> #1,-0.71765,-0.64782,0.25555,397.18,0.46452,-0.71869,-0.51741,447.78,0.51885,-0.25261,0.81669,503.74
> view matrix models
> #1,-0.71765,-0.64782,0.25555,402.1,0.46452,-0.71869,-0.51741,448.29,0.51885,-0.25261,0.81669,518.11
> view matrix models
> #1,-0.71765,-0.64782,0.25555,404.14,0.46452,-0.71869,-0.51741,447.1,0.51885,-0.25261,0.81669,518.5
> view matrix models
> #1,-0.71765,-0.64782,0.25555,404.87,0.46452,-0.71869,-0.51741,453,0.51885,-0.25261,0.81669,517.06
> view matrix models
> #1,-0.71765,-0.64782,0.25555,404.53,0.46452,-0.71869,-0.51741,456.09,0.51885,-0.25261,0.81669,517.88
> view matrix models
> #1,-0.71765,-0.64782,0.25555,412.45,0.46452,-0.71869,-0.51741,477.74,0.51885,-0.25261,0.81669,525.76
> open
> /Users/egelmanlab01/Documents/milano/base_plate/J190-WINregion_65366.mrc
Opened J190-WINregion_65366.mrc as #5, grid size 62,101,83, pixel
1.08,1.08,1.08, shown at level 0.46, step 1, values float32
> select add #1
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #5
2 models selected
> view clip false
> close#5
Unknown command: close#5
> close #5
> open
> /Users/egelmanlab01/Documents/milano/base_plate/cryosparc_P101_J190_003_volume_map_sharp-
> WINDOWED.mrc
Opened cryosparc_P101_J190_003_volume_map_sharp-WINDOWED.mrc as #5, grid size
448,448,448, pixel 1.08, shown at level 0.29, step 2, values float32
> volume #5 step 1
> close #5
> open
> /Users/egelmanlab01/Documents/milano/base_plate/cryosparc_P101_J258_002_volume_map_sharp_WIN480.mrc
Opened cryosparc_P101_J258_002_volume_map_sharp_WIN480.mrc as #5, grid size
480,480,480, pixel 1.08, shown at level 0.239, step 2, values float32
> volume #5 step 1
> view clip false
> hide #!2 models
> hide #1 models
> view clip false
> volume #5 level 0.25
> volume #2 level 0.15
> volume #5 level 0.3
> volume #5 level 0.2592
> volume #5 level 0.28
> volume #5 level 0.23
> volume #5 color #929000
> volume #5 color #fffb00
> volume #5 color #945200
> volume #5 color darkgrey
> open
> /Users/egelmanlab01/Documents/milano/ravi2/A0A482MHK7_unrelaxed_rank_1_model_3.pdb
Chain information for A0A482MHK7_unrelaxed_rank_1_model_3.pdb #6
---
Chain | Description
A | No description available
> view clip false
> select add #6
448 atoms, 457 bonds, 55 residues, 1 model selected
> view clip false
> hide #!5 models
> show #!5 models
> view matrix models #6,1,0,0,-25.766,0,1,0,1.1501,0,0,1,83.162
> color #6 #ff9300 transparency 0
> view matrix models #6,1,0,0,-35.585,0,1,0,-4.2844,0,0,1,93.703
> view matrix models #6,1,0,0,-33.983,0,1,0,4.6088,0,0,1,100.79
> view matrix models
> #6,-0.14373,-0.71949,0.67946,-23.655,0.36393,0.60005,0.71238,0.69683,-0.92027,0.34967,0.1756,110.02
> view matrix models
> #6,-0.14373,-0.71949,0.67946,-15.371,0.36393,0.60005,0.71238,8.009,-0.92027,0.34967,0.1756,115.96
> view matrix models
> #6,0.10361,-0.53464,0.8387,-17.664,0.96859,0.24587,0.037077,2.1714,-0.22603,0.80852,0.54333,109.5
> view matrix models
> #6,0.10361,-0.53464,0.8387,-4.9673,0.96859,0.24587,0.037077,5.1564,-0.22603,0.80852,0.54333,113.79
> view matrix models
> #6,0.10361,-0.53464,0.8387,0.56456,0.96859,0.24587,0.037077,-0.40273,-0.22603,0.80852,0.54333,117.31
> view matrix models
> #6,0.3401,-0.46819,0.81555,-1.6517,0.8638,0.49834,-0.074127,0.78547,-0.37172,0.72969,0.57391,118.65
> view matrix models
> #6,0.3401,-0.46819,0.81555,-1.3917,0.8638,0.49834,-0.074127,-0.5241,-0.37172,0.72969,0.57391,115.85
> view matrix models
> #6,0.3862,-0.39297,0.83452,-1.7909,0.79706,0.59753,-0.087482,0.17988,-0.46428,0.69895,0.54399,116.73
> view matrix models
> #6,0.3862,-0.39297,0.83452,-1.332,0.79706,0.59753,-0.087482,-0.75593,-0.46428,0.69895,0.54399,115.3
> view matrix models
> #6,0.38384,-0.47959,0.78909,-1.3518,0.69411,0.71344,0.095984,0.25531,-0.609,0.51087,0.60673,116.55
> view matrix models
> #6,0.38384,-0.47959,0.78909,-3.2319,0.69411,0.71344,0.095984,-1.9325,-0.609,0.51087,0.60673,115.87
> view matrix models
> #6,0.42125,-0.51991,0.74313,-3.6035,0.79376,0.60773,-0.024764,-2.9217,-0.43874,0.6003,0.66869,114.28
> view matrix models
> #6,0.13603,-0.48114,0.86602,-0.88043,0.92754,0.36899,0.059315,-4.3719,-0.3481,0.7952,0.49647,113.58
> view matrix models
> #6,0.13603,-0.48114,0.86602,-4.8487,0.92754,0.36899,0.059315,-2.6672,-0.3481,0.7952,0.49647,115.94
> view matrix models
> #6,0.13603,-0.48114,0.86602,-15.97,0.92754,0.36899,0.059315,-9.4834,-0.3481,0.7952,0.49647,128.02
> view matrix models
> #6,-0.62689,-0.46786,0.62299,-8.598,0.73455,-0.088396,0.67277,-8.0758,-0.25969,0.87937,0.39908,127.25
> view matrix models
> #6,-0.62689,-0.46786,0.62299,-1.8234,0.73455,-0.088396,0.67277,-3.8479,-0.25969,0.87937,0.39908,118.17
> view matrix models
> #6,-0.56908,-0.66178,0.48806,-2.4634,0.71466,-0.10449,0.69162,-3.6723,-0.4067,0.74238,0.53241,119.46
> view matrix models
> #6,-0.56908,-0.66178,0.48806,1.5398,0.71466,-0.10449,0.69162,-5.0428,-0.4067,0.74238,0.53241,116.95
> view matrix models
> #6,-0.61445,-0.68726,0.38746,1.9835,0.63521,-0.13967,0.7596,-4.3214,-0.46793,0.71285,0.52238,117.52
> close #6
> show #!2 models
> hide #!5 models
> view clip false
> volume #2 level 0.2
> volume #2 level 0.22
> volume #2 level 0.25
> open
> /Users/egelmanlab01/Documents/milano/ravi2/A0A482MFT5_unrelaxed_rank_1_model_3.pdb
Chain information for A0A482MFT5_unrelaxed_rank_1_model_3.pdb #6
---
Chain | Description
A | No description available
> view clip false
Drag select of 11 residues
> view matrix models #6,1,0,0,59.636,0,1,0,484.2,0,0,1,486.07
> view matrix models #6,1,0,0,368.98,0,1,0,373.46,0,0,1,501.73
> view matrix models #6,1,0,0,378.42,0,1,0,410.97,0,0,1,515.26
> color #6 #941100 transparency 0
> color #6 #ff2600 transparency 0
> view matrix models
> #6,-0.78042,0.029055,-0.62458,387.92,0.047709,-0.99324,-0.10582,418.08,-0.62344,-0.11238,0.77376,519.04
> view matrix models
> #6,-0.6465,-0.70965,-0.28005,388.2,0.60531,-0.70057,0.37789,412.63,-0.46436,0.074791,0.88248,517.29
> view matrix models
> #6,-0.6465,-0.70965,-0.28005,401.18,0.60531,-0.70057,0.37789,393.97,-0.46436,0.074791,0.88248,515.18
> view matrix models
> #6,-0.6465,-0.70965,-0.28005,417.86,0.60531,-0.70057,0.37789,405.52,-0.46436,0.074791,0.88248,511.35
> view matrix models
> #6,-0.6465,-0.70965,-0.28005,418.85,0.60531,-0.70057,0.37789,404.48,-0.46436,0.074791,0.88248,511.14
> view matrix models
> #6,-0.81537,0.53664,-0.21723,414.93,0.23962,0.6544,0.71718,399.51,0.52702,0.53272,-0.66217,513.76
> view matrix models
> #6,-0.80672,0.4715,-0.35621,415.82,-0.15986,-0.75445,-0.63659,412.53,-0.5689,-0.45661,0.68401,514.32
> view matrix models
> #6,-0.80672,0.4715,-0.35621,395.36,-0.15986,-0.75445,-0.63659,437.16,-0.5689,-0.45661,0.68401,528.15
> view matrix models
> #6,-0.84449,-0.014671,-0.53536,398.04,0.26367,-0.88148,-0.39176,434.82,-0.46617,-0.47199,0.74827,527.51
> view matrix models
> #6,-0.62443,-0.35527,-0.69561,397.69,0.50281,-0.86434,-0.0099129,431.59,-0.59772,-0.35595,0.71835,528.16
> view matrix models
> #6,-0.48116,-0.55664,-0.67723,397.76,0.67863,-0.72555,0.1142,429.86,-0.55493,-0.40464,0.72685,528.12
> view matrix models
> #6,-0.48116,-0.55664,-0.67723,411,0.67863,-0.72555,0.1142,434.72,-0.55493,-0.40464,0.72685,538.07
> view matrix models
> #6,-0.0026144,-0.99453,-0.10439,407.86,0.99933,0.0012205,-0.036657,431.85,0.036584,-0.10441,0.99386,533.57
> view matrix models
> #6,-0.0026144,-0.99453,-0.10439,415.97,0.99933,0.0012205,-0.036657,413.67,0.036584,-0.10441,0.99386,537.66
> view matrix models
> #6,-0.0026144,-0.99453,-0.10439,414,0.99933,0.0012205,-0.036657,412.86,0.036584,-0.10441,0.99386,536.95
> view matrix models
> #6,-0.27553,-0.7713,-0.57374,416.6,0.95924,-0.18162,-0.2165,414.53,0.062784,-0.61001,0.7899,539.59
> view matrix models
> #6,-0.27553,-0.7713,-0.57374,411.58,0.95924,-0.18162,-0.2165,407.07,0.062784,-0.61001,0.7899,535.12
> view matrix models
> #6,-0.27553,-0.7713,-0.57374,408.45,0.95924,-0.18162,-0.2165,407.36,0.062784,-0.61001,0.7899,536.46
> view matrix models
> #6,0.54872,0.78609,0.28454,395.88,-0.16033,0.43299,-0.88703,412.71,-0.82049,0.44111,0.36362,538.25
> view matrix models
> #6,0.54775,0.7863,0.28584,395.88,-0.15877,0.43314,-0.88723,412.71,-0.82144,0.4406,0.3621,538.26
> view matrix models
> #6,0.096423,0.81937,0.5651,396,-0.13551,0.57326,-0.80809,411.75,-0.98607,0.0013423,0.16631,541.33
> view matrix models
> #6,0.096423,0.81937,0.5651,410.32,-0.13551,0.57326,-0.80809,401.94,-0.98607,0.0013423,0.16631,535.79
> view matrix models
> #6,0.096423,0.81937,0.5651,409.23,-0.13551,0.57326,-0.80809,407.07,-0.98607,0.0013423,0.16631,529.66
> view matrix models
> #6,-0.0047763,0.45442,0.89078,409.21,-0.29629,0.85014,-0.43528,404.84,-0.95509,-0.26601,0.13058,530.66
> view matrix models
> #6,-0.0047763,0.45442,0.89078,412.78,-0.29629,0.85014,-0.43528,403.14,-0.95509,-0.26601,0.13058,534.51
> view matrix models
> #6,-0.24894,0.72404,0.64327,414,-0.56619,0.43007,-0.70318,406.88,-0.78578,-0.53927,0.30288,533.95
> hide #!2 models
> show #!2 models
> volume #2 level 0.24
> volume #2 level 0.27
> view matrix models
> #6,0.10448,-0.99415,0.027335,421.62,0.058202,-0.021327,-0.99808,407.63,0.99282,0.10587,0.055633,526.56
> view matrix models
> #6,0.10448,-0.99415,0.027335,418.29,0.058202,-0.021327,-0.99808,420.36,0.99282,0.10587,0.055633,518.89
> view matrix models
> #6,0.10448,-0.99415,0.027335,417.9,0.058202,-0.021327,-0.99808,429.5,0.99282,0.10587,0.055633,531.98
> view matrix models
> #6,0.10448,-0.99415,0.027335,400.42,0.058202,-0.021327,-0.99808,427.57,0.99282,0.10587,0.055633,530.27
> view matrix models
> #6,-0.33398,-0.92991,0.15406,401.15,0.0074257,-0.16603,-0.98609,428.19,0.94255,-0.32819,0.062356,531.88
Drag select of 3 residues
> view matrix models
> #6,-0.73602,-0.61871,0.27471,400.95,-0.11838,-0.28192,-0.95211,428.86,0.66653,-0.73329,0.13425,533.89
> view matrix models
> #6,-0.93108,-0.13445,0.33915,399.7,-0.28411,-0.31594,-0.90524,429.34,0.22886,-0.9392,0.25597,535.57
> view matrix models
> #6,-0.98673,0.15822,0.036575,400.43,0.15383,0.83845,0.52281,416.67,0.052054,0.5215,-0.85166,536.83
> view matrix models
> #6,0.012282,-0.18512,-0.98264,403.09,-0.26313,0.94748,-0.18178,421.36,0.96468,0.26079,-0.037072,530.31
> view matrix models
> #6,0.012282,-0.18512,-0.98264,409.9,-0.26313,0.94748,-0.18178,417.32,0.96468,0.26079,-0.037072,517.08
> view matrix models
> #6,0.012282,-0.18512,-0.98264,411.29,-0.26313,0.94748,-0.18178,410.88,0.96468,0.26079,-0.037072,516.84
> view matrix models
> #6,-0.17599,0.43499,-0.88307,409.38,-0.12076,0.88075,0.45792,407.37,0.97696,0.18723,-0.10247,517.38
> view matrix models
> #6,0.16483,-0.98363,-0.072825,408.87,-0.96785,-0.14708,-0.20403,417.25,0.18998,0.10411,-0.97625,524.9
> view matrix models
> #6,0.16483,-0.98363,-0.072825,405.15,-0.96785,-0.14708,-0.20403,420.29,0.18998,0.10411,-0.97625,529.75
> view matrix models
> #6,0.6782,-0.66033,0.32249,400.2,-0.67919,-0.7308,-0.068056,420.53,0.28061,-0.17287,-0.94412,530.2
> view matrix models
> #6,0.6782,-0.66033,0.32249,398.62,-0.67919,-0.7308,-0.068056,424.98,0.28061,-0.17287,-0.94412,529.57
> view matrix models
> #6,0.82488,-0.44021,0.35466,397.18,-0.46605,-0.88464,-0.014078,424.46,0.31995,-0.15368,-0.93489,529.32
> view matrix models
> #6,0.82488,-0.44021,0.35466,397.5,-0.46605,-0.88464,-0.014078,424.23,0.31995,-0.15368,-0.93489,529.87
> view matrix models
> #6,0.82488,-0.44021,0.35466,397.4,-0.46605,-0.88464,-0.014078,424.39,0.31995,-0.15368,-0.93489,528.98
> view matrix models
> #6,0.58424,-0.78216,0.21654,400.13,-0.79832,-0.6019,-0.020194,424.67,0.14613,-0.16107,-0.97606,529.84
> view matrix models
> #6,0.58424,-0.78216,0.21654,400.01,-0.79832,-0.6019,-0.020194,423.99,0.14613,-0.16107,-0.97606,532.04
> view matrix models
> #6,0.73368,-0.66963,-0.11538,400.76,-0.66374,-0.66991,-0.33267,425.3,0.14547,0.32065,-0.93596,530.21
> view matrix models
> #6,0.7726,-0.63356,0.041141,399.71,-0.62626,-0.77114,-0.11461,424.41,0.10434,0.062781,-0.99256,531.52
> view matrix models
> #6,0.79907,-0.60116,-0.010116,399.76,-0.59088,-0.78208,-0.198,424.74,0.11111,0.16419,-0.98015,531.09
> show #3 models
> hide #3 models
> open
> /Users/egelmanlab01/Documents/milano/ravi2/A0A482MFZ0_unrelaxed_rank_1_model_3.pdb
Chain information for A0A482MFZ0_unrelaxed_rank_1_model_3.pdb #7
---
Chain | Description
A | No description available
> view clip false
> sym #7 C3
> select #8.2/A:80
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #8.1/A:123
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #8.1/A:123
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #8.1
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> view matrix models
> #8.1,0.65416,0.64068,0.402,-4.376,-0.71019,0.70313,0.035073,-1.6592,-0.26019,-0.30844,0.91497,0.29943
> color #8.2 #008f00 transparency 0
> color #8.3 #73fdff transparency 0
> select #8.1/A:32
4 atoms, 3 bonds, 1 residue, 1 model selected
> view matrix models
> #8.1,0.62144,0.55952,0.5484,-4.7428,-0.7056,0.70392,0.081377,-1.8014,-0.3405,-0.43752,0.83225,0.6796
> view matrix models
> #8.1,0.62144,0.55952,0.5484,-7.362,-0.7056,0.70392,0.081377,1.8858,-0.3405,-0.43752,0.83225,-2.196
> view matrix models
> #8.1,0.72454,0.49774,0.47676,-6.5938,-0.56841,0.82273,0.004892,2.2621,-0.38981,-0.27454,0.87902,-2.9921
> select up
50 atoms, 49 bonds, 8 residues, 1 model selected
> hide #!8 models
> hide #8.1 models
> hide #8.2 models
> hide #8.3 models
> select add #8
4371 atoms, 4467 bonds, 564 residues, 4 models selected
> select subtract #8.1
2914 atoms, 2978 bonds, 376 residues, 3 models selected
> select add #8
4371 atoms, 4467 bonds, 564 residues, 4 models selected
> select subtract #8.1
2914 atoms, 2978 bonds, 376 residues, 3 models selected
> select add #8
4371 atoms, 4467 bonds, 564 residues, 4 models selected
> view clip false
> volume #2 level 0.25
> volume #2 level 0.23
> show #7 models
> view clip false
Drag select of 57 residues
Drag select of 102 residues
> view matrix models #7,1,0,0,144.27,0,1,0,-74.994,0,0,1,472.06
> view matrix models #7,1,0,0,402.89,0,1,0,407.24,0,0,1,526.03
> view matrix models
> #7,0.80675,0.078489,0.58565,400.04,0.30401,0.79477,-0.52529,410.62,-0.50669,0.60182,0.61732,523.85
> view matrix models
> #7,0.80675,0.078489,0.58565,403.7,0.30401,0.79477,-0.52529,421.32,-0.50669,0.60182,0.61732,489.81
> view matrix models
> #7,0.80675,0.078489,0.58565,409.14,0.30401,0.79477,-0.52529,416.08,-0.50669,0.60182,0.61732,493.01
> hide #6 models
> view matrix models
> #7,0.80675,0.078489,0.58565,405.44,0.30401,0.79477,-0.52529,419.63,-0.50669,0.60182,0.61732,490.32
> view matrix models
> #7,0.80675,0.078489,0.58565,407.09,0.30401,0.79477,-0.52529,418.49,-0.50669,0.60182,0.61732,487.7
> select add #7
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> volume zone #2 nearAtoms sel & #7 range 6.48
> volume zone #2 nearAtoms sel & #7 range 15
> view matrix models
> #7,0.86478,-0.038512,0.50067,407.91,0.39408,0.66999,-0.62914,419.51,-0.31121,0.74137,0.59457,488.03
> view matrix models
> #7,0.86478,-0.038512,0.50067,410.97,0.39408,0.66999,-0.62914,425,-0.31121,0.74137,0.59457,491.6
Drag select of 2 cryosparc_P101_J257_005_volume_map_sharp.mrc , 2 residues
> select clear
> select #7/A:98
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #7/A:98
4 atoms, 3 bonds, 1 residue, 1 model selected
Drag select of 3 residues
> view matrix models
> #7,-0.92308,-0.36091,0.13293,407.09,0.38459,-0.86268,0.32845,426.2,-0.0038663,0.35431,0.93512,492.62
> view matrix models
> #7,-0.92308,-0.36091,0.13293,414.02,0.38459,-0.86268,0.32845,419.48,-0.0038663,0.35431,0.93512,494.91
> view matrix models
> #7,-0.61842,-0.78155,0.082073,416.44,0.67094,-0.47072,0.57294,418.49,-0.40915,0.40938,0.81548,493.78
> view matrix models
> #7,-0.61842,-0.78155,0.082073,440.41,0.67094,-0.47072,0.57294,405.7,-0.40915,0.40938,0.81548,503.02
> view matrix models
> #7,-0.61842,-0.78155,0.082073,433.04,0.67094,-0.47072,0.57294,418.17,-0.40915,0.40938,0.81548,495.14
> view matrix models
> #7,-0.66498,-0.73685,-0.12183,433.44,0.54119,-0.58782,0.60132,417.97,-0.5147,0.33394,0.78967,495.08
> view matrix models
> #7,-0.66498,-0.73685,-0.12183,430.35,0.54119,-0.58782,0.60132,421.74,-0.5147,0.33394,0.78967,495.68
> view matrix models
> #7,-0.66498,-0.73685,-0.12183,428.59,0.54119,-0.58782,0.60132,421.13,-0.5147,0.33394,0.78967,496.98
> view matrix models
> #7,0.78703,-0.28814,0.54549,429.96,0.41012,0.90491,-0.11373,418.76,-0.46085,0.31323,0.83036,497.08
> view matrix models
> #7,0.48472,-0.47654,0.73346,428.85,0.61603,0.78129,0.1005,419.1,-0.62094,0.40311,0.67226,496.81
> view matrix models
> #7,0.48472,-0.47654,0.73346,429.37,0.61603,0.78129,0.1005,415.88,-0.62094,0.40311,0.67226,495.45
> view matrix models
> #7,0.48472,-0.47654,0.73346,430.13,0.61603,0.78129,0.1005,419.29,-0.62094,0.40311,0.67226,502.35
> view matrix models
> #7,0.1591,-0.4312,0.88812,428.38,0.71821,0.66778,0.19556,419.65,-0.67739,0.60675,0.41594,502.43
> view matrix models
> #7,0.1591,-0.4312,0.88812,426.13,0.71821,0.66778,0.19556,414.98,-0.67739,0.60675,0.41594,487.45
> view matrix models
> #7,0.1591,-0.4312,0.88812,419.5,0.71821,0.66778,0.19556,415.45,-0.67739,0.60675,0.41594,489.61
> view matrix models
> #7,-0.55874,-0.79287,0.24322,420.28,0.67776,-0.26753,0.68489,416.38,-0.47796,0.54752,0.68686,489.55
> view matrix models
> #7,-0.55839,-0.79195,0.24702,420.27,0.67771,-0.26375,0.6864,416.36,-0.47844,0.55069,0.68399,489.55
> view matrix models
> #7,-0.55839,-0.79195,0.24702,419.31,0.67771,-0.26375,0.6864,417.32,-0.47844,0.55069,0.68399,489.17
> volume zone #2 nearAtoms sel & #7 range 15
> select clear
> select add #7
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> volume zone #2 nearAtoms sel & #7 range 15
> view matrix models
> #7,-0.65211,-0.75399,-0.079096,419.98,0.62622,-0.59451,0.50439,418.72,-0.42733,0.27939,0.85984,489.54
> view matrix models
> #7,-0.28425,-0.95422,0.093109,421.22,0.92058,-0.24451,0.30455,419.37,-0.26784,0.17228,0.94794,490.09
> view matrix models
> #7,0.1494,-0.95593,0.25275,422.16,0.96129,0.20028,0.18926,418.61,-0.23153,0.21469,0.94884,490.09
> view matrix models
> #7,0.1494,-0.95593,0.25275,424.71,0.96129,0.20028,0.18926,420.98,-0.23153,0.21469,0.94884,487.38
> view matrix models
> #7,-0.022826,-0.98137,0.19075,424.41,0.97167,0.023121,0.23522,421.37,-0.23525,0.19072,0.95304,487.42
> view matrix models
> #7,-0.071407,-0.97821,0.19495,424.22,0.97943,-0.031781,0.19928,421.68,-0.18874,0.20517,0.96036,487.51
> view matrix models
> #7,-0.23547,-0.96427,0.12142,423.88,0.92734,-0.18553,0.32499,421.52,-0.29085,0.18912,0.93789,487.29
> open /Users/egelmanlab01/Documents/milano/base_plate/allCombo_J190_1305.pdb
Chain information for allCombo_J190_1305.pdb #9
---
Chain | Description
0 0E 0J 0N 0S 0X 0c 0h 0m 5 u z | No description available
0A 0F 0O 0T 0Y 0d 0i 0n 1 6 q v | No description available
0B 0G 0K 0P 0U 0Z 0e 0j 2 7 r w | No description available
0C 0H 0L 0Q 0V 0a 0f 0k 3 8 s x | No description available
0D 0I 0M 0R 0W 0b 0g 0l 4 9 t y | No description available
0o 0p 0q | No description available
0r 0s 0t 0u 0v 0w j k l m n o | No description available
A P a d g p | No description available
B C D E F G | No description available
H I J K L M | No description available
N Q Y b e h | No description available
O R Z c f i | No description available
S T U V W X | No description available
> view clip false
> open
> /Users/egelmanlab01/Documents/milano/base_plate/baseplate/MFS1/GoodFit/MSF1_partial_fit_Map257.pdb
Chain information for MSF1_partial_fit_Map257.pdb #10
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
> view clip false
> hide #10 models
> show #10 models
> open
> /Users/egelmanlab01/Documents/milano/base_plate/baseplate/MFS1/GoodFit/MFS1_partial_good_baseFit-
> coot-0.pdb
Summary of feedback from opening
/Users/egelmanlab01/Documents/milano/base_plate/baseplate/MFS1/GoodFit/MFS1_partial_good_baseFit-
coot-0.pdb
---
warning | Start residue of secondary structure not found: SHEET 4 4 4 GLU B 56
ILE B 61 0
Chain information for MFS1_partial_good_baseFit-coot-0.pdb #11
---
Chain | Description
A | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
> hide target m
> show #11 models
> show #10 models
> open
> /Users/egelmanlab01/Documents/milano/base_plate/baseplate/MFS1/MFS1_baseFit.pdb
Chain information for MFS1_baseFit.pdb #12
---
Chain | Description
A | No description available
> hide #11 models
> hide #10 models
> open
> /Users/egelmanlab01/Documents/milano/base_plate/baseplate/MFQ9_398_baseFit.pdb
Summary of feedback from opening
/Users/egelmanlab01/Documents/milano/base_plate/baseplate/MFQ9_398_baseFit.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU A 76
GLN A 80 1 5
Start residue of secondary structure not found: HELIX 2 2 PHE B 27 ASP B 29 1
3
Start residue of secondary structure not found: HELIX 3 3 GLU B 32 LEU B 42 1
11
Start residue of secondary structure not found: HELIX 4 4 PRO B 47 ALA B 63 1
17
Start residue of secondary structure not found: HELIX 5 5 LEU B 78 ARG B 95 1
18
90 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (33 )
Cannot find LINK/SSBOND residue CYS (125 )
Cannot find LINK/SSBOND residue CYS (212 )
Cannot find LINK/SSBOND residue CYS (26 )
Cannot find LINK/SSBOND residue CYS (73 )
7 messages similar to the above omitted
Chain information for MFQ9_398_baseFit.pdb #13
---
Chain | Description
C | No description available
> hide #12 models
> open
> /Users/egelmanlab01/Documents/milano/base_plate/baseplate/MFQ9_138_baseFit.pdb
Chain information for MFQ9_138_baseFit.pdb #14
---
Chain | Description
C | No description available
> select clear
[Repeated 1 time(s)]
> combine #13 #14
Remapping chain ID 'C' in MFQ9_138_baseFit.pdb #14 to 'D'
> hide #14 models
> hide #13 models
> hide #15 models
> show #15 models
> save MFQ9_combo.pdb #15
> clsoe all
Unknown command: clsoe all
> close all
> open
> /Users/egelmanlab01/Documents/milano/base_plate/cryosparc_P101_J257_005_volume_map_sharp.mrc
Opened cryosparc_P101_J257_005_volume_map_sharp.mrc as #1, grid size
768,768,768, pixel 1.08, shown at step 1, values float32
> volume #1 region 0,0,0,767,767,767 step 4
[Repeated 1 time(s)]
> volume #1 step 1
> volume #1 level 0.22
> volume #1 change image level -0.055,0 level 0.2541,0.8 level 0.9056,1
> open
> /Users/egelmanlab01/Documents/milano/base_plate/baseplate/MFS1/GoodFit/MSF1_partial_fit_Map257.pdb
Chain information for MSF1_partial_fit_Map257.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
> transparency 50
> hide atoms
> show cartoons
> volume zone #1 nearAtoms #2 range 6.48
> open
> /Users/egelmanlab01/Documents/milano/ravi2/A0A482MFZ0_unrelaxed_rank_1_model_3.pdb
Chain information for A0A482MFZ0_unrelaxed_rank_1_model_3.pdb #3
---
Chain | Description
A | No description available
> view clip false
Drag select of 188 residues
> view matrix models #3,1,0,0,-63.501,0,1,0,8.074,0,0,1,263.44
> view matrix models #3,1,0,0,242.52,0,1,0,491.63,0,0,1,245.53
> view matrix models #3,1,0,0,275.01,0,1,0,562.86,0,0,1,331.28
> view matrix models #3,1,0,0,347.16,0,1,0,576.66,0,0,1,401.5
> view matrix models #3,1,0,0,408.25,0,1,0,531.18,0,0,1,455.55
> view matrix models #3,1,0,0,435.83,0,1,0,484.18,0,0,1,425.44
> volume zone #1 nearAtoms #2 range 20
> view matrix models
> #3,-0.07048,0.91613,0.39464,428.23,0.99699,0.051855,0.057677,490.1,0.032375,0.39751,-0.91702,430.83
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #1 region 0,0,0,705,767,767
> volume #1 region 0,0,0,684,767,767
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.07048,0.91613,0.39464,411.52,0.99699,0.051855,0.057677,432.16,0.032375,0.39751,-0.91702,434.51
> view matrix models
> #3,0.29497,0.68904,-0.66198,416.96,0.85197,0.12399,0.50869,429.95,0.43259,-0.71404,-0.55047,437.86
> view matrix models
> #3,0.29497,0.68904,-0.66198,416,0.85197,0.12399,0.50869,415.94,0.43259,-0.71404,-0.55047,439.13
> select add #3
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> volume zone #1 nearAtoms sel & #3 range 6.48
> view matrix models
> #3,0.29497,0.68904,-0.66198,409.91,0.85197,0.12399,0.50869,413.51,0.43259,-0.71404,-0.55047,453.69
> volume zone #1 nearAtoms sel & #3 range 6.48
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #1 region 0,0,0,767,767,767
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.056529,0.88517,-0.46183,407.86,0.84542,0.20363,0.49377,413.31,0.53111,-0.41835,-0.73682,453.79
> view matrix models
> #3,0.056529,0.88517,-0.46183,421.82,0.84542,0.20363,0.49377,409.26,0.53111,-0.41835,-0.73682,474.93
> view matrix models
> #3,0.056529,0.88517,-0.46183,418.61,0.84542,0.20363,0.49377,408.51,0.53111,-0.41835,-0.73682,476.24
> view matrix models
> #3,-0.91582,-0.068543,-0.39569,417.87,-0.1891,-0.79564,0.57549,407.64,-0.35427,0.60187,0.71571,465.41
> view matrix models
> #3,-0.91582,-0.068543,-0.39569,411.01,-0.1891,-0.79564,0.57549,401.89,-0.35427,0.60187,0.71571,470.99
> view matrix models
> #3,-0.91582,-0.068543,-0.39569,416.61,-0.1891,-0.79564,0.57549,409.6,-0.35427,0.60187,0.71571,473.04
> view matrix models
> #3,-0.91582,-0.068543,-0.39569,418.64,-0.1891,-0.79564,0.57549,412.78,-0.35427,0.60187,0.71571,472.35
> view matrix models
> #3,-0.84582,-0.10917,-0.52218,419.42,-0.15982,-0.88202,0.44327,413.57,-0.50896,0.45839,0.72859,472.2
> view matrix models
> #3,-0.84582,-0.10917,-0.52218,418.52,-0.15982,-0.88202,0.44327,414.73,-0.50896,0.45839,0.72859,471.87
> volume zone #1 nearAtoms sel & #3 range 6.48
> select clear
> select #3/A:142
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #3,-0.84582,-0.10917,-0.52218,424.32,-0.15982,-0.88202,0.44327,417.98,-0.50896,0.45839,0.72859,468.64
> view matrix models
> #3,0.6458,0.75709,0.098755,424.77,-0.60566,0.58674,-0.53751,415.51,-0.46488,0.28731,0.83746,468.92
> view matrix models
> #3,0.6458,0.75709,0.098755,427.92,-0.60566,0.58674,-0.53751,412.68,-0.46488,0.28731,0.83746,466.93
> view matrix models
> #3,0.6458,0.75709,0.098755,421.03,-0.60566,0.58674,-0.53751,426.4,-0.46488,0.28731,0.83746,484.96
> view matrix models
> #3,0.75541,0.65148,0.070207,421.81,-0.46906,0.61245,-0.63631,427.12,-0.45754,0.44774,0.76824,484.76
> view matrix models
> #3,0.75541,0.65148,0.070207,423.11,-0.46906,0.61245,-0.63631,419.5,-0.45754,0.44774,0.76824,485.69
> view matrix models
> #3,0.97642,0.11956,0.17973,425.03,-0.0023943,0.83856,-0.54481,420.11,-0.21585,0.53153,0.81907,486.09
> view matrix models
> #3,-0.50925,-0.85748,0.073399,423.2,0.65741,-0.33255,0.67618,421.64,-0.55541,0.3926,0.73307,485.64
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit molecule A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 1457 atoms
average map value = 0.1542, steps = 148
shifted from previous position = 7
rotated from previous position = 20.2 degrees
atoms outside contour = 998, contour level = 0.22
Position of A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.28866663 -0.90751560 0.30510162 416.13740396
0.85405363 -0.10004269 0.51047414 420.74289500
-0.43274006 0.40793001 0.80394599 486.20539513
Axis -0.05361495 0.38577871 0.92103215
Axis point 144.30001381 288.36790048 0.00000000
Rotation angle (degrees) 107.00059692
Shift along axis 587.81326736
> volume zone #1 nearAtoms #2 range 40
> select #3/A:124
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #3
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> volume zone #1 nearAtoms #3 range 40
> volume zone #1 nearAtoms #3 range 30
> view matrix models
> #3,-0.28867,-0.90752,0.3051,431.13,0.85405,-0.10004,0.51047,440.82,-0.43274,0.40793,0.80395,507.62
> view matrix models
> #3,-0.26526,-0.82128,0.5051,430.29,0.93746,-0.097213,0.33425,441.68,-0.22541,0.56218,0.7957,507.91
> view matrix models
> #3,-0.26526,-0.82128,0.5051,421.44,0.93746,-0.097213,0.33425,416.01,-0.22541,0.56218,0.7957,474.01
> view matrix models
> #3,-0.26526,-0.82128,0.5051,405.16,0.93746,-0.097213,0.33425,417.39,-0.22541,0.56218,0.7957,485.02
> view matrix models
> #3,-0.30604,-0.77932,0.54681,404.76,0.95103,-0.2241,0.21288,418.22,-0.043358,0.58518,0.80974,485.52
> view matrix models
> #3,-0.30604,-0.77932,0.54681,400.66,0.95103,-0.2241,0.21288,412.52,-0.043358,0.58518,0.80974,482.69
> view matrix models
> #3,-0.30604,-0.77932,0.54681,405.92,0.95103,-0.2241,0.21288,411.36,-0.043358,0.58518,0.80974,481.88
> view matrix models
> #3,-0.22916,-0.75048,0.61989,405.86,0.97219,-0.208,0.10757,411.74,0.048207,0.6273,0.77728,482.18
> view matrix models
> #3,-0.22916,-0.75048,0.61989,406.66,0.97219,-0.208,0.10757,409.32,0.048207,0.6273,0.77728,480.45
> view matrix models
> #3,-0.58417,-0.71628,0.3817,406.16,0.78828,-0.61271,0.056642,410.04,0.1933,0.33397,0.92255,481.3
> view matrix models
> #3,-0.25065,0.8529,0.45798,402.49,-0.015696,0.46943,-0.88283,407.34,-0.96795,-0.22846,-0.10427,482.45
> view matrix models
> #3,0.42131,0.87093,-0.25294,407.09,-0.74217,0.1708,-0.64808,404.96,-0.52123,0.46076,0.71834,479.2
> view matrix models
> #3,0.42131,0.87093,-0.25294,381.02,-0.74217,0.1708,-0.64808,415.03,-0.52123,0.46076,0.71834,498.47
> view matrix models
> #3,0.56984,0.16014,0.806,380.03,-0.32324,0.94544,0.04068,411.89,-0.75551,-0.28371,0.59051,500.26
> view matrix models
> #3,0.52184,0.11869,0.84475,379.86,0.17466,0.95443,-0.242,414.49,-0.83497,0.27383,0.47732,498.76
> view matrix models
> #3,0.52184,0.11869,0.84475,412.49,0.17466,0.95443,-0.242,418.85,-0.83497,0.27383,0.47732,496.91
> view matrix models
> #3,0.63714,0.74721,0.18905,413.26,-0.72586,0.66418,-0.17887,416.44,-0.25921,-0.02326,0.96554,498.08
> view matrix models
> #3,0.63714,0.74721,0.18905,400.29,-0.72586,0.66418,-0.17887,421.7,-0.25921,-0.02326,0.96554,496.12
> view matrix models
> #3,0.63714,0.74721,0.18905,401.03,-0.72586,0.66418,-0.17887,421.04,-0.25921,-0.02326,0.96554,493.88
> view matrix models
> #3,0.63714,0.74721,0.18905,401.59,-0.72586,0.66418,-0.17887,422.86,-0.25921,-0.02326,0.96554,493.35
> view matrix models
> #3,0.63714,0.74721,0.18905,403.94,-0.72586,0.66418,-0.17887,424.45,-0.25921,-0.02326,0.96554,493.77
> view matrix models
> #3,0.63714,0.74721,0.18905,403.33,-0.72586,0.66418,-0.17887,426.13,-0.25921,-0.02326,0.96554,493.42
> fitmap #3 inMap #1
Fit molecule A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 1457 atoms
average map value = 0.1048, steps = 160
shifted from previous position = 11.2
rotated from previous position = 15 degrees
atoms outside contour = 1114, contour level = 0.22
Position of A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.53865773 0.80490921 0.24893575 411.22652889
-0.69431407 0.59145194 -0.41001534 418.51594890
-0.47725866 0.04801834 0.87744995 497.91923797
Axis 0.26511731 0.42033308 -0.86777469
Axis point 763.49860676 -121.75575503 0.00000000
Rotation angle (degrees) 59.74961336
Shift along axis -147.14234826
> volume zone #1 nearAtoms #3 range 25
> view matrix models
> #3,-0.25662,0.81489,-0.51972,411.09,-0.91928,-0.37183,-0.12908,419.6,-0.29843,0.44464,0.84453,497.48
> view matrix models
> #3,-0.73952,0.52046,-0.42689,410,-0.64,-0.74015,0.20634,420.49,-0.20857,0.4258,0.88045,497.72
> view matrix models
> #3,-0.73952,0.52046,-0.42689,429.46,-0.64,-0.74015,0.20634,421.26,-0.20857,0.4258,0.88045,484.88
> view matrix models
> #3,-0.73952,0.52046,-0.42689,426.98,-0.64,-0.74015,0.20634,410.95,-0.20857,0.4258,0.88045,490.45
> view matrix models
> #3,-0.62922,0.70358,-0.33024,426.5,-0.76938,-0.5036,0.39299,409.2,0.11019,0.50135,0.8582,491.38
> view matrix models
> #3,-0.66682,0.7303,-0.14838,425.69,-0.73875,-0.62163,0.26042,410.09,0.097946,0.28327,0.95402,491.65
> view matrix models
> #3,-0.65259,0.74237,-0.15172,430.34,-0.75146,-0.60844,0.25517,415.02,0.097118,0.28053,0.95492,487.26
> view matrix models
> #3,-0.2344,0.97008,-0.063314,430.8,-0.55577,-0.18716,-0.80999,418.04,-0.79761,-0.15467,0.58301,486.74
> view matrix models
> #3,-0.2344,0.97008,-0.063314,419.83,-0.55577,-0.18716,-0.80999,406.79,-0.79761,-0.15467,0.58301,486.3
> view matrix models
> #3,-0.2344,0.97008,-0.063314,415.83,-0.55577,-0.18716,-0.80999,402.76,-0.79761,-0.15467,0.58301,484.65
> fitmap #3 inMap #1
Fit molecule A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 1457 atoms
average map value = 0.09268, steps = 100
shifted from previous position = 5.35
rotated from previous position = 8.51 degrees
atoms outside contour = 1151, contour level = 0.22
Position of A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.25249443 0.96396067 0.08382352 420.08089932
-0.58009951 -0.08147242 -0.81046086 405.56655928
-0.77442309 -0.25326284 0.57976444 482.28714053
Axis 0.30080697 0.46333001 -0.83357092
Axis point 477.07398253 156.70449022 0.00000000
Rotation angle (degrees) 112.15423997
Shift along axis -87.74611363
> view matrix models
> #3,-0.48692,0.72259,-0.49069,421.92,-0.52755,-0.69104,-0.49412,406.45,-0.69613,0.018262,0.71768,481.3
> view matrix models
> #3,-0.48692,0.72259,-0.49069,422.83,-0.52755,-0.69104,-0.49412,407.4,-0.69613,0.018262,0.71768,482.19
> view matrix models
> #3,-0.71238,0.65216,-0.25921,421.49,-0.63712,-0.75588,-0.15075,406.07,-0.29425,0.057756,0.95398,482.65
> view matrix models
> #3,-0.70881,0.64551,-0.28443,417.47,-0.63911,-0.75833,-0.12833,399.98,-0.29853,0.090819,0.95007,487.57
> view matrix models
> #3,-0.7137,0.6452,-0.27268,417.42,-0.63497,-0.76029,-0.13701,400.03,-0.29571,0.075357,0.9523,487.62
> fitmap #3 inMap #1
Fit molecule A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 1457 atoms
average map value = 0.08946, steps = 64
shifted from previous position = 4.76
rotated from previous position = 3.23 degrees
atoms outside contour = 1175, contour level = 0.22
Position of A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.71997239 0.61605513 -0.31955569 417.92084030
-0.60842992 -0.78180185 -0.13637778 404.20479658
-0.33384546 0.09623901 0.93770212 485.56951227
Axis 0.18662099 0.01146423 -0.98236509
Axis point 327.83761887 117.44282333 0.00000000
Rotation angle (degrees) 141.44737494
Shift along axis -394.37984212
> view matrix models
> #3,-0.16971,0.94424,-0.28215,418.71,-0.88648,-0.27134,-0.37487,402.59,-0.43053,0.1865,0.8831,485.16
> view matrix models
> #3,-0.69359,0.51233,-0.5064,418.94,-0.56616,-0.82236,-0.056548,404.2,-0.44542,0.24748,0.86044,485.01
> volume zone #1 nearAtoms #3 range 10
> view matrix models
> #3,0.14944,0.97747,0.14907,418.24,-0.74389,0.21046,-0.63429,402.54,-0.65138,-0.016105,0.75858,485.42
> view matrix models
> #3,0.14944,0.97747,0.14907,418.67,-0.74389,0.21046,-0.63429,405.4,-0.65138,-0.016105,0.75858,486.39
> view matrix models
> #3,0.14944,0.97747,0.14907,416.81,-0.74389,0.21046,-0.63429,406.2,-0.65138,-0.016105,0.75858,485.54
> view matrix models
> #3,0.14944,0.97747,0.14907,422.8,-0.74389,0.21046,-0.63429,407.3,-0.65138,-0.016105,0.75858,485.43
> volume zone #1 nearAtoms #3 range 8
> view matrix models
> #3,0.49994,0.15259,0.85251,424.02,-0.19019,0.97967,-0.063813,405.03,-0.84492,-0.13024,0.51879,485.91
> view matrix models
> #3,0.42029,-0.42794,0.80014,425.61,0.041168,0.88989,0.45432,404.33,-0.90645,-0.15801,0.39163,486.21
> view matrix models
> #3,0.42029,-0.42794,0.80014,420.72,0.041168,0.88989,0.45432,414.45,-0.90645,-0.15801,0.39163,486.32
> view matrix models
> #3,0.301,0.66476,0.68374,417.54,-0.21457,0.74581,-0.63066,417.64,-0.92917,0.043118,0.36712,485.74
> view matrix models
> #3,0.301,0.66476,0.68374,412.8,-0.21457,0.74581,-0.63066,413.34,-0.92917,0.043118,0.36712,490.22
> fitmap #3 inMap #1
Fit molecule A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 1457 atoms
average map value = 0.1283, steps = 280
shifted from previous position = 9.42
rotated from previous position = 25.1 degrees
atoms outside contour = 1071, contour level = 0.22
Position of A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.46419225 0.47288553 0.74893579 411.32957598
0.18149903 0.77682749 -0.60299018 414.86748859
-0.86693924 0.41583449 0.27476903 480.87891492
Axis 0.52724747 0.83622439 -0.15079415
Axis point 506.89104603 0.00000000 159.28371531
Rotation angle (degrees) 75.05484098
Shift along axis 491.28106606
> view matrix models
> #3,0.46419,0.47289,0.74894,430.82,0.1815,0.77683,-0.60299,427.28,-0.86694,0.41583,0.27477,509.32
> view matrix models
> #3,-0.43863,-0.8981,0.031906,434.15,0.23134,-0.078537,0.9697,424.65,-0.86838,0.43272,0.24222,509.38
> view matrix models
> #3,-0.43863,-0.8981,0.031906,432.95,0.23134,-0.078537,0.9697,422.64,-0.86838,0.43272,0.24222,509.81
> view matrix models
> #3,-0.43863,-0.8981,0.031906,418.98,0.23134,-0.078537,0.9697,425.86,-0.86838,0.43272,0.24222,496.24
> view matrix models
> #3,-0.68641,-0.70929,0.16045,417.17,0.42904,-0.21684,0.87687,427.24,-0.58717,0.67073,0.45315,495.79
> view matrix models
> #3,-0.68641,-0.70929,0.16045,424.21,0.42904,-0.21684,0.87687,415.32,-0.58717,0.67073,0.45315,503.35
> volume #1 level 0.2
> volume #1 level 0.25
> view matrix models
> #3,-0.77468,-0.62302,0.10827,423.83,0.31093,-0.2262,0.92312,414.79,-0.55063,0.74879,0.36895,503.53
> view matrix models
> #3,0.31245,0.9291,0.19783,422.71,-0.91254,0.35143,-0.20919,412.78,-0.26389,-0.11517,0.95765,505.02
> view matrix models
> #3,0.31245,0.9291,0.19783,417.92,-0.91254,0.35143,-0.20919,423.24,-0.26389,-0.11517,0.95765,492.36
> volume zone #1 nearAtoms #3 range 8
> view matrix models
> #3,0.31245,0.9291,0.19783,412.46,-0.91254,0.35143,-0.20919,423.9,-0.26389,-0.11517,0.95765,489.67
> view matrix models
> #3,0.28221,0.93641,0.20853,412.3,-0.91289,0.32895,-0.24171,424.07,-0.29494,-0.12215,0.94768,489.62
> volume zone #1 nearAtoms #3 range 8
> view matrix models
> #3,0.28221,0.93641,0.20853,411.47,-0.91289,0.32895,-0.24171,421.5,-0.29494,-0.12215,0.94768,487.55
> view matrix models
> #3,0.59063,-0.39606,0.70306,414.72,0.037754,0.88387,0.46621,420.73,-0.80606,-0.24881,0.53699,487.56
> view matrix models
> #3,0.032723,0.98618,0.16241,410.64,-0.97487,0.067317,-0.21234,421.95,-0.22034,-0.15138,0.96361,487.83
> view matrix models
> #3,0.032723,0.98618,0.16241,417.72,-0.97487,0.067317,-0.21234,420.7,-0.22034,-0.15138,0.96361,490.76
> view matrix models
> #3,0.032723,0.98618,0.16241,418.03,-0.97487,0.067317,-0.21234,418.64,-0.22034,-0.15138,0.96361,486.16
> volume zone #1 nearAtoms #3 range 8
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #1 region 0,0,0,767,767,767
> select #3/A:117
14 atoms, 15 bonds, 1 residue, 1 model selected
> volume #1 region 0,0,0,767,767,767
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.032723,0.98618,0.16241,422.52,-0.97487,0.067317,-0.21234,421.73,-0.22034,-0.15138,0.96361,485.78
> view matrix models
> #3,-0.86869,-0.42277,-0.25816,424.96,0.18741,-0.7629,0.61876,425.28,-0.45854,0.48912,0.74195,483.86
> view matrix models
> #3,-0.86869,-0.42277,-0.25816,415.63,0.18741,-0.7629,0.61876,413.39,-0.45854,0.48912,0.74195,493.8
> view matrix models
> #3,-0.87194,-0.34043,-0.3519,415.69,0.12995,-0.85385,0.50404,413.85,-0.47206,0.39376,0.78874,493.87
> open
> /Users/egelmanlab01/Documents/milano/base_plate/baseplate/MFS1/C3_MFS1_baseFitJ190.pdb
Chain information for C3_MFS1_baseFitJ190.pdb #4
---
Chain | Description
A B C | No description available
> select add #4
10502 atoms, 10695 bonds, 1372 residues, 2 models selected
> select subtract #4
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide #4 models
> show #4 models
> view clip false
> mmaker #4 #2
> matchmaker #4 #2
Missing required "to" argument
> mmaker #4 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker MSF1_partial_fit_Map257.pdb, chain G (#2) with
C3_MFS1_baseFitJ190.pdb, chain A (#4), sequence alignment score = 212.1
RMSD between 40 pruned atom pairs is 0.001 angstroms; (across all 40 pairs:
0.001)
> view matrix models
> #3,-0.87194,-0.34043,-0.3519,414.72,0.12995,-0.85385,0.50404,423.1,-0.47206,0.39376,0.78874,489.96
> view matrix models
> #3,-0.80464,-0.38939,-0.44825,415.41,0.1793,-0.87904,0.44175,423.55,-0.56604,0.27508,0.77713,490.02
> view matrix models
> #3,-0.80464,-0.38939,-0.44825,415.72,0.1793,-0.87904,0.44175,423.91,-0.56604,0.27508,0.77713,490.88
> transparency 0
> view matrix models
> #3,-0.80464,-0.38939,-0.44825,428.7,0.1793,-0.87904,0.44175,410.66,-0.56604,0.27508,0.77713,486.39
> view matrix models
> #3,-0.57403,-0.80302,0.16012,428.64,0.22158,0.03592,0.97448,406.36,-0.78828,0.59486,0.15731,486.79
> view matrix models
> #3,0.1573,-0.86271,0.48062,430.21,0.12209,0.49993,0.85742,405.07,-0.97997,-0.076193,0.18397,487.99
> view matrix models
> #3,-0.73982,-0.67165,0.039385,428.11,0.090725,-0.041586,0.99501,406.08,-0.66666,0.7397,0.091702,487
> view matrix models
> #3,-0.65202,-0.7576,-0.030134,428.88,0.14564,-0.16415,0.97563,406.68,-0.74408,0.63174,0.21736,486.63
> view matrix models
> #3,-0.65202,-0.7576,-0.030134,419.63,0.14564,-0.16415,0.97563,416.2,-0.74408,0.63174,0.21736,483.15
> view matrix models
> #3,-0.65202,-0.7576,-0.030134,412.35,0.14564,-0.16415,0.97563,419.74,-0.74408,0.63174,0.21736,493.51
> view matrix models
> #3,-0.26294,-0.96442,0.027624,414.08,-0.057432,0.044226,0.99737,418.38,-0.9631,0.26066,-0.067017,494.8
> view matrix models
> #3,-0.26294,-0.96442,0.027624,411.56,-0.057432,0.044226,0.99737,417.4,-0.9631,0.26066,-0.067017,495.22
> view matrix models
> #3,-0.71916,-0.34214,-0.60477,410.33,-0.34648,-0.57786,0.73894,419.09,-0.60229,0.74095,0.29703,493.83
> view matrix models
> #3,-0.71916,-0.34214,-0.60477,406.25,-0.34648,-0.57786,0.73894,417.96,-0.60229,0.74095,0.29703,492.88
> view matrix models
> #3,-0.36435,-0.90138,-0.23402,407.83,0.16479,-0.30973,0.93644,418.24,-0.91657,0.30262,0.26139,493.21
> view matrix models
> #3,-0.36435,-0.90138,-0.23402,400,0.16479,-0.30973,0.93644,417.9,-0.91657,0.30262,0.26139,493.19
> view matrix models
> #3,-0.36435,-0.90138,-0.23402,397.94,0.16479,-0.30973,0.93644,416.77,-0.91657,0.30262,0.26139,494.57
> view matrix models
> #3,-0.36435,-0.90138,-0.23402,399.42,0.16479,-0.30973,0.93644,415.13,-0.91657,0.30262,0.26139,494.68
> view matrix models
> #3,-0.24309,-0.94994,-0.19628,399.85,0.3062,-0.26715,0.91371,415.56,-0.92041,0.16201,0.35581,494.76
> view matrix models
> #3,-0.24309,-0.94994,-0.19628,396.91,0.3062,-0.26715,0.91371,414.27,-0.92041,0.16201,0.35581,494.27
> fitmap #3 inMap #1
Fit molecule A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 1457 atoms
average map value = 0.07835, steps = 104
shifted from previous position = 3.07
rotated from previous position = 7.84 degrees
atoms outside contour = 1228, contour level = 0.25
Position of A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.27949750 -0.90570672 -0.31871064 397.85056683
0.25227979 -0.38955090 0.88577931 417.10323288
-0.92641030 0.16716886 0.33737001 493.43083218
Axis -0.48158089 0.40725339 0.77603126
Axis point 274.11270283 244.08001770 0.00000000
Rotation angle (degrees) 131.74673857
Shift along axis 361.18722493
> transparency 50
> volume #1 color #d6d6d6
> transparency 50
> view matrix models
> #3,-0.16568,-0.97511,-0.14732,397.86,0.11381,-0.1673,0.97932,415.68,-0.97959,0.14548,0.1387,493.98
> view matrix models
> #3,0.90828,0.022964,0.41774,396.7,0.033407,0.99132,-0.12713,415.76,-0.41703,0.12943,0.89963,493.38
> view matrix models
> #3,0.90828,0.022964,0.41774,412.85,0.033407,0.99132,-0.12713,409.71,-0.41703,0.12943,0.89963,478.62
> view matrix models
> #3,0.90828,0.022964,0.41774,417.69,0.033407,0.99132,-0.12713,407.1,-0.41703,0.12943,0.89963,480.63
> view matrix models
> #3,0.90828,0.022964,0.41774,420.33,0.033407,0.99132,-0.12713,412.61,-0.41703,0.12943,0.89963,487.47
> view matrix models
> #3,0.32255,-0.84726,0.42203,420.86,0.90214,0.41014,0.1339,416.35,-0.28654,0.33754,0.89664,487.32
> view matrix models
> #3,0.32255,-0.84726,0.42203,419.01,0.90214,0.41014,0.1339,422.91,-0.28654,0.33754,0.89664,488.08
> view matrix models
> #3,0.23521,-0.89586,0.37698,419,0.91469,0.33518,0.22582,422.87,-0.32866,0.29171,0.89827,488.06
> view matrix models
> #3,0.51465,-0.79075,0.33144,419.8,0.78216,0.59134,0.1963,421.77,-0.35122,0.15821,0.92283,488.29
> view matrix models
> #3,0.51465,-0.79075,0.33144,422.41,0.78216,0.59134,0.1963,433.19,-0.35122,0.15821,0.92283,489.06
> view matrix models
> #3,0.9601,-0.1028,0.26009,422.16,0.16023,0.96442,-0.21031,431.37,-0.22921,0.24359,0.9424,489.15
> view matrix models
> #3,0.96147,0.17067,0.21551,421.52,-0.11923,0.96526,-0.23249,430.49,-0.2477,0.19783,0.94842,489.2
> view matrix models
> #3,0.96147,0.17067,0.21551,426,-0.11923,0.96526,-0.23249,429.1,-0.2477,0.19783,0.94842,486.51
> view matrix models
> #3,0.88495,0.44308,0.14332,425.19,-0.38498,0.86925,-0.31016,428.74,-0.26201,0.2193,0.93982,486.42
> view matrix models
> #3,0.88495,0.44308,0.14332,430.4,-0.38498,0.86925,-0.31016,430.32,-0.26201,0.2193,0.93982,494.45
> view matrix models
> #3,0.88495,0.44308,0.14332,416.05,-0.38498,0.86925,-0.31016,419.21,-0.26201,0.2193,0.93982,492.01
> view matrix models
> #3,0.88495,0.44308,0.14332,413.3,-0.38498,0.86925,-0.31016,423.41,-0.26201,0.2193,0.93982,486.91
> view matrix models
> #3,0.79316,-0.28368,0.53891,413.76,0.48903,0.82406,-0.28596,426.41,-0.36297,0.49036,0.79234,486.28
> view matrix models
> #3,0.79316,-0.28368,0.53891,417.77,0.48903,0.82406,-0.28596,417.91,-0.36297,0.49036,0.79234,487.92
> view matrix models
> #3,0.79316,-0.28368,0.53891,417.4,0.48903,0.82406,-0.28596,408.76,-0.36297,0.49036,0.79234,491.79
> view matrix models
> #3,0.63934,0.61526,0.4612,414.54,-0.24989,0.73349,-0.6321,407.68,-0.72719,0.28887,0.62269,491.71
> view matrix models
> #3,0.63934,0.61526,0.4612,415.69,-0.24989,0.73349,-0.6321,414.13,-0.72719,0.28887,0.62269,494.39
> view matrix models
> #3,0.63934,0.61526,0.4612,419.55,-0.24989,0.73349,-0.6321,413.91,-0.72719,0.28887,0.62269,493.89
> volume zone #1 nearAtoms sel & #3 range 6.48
> select clear
> select add #3
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> volume zone #1 nearAtoms sel & #3 range 6.48
> select clear
> transparency 0
> volume #1 color #929292
> select #3/A:110
9 atoms, 8 bonds, 1 residue, 1 model selected
> view matrix models
> #3,0.63934,0.61526,0.4612,419.41,-0.24989,0.73349,-0.6321,414.31,-0.72719,0.28887,0.62269,494.1
> select clear
> select add #3
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> volume zone #1 nearAtoms sel & #3 range 6.48
> volume zone #1 nearAtoms sel & #3 range 10
> select clear
> volume zone #1 nearAtoms sel & #3 range 13
no atoms specified for zone
> select add #2
1391 atoms, 1406 bonds, 177 residues, 1 model selected
> select add #3
2848 atoms, 2895 bonds, 365 residues, 2 models selected
> select subtract #2
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> volume zone #1 nearAtoms sel & #3 range 13
> select clear
> select #3/A:117
14 atoms, 15 bonds, 1 residue, 1 model selected
> view matrix models
> #3,0.63934,0.61526,0.4612,430.45,-0.24989,0.73349,-0.6321,378.8,-0.72719,0.28887,0.62269,513.37
> view matrix models
> #3,-0.37664,0.84832,-0.37215,429.14,-0.76941,-0.51021,-0.38432,379.82,-0.5159,0.14159,0.84487,513.76
> view matrix models
> #3,-0.80593,-0.31443,-0.50161,431.49,0.24261,-0.9483,0.20464,382.54,-0.54002,0.043235,0.84054,513.98
> view #2 clip false
> select #3/A:14
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #3,0.54468,-0.8362,0.063985,435.67,0.39277,0.32177,0.86151,377.16,-0.74098,-0.44412,0.5037,515.84
> view matrix models
> #3,0.54468,-0.8362,0.063985,434.44,0.39277,0.32177,0.86151,424.02,-0.74098,-0.44412,0.5037,487.01
> view matrix models
> #3,0.6525,-0.75642,0.045571,434.63,0.49828,0.47358,0.72625,424.39,-0.57093,-0.45118,0.68591,486.99
> view matrix models
> #3,0.6525,-0.75642,0.045571,411.37,0.49828,0.47358,0.72625,435.36,-0.57093,-0.45118,0.68591,494.91
> hide #4 models
> view matrix models
> #3,0.6525,-0.75642,0.045571,402.72,0.49828,0.47358,0.72625,430.38,-0.57093,-0.45118,0.68591,487.62
> view matrix models
> #3,0.6525,-0.75642,0.045571,402.51,0.49828,0.47358,0.72625,432.82,-0.57093,-0.45118,0.68591,487.77
> view matrix models
> #3,0.6525,-0.75642,0.045571,398.43,0.49828,0.47358,0.72625,432.03,-0.57093,-0.45118,0.68591,484.73
> view matrix models
> #3,0.6525,-0.75642,0.045571,398.55,0.49828,0.47358,0.72625,432.7,-0.57093,-0.45118,0.68591,484.47
> view matrix models
> #3,0.59152,-0.79593,0.12884,398.17,0.49819,0.48644,0.71777,432.69,-0.63397,-0.36039,0.68426,484
> view matrix models
> #3,0.59152,-0.79593,0.12884,398.58,0.49819,0.48644,0.71777,432.27,-0.63397,-0.36039,0.68426,484.7
> view matrix models
> #3,0.59152,-0.79593,0.12884,401.73,0.49819,0.48644,0.71777,431.92,-0.63397,-0.36039,0.68426,486.79
> view matrix models
> #3,0.61403,-0.77227,0.16299,401.62,0.49398,0.53706,0.68378,431.87,-0.6156,-0.33934,0.71126,486.7
> view matrix models
> #3,0.61814,-0.77454,0.13415,401.74,0.49544,0.51637,0.6985,431.89,-0.61029,-0.36531,0.70292,486.83
> transparency 50
> select add #3
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> volume zone #1 nearAtoms sel & #3 range 6.48
> view matrix models
> #3,0.61814,-0.77454,0.13415,402.15,0.49544,0.51637,0.6985,432.09,-0.61029,-0.36531,0.70292,487.14
> transparency 0
> view matrix models
> #3,0.61814,-0.77454,0.13415,402.99,0.49544,0.51637,0.6985,431.96,-0.61029,-0.36531,0.70292,486.95
> open /Users/egelmanlab01/Downloads/3qr8_3qr8_01000000_3qr8_02000000.pdb
Summary of feedback from opening
/Users/egelmanlab01/Downloads/3qr8_3qr8_01000000_3qr8_02000000.pdb
---
note | Combining 3 symmetry atoms into CL /A:212 CL
Chain information for 3qr8_3qr8_01000000_3qr8_02000000.pdb #5
---
Chain | Description
A | No description available
A | No description available
> mmaker #5 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A0A482MFZ0_unrelaxed_rank_1_model_3.pdb, chain A (#3) with
3qr8_3qr8_01000000_3qr8_02000000.pdb, chain A (#5), sequence alignment score =
115
RMSD between 40 pruned atom pairs is 1.215 angstroms; (across all 146 pairs:
8.498)
> hide sel atoms
> show sel cartoons
> select #5/A:150
21 atoms, 18 bonds, 3 residues, 1 model selected
> view matrix models
> #5,0.21677,0.97026,0.10775,360.63,0.97371,-0.2228,0.04736,425.91,0.069958,0.09465,-0.99305,523.77
> view matrix models
> #5,0.21677,0.97026,0.10775,366.94,0.97371,-0.2228,0.04736,431.43,0.069958,0.09465,-0.99305,525.4
> view matrix models
> #5,0.21677,0.97026,0.10775,372.21,0.97371,-0.2228,0.04736,425.13,0.069958,0.09465,-0.99305,525.93
> view matrix models
> #5,0.21677,0.97026,0.10775,371.15,0.97371,-0.2228,0.04736,423.71,0.069958,0.09465,-0.99305,525.82
> view matrix models
> #5,0.073097,0.99708,-0.022122,377.83,0.99292,-0.070675,0.095432,415.32,0.09359,-0.028941,-0.99519,530.02
> view matrix models
> #5,-0.029972,0.99922,-0.02574,378.72,0.99692,0.028016,-0.073266,420.58,-0.072488,-0.027857,-0.99698,531.33
> select add #5
4216 atoms, 3611 bonds, 445 pseudobonds, 1147 residues, 2 models selected
> volume zone #1 nearAtoms sel & #5 range 6.48
> select #5/A:101
30 atoms, 30 bonds, 3 residues, 1 model selected
> select #5/A:101
30 atoms, 30 bonds, 3 residues, 1 model selected
> view matrix models
> #5,-0.088951,0.99599,-0.0099,378.15,0.99568,0.08918,0.025765,413.33,0.026544,-0.0075655,-0.99962,529.82
> view matrix models
> #5,-0.088951,0.99599,-0.0099,377.82,0.99568,0.08918,0.025765,411.8,0.026544,-0.0075655,-0.99962,530.95
> view matrix models
> #5,-0.39205,0.91721,0.070922,379.02,0.91979,0.38938,0.048749,400.99,0.017097,0.084345,-0.99629,527.71
> view matrix models
> #5,-0.098791,0.97341,0.20666,365.63,0.99405,0.086946,0.065653,412.01,0.045938,0.21192,-0.97621,523.41
> view matrix models
> #5,-0.098791,0.97341,0.20666,369.06,0.99405,0.086946,0.065653,407.91,0.045938,0.21192,-0.97621,522.3
> fitmap #5 inMap #1
Fit molecule 3qr8_3qr8_01000000_3qr8_02000000.pdb (#5) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 4216 atoms
average map value = 0.1398, steps = 160
shifted from previous position = 5.63
rotated from previous position = 12.9 degrees
atoms outside contour = 3253, contour level = 0.25
Position of 3qr8_3qr8_01000000_3qr8_02000000.pdb (#5) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.11798354 0.99301074 -0.00308945 375.35077328
0.99298017 0.11795250 -0.00880815 410.51251538
-0.00838218 -0.00410698 -0.99995643 527.93899689
Axis 0.66408319 0.74764622 -0.00431863
Axis point 5.98793009 0.00000000 265.14622795
Rotation angle (degrees) 179.79719594
Shift along axis 553.90229418
> select #5/A:116
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #5/A:116
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #5/A:116
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #5/A:116
21 atoms, 18 bonds, 3 residues, 1 model selected
> view matrix models
> #5,-0.33846,0.93701,0.086419,374.61,0.93958,0.34153,-0.023227,404.13,-0.051279,0.073336,-0.99599,525.41
> view matrix models
> #5,-0.33846,0.93701,0.086419,374.5,0.93958,0.34153,-0.023227,403.12,-0.051279,0.073336,-0.99599,527.31
> view matrix models
> #5,-0.33846,0.93701,0.086419,374.46,0.93958,0.34153,-0.023227,402.63,-0.051279,0.073336,-0.99599,525.77
> fitmap #5 inMap #1
Fit molecule 3qr8_3qr8_01000000_3qr8_02000000.pdb (#5) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 4216 atoms
average map value = 0.1442, steps = 64
shifted from previous position = 1.79
rotated from previous position = 6.94 degrees
atoms outside contour = 3228, contour level = 0.25
Position of 3qr8_3qr8_01000000_3qr8_02000000.pdb (#5) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.41420352 0.91018061 -0.00258721 378.83208066
0.91018282 0.41419608 -0.00297303 398.57753341
-0.00163438 -0.00358628 -0.99999223 527.79672135
Axis -0.54120071 -0.84089119 0.00194991
Axis point 61.06396567 -0.00000000 264.37514598
Rotation angle (degrees) 179.96753858
Shift along axis -539.15536802
> select add #5
4216 atoms, 3611 bonds, 445 pseudobonds, 1147 residues, 2 models selected
> volume zone #1 nearAtoms sel & #5 range 6.48
> volume zone #1 nearAtoms sel & #5 range 3
> mmaker #3 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3qr8_3qr8_01000000_3qr8_02000000.pdb, chain A (#5) with
A0A482MFZ0_unrelaxed_rank_1_model_3.pdb, chain A (#3), sequence alignment
score = 115
RMSD between 40 pruned atom pairs is 1.215 angstroms; (across all 146 pairs:
8.498)
> hide #!5 models
> transparency 50
> select #3:1-118
925 atoms, 947 bonds, 118 residues, 1 model selected
> select #3:1-120
942 atoms, 964 bonds, 120 residues, 1 model selected
> save /Users/egelmanlab01/Desktop/1-118_MFZ0.pdb models #3 selectedOnly true
> open /Users/egelmanlab01/Desktop/1-118_MFZ0.pdb
Summary of feedback from opening /Users/egelmanlab01/Desktop/1-118_MFZ0.pdb
---
warnings | Start residue of secondary structure not found: SHEET 9 9 1 LYS A
122 LEU A 125 0
Start residue of secondary structure not found: SHEET 10 10 1 LEU A 131 SER A
136 0
Start residue of secondary structure not found: SHEET 11 11 1 LEU A 139 SER A
144 0
Chain information for 1-118_MFZ0.pdb #6
---
Chain | Description
A | No description available
> hide #3 models
> select #6/A:27
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #6
942 atoms, 964 bonds, 120 residues, 1 model selected
> transparency 0
> volume zone #1 nearAtoms sel & #6 range 6.48
> color #6 #ff9300 transparency 0
> fitmap #6 inMap #1
Fit molecule 1-118_MFZ0.pdb (#6) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 942 atoms
average map value = 0.1589, steps = 64
shifted from previous position = 1.97
rotated from previous position = 4.32 degrees
atoms outside contour = 694, contour level = 0.25
Position of 1-118_MFZ0.pdb (#6) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99818749 0.05750775 -0.01773675 -16.30461819
-0.05825348 0.99729301 -0.04486842 46.38671594
0.01510845 0.04582032 0.99883544 -23.51493634
Axis 0.60187037 -0.21798245 -0.76826799
Axis point 775.92741921 288.51985523 0.00000000
Rotation angle (degrees) 4.32070592
Shift along axis -1.85898345
> select #6/A:14
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #6,0.99819,0.057508,-0.017737,-21.272,-0.058253,0.99729,-0.044868,50.326,0.015108,0.04582,0.99884,-14.551
> view matrix models
> #6,0.99819,0.057508,-0.017737,-19.902,-0.058253,0.99729,-0.044868,45.425,0.015108,0.04582,0.99884,-14.047
> view matrix models
> #6,0.99819,0.057508,-0.017737,-20.056,-0.058253,0.99729,-0.044868,47.582,0.015108,0.04582,0.99884,-13.174
> select add #5
4224 atoms, 3618 bonds, 445 pseudobonds, 1148 residues, 3 models selected
> show #!5 models
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 3 atomic
models, 1 maps.
> select subtract #5
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #6
942 atoms, 964 bonds, 120 residues, 1 model selected
> volume zone #1 nearAtoms sel & #6 range 6.48
> select add #5
5158 atoms, 4575 bonds, 445 pseudobonds, 1267 residues, 3 models selected
> select subtract #6
4216 atoms, 3611 bonds, 445 pseudobonds, 1147 residues, 2 models selected
> volume zone #1 nearAtoms sel & #5 range 6.48
> hide #!5 models
> select subtract #5
Nothing selected
> select #6/A:33
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #6/A:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #6,0.99819,0.057508,-0.017737,-20.102,-0.058253,0.99729,-0.044868,47.548,0.015108,0.04582,0.99884,-13.013
> view matrix models
> #6,-0.93263,-0.31145,0.1822,847.1,0.15944,-0.80868,-0.56622,954.36,0.32369,-0.49903,0.80386,176.71
> view matrix models
> #6,-0.93263,-0.31145,0.1822,887.33,0.15944,-0.80868,-0.56622,966.37,0.32369,-0.49903,0.80386,185.02
> view matrix models
> #6,-0.93263,-0.31145,0.1822,888.35,0.15944,-0.80868,-0.56622,967.87,0.32369,-0.49903,0.80386,185.31
> view matrix models
> #6,-0.83182,-0.52955,-0.16632,1099.6,0.53959,-0.70127,-0.4659,717.6,0.13008,-0.47728,0.86907,226.7
> view matrix models
> #6,-0.82218,-0.47684,-0.31087,1140.8,0.53728,-0.83048,-0.1471,624.28,-0.18803,-0.28797,0.939,247.79
> view matrix models
> #6,-0.82218,-0.47684,-0.31087,1115.1,0.53728,-0.83048,-0.1471,610.26,-0.18803,-0.28797,0.939,238.26
> view matrix models
> #6,-0.82218,-0.47684,-0.31087,1116.1,0.53728,-0.83048,-0.1471,625.99,-0.18803,-0.28797,0.939,239.33
> view matrix models
> #6,-0.82218,-0.47684,-0.31087,1108.5,0.53728,-0.83048,-0.1471,626.65,-0.18803,-0.28797,0.939,233.85
> view matrix models
> #6,-0.74328,-0.66081,-0.10422,1056.4,0.65617,-0.68982,-0.30591,592.1,0.13026,-0.29577,0.94634,100.84
> view matrix models
> #6,-0.74328,-0.66081,-0.10422,1053.7,0.65617,-0.68982,-0.30591,591.6,0.13026,-0.29577,0.94634,100.12
> view matrix models
> #6,-0.74328,-0.66081,-0.10422,1053.4,0.65617,-0.68982,-0.30591,587.61,0.13026,-0.29577,0.94634,96.59
> fitmap #6 inMap #1
Fit molecule 1-118_MFZ0.pdb (#6) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 942 atoms
average map value = 0.1456, steps = 100
shifted from previous position = 6.62
rotated from previous position = 16.4 degrees
atoms outside contour = 706, contour level = 0.25
Position of 1-118_MFZ0.pdb (#6) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.69904951 -0.71034088 -0.08213176 1046.97680244
0.62623707 -0.55270647 -0.54985698 649.64942583
0.34519114 -0.43581120 0.83121097 118.66238806
Axis 0.08100684 -0.30352792 0.94937279
Axis point 377.58412803 570.74001473 0.00000000
Rotation angle (degrees) 135.25709088
Shift along axis 0.28038572
> view matrix models
> #6,-0.69905,-0.71034,-0.082132,1077.3,0.62624,-0.55271,-0.54986,654.52,0.34519,-0.43581,0.83121,124.09
> volume #1 level 0.2
> volume #1 level 0.28
> view matrix models
> #6,0.87714,0.45176,0.16293,-180.54,-0.35611,0.83946,-0.41048,417.62,-0.32221,0.30203,0.8972,63.457
> view matrix models
> #6,0.87714,0.45176,0.16293,-181.98,-0.35611,0.83946,-0.41048,417.02,-0.32221,0.30203,0.8972,61.403
> view matrix models
> #6,-0.65164,-0.73432,0.19011,939.42,0.71764,-0.67801,-0.15903,486.34,0.24568,0.032806,0.9688,-96.379
> view matrix models
> #6,-0.63365,-0.74287,0.21594,923.48,0.73236,-0.66596,-0.14197,467.22,0.24927,0.068182,0.96603,-111.38
> view matrix models
> #6,-0.63365,-0.74287,0.21594,893.93,0.73236,-0.66596,-0.14197,447.88,0.24927,0.068182,0.96603,-116.31
> view matrix models
> #6,-0.63365,-0.74287,0.21594,894.87,0.73236,-0.66596,-0.14197,458.22,0.24927,0.068182,0.96603,-112.27
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume zone #1 nearAtoms sel & #6 range 6.48
> select add #6
942 atoms, 964 bonds, 120 residues, 1 model selected
> select add #5
5158 atoms, 4575 bonds, 445 pseudobonds, 1267 residues, 3 models selected
> select subtract #6
4216 atoms, 3611 bonds, 445 pseudobonds, 1147 residues, 2 models selected
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.
[Repeated 1 time(s)]
> show #!5 models
> volume zone #1 nearAtoms sel & #5 range 6.48
> hide #!5 models
> select #6/A:116
8 atoms, 7 bonds, 1 residue, 1 model selected
> volume #1 region 0,0,0,767,767,767
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.63365,-0.74287,0.21594,860.01,0.73236,-0.66596,-0.14197,456.07,0.24927,0.068182,0.96603,-104.51
> view matrix models
> #6,0.11991,-0.99277,0.0060633,747.6,0.98621,0.11841,-0.11563,9.8926,0.11408,0.019845,0.99327,-40.539
> view matrix models
> #6,0.96944,0.12886,0.20878,-170.29,-0.15119,0.98396,0.094707,24.886,-0.19322,-0.12338,0.97337,156.88
> view matrix models
> #6,0.96584,-0.058526,0.25245,-110.76,0.043472,0.99695,0.064808,-47.888,-0.25547,-0.05162,0.96544,156.54
> view matrix models
> #6,0.96584,-0.058526,0.25245,-106.06,0.043472,0.99695,0.064808,-46.94,-0.25547,-0.05162,0.96544,150.49
> view matrix models
> #6,0.81847,-0.49221,0.29638,116.35,0.40129,0.8589,0.31822,-256.47,-0.41119,-0.14152,0.90049,283.3
> view matrix models
> #6,0.81847,-0.49221,0.29638,120.28,0.40129,0.8589,0.31822,-257.39,-0.41119,-0.14152,0.90049,287.23
> view matrix models
> #6,0.5022,-0.83158,0.23719,421.73,0.83972,0.53448,0.095928,-201.32,-0.20654,0.151,0.96672,48.693
> view matrix models
> #6,0.5022,-0.83158,0.23719,421.35,0.83972,0.53448,0.095928,-201.42,-0.20654,0.151,0.96672,47.037
> view matrix models
> #6,0.79918,-0.5556,0.22941,185.61,0.5526,0.82927,0.083313,-198.97,-0.23653,0.060191,0.96976,96.108
> view matrix models
> #6,0.79918,-0.5556,0.22941,186.7,0.5526,0.82927,0.083313,-199.79,-0.23653,0.060191,0.96976,98.07
> view matrix models
> #6,0.79918,-0.5556,0.22941,186.33,0.5526,0.82927,0.083313,-199.99,-0.23653,0.060191,0.96976,96.057
> view matrix models
> #6,0.81026,-0.58208,0.06836,267.71,0.58582,0.80784,-0.06488,-135.95,-0.017459,0.092615,0.99555,-20.943
> view matrix models
> #6,0.81026,-0.58208,0.06836,266.55,0.58582,0.80784,-0.06488,-135.1,-0.017459,0.092615,0.99555,-22.254
> view matrix models
> #6,0.83191,-0.52685,0.1742,185.18,0.52542,0.84886,0.058088,-184.25,-0.17847,0.043202,0.983,71.456
> view matrix models
> #6,0.92712,-0.32673,0.18356,57.406,0.32333,0.94502,0.049027,-135.88,-0.18949,0.013896,0.98179,88.869
> view matrix models
> #6,0.92712,-0.32673,0.18356,58.091,0.32333,0.94502,0.049027,-136.96,-0.18949,0.013896,0.98179,88.575
> view matrix models
> #6,0.8735,-0.45572,0.17121,140.15,0.44856,0.8901,0.080719,-181.01,-0.18918,0.0062889,0.98192,91.564
> view matrix models
> #6,0.8735,-0.45572,0.17121,140.72,0.44856,0.8901,0.080719,-181.9,-0.18918,0.0062889,0.98192,86.646
> view matrix models
> #6,0.84281,-0.52357,0.12471,203.54,0.51806,0.85198,0.07574,-192.65,-0.14591,0.00077461,0.9893,67.459
> view matrix models
> #6,0.84281,-0.52357,0.12471,205.33,0.51806,0.85198,0.07574,-193.68,-0.14591,0.00077461,0.9893,64.897
> view matrix models
> #6,0.79449,-0.60721,0.0086431,314.47,0.60723,0.79453,0.00070358,-171.97,-0.0072944,0.0046893,0.99996,0.43974
> view matrix models
> #6,0.79449,-0.60721,0.0086431,315.39,0.60723,0.79453,0.00070358,-172.46,-0.0072944,0.0046893,0.99996,2.6908
> view matrix models
> #6,0.79449,-0.60721,0.0086431,315.6,0.60723,0.79453,0.00070358,-172.6,-0.0072944,0.0046893,0.99996,1.9411
> fitmap #6 inMap #1
Fit molecule 1-118_MFZ0.pdb (#6) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 942 atoms
average map value = 0.139, steps = 68
shifted from previous position = 3.84
rotated from previous position = 8.22 degrees
atoms outside contour = 764, contour level = 0.28
Position of 1-118_MFZ0.pdb (#6) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.84833411 -0.52326892 -0.08073950 302.79528034
0.52119654 0.85216378 -0.04659449 -137.36853739
0.09318473 -0.00255346 0.99564556 -35.47621370
Axis 0.04155744 -0.16411618 0.98556525
Axis point 395.15722967 464.11433351 0.00000000
Rotation angle (degrees) 31.99744458
Shift along axis 0.16367268
> select #6:93-118
205 atoms, 212 bonds, 26 residues, 1 model selected
> volume zone #1 nearAtoms sel & #6 range 6.48
> save /Users/egelmanlab01/Desktop/93-118_RBF_MFZ0.pdb models #6 selectedOnly
> true
> select add #6
942 atoms, 964 bonds, 120 residues, 1 model selected
> volume zone #1 nearAtoms sel & #6 range 6.48
> select add #5
5158 atoms, 4575 bonds, 445 pseudobonds, 1267 residues, 3 models selected
> select subtract #6
4216 atoms, 3611 bonds, 445 pseudobonds, 1147 residues, 2 models selected
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.
> show #!5 models
> volume zone #1 nearAtoms sel & #5 range 6.48
> hide #!5 models
> hide #!1 models
> select #6:65-92
227 atoms, 232 bonds, 28 residues, 1 model selected
> save /Users/egelmanlab01/Desktop/65-92_MFZ0.pdb models #6 selectedOnly true
> open /Users/egelmanlab01/Desktop/65-92_MFZ0.pdb
Summary of feedback from opening /Users/egelmanlab01/Desktop/65-92_MFZ0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR A 7
GLN A 15 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP A 16 PHE A 18 1
3
Start residue of secondary structure not found: SHEET 1 1 1 HIS A 21 THR A 29
0
Start residue of secondary structure not found: SHEET 2 2 1 GLY A 32 GLY A 39
0
Start residue of secondary structure not found: SHEET 3 3 1 GLU A 45 PRO A 48
0
3 messages similar to the above omitted
Chain information for 65-92_MFZ0.pdb #7
---
Chain | Description
A | No description available
> hide #6 models
> select #7/A:81
7 atoms, 6 bonds, 1 residue, 1 model selected
> show #!1 models
> view matrix models
> #7,-0.18418,-0.8945,-0.40737,1037.8,0.96273,-0.24769,0.1086,81.659,-0.19804,-0.37219,0.90678,277.85
> open /Users/egelmanlab01/Desktop/93-118_RBF_MFZ0.pdb
Summary of feedback from opening
/Users/egelmanlab01/Desktop/93-118_RBF_MFZ0.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR A 7
GLN A 15 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP A 16 PHE A 18 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 86 LYS A 88 1
3
Start residue of secondary structure not found: SHEET 1 1 1 HIS A 21 THR A 29
0
Start residue of secondary structure not found: SHEET 2 2 1 GLY A 32 GLY A 39
0
3 messages similar to the above omitted
Chain information for 93-118_RBF_MFZ0.pdb #8
---
Chain | Description
A | No description available
> transparency 50
> select #7/A:87
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #7,-0.18418,-0.8945,-0.40737,1036.6,0.96273,-0.24769,0.1086,83.594,-0.19804,-0.37219,0.90678,280.98
Drag select of 1 residues
> select #7/A:87
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #7,0.15201,0.46792,0.8706,-258.85,-0.64833,-0.61765,0.44517,729.54,0.74603,-0.63211,0.20948,332.97
> view matrix models
> #7,-0.53741,0.41481,-0.73425,785.36,0.24556,0.90991,0.33432,-214.5,0.80678,-0.00062785,-0.59085,417.07
> view matrix models
> #7,-0.54781,0.38736,-0.74152,804.34,0.056196,0.90138,0.42936,-178.87,0.83471,0.19354,-0.51556,290.07
> view matrix models
> #7,0.24232,0.83411,-0.49553,186.36,0.55919,0.2973,0.77389,-289.66,0.79283,-0.46462,-0.39438,524.65
> view matrix models
> #7,0.24232,0.83411,-0.49553,191.76,0.55919,0.2973,0.77389,-292.65,0.79283,-0.46462,-0.39438,530.45
> view matrix models
> #7,-0.28293,-0.22854,-0.93152,1047.7,0.91805,-0.34576,-0.19401,279.83,-0.27774,-0.91007,0.30763,820.79
> view matrix models
> #7,-0.83197,-0.475,-0.28671,1072,0.30433,-0.82278,0.48003,412.5,-0.46391,0.31212,0.82908,144.95
> view matrix models
> #7,-0.9002,-0.43031,0.066915,916.71,0.34412,-0.60873,0.71486,198.41,-0.26688,0.66655,0.69605,-20.114
> view matrix models
> #7,-0.9002,-0.43031,0.066915,915.31,0.34412,-0.60873,0.71486,199.69,-0.26688,0.66655,0.69605,-20.288
> view matrix models
> #7,-0.9002,-0.43031,0.066915,911.58,0.34412,-0.60873,0.71486,196.58,-0.26688,0.66655,0.69605,-20.774
> view matrix models
> #7,-0.96826,-0.19737,0.15333,801.9,0.22441,-0.41648,0.88101,87.62,-0.11003,0.88746,0.44756,-60.515
> fitmap #7 inMap #1
Fit molecule 65-92_MFZ0.pdb (#7) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 227 atoms
average map value = 0.1774, steps = 156
shifted from previous position = 3.85
rotated from previous position = 38.8 degrees
atoms outside contour = 174, contour level = 0.28
Position of 65-92_MFZ0.pdb (#7) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.67019137 -0.28224242 0.68642752 472.27695012
0.71889287 -0.01696341 0.69491387 -193.70171822
-0.18449002 0.95919313 0.21427080 46.42744890
Axis 0.19532815 0.64369301 0.73993663
Axis point 281.32927775 7.18742459 0.00000000
Rotation angle (degrees) 137.42920339
Shift along axis 1.91791088
> view matrix models
> #7,-0.75899,-0.43658,0.48303,666.63,0.63697,-0.3442,0.68978,-22.148,-0.13489,0.83122,0.53934,-71.106
> volume #1 level 0.25
> select clear
[Repeated 1 time(s)]
> select #7/A:75
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.75899,-0.43658,0.48303,665.09,0.63697,-0.3442,0.68978,-24.015,-0.13489,0.83122,0.53934,-64.687
> view matrix models
> #7,-0.65901,0.73811,-0.14454,427.13,-0.72641,-0.67444,-0.13212,1043.3,-0.195,0.01793,0.98064,93.244
> select clear
> select #7/A:87
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #7,-0.65901,0.73811,-0.14454,441.43,-0.72641,-0.67444,-0.13212,1047.4,-0.195,0.01793,0.98064,86.216
> show #6 models
> select add #5
4224 atoms, 3618 bonds, 445 pseudobonds, 1148 residues, 3 models selected
> show #!5 models
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 5 atomic
models, 1 maps.
> select add #7
4443 atoms, 3843 bonds, 445 pseudobonds, 1175 residues, 3 models selected
> select subtract #7
4216 atoms, 3611 bonds, 445 pseudobonds, 1147 residues, 2 models selected
> volume zone #1 nearAtoms sel & #5 range 6.48
> volume zone #1 nearAtoms sel & #5 range 10
> select subtract #5
Nothing selected
> hide #!5 models
> transparency 0
> select #6/A:46
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #6,0.84833,-0.52327,-0.08074,309.3,0.5212,0.85216,-0.046594,-134.97,0.093185,-0.0025535,0.99565,-23.22
> view matrix models
> #6,-0.5055,-0.71234,0.48687,689.38,0.56854,-0.69944,-0.43306,673.84,0.64902,0.057894,0.75857,-170.21
> view matrix models
> #6,-0.5055,-0.71234,0.48687,691.5,0.56854,-0.69944,-0.43306,678.57,0.64902,0.057894,0.75857,-169.31
> view matrix models
> #6,-0.49669,0.55044,0.67106,74.124,-0.71381,-0.6989,0.04494,991.22,0.49374,-0.45669,0.74004,119.29
> view matrix models
> #6,-0.49669,0.55044,0.67106,77.993,-0.71381,-0.6989,0.04494,995.87,0.49374,-0.45669,0.74004,117.28
> view matrix models
> #6,-0.49669,0.55044,0.67106,71.87,-0.71381,-0.6989,0.04494,994.38,0.49374,-0.45669,0.74004,117.54
> view matrix models
> #6,-0.82465,-0.47781,0.30273,810.07,0.42069,-0.87586,-0.23641,725.72,0.37811,-0.067604,0.92329,-82.138
> view matrix models
> #6,-0.82465,-0.47781,0.30273,807.74,0.42069,-0.87586,-0.23641,724.77,0.37811,-0.067604,0.92329,-86.58
> view matrix models
> #6,-0.8537,-0.22727,0.46855,637.95,-0.043193,-0.86574,-0.49862,1036.2,0.51897,-0.44591,0.72927,103.07
> view matrix models
> #6,-0.8537,-0.22727,0.46855,636.22,-0.043193,-0.86574,-0.49862,1033.3,0.51897,-0.44591,0.72927,102.11
> view matrix models
> #6,-0.81152,-0.44127,0.38304,747.88,0.18642,-0.81678,-0.546,939.03,0.55379,-0.37168,0.7451,49.17
> fitmap #6 inMap #1
Fit molecule 1-118_MFZ0.pdb (#6) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 942 atoms
average map value = 0.1347, steps = 120
shifted from previous position = 5.11
rotated from previous position = 18.5 degrees
atoms outside contour = 721, contour level = 0.25
Position of 1-118_MFZ0.pdb (#6) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.77787484 -0.48186946 0.40337643 746.28035590
0.38387489 -0.87256997 -0.30209552 766.07460118
0.49754477 -0.08014642 0.86372782 -106.83702886
Axis 0.24696979 -0.10478409 0.96334117
Axis point 292.45628831 469.11899183 0.00000000
Rotation angle (degrees) 153.29835645
Shift along axis 1.11576311
> select add #6
942 atoms, 964 bonds, 120 residues, 1 model selected
> volume zone #1 nearAtoms sel & #6 range 6.48
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume zone #1 nearAtoms sel & #6 range 6.48
> show #!5 models
> hide #!5 models
> volume zone #1 nearAtoms sel & #6 range 10
> volume zone #1 nearAtoms sel & #6 range 20
> select #1
3 models selected
> select #6/A:22
7 atoms, 6 bonds, 1 residue, 1 model selected
> volume #1 region 2,0,0,767,767,767
> select #6/A:22
7 atoms, 6 bonds, 1 residue, 1 model selected
> volume #1 region 4,0,0,767,767,767
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.77787,-0.48187,0.40338,747.42,0.38387,-0.87257,-0.3021,765.96,0.49754,-0.080146,0.86373,-105.25
Drag select of 1 cryosparc_P101_J257_005_volume_map_sharp.mrc , 1 residues
> select #6/A:22
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models
> #6,-0.77787,-0.48187,0.40338,748.15,0.38387,-0.87257,-0.3021,766.88,0.49754,-0.080146,0.86373,-103.35
> view matrix models
> #6,-0.76641,-0.48473,0.42149,736.13,0.38719,-0.87217,-0.29901,763.89,0.51255,-0.065964,0.85612,-112
> view matrix models
> #6,-0.085653,0.62947,0.77229,-177.1,-0.99224,-0.12401,-0.0089722,891.92,0.090122,-0.76706,0.63521,460.25
> view matrix models
> #6,-0.085653,0.62947,0.77229,-177.65,-0.99224,-0.12401,-0.0089722,894.53,0.090122,-0.76706,0.63521,456.7
> view matrix models
> #6,-0.085653,0.62947,0.77229,-179.38,-0.99224,-0.12401,-0.0089722,898.24,0.090122,-0.76706,0.63521,459.23
> view matrix models
> #6,0.55461,0.82805,0.082081,-208.55,-0.83184,0.5492,0.080177,508.33,0.021312,-0.11274,0.9934,47.72
> view matrix models
> #6,0.55461,0.82805,0.082081,-214.81,-0.83184,0.5492,0.080177,511.78,0.021312,-0.11274,0.9934,52.856
> view matrix models
> #6,0.25185,0.84282,0.47564,-277.7,-0.94542,0.10926,0.30699,637.61,0.20677,-0.52699,0.82433,227.31
> view matrix models
> #6,0.25185,0.84282,0.47564,-279.32,-0.94542,0.10926,0.30699,664.55,0.20677,-0.52699,0.82433,234.06
Drag select of 1 cryosparc_P101_J257_005_volume_map_sharp.mrc , 16 residues
> show sel atoms
> view matrix models
> #1,1,0,0,-1.2109,0,1,0,-1.5529,0,0,1,-0.87294,#6,0.25185,0.84282,0.47564,-280.53,-0.94542,0.10926,0.30699,663,0.20677,-0.52699,0.82433,233.19
> close #1
> open
> /Users/egelmanlab01/Documents/milano/base_plate/cryosparc_P101_J257_005_volume_map_sharp.mrc
Opened cryosparc_P101_J257_005_volume_map_sharp.mrc as #1, grid size
768,768,768, pixel 1.08, shown at step 1, values float32
> volume #1 region 0,0,0,767,767,767 step 4
[Repeated 1 time(s)]
> volume #1 step 1
> volume #1 color #929292
> volume #1 level 0.2
> volume #1 level 0.25
> volume #1 level 0.35
> volume #1 level 0.28
> select #6/A:67
11 atoms, 11 bonds, 1 residue, 1 model selected
> view matrix models
> #6,0.25185,0.84282,0.47564,-269.56,-0.94542,0.10926,0.30699,641.82,0.20677,-0.52699,0.82433,237.73
> select add #5
4227 atoms, 3622 bonds, 445 pseudobonds, 1148 residues, 3 models selected
> show #!5 models
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 5 atomic
models, 1 maps.
> select add #6
5158 atoms, 4575 bonds, 445 pseudobonds, 1267 residues, 3 models selected
> select subtract #6
4216 atoms, 3611 bonds, 445 pseudobonds, 1147 residues, 2 models selected
> volume zone #1 nearAtoms sel & #5 range 6.48
> select add #6
5158 atoms, 4575 bonds, 445 pseudobonds, 1267 residues, 3 models selected
> view clip false
> fitmap #5 inMap #1
Fit molecule 3qr8_3qr8_01000000_3qr8_02000000.pdb (#5) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 4216 atoms
average map value = 0.1442, steps = 48
shifted from previous position = 0.021
rotated from previous position = 0.0291 degrees
atoms outside contour = 3415, contour level = 0.28
Position of 3qr8_3qr8_01000000_3qr8_02000000.pdb (#5) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.41415669 0.91020296 -0.00219065 378.81110148
0.91020434 0.41415091 -0.00266017 398.56320506
-0.00151404 -0.00309566 -0.99999406 527.75638644
Axis -0.54122238 -0.84087776 0.00171099
Axis point 61.07674496 -0.00000000 264.29408442
Rotation angle (degrees) 179.97694865
Shift along axis -539.26099757
> fitmap #5 inMap #1
Fit molecule 3qr8_3qr8_01000000_3qr8_02000000.pdb (#5) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 4216 atoms
average map value = 0.1443, steps = 44
shifted from previous position = 0.0238
rotated from previous position = 0.0115 degrees
atoms outside contour = 3420, contour level = 0.28
Position of 3qr8_3qr8_01000000_3qr8_02000000.pdb (#5) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.41417976 0.91019232 -0.00225043 378.81487913
0.91019358 0.41417329 -0.00285038 398.57172221
-0.00166232 -0.00322889 -0.99999340 527.78546528
Axis -0.54121174 -0.84088441 0.00180709
Axis point 61.08769373 -0.00000000 264.33004829
Rotation angle (degrees) 179.97996405
Shift along axis -539.21805044
> hide #!5 models
> select subtract #5
942 atoms, 964 bonds, 120 residues, 1 model selected
> volume #1 level 0.25
> select #6/A:80
5 atoms, 4 bonds, 1 residue, 1 model selected
> view matrix models
> #6,0.25185,0.84282,0.47564,-269.49,-0.94542,0.10926,0.30699,642.02,0.20677,-0.52699,0.82433,231.95
> view matrix models
> #6,0.25185,0.84282,0.47564,-279,-0.94542,0.10926,0.30699,632.64,0.20677,-0.52699,0.82433,223.11
> select add #6
942 atoms, 964 bonds, 120 residues, 1 model selected
> volume zone #1 nearAtoms sel & #6 range 6.48
> volume zone #1 nearAtoms sel & #6 range 12
> volume zone #1 nearAtoms sel & #6 range 25
> select #6/A:66
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models
> #6,0.25185,0.84282,0.47564,-278.26,-0.94542,0.10926,0.30699,636.21,0.20677,-0.52699,0.82433,223.74
> view matrix models
> #6,0.25185,0.84282,0.47564,-270.53,-0.94542,0.10926,0.30699,648.88,0.20677,-0.52699,0.82433,231.4
> view matrix models
> #6,0.8223,0.51413,0.24392,-263.4,-0.54351,0.83657,0.068962,287.75,-0.1686,-0.18928,0.96734,180.34
> view matrix models
> #6,0.51798,0.55157,0.65381,-342.73,-0.85182,0.26284,0.45312,477.61,0.078083,-0.79164,0.60598,497.35
> view matrix models
> #6,0.51798,0.55157,0.65381,-346.33,-0.85182,0.26284,0.45312,467.79,0.078083,-0.79164,0.60598,494.51
> view matrix models
> #6,0.70069,0.44162,0.56035,-333.15,-0.67248,0.67116,0.31195,287.88,-0.23832,-0.59541,0.76726,469.5
> view matrix models
> #6,0.70069,0.44162,0.56035,-328.8,-0.67248,0.67116,0.31195,284.14,-0.23832,-0.59541,0.76726,468.65
> view matrix models
> #6,0.70069,0.44162,0.56035,-327.73,-0.67248,0.67116,0.31195,284.64,-0.23832,-0.59541,0.76726,470.55
> view matrix models
> #6,0.12168,0.84279,0.52431,-237.01,-0.99015,0.066246,0.12331,757.93,0.069195,-0.53416,0.84255,281.55
> view matrix models
> #6,0.12168,0.84279,0.52431,-236.89,-0.99015,0.066246,0.12331,754.07,0.069195,-0.53416,0.84255,281.49
> view matrix models
> #6,0.12168,0.84279,0.52431,-239.83,-0.99015,0.066246,0.12331,751.7,0.069195,-0.53416,0.84255,282.33
> view matrix models
> #6,0.12168,0.84279,0.52431,-240.01,-0.99015,0.066246,0.12331,756.59,0.069195,-0.53416,0.84255,282.07
> view matrix models
> #6,0.12168,0.84279,0.52431,-242.9,-0.99015,0.066246,0.12331,769.93,0.069195,-0.53416,0.84255,288.06
> view matrix models
> #6,0.12168,0.84279,0.52431,-242.87,-0.99015,0.066246,0.12331,765.51,0.069195,-0.53416,0.84255,284.39
> view matrix models
> #6,-0.4405,-0.53573,0.72038,476.96,0.57989,-0.78236,-0.22724,628.07,0.68534,0.31764,0.65529,-241.83
> view matrix models
> #6,0.82969,-0.49657,0.25502,146.91,0.4714,0.86794,0.15639,-195.16,-0.299,-0.0095364,0.95421,166.78
> view matrix models
> #6,0.33833,-0.88722,0.31366,488.06,0.93946,0.33768,-0.05817,-68.994,-0.05431,0.31436,0.94775,-67.783
> view matrix models
> #6,-0.53902,-0.83444,0.11477,924.74,0.64181,-0.49513,-0.5856,648.85,0.54547,-0.24198,0.80244,-17.911
> view matrix models
> #6,-0.20747,-0.83694,0.50645,605.17,0.6614,-0.50146,-0.55775,630.36,0.72077,0.21925,0.65759,-216.55
> view matrix models
> #6,-0.20747,-0.83694,0.50645,601.78,0.6614,-0.50146,-0.55775,617.34,0.72077,0.21925,0.65759,-221.21
> view matrix models
> #6,-0.20747,-0.83694,0.50645,609.5,0.6614,-0.50146,-0.55775,613.59,0.72077,0.21925,0.65759,-231.14
> view matrix models
> #6,-0.1141,-0.83581,0.53703,555.83,0.71926,-0.44239,-0.53569,554.48,0.68531,0.32514,0.65164,-257.85
> view matrix models
> #6,-0.1141,-0.83581,0.53703,556.62,0.71926,-0.44239,-0.53569,549.49,0.68531,0.32514,0.65164,-258.92
> view matrix models
> #6,-0.1141,-0.83581,0.53703,557.91,0.71926,-0.44239,-0.53569,550.1,0.68531,0.32514,0.65164,-260.06
> view matrix models
> #6,-0.1141,-0.83581,0.53703,557.57,0.71926,-0.44239,-0.53569,550.52,0.68531,0.32514,0.65164,-260.68
> view matrix models
> #6,-0.1141,-0.83581,0.53703,558.15,0.71926,-0.44239,-0.53569,549.32,0.68531,0.32514,0.65164,-261.1
> fitmap #6 inMap #1
Fit molecule 1-118_MFZ0.pdb (#6) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 942 atoms
average map value = 0.1449, steps = 68
shifted from previous position = 1.59
rotated from previous position = 8.57 degrees
atoms outside contour = 698, contour level = 0.25
Position of 1-118_MFZ0.pdb (#6) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.10481050 -0.83355526 0.54240241 550.09926538
0.81362753 -0.38549640 -0.43520428 439.97137205
0.57186100 0.39569955 0.71860758 -275.05604183
Axis 0.45032428 -0.01596565 0.89272232
Axis point 180.41019642 423.44436178 0.00000000
Rotation angle (degrees) 112.69649829
Shift along axis -4.85004032
> select #6/A:24
9 atoms, 8 bonds, 1 residue, 1 model selected
> view matrix models
> #6,-0.16462,-0.86415,0.47554,618.97,0.8056,-0.39598,-0.44069,450.25,0.56913,0.31055,0.76135,-258.2
> view matrix models
> #6,-0.075908,-0.82702,0.55702,528.5,0.82069,-0.36909,-0.43616,430.61,0.56631,0.42404,0.70675,-279.07
> view matrix models
> #6,0.36351,-0.88416,0.29346,491.59,0.78101,0.11752,-0.61336,326.15,0.50782,0.45216,0.73326,-278.75
> hide #6 models
> hide #8 models
> hide #7 models
> show #!5 models
> hide #5.1 models
> show #5.1 models
> hide #5.1 models
> ui tool show "Color Actions"
> color sel bychain
> select add #5
4225 atoms, 3619 bonds, 445 pseudobonds, 1148 residues, 3 models selected
> ui tool show "Color Actions"
[Repeated 2 time(s)]
> color sel bychain
> select subtract #5.1
4225 atoms, 3619 bonds, 1148 residues, 2 models selected
> select add #5
4225 atoms, 3619 bonds, 445 pseudobonds, 1148 residues, 3 models selected
> select add #6
5158 atoms, 4575 bonds, 445 pseudobonds, 1267 residues, 3 models selected
> select subtract #6
4216 atoms, 3611 bonds, 445 pseudobonds, 1147 residues, 2 models selected
> volume zone #1 nearAtoms sel & #5 range 6.48
> transparency 50
> volume zone #1 nearAtoms sel & #5 range 3
> ui tool show "Fit in Map"
> fitmap #5 inMap #1
Fit molecule 3qr8_3qr8_01000000_3qr8_02000000.pdb (#5) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 4216 atoms
average map value = 0.1443, steps = 48
shifted from previous position = 0.00128
rotated from previous position = 0.00294 degrees
atoms outside contour = 3225, contour level = 0.25
Position of 3qr8_3qr8_01000000_3qr8_02000000.pdb (#5) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.41417819 0.91019297 -0.00227592 378.81675653
0.91019439 0.41417182 -0.00280589 398.56916577
-0.00161128 -0.00323367 -0.99999347 527.78675860
Axis -0.54121245 -0.84088397 0.00179532
Axis point 61.08206715 0.00000000 264.32908003
Rotation angle (degrees) 179.97735673
Shift along axis -539.22322291
> select subtract #5.1
4216 atoms, 3611 bonds, 1147 residues, 1 model selected
> show #6 models
> mmaker #6 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3qr8_3qr8_01000000_3qr8_02000000.pdb, chain A (#5) with
1-118_MFZ0.pdb, chain A (#6), sequence alignment score = 72
RMSD between 37 pruned atom pairs is 1.139 angstroms; (across all 110 pairs:
6.194)
> transparency 0
> transparency 50
> fitmap #6 inMap #1
Fit molecule 1-118_MFZ0.pdb (#6) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) using 942 atoms
average map value = 0.158, steps = 72
shifted from previous position = 1.53
rotated from previous position = 3.86 degrees
atoms outside contour = 692, contour level = 0.25
Position of 1-118_MFZ0.pdb (#6) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.53032930 0.84717964 0.03220991 267.83921123
-0.84606605 -0.53129057 0.04361829 966.65208388
0.05406536 -0.00411965 0.99852890 -19.41803155
Axis -0.02817962 -0.01290123 -0.99951962
Axis point 401.62578263 409.35553604 0.00000000
Rotation angle (degrees) 122.10993674
Shift along axis -0.60989936
> transparency 0
> hide #!5 models
> transparency 50
> select add #6
5158 atoms, 4575 bonds, 1267 residues, 2 models selected
> select add #5
5158 atoms, 4575 bonds, 445 pseudobonds, 1267 residues, 3 models selected
> volume zone #1 nearAtoms sel & #6 range 6.48
> view matrix models
> #5,0.56924,0.7256,-0.38661,412.99,0.70342,-0.67326,-0.22786,454.36,-0.42562,-0.14225,-0.89365,525.29,#6,-0.8985,-0.07658,0.43225,621.67,0.18527,-0.95882,0.21525,635.06,0.39796,0.27349,0.87569,-221.89
> view matrix models
> #5,0.56924,0.7256,-0.38661,418.34,0.70342,-0.67326,-0.22786,462.26,-0.42562,-0.14225,-0.89365,521.5,#6,-0.8985,-0.07658,0.43225,627.02,0.18527,-0.95882,0.21525,642.96,0.39796,0.27349,0.87569,-225.68
> view matrix models
> #5,0.18036,0.88161,-0.43617,414.02,0.81433,-0.38254,-0.43649,464.11,-0.55166,-0.27646,-0.78691,519.76,#6,-0.81191,0.33372,0.479,397.57,-0.1075,-0.89194,0.43919,633.01,0.5738,0.30509,0.76004,-258.49
> view matrix models
> #5,0.18036,0.88161,-0.43617,420.7,0.81433,-0.38254,-0.43649,456.87,-0.55166,-0.27646,-0.78691,521.63,#6,-0.81191,0.33372,0.479,404.26,-0.1075,-0.89194,0.43919,625.77,0.5738,0.30509,0.76004,-256.62
> view matrix models
> #5,0.26428,0.95266,-0.15031,400.56,0.77313,-0.30244,-0.5575,461.06,-0.57657,0.031126,-0.81646,511.32,#6,-0.93175,0.30389,0.19872,597.15,-0.14546,-0.81386,0.56256,551.57,0.33269,0.49526,0.80251,-255.25
> view matrix models
> #5,0.26428,0.95266,-0.15031,401.44,0.77313,-0.30244,-0.5575,461.42,-0.57657,0.031126,-0.81646,510.2,#6,-0.93175,0.30389,0.19872,598.03,-0.14546,-0.81386,0.56256,551.94,0.33269,0.49526,0.80251,-256.36
> view matrix models
> #5,0.29,0.89654,-0.33484,415.11,0.71154,-0.43596,-0.55105,466.06,-0.64001,-0.07845,-0.76435,511.08,#6,-0.88983,0.25083,0.38118,517.83,-0.00061247,-0.83602,0.5487,507.2,0.4563,0.48802,0.74406,-277.74
> view matrix models
> #5,0.18567,0.9579,0.21898,378.2,0.95104,-0.11914,-0.2852,438.03,-0.2471,0.26121,-0.93312,509.47,#6,-0.91148,0.37374,-0.1718,732.75,-0.40989,-0.8603,0.30311,802.45,-0.034519,0.3467,0.93734,-103.7
> view matrix models
> #5,0.18567,0.9579,0.21898,379.21,0.95104,-0.11914,-0.2852,439.37,-0.2471,0.26121,-0.93312,507.46,#6,-0.91148,0.37374,-0.1718,733.76,-0.40989,-0.8603,0.30311,803.78,-0.034519,0.3467,0.93734,-105.7
> view matrix models
> #5,0.039873,0.97321,0.22645,377.67,0.93865,0.041211,-0.3424,436.57,-0.34255,0.22621,-0.91186,507.21,#6,-0.84435,0.50386,-0.1822,656.16,-0.5338,-0.76181,0.36701,784.6,0.046121,0.40714,0.9122,-152.93
> view matrix models
> #5,0.039873,0.97321,0.22645,377.66,0.93865,0.041211,-0.3424,438.24,-0.34255,0.22621,-0.91186,508.48,#6,-0.84435,0.50386,-0.1822,656.15,-0.5338,-0.76181,0.36701,786.26,0.046121,0.40714,0.9122,-151.67
> view matrix models
> #5,0.26019,0.94791,-0.18376,404.71,0.91716,-0.30213,-0.25986,446.52,-0.30184,-0.10092,-0.948,523.65,#6,-0.92385,0.30456,0.23182,580.08,-0.24004,-0.93278,0.26889,780.78,0.29813,0.19277,0.93486,-177.76
> view matrix models
> #5,0.71569,0.48867,0.49899,382.08,0.27612,0.45828,-0.84483,450.72,-0.64152,0.74242,0.19305,419.12,#6,-0.8264,-0.32608,-0.45906,1124.5,-0.49124,0.019018,0.87082,207.62,-0.27523,0.94515,-0.1759,263.74
> view matrix models
> #5,0.23791,0.96623,-0.098985,398.69,0.79274,-0.25205,-0.55501,462.36,-0.56122,0.053571,-0.82593,509.22,#6,-0.93113,0.33357,0.14741,610.26,-0.19837,-0.80244,0.56279,572.15,0.30602,0.49479,0.81335,-250.81
> view matrix models
> #5,0.23791,0.96623,-0.098985,397.68,0.79274,-0.25205,-0.55501,459.41,-0.56122,0.053571,-0.82593,509.59,#6,-0.93113,0.33357,0.14741,609.26,-0.19837,-0.80244,0.56279,569.2,0.30602,0.49479,0.81335,-250.44
> view matrix models
> #5,0.23791,0.96623,-0.098985,397.72,0.79274,-0.25205,-0.55501,459.42,-0.56122,0.053571,-0.82593,509.75,#6,-0.93113,0.33357,0.14741,609.29,-0.19837,-0.80244,0.56279,569.21,0.30602,0.49479,0.81335,-250.28
> view matrix models
> #5,0.43448,0.89479,-0.10289,401.4,0.73757,-0.41903,-0.52954,464.21,-0.51693,0.15419,-0.84202,506.95,#6,-0.97962,0.13015,0.15302,711.98,-0.030138,-0.84833,0.52861,534.08,0.19861,0.51323,0.83496,-223.21
> view matrix models
> #5,0.43448,0.89479,-0.10289,401.38,0.73757,-0.41903,-0.52954,464.46,-0.51693,0.15419,-0.84202,505.87,#6,-0.97962,0.13015,0.15302,711.96,-0.030138,-0.84833,0.52861,534.33,0.19861,0.51323,0.83496,-224.29
> view matrix models
> #5,0.10919,0.9907,-0.081155,395.23,0.99398,-0.10805,0.018374,419.32,0.0094345,-0.082673,-0.99653,526.4,#6,-0.88156,0.45452,0.1275,547.28,-0.4581,-0.8889,0.0014811,975.16,0.11401,-0.0571,0.99184,-23.495
> open
> /Users/egelmanlab01/Downloads/cryosparc_P101_J122_009_volume_map_sharp.mrc
Opened cryosparc_P101_J122_009_volume_map_sharp.mrc as #9, grid size
512,512,512, pixel 1.08, shown at level 0.116, step 2, values float32
> close #1-8
> volume #9 step 1
> volume #9 color darkgrey
> view clip false
> volume #9 level 0.1576
> volume #9 level 0.09999
> ui tool show "Segment Map"
> volume #9 level 0.15
> volume #9 level 0.11
Segmenting cryosparc_P101_J122_009_volume_map_sharp.mrc, density threshold
0.110000
Only showing 60 of 2538 regions.
Showing 60 of 2538 region surfaces
11302 watershed regions, grouped to 2538 regions
Showing cryosparc_P101_J122_009_volume_map_sharp.seg - 2538 regions, 60
surfaces
> volume #9 level 0.09
Segmenting cryosparc_P101_J122_009_volume_map_sharp.mrc, density threshold
0.090000
Only showing 60 of 2839 regions.
Showing 60 of 2839 region surfaces
15422 watershed regions, grouped to 2839 regions
Showing cryosparc_P101_J122_009_volume_map_sharp.seg - 2839 regions, 60
surfaces
> volume #9 level 0.08
Segmenting cryosparc_P101_J122_009_volume_map_sharp.mrc, density threshold
0.080000
Only showing 60 of 2789 regions.
Showing 60 of 2789 region surfaces
17550 watershed regions, grouped to 2789 regions
Showing cryosparc_P101_J122_009_volume_map_sharp.seg - 2789 regions, 60
surfaces
> open
> /Users/egelmanlab01/Documents/milano/base_plate/cryosparc_P101_J257_005_volume_map_sharp.mrc
Opened cryosparc_P101_J257_005_volume_map_sharp.mrc as #2, grid size
768,768,768, pixel 1.08, shown at step 1, values float32
> close #9
> volume #2 region 0,0,0,767,767,767 step 4
[Repeated 1 time(s)]
> volume #2 change image level -0.055,0 level 0.2541,0.8 level 0.9056,1
> volume #2 step 1
> close #1
> volume #2 level 0.2
> view clip false
> open /Users/egelmanlab01/Downloads/3qr8_3qr8_01000000_3qr8_02000000.pdb
Summary of feedback from opening
/Users/egelmanlab01/Downloads/3qr8_3qr8_01000000_3qr8_02000000.pdb
---
note | Combining 3 symmetry atoms into CL /A:212 CL
Chain information for 3qr8_3qr8_01000000_3qr8_02000000.pdb #1
---
Chain | Description
A | No description available
A | No description available
> open /Users/egelmanlab01/Downloads/3qr8_3qr8_01000000_3qr8_02000000.pdb
Summary of feedback from opening
/Users/egelmanlab01/Downloads/3qr8_3qr8_01000000_3qr8_02000000.pdb
---
note | Combining 3 symmetry atoms into CL /A:212 CL
Chain information for 3qr8_3qr8_01000000_3qr8_02000000.pdb #3
---
Chain | Description
A | No description available
A | No description available
> close #3
> view clip false
Drag select of 227 atoms, 471 residues, 206 pseudobonds, 15 bonds
> hide sel atoms
Drag select of 455 residues
> view matrix models #1,1,0,0,374.44,0,1,0,361.13,0,0,1,514.23
> view matrix models #1,1,0,0,424,0,1,0,362.61,0,0,1,496.73
> view matrix models #1,1,0,0,419.35,0,1,0,384.42,0,0,1,487.04
> view matrix models
> #1,0.5129,-0.83381,0.20419,442.07,-0.85676,-0.48227,0.1827,433.98,-0.05386,-0.26864,-0.96173,597.37
> view matrix models
> #1,0.5129,-0.83381,0.20419,444.09,-0.85676,-0.48227,0.1827,440.39,-0.05386,-0.26864,-0.96173,594.13
> view matrix models
> #1,0.5129,-0.83381,0.20419,446.34,-0.85676,-0.48227,0.1827,423.13,-0.05386,-0.26864,-0.96173,590.67
> view matrix models
> #1,0.532,-0.84207,0.088836,452.53,-0.84305,-0.51697,0.14834,426.25,-0.078987,-0.15381,-0.98494,587.29
> view matrix models
> #1,0.532,-0.84207,0.088836,445.65,-0.84305,-0.51697,0.14834,426.75,-0.078987,-0.15381,-0.98494,588.1
> ui tool show "Side View"
> view matrix models
> #1,0.532,-0.84207,0.088836,447.33,-0.84305,-0.51697,0.14834,427.93,-0.078987,-0.15381,-0.98494,580.21
> view matrix models
> #1,0.532,-0.84207,0.088836,450.57,-0.84305,-0.51697,0.14834,429.72,-0.078987,-0.15381,-0.98494,566.4
> view matrix models
> #1,0.532,-0.84207,0.088836,443.2,-0.84305,-0.51697,0.14834,431.08,-0.078987,-0.15381,-0.98494,555.68
> view matrix models
> #1,0.80044,-0.59733,0.049893,435.46,-0.58596,-0.76223,0.27506,434.37,-0.12627,-0.24941,-0.96013,558.23
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule 3qr8_3qr8_01000000_3qr8_02000000.pdb (#1) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 4216 atoms
average map value = 0.1125, steps = 152
shifted from previous position = 6.17
rotated from previous position = 21.2 degrees
atoms outside contour = 3179, contour level = 0.2
Position of 3qr8_3qr8_01000000_3qr8_02000000.pdb (#1) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.91874608 -0.39484734 -0.00110521 430.36118401
-0.39484079 -0.91874156 0.00383240 450.89003481
-0.00252862 -0.00308462 -0.99999205 545.65015476
Axis -0.97947584 0.20155945 0.00092754
Axis point 0.00000000 270.21756027 272.56251469
Rotation angle (degrees) 179.79768912
Shift along axis -330.14112111
> view matrix models
> #1,0.91875,-0.39485,-0.0011052,431.25,-0.39484,-0.91874,0.0038324,452.93,-0.0025286,-0.0030846,-0.99999,528.21
> fitmap #1 inMap #2
Fit molecule 3qr8_3qr8_01000000_3qr8_02000000.pdb (#1) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 4216 atoms
average map value = 0.1398, steps = 76
shifted from previous position = 2.34
rotated from previous position = 0.764 degrees
atoms outside contour = 2861, contour level = 0.2
Position of 3qr8_3qr8_01000000_3qr8_02000000.pdb (#1) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.91721297 -0.39838529 -0.00308745 430.41344004
-0.39839671 -0.91717130 -0.00876736 451.46642860
0.00066107 0.00927157 -0.99995680 527.42633401
Axis 0.97908406 -0.20345520 -0.00061955
Axis point 0.00000000 269.21236980 265.06888881
Rotation angle (degrees) 179.47217554
Shift along axis 329.23098211
> select add #1
4216 atoms, 3611 bonds, 445 pseudobonds, 1147 residues, 2 models selected
> volume zone #2 nearAtoms sel & #1 range 6.48
> select clear
> select /A:124
24 atoms, 21 bonds, 3 residues, 1 model selected
> view matrix models
> #1,0.27287,-0.95553,-0.11182,458.06,-0.96001,-0.27802,0.033073,423.98,-0.06269,0.098323,-0.99318,523.55
> fitmap #1 inMap #2
Fit molecule 3qr8_3qr8_01000000_3qr8_02000000.pdb (#1) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 4216 atoms
average map value = 0.1428, steps = 80
shifted from previous position = 0.32
rotated from previous position = 10.8 degrees
atoms outside contour = 2853, contour level = 0.2
Position of 3qr8_3qr8_01000000_3qr8_02000000.pdb (#1) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.41420108 -0.91018326 0.00197543 450.68623962
-0.91018518 -0.41420151 0.00020294 431.06087828
0.00063351 -0.00188207 -0.99999803 527.85425033
Axis -0.84089270 0.54120131 -0.00077561
Axis point 0.00000000 360.75653078 263.53125115
Rotation angle (degrees) 179.92896701
Shift along axis -146.09746456
> ui tool show "Color Actions"
[Repeated 1 time(s)]
> volume zone #2 nearAtoms sel & #1 range 6.48
> select clear
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume zone #2 nearAtoms #1 range 6.48
> transparency 50
> select /A:101
30 atoms, 30 bonds, 3 residues, 1 model selected
Drag select of 2 cryosparc_P101_J257_005_volume_map_sharp.mrc , 2 residues
> select clear
> ui mousemode right "play coordinates"
> ui mousemode right "translate selected models"
> select /A:106
24 atoms, 21 bonds, 3 residues, 1 model selected
> view matrix models
> #1,0.22087,-0.97498,0.025226,452.08,-0.97459,-0.21964,0.043929,421.12,-0.037289,-0.034288,-0.99872,529.08
> fitmap #1 inMap #2
Fit molecule 3qr8_3qr8_01000000_3qr8_02000000.pdb (#1) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 4216 atoms
average map value = 0.1448, steps = 264
shifted from previous position = 0.172
rotated from previous position = 16.5 degrees
atoms outside contour = 2818, contour level = 0.2
Position of 3qr8_3qr8_01000000_3qr8_02000000.pdb (#1) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.06090683 -0.99810175 0.00912426 453.82470038
-0.99813026 0.06085647 -0.00569861 412.62991057
0.00513252 -0.00945429 -0.99994214 528.32380743
Axis -0.68523401 0.72830440 -0.00520146
Axis point 421.52319710 0.00000000 265.21698220
Rotation angle (degrees) 179.84298467
Shift along axis -13.20399405
> ui tool show "Color Actions"
> color sel bychain
[Repeated 6 time(s)]
> select add #1
4216 atoms, 3611 bonds, 445 pseudobonds, 1147 residues, 2 models selected
> color sel bychain
[Repeated 2 time(s)]
> color sel red
> color sel orange
> select /A:117
18 atoms, 15 bonds, 3 residues, 1 model selected
> view matrix models
> #1,0.22666,-0.97078,0.078846,449.19,-0.97224,-0.22069,0.077733,419.57,-0.058061,-0.094276,-0.99385,531.38
> fitmap #1 inMap #2
Fit molecule 3qr8_3qr8_01000000_3qr8_02000000.pdb (#1) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 4216 atoms
average map value = 0.1449, steps = 284
shifted from previous position = 0.134
rotated from previous position = 17.5 degrees
atoms outside contour = 2822, contour level = 0.2
Position of 3qr8_3qr8_01000000_3qr8_02000000.pdb (#1) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.06048150 -0.99812869 0.00900653 453.82985246
-0.99815654 0.06043260 -0.00560646 412.64381678
0.00505168 -0.00932902 -0.99994372 528.34253840
Axis -0.68538918 0.72815889 -0.00512785
Axis point 421.61069659 0.00000000 265.20958713
Rotation angle (degrees) 179.84440445
Shift along axis -13.28906820
> select clear
> select add #1
4216 atoms, 3611 bonds, 445 pseudobonds, 1147 residues, 2 models selected
> volume zone #2 nearAtoms sel & #1 range 6.48
> volume zone #2 nearAtoms sel & #1 range 3
> view matrix models
> #1,-0.057489,-0.99771,0.035717,452.46,-0.99776,0.056193,-0.036284,414.37,0.034193,-0.037723,-0.9987,529.41
> view matrix models
> #1,-0.057489,-0.99771,0.035717,453.2,-0.99776,0.056193,-0.036284,416.06,0.034193,-0.037723,-0.9987,534.21
> fitmap #1 inMap #2
Fit molecule 3qr8_3qr8_01000000_3qr8_02000000.pdb (#1) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 4216 atoms
average map value = 0.1338, steps = 60
shifted from previous position = 1.79
rotated from previous position = 5.48 degrees
atoms outside contour = 2945, contour level = 0.2
Position of 3qr8_3qr8_01000000_3qr8_02000000.pdb (#1) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.01561681 -0.99551801 0.09327387 451.27223186
-0.99937577 0.01849736 0.03009839 412.75384525
-0.03168881 -0.09274561 -0.99518545 535.97382501
Axis -0.70086575 0.71295355 -0.02200984
Axis point 444.99353015 0.00000000 261.19301343
Rotation angle (degrees) 174.97230166
Shift along axis -33.80363216
> select clear
> select /A:124
24 atoms, 21 bonds, 3 residues, 1 model selected
> view matrix models
> #1,-0.015989,-0.99667,0.080009,451.99,-0.99879,0.01964,0.045051,411.95,-0.046472,-0.079192,-0.99578,535.47
> view matrix models
> #1,-0.015989,-0.99667,0.080009,450.07,-0.99879,0.01964,0.045051,414.12,-0.046472,-0.079192,-0.99578,535.52
> view matrix models
> #1,-0.016852,-0.99798,0.061238,451.07,-0.99759,0.020907,0.066202,412.99,-0.067349,-0.059975,-0.99593,534.77
> view matrix models
> #1,-0.016852,-0.99798,0.061238,450.91,-0.99759,0.020907,0.066202,413.18,-0.067349,-0.059975,-0.99593,535.19
> view matrix models
> #1,-0.017942,-0.99884,0.044642,451.78,-0.99615,0.021688,0.084895,412.19,-0.085765,-0.042948,-0.99539,534.48
> view matrix models
> #1,-0.017942,-0.99884,0.044642,451.58,-0.99615,0.021688,0.084895,412.43,-0.085765,-0.042948,-0.99539,534.16
> view matrix models
> #1,-0.018241,-0.999,0.040767,451.78,-0.99577,0.021824,0.08926,412.2,-0.09006,-0.038966,-0.99517,533.99
> fitmap #1 inMap #2
Fit molecule 3qr8_3qr8_01000000_3qr8_02000000.pdb (#1) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 4216 atoms
average map value = 0.1337, steps = 76
shifted from previous position = 3.54
rotated from previous position = 4.56 degrees
atoms outside contour = 2944, contour level = 0.2
Position of 3qr8_3qr8_01000000_3qr8_02000000.pdb (#1) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.01559959 -0.99548553 0.09362272 451.25215733
-0.99937501 0.01849380 0.03012589 412.75300401
-0.03172132 -0.09309426 -0.99515186 535.99428542
Axis -0.70086761 0.71294822 -0.02212310
Axis point 445.03634944 0.00000000 261.19725093
Rotation angle (degrees) 174.95688024
Shift along axis -33.85435677
> transparency 0
> view matrix models
> #1,-0.0156,-0.99549,0.093623,453.71,-0.99938,0.018494,0.030126,456.04,-0.031721,-0.093094,-0.99515,540.42
> view matrix models
> #1,-0.1207,-0.99022,0.070044,454.7,-0.99241,0.11869,-0.032209,455.24,0.023581,-0.073399,-0.99702,539.73
> view matrix models
> #1,0.69709,-0.70515,0.12977,440.34,-0.68563,-0.70853,-0.16702,494.91,0.20972,0.027452,-0.97737,534.73
> view matrix models
> #1,0.70182,-0.71229,-0.0095731,447.7,-0.70344,-0.6951,0.14836,478.36,-0.11233,-0.097385,-0.98889,540.27
> open
> /Users/egelmanlab01/Documents/milano/ravi2/A0A482MFZ0_unrelaxed_rank_1_model_3.pdb
Chain information for A0A482MFZ0_unrelaxed_rank_1_model_3.pdb #3
---
Chain | Description
A | No description available
> view clip false
Drag select of 188 residues
> view matrix models #3,1,0,0,114.19,0,1,0,398.09,0,0,1,517.67
> view matrix models #3,1,0,0,286.14,0,1,0,287.88,0,0,1,557.53
> view matrix models #3,1,0,0,434.53,0,1,0,316.77,0,0,1,505.98
> view matrix models
> #3,0.9764,0.0862,0.198,433.53,-0.10006,0.9931,0.061085,316.25,-0.19137,-0.079456,0.9783,505.64
> view matrix models
> #3,0.99947,0.013944,0.029553,434.39,-0.014258,0.99984,0.010432,316.69,-0.029403,-0.010848,0.99951,505.91
> view matrix models
> #3,0.14838,0.88117,-0.44891,430.6,-0.988,0.1518,-0.02859,315.99,0.042953,0.44776,0.89312,505.19
> view matrix models
> #3,0.25338,0.73081,-0.63381,432.01,-0.96734,0.19609,-0.16062,316.37,0.0069044,0.65381,0.75663,504.93
> view matrix models
> #3,0.25338,0.73081,-0.63381,453.62,-0.96734,0.19609,-0.16062,332.74,0.0069044,0.65381,0.75663,522.83
> view matrix models
> #3,0.25338,0.73081,-0.63381,402.31,-0.96734,0.19609,-0.16062,344.98,0.0069044,0.65381,0.75663,502.16
> view matrix models
> #3,0.25338,0.73081,-0.63381,431.15,-0.96734,0.19609,-0.16062,411.74,0.0069044,0.65381,0.75663,511.6
> view matrix models
> #3,0.71323,0.6851,-0.14813,431.2,-0.66041,0.58601,-0.46953,412.68,-0.23486,0.43271,0.8704,511.04
> view matrix models
> #3,0.71323,0.6851,-0.14813,431.58,-0.66041,0.58601,-0.46953,414.27,-0.23486,0.43271,0.8704,502.35
> view matrix models
> #3,-0.47322,0.36097,-0.8036,430.7,-0.65213,-0.75683,0.044063,416.46,-0.59228,0.5449,0.59354,501.74
> view matrix models
> #3,-0.47322,0.36097,-0.8036,422.08,-0.65213,-0.75683,0.044063,413.65,-0.59228,0.5449,0.59354,500.96
> fitmap #3 inMap #2
Fit molecule A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 1457 atoms
average map value = 0.1336, steps = 244
shifted from previous position = 7.59
rotated from previous position = 8.21 degrees
atoms outside contour = 1000, contour level = 0.2
Position of A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.38150610 0.46746846 -0.79744990 415.72413253
-0.69614595 -0.71286893 -0.08484522 417.84997250
-0.60813972 0.52277255 0.59739011 502.03208701
Axis 0.45813459 -0.14273701 -0.87734762
Axis point 419.70051269 47.56921522 0.00000000
Rotation angle (degrees) 138.45995791
Shift along axis -309.64170695
> view matrix models
> #3,-0.38151,0.46747,-0.79745,418.2,-0.69615,-0.71287,-0.084845,382.94,-0.60814,0.52277,0.59739,507.56
> view matrix models
> #3,0.36209,0.89369,-0.26498,417.69,-0.73248,0.096974,-0.67385,382.45,-0.57651,0.43808,0.68972,507.6
> view matrix models
> #3,0.36209,0.89369,-0.26498,423.42,-0.73248,0.096974,-0.67385,412.15,-0.57651,0.43808,0.68972,490.92
> view matrix models
> #3,0.36209,0.89369,-0.26498,426.14,-0.73248,0.096974,-0.67385,409.27,-0.57651,0.43808,0.68972,490.79
> fitmap #3 inMap #2
Fit molecule A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 1457 atoms
average map value = 0.1551, steps = 356
shifted from previous position = 10.9
rotated from previous position = 17.3 degrees
atoms outside contour = 922, contour level = 0.2
Position of A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.59231162 0.78926852 -0.16193258 415.09927052
-0.67372108 0.37494735 -0.63680012 410.78072343
-0.44189009 0.48628150 0.75383251 491.27888746
Axis 0.60203260 0.15007240 -0.78424169
Axis point 788.42429372 -174.91697509 0.00000000
Rotation angle (degrees) 68.86628429
Shift along axis -73.73124539
> view matrix models
> #3,0.63953,0.75811,-0.12758,415.23,-0.62232,0.41309,-0.66488,410.94,-0.45135,0.50461,0.73597,491.25
> view matrix models
> #3,0.7385,0.66395,0.11745,415.02,-0.37125,0.5458,-0.75118,411.69,-0.56285,0.51114,0.64956,491.15
> view matrix models
> #3,0.7385,0.66395,0.11745,452.9,-0.37125,0.5458,-0.75118,423.01,-0.56285,0.51114,0.64956,534.05
> select #3:1-20
171 atoms, 172 bonds, 20 residues, 1 model selected
> save /Users/egelmanlab01/Desktop/1-20.pdb models #3 selectedOnly true
> open /Users/egelmanlab01/Desktop/1-20.pdb
Summary of feedback from opening /Users/egelmanlab01/Desktop/1-20.pdb
---
warnings | Start residue of secondary structure not found: HELIX 3 3 ARG A 86
LYS A 88 1 3
Start residue of secondary structure not found: SHEET 1 1 1 HIS A 21 THR A 29
0
Start residue of secondary structure not found: SHEET 2 2 1 GLY A 32 GLY A 39
0
Start residue of secondary structure not found: SHEET 3 3 1 GLU A 45 PRO A 48
0
Start residue of secondary structure not found: SHEET 4 4 1 VAL A 66 GLY A 70
0
7 messages similar to the above omitted
Chain information for 1-20.pdb #4
---
Chain | Description
A | No description available
> hide #3 models
> select add #3
1457 atoms, 1489 bonds, 188 residues, 1 model selected
Drag select of 7 residues
> view matrix models #4,1,0,0,-46.382,0,1,0,-9.4978,0,0,1,-34.644
> view matrix models #4,1,0,0,-49.467,0,1,0,-16.756,0,0,1,-41.217
> select add #4
171 atoms, 172 bonds, 20 residues, 1 model selected
> volume zone #2 nearAtoms sel & #4 range 6.48
> volume zone #2 nearAtoms sel & #4 range 5
> hide #!1 models
> volume zone #2 nearAtoms sel & #4 range 10
> volume zone #2 nearAtoms sel & #4 range 15
> view matrix models #4,1,0,0,-46.968,0,1,0,-15.251,0,0,1,-40.377
> volume zone #2 nearAtoms sel & #4 range 10
> view matrix models #4,1,0,0,-48.234,0,1,0,-20.623,0,0,1,-44.92
> volume zone #2 nearAtoms sel & #4 range 10
> view matrix models
> #4,0.55937,0.48943,0.669,-391.64,-0.74976,0.64292,0.15655,397.24,-0.3535,-0.58916,0.72659,506.53
> view matrix models
> #4,0.55937,0.48943,0.669,-395.3,-0.74976,0.64292,0.15655,420.56,-0.3535,-0.58916,0.72659,509.17
> show sel atoms
> view matrix models
> #4,0.82097,-0.56918,0.045285,251.29,0.30511,0.50435,0.8078,-325.26,-0.48262,-0.64936,0.58772,663.1
> view matrix models
> #4,0.82097,-0.56918,0.045285,249.79,0.30511,0.50435,0.8078,-351.52,-0.48262,-0.64936,0.58772,663.55
> view matrix models
> #4,0.82097,-0.56918,0.045285,246.91,0.30511,0.50435,0.8078,-349.34,-0.48262,-0.64936,0.58772,661.96
> view matrix models
> #4,0.61385,-0.7894,-0.0056739,461.27,0.39394,0.30009,0.86877,-332.47,-0.6841,-0.53553,0.49519,751
> view matrix models
> #4,0.61385,-0.7894,-0.0056739,461.31,0.39394,0.30009,0.86877,-333.58,-0.6841,-0.53553,0.49519,750.4
> view matrix models
> #4,0.31929,-0.94251,-0.098606,707.6,0.65613,0.14479,0.74062,-322.4,-0.68377,-0.30117,0.66465,565.07
> fitmap #3 inMap #2
Fit molecule A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 1457 atoms
average map value = 0.1501, steps = 304
shifted from previous position = 41.9
rotated from previous position = 10.8 degrees
atoms outside contour = 995, contour level = 0.2
Position of A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.77927026 0.57547851 0.24811763 481.38256565
-0.30040157 0.69048610 -0.65801812 449.73049474
-0.54999706 0.43823902 0.71094993 518.62365851
Axis 0.67909548 0.49440597 -0.54257909
Axis point 0.00000000 -913.57951419 911.92711674
Rotation angle (degrees) 53.81792769
Shift along axis 267.85981288
> fitmap #4 inMap #2
Fit molecule 1-20.pdb (#4) to map cryosparc_P101_J257_005_volume_map_sharp.mrc
(#2) using 171 atoms
average map value = 0.1717, steps = 56
shifted from previous position = 3.55
rotated from previous position = 12 degrees
atoms outside contour = 100, contour level = 0.2
Position of 1-20.pdb (#4) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.27590911 -0.92185619 -0.27213108 805.78660916
0.76829549 0.04138868 0.63875584 -281.51892876
-0.57757788 -0.38531563 0.71967747 527.04469300
Axis -0.51212326 0.15274951 0.84522030
Axis point 731.26808056 294.03818080 0.00000000
Rotation angle (degrees) 88.94067676
Shift along axis -10.19507382
> view matrix models
> #4,0.27591,-0.92186,-0.27213,801.95,0.7683,0.041389,0.63876,-279.98,-0.57758,-0.38532,0.71968,529.14
> volume zone #2 nearAtoms sel & #4 range 5
> view matrix models
> #4,0.656,-0.7478,-0.10222,469.3,0.62693,0.46447,0.62548,-390.69,-0.42026,-0.4744,0.77352,468.88
> view matrix models
> #4,0.656,-0.7478,-0.10222,469.3,0.62693,0.46447,0.62548,-390.51,-0.42026,-0.4744,0.77352,467.31
> view matrix models
> #4,0.656,-0.7478,-0.10222,470,0.62693,0.46447,0.62548,-389.29,-0.42026,-0.4744,0.77352,468.58
> view matrix models
> #4,0.55304,-0.81751,0.16067,415.74,0.59112,0.52092,0.6158,-392.4,-0.58713,-0.24559,0.77134,447.4
> view matrix models
> #4,0.55304,-0.81751,0.16067,414.71,0.59112,0.52092,0.6158,-391.77,-0.58713,-0.24559,0.77134,444.45
> view matrix models
> #4,0.55304,-0.81751,0.16067,414.84,0.59112,0.52092,0.6158,-391.71,-0.58713,-0.24559,0.77134,444.75
> view matrix models
> #4,0.55304,-0.81751,0.16067,416.67,0.59112,0.52092,0.6158,-392.59,-0.58713,-0.24559,0.77134,445.05
> view matrix models
> #4,0.36487,-0.91425,0.17613,536.23,0.50773,0.35395,0.78545,-367.48,-0.78044,-0.19716,0.59333,601.09
> view matrix models
> #4,0.36487,-0.91425,0.17613,536.03,0.50773,0.35395,0.78545,-367.19,-0.78044,-0.19716,0.59333,601.13
> fitmap #4 inMap #2
Fit molecule 1-20.pdb (#4) to map cryosparc_P101_J257_005_volume_map_sharp.mrc
(#2) using 171 atoms
average map value = 0.1731, steps = 64
shifted from previous position = 2.59
rotated from previous position = 13.6 degrees
atoms outside contour = 104, contour level = 0.2
Position of 1-20.pdb (#4) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.32020292 -0.94579782 -0.05419026 685.30378608
0.58205385 0.15127948 0.79895421 -319.78403191
-0.74745127 -0.28736912 0.59894540 624.17425930
Axis -0.54349874 0.34684562 0.76439992
Axis point 779.75267756 160.52966091 0.00000000
Rotation angle (degrees) 87.98197509
Shift along axis -6.25868458
> transparency 50
> view matrix models
> #4,0.25013,-0.96545,0.073113,662.18,0.54436,0.20268,0.814,-332.19,-0.80069,-0.1638,0.57625,606.67
> fitmap #4 inMap #2
Fit molecule 1-20.pdb (#4) to map cryosparc_P101_J257_005_volume_map_sharp.mrc
(#2) using 171 atoms
average map value = 0.173, steps = 60
shifted from previous position = 0.291
rotated from previous position = 8.59 degrees
atoms outside contour = 106, contour level = 0.2
Position of 1-20.pdb (#4) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.32044818 -0.94567892 -0.05481186 685.44959502
0.58275498 0.15119054 0.79845980 -319.80554490
-0.74679957 -0.28780688 0.59954783 623.78522438
Axis -0.54347771 0.34621323 0.76470150
Axis point 779.61021218 161.02066190 0.00000000
Rotation angle (degrees) 87.96022483
Shift along axis -6.23799278
> view matrix models
> #4,0.23732,-0.97121,0.020894,696.53,0.75022,0.1969,0.63118,-332.31,-0.61712,-0.13412,0.77535,411.02
> view matrix models
> #4,0.23732,-0.97121,0.020894,696.08,0.75022,0.1969,0.63118,-332.25,-0.61712,-0.13412,0.77535,410.53
> view matrix models
> #4,0.23732,-0.97121,0.020894,696.19,0.75022,0.1969,0.63118,-332.45,-0.61712,-0.13412,0.77535,409.49
> fitmap #4 inMap #2
Fit molecule 1-20.pdb (#4) to map cryosparc_P101_J257_005_volume_map_sharp.mrc
(#2) using 171 atoms
average map value = 0.1856, steps = 72
shifted from previous position = 3.61
rotated from previous position = 17.7 degrees
atoms outside contour = 104, contour level = 0.2
Position of 1-20.pdb (#4) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.01756565 -0.98852612 -0.15002518 903.73798502
0.78746050 -0.10613902 0.60715770 -208.26756429
-0.61611478 -0.10747379 0.78028967 398.59954739
Axis -0.36270261 0.23655816 0.90138064
Axis point 627.23707842 262.04613437 0.00000000
Rotation angle (degrees) 99.88711166
Shift along axis -17.76560744
> show #3 models
> select #3:21-40
146 atoms, 148 bonds, 20 residues, 1 model selected
> save /Users/egelmanlab01/Desktop/21-40.pdb models #3 selectedOnly true
> open /Users/egelmanlab01/Desktop/21-40.pdb
Summary of feedback from opening /Users/egelmanlab01/Desktop/21-40.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR A 7
GLN A 15 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP A 16 PHE A 18 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 86 LYS A 88 1
3
Start residue of secondary structure not found: SHEET 3 3 1 GLU A 45 PRO A 48
0
Start residue of secondary structure not found: SHEET 4 4 1 VAL A 66 GLY A 70
0
7 messages similar to the above omitted
Chain information for 21-40.pdb #5
---
Chain | Description
A | No description available
> hide #3 models
Drag select of 19 residues
> view matrix models #5,1,0,0,-68.494,0,1,0,7.5967,0,0,1,-6.2166
> view matrix models
> #5,0.87445,0.38704,0.29246,-326.53,-0.45928,0.46644,0.75597,97.606,0.15617,-0.79539,0.58564,481.27
> view matrix models
> #5,-0.16069,0.55805,0.8141,-155.87,-0.29617,-0.81407,0.49957,721.86,0.94152,-0.16083,0.29609,-45.214
> view matrix models
> #5,-0.16069,0.55805,0.8141,-158.83,-0.29617,-0.81407,0.49957,716.31,0.94152,-0.16083,0.29609,-65.862
> view matrix models
> #5,0.43537,0.6356,0.63754,-397.83,-0.71289,0.67588,-0.187,589.68,-0.54976,-0.37308,0.74737,535.56
> view matrix models
> #5,0.43537,0.6356,0.63754,-405,-0.71289,0.67588,-0.187,558.83,-0.54976,-0.37308,0.74737,531.5
> view matrix models
> #5,0.43537,0.6356,0.63754,-399.47,-0.71289,0.67588,-0.187,557.98,-0.54976,-0.37308,0.74737,535.88
> view matrix models
> #5,0.43537,0.6356,0.63754,-396.21,-0.71289,0.67588,-0.187,550.41,-0.54976,-0.37308,0.74737,536.71
> view matrix models
> #5,0.43537,0.6356,0.63754,-396.87,-0.71289,0.67588,-0.187,550.33,-0.54976,-0.37308,0.74737,535.14
> select add #5
146 atoms, 148 bonds, 20 residues, 1 model selected
> volume zone #2 nearAtoms sel & #5 range 6.48
> view matrix models
> #5,0.92855,0.31555,0.19551,-274.68,-0.2526,0.92306,-0.29009,264.9,-0.272,0.21997,0.93682,38.062
> view matrix models
> #5,0.92855,0.31555,0.19551,-279.48,-0.2526,0.92306,-0.29009,265.31,-0.272,0.21997,0.93682,38.653
> view matrix models
> #5,0.93095,0.33649,0.14179,-263.44,-0.27248,0.89869,-0.34368,312.61,-0.24307,0.28131,0.92832,1.0833
> volume zone #2 nearAtoms sel & #5 range 6.48
> show #3 models
> select #3:21-84
471 atoms, 480 bonds, 64 residues, 1 model selected
> save /Users/egelmanlab01/Desktop/21-84.pdb models #3 selectedOnly true
> open /Users/egelmanlab01/Desktop/21-84.pdb
Summary of feedback from opening /Users/egelmanlab01/Desktop/21-84.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR A 7
GLN A 15 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP A 16 PHE A 18 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 86 LYS A 88 1
3
Start residue of secondary structure not found: SHEET 6 6 1 GLY A 97 GLN A 100
0
Start residue of secondary structure not found: SHEET 7 7 1 PHE A 108 PHE A
111 0
4 messages similar to the above omitted
Chain information for 21-84.pdb #6
---
Chain | Description
A | No description available
> mmaker #3 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1-20.pdb, chain A (#4) with
A0A482MFZ0_unrelaxed_rank_1_model_3.pdb, chain A (#3), sequence alignment
score = 105.4
RMSD between 20 pruned atom pairs is 0.000 angstroms; (across all 20 pairs:
0.000)
> select add #3
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> volume zone #2 nearAtoms sel & #3 range 6.48
> view matrix models
> #3,0.63206,-0.051366,0.77321,396.05,-0.14683,0.97179,0.18459,427,-0.76088,-0.2302,0.60669,491.29
> view matrix models
> #3,0.63206,-0.051366,0.77321,398.12,-0.14683,0.97179,0.18459,421.83,-0.76088,-0.2302,0.60669,488.87
> view matrix models
> #3,0.63206,-0.051366,0.77321,407.61,-0.14683,0.97179,0.18459,425.09,-0.76088,-0.2302,0.60669,490.19
> view matrix models
> #3,0.37813,-0.56103,0.73638,408.36,0.17103,0.82409,0.54003,425.4,-0.90982,-0.078253,0.40756,489.91
> view matrix models
> #3,0.37813,-0.56103,0.73638,407.71,0.17103,0.82409,0.54003,425.3,-0.90982,-0.078253,0.40756,491.14
> view matrix models
> #3,0.37813,-0.56103,0.73638,405.14,0.17103,0.82409,0.54003,426.81,-0.90982,-0.078253,0.40756,490.78
> fitmap #3 inMap #2
Fit molecule A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 1457 atoms
average map value = 0.07891, steps = 84
shifted from previous position = 3.8
rotated from previous position = 2.65 degrees
atoms outside contour = 1157, contour level = 0.2
Position of A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.38815160 -0.55448029 0.73613175 407.10907004
0.20866222 0.83089012 0.51583106 423.80640225
-0.89766275 -0.04661777 0.43821042 492.28095756
Axis -0.29776209 0.86493568 0.40400992
Axis point 530.88399422 0.00000000 -291.47419270
Rotation angle (degrees) 70.81459515
Shift along axis 444.23002223
> volume #2 level 0.23
> view matrix models
> #3,0.38815,-0.55448,0.73613,401.13,0.20866,0.83089,0.51583,426.32,-0.89766,-0.046618,0.43821,484
> fitmap #3 inMap #2
Fit molecule A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 1457 atoms
average map value = 0.09061, steps = 184
shifted from previous position = 3.97
rotated from previous position = 11.9 degrees
atoms outside contour = 1183, contour level = 0.23
Position of A0A482MFZ0_unrelaxed_rank_1_model_3.pdb (#3) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.24647081 -0.65887825 0.71072611 402.79658053
0.34907597 0.74448158 0.56911612 423.07013841
-0.90410072 0.10782689 0.41349154 486.11840359
Axis -0.23551032 0.82444672 0.51460907
Axis point 430.60503974 0.00000000 -277.24203650
Rotation angle (degrees) 78.33307653
Shift along axis 504.09697690
> volume zone #2 nearAtoms sel & #3 range 6.48
> volume zone #2 nearAtoms sel & #3 range 3
> hide #4 models
> hide #5 models
> select up
6461 atoms, 5900 bonds, 1439 residues, 7 models selected
> select down
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> select #3/1-20
Nothing selected
> select #3:1-20
171 atoms, 172 bonds, 20 residues, 1 model selected
> save /Users/egelmanlab01/Desktop/1-20_MFZ0_RBF_j257.pdb models #3
> selectedOnly true
> close #4 #5
> open /Users/egelmanlab01/Desktop/1-20_MFZ0_RBF_j257.pdb
Summary of feedback from opening
/Users/egelmanlab01/Desktop/1-20_MFZ0_RBF_j257.pdb
---
warnings | Start residue of secondary structure not found: HELIX 3 3 ARG A 86
LYS A 88 1 3
Start residue of secondary structure not found: SHEET 1 1 1 HIS A 21 THR A 29
0
Start residue of secondary structure not found: SHEET 2 2 1 GLY A 32 GLY A 39
0
Start residue of secondary structure not found: SHEET 3 3 1 GLU A 45 PRO A 48
0
Start residue of secondary structure not found: SHEET 4 4 1 VAL A 66 GLY A 70
0
7 messages similar to the above omitted
Chain information for 1-20_MFZ0_RBF_j257.pdb #4
---
Chain | Description
A | No description available
> hide #3 models
> select add #3
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> hide #6 models
> show #6 models
Drag select of 63 residues
> view matrix models #6,1,0,0,-28.388,0,1,0,-13.307,0,0,1,-74.031
> view matrix models #6,1,0,0,-82.068,0,1,0,-8.1416,0,0,1,-50.163
> view matrix models #6,1,0,0,-80.532,0,1,0,-29.191,0,0,1,-39.834
> view matrix models #6,1,0,0,-80.433,0,1,0,-27.098,0,0,1,-40.147
> view matrix models
> #6,0.47067,-0.88168,-0.033236,590.64,0.8671,0.46919,-0.16733,-128.05,0.16313,0.049938,0.98534,-134.86
> view matrix models
> #6,0.47067,-0.88168,-0.033236,590.36,0.8671,0.46919,-0.16733,-137.95,0.16313,0.049938,0.98534,-131.49
> view matrix models
> #6,0.47067,-0.88168,-0.033236,589.27,0.8671,0.46919,-0.16733,-137.43,0.16313,0.049938,0.98534,-130.55
> view matrix models
> #6,0.47067,-0.88168,-0.033236,586.5,0.8671,0.46919,-0.16733,-137.61,0.16313,0.049938,0.98534,-132.05
> view matrix models
> #6,0.43582,-0.83024,-0.34752,736,0.88853,0.45841,0.019122,-235.55,0.14343,-0.31712,0.93748,66.368
> view matrix models
> #6,0.4429,-0.82582,-0.3491,731.34,0.79343,0.54233,-0.2763,-80.634,0.4175,-0.15461,0.89543,-119.49
> view matrix models
> #6,0.4429,-0.82582,-0.3491,729.77,0.79343,0.54233,-0.2763,-78.934,0.4175,-0.15461,0.89543,-118.1
> view matrix models
> #6,0.4429,-0.82582,-0.3491,729.8,0.79343,0.54233,-0.2763,-77.856,0.4175,-0.15461,0.89543,-119.4
> fitmap #6 inMap #2
Fit molecule 21-84.pdb (#6) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 471 atoms
average map value = 0.1695, steps = 112
shifted from previous position = 3.08
rotated from previous position = 23.4 degrees
atoms outside contour = 307, contour level = 0.23
Position of 21-84.pdb (#6) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.59344498 -0.80443505 0.02659532 462.29014558
0.78360471 0.56990084 -0.24733922 -102.37393830
0.18381164 0.16762244 0.96856388 -187.47893350
Axis 0.25166389 -0.09534778 0.96310648
Axis point 361.71018412 408.90870838 0.00000000
Rotation angle (degrees) 55.53137564
Shift along axis -54.45931046
> select add #6
471 atoms, 480 bonds, 64 residues, 1 model selected
> volume zone #2 nearAtoms sel & #6 range 6.48
> select clear
> select add #6
471 atoms, 480 bonds, 64 residues, 1 model selected
> volume zone #2 nearAtoms sel & #6 range 3
> select up
6315 atoms, 5752 bonds, 1419 residues, 6 models selected
> select #6/21-40
Nothing selected
> select #6:21-40
146 atoms, 148 bonds, 20 residues, 1 model selected
> save /Users/egelmanlab01/Desktop/21-40_MFZ0_RBF_j257.pdb models #6
> selectedOnly true
> hide #6 models
> select add #6
471 atoms, 480 bonds, 64 residues, 1 model selected
> select subtract #6
Nothing selected
> show #6 models
> select add #4
171 atoms, 172 bonds, 20 residues, 1 model selected
> select add #6
642 atoms, 652 bonds, 84 residues, 2 models selected
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.
> select subtract #6
171 atoms, 172 bonds, 20 residues, 1 model selected
> select subtract #4
Nothing selected
> volume #2 level 0.2
> select #6:41-60
144 atoms, 147 bonds, 20 residues, 1 model selected
> save /Users/egelmanlab01/Desktop/41-60.pdb models #6 selectedOnly true
> open /Users/egelmanlab01/Desktop/41-60.pdb
Summary of feedback from opening /Users/egelmanlab01/Desktop/41-60.pdb
---
warnings | Start residue of secondary structure not found: SHEET 1 1 1 HIS A
21 THR A 29 0
Start residue of secondary structure not found: SHEET 2 2 1 GLY A 32 GLY A 39
0
Start residue of secondary structure not found: SHEET 4 4 1 VAL A 66 GLY A 70
0
Start residue of secondary structure not found: SHEET 5 5 1 LYS A 78 MET A 82
0
Chain information for 41-60.pdb #5
---
Chain | Description
A | No description available
> select #5/A:41
4 atoms, 3 bonds, 1 residue, 1 model selected
> view matrix models #5,1,0,0,1.0246,0,1,0,-1.5472,0,0,1,-0.51006
> view matrix models
> #5,0.4395,-0.031057,-0.8977,649.99,0.65879,0.69052,0.29864,-275.69,0.6106,-0.72265,0.32394,360.88
> view matrix models
> #5,0.41582,-0.020288,-0.90922,660.35,0.67454,0.67744,0.29338,-274.23,0.60999,-0.7353,0.29538,379.4
> view matrix models
> #5,0.3655,0.61195,-0.70138,324.99,0.8872,-0.0010911,0.46138,-157.04,0.28158,-0.79089,-0.54332,918.12
> view matrix models
> #5,0.3655,0.61195,-0.70138,321.07,0.8872,-0.0010911,0.46138,-160.54,0.28158,-0.79089,-0.54332,904.66
> view matrix models
> #5,0.3655,0.61195,-0.70138,321.87,0.8872,-0.0010911,0.46138,-162.87,0.28158,-0.79089,-0.54332,901.4
> view matrix models
> #5,0.3655,0.61195,-0.70138,322.39,0.8872,-0.0010911,0.46138,-157.91,0.28158,-0.79089,-0.54332,899.72
> select add #5
144 atoms, 147 bonds, 20 residues, 1 model selected
> volume zone #2 nearAtoms sel & #5 range 6.48
> view matrix models
> #5,0.3655,0.61195,-0.70138,323.57,0.8872,-0.0010911,0.46138,-158.88,0.28158,-0.79089,-0.54332,899.81
> volume #2 level 0.25
> volume #2 level 0.225
> view matrix models
> #5,0.36535,0.83908,-0.40307,93.571,0.52714,0.1704,0.83252,-254.46,0.76723,-0.51664,-0.38006,516.71
> view matrix models
> #5,0.36535,0.83908,-0.40307,95.284,0.52714,0.1704,0.83252,-255.41,0.76723,-0.51664,-0.38006,515.95
> view matrix models
> #5,0.36535,0.83908,-0.40307,95.187,0.52714,0.1704,0.83252,-249.88,0.76723,-0.51664,-0.38006,515.23
> view matrix models
> #5,0.47173,0.67929,-0.56217,191.01,0.78461,-0.032482,0.61914,-172.26,0.40231,-0.73315,-0.5483,828.24
> view matrix models
> #5,0.47173,0.67929,-0.56217,192.74,0.78461,-0.032482,0.61914,-173.75,0.40231,-0.73315,-0.5483,830.29
> view matrix models
> #5,0.47173,0.67929,-0.56217,192.84,0.78461,-0.032482,0.61914,-174.45,0.40231,-0.73315,-0.5483,831.49
> view matrix models
> #5,0.42534,0.87138,-0.24451,-12.968,0.5165,-0.01186,0.8562,-183.52,0.74318,-0.49047,-0.45511,551.72
> view matrix models
> #5,0.25044,0.96813,-0.0030243,-92.941,0.42646,-0.10751,0.89809,-127.04,0.86914,-0.22621,-0.43979,385.13
> view matrix models
> #5,0.25044,0.96813,-0.0030243,-92.481,0.42646,-0.10751,0.89809,-128.15,0.86914,-0.22621,-0.43979,380.46
> view matrix models
> #5,0.1225,0.99247,-0.0002563,-52.301,0.36782,-0.045159,0.9288,-144.3,0.92179,-0.11387,-0.37059,281.32
> view matrix models
> #5,0.87881,0.46637,0.10091,-186.08,-0.37764,0.55051,0.74453,-5.5396,0.29168,-0.69241,0.65992,301.83
> view matrix models
> #5,0.87881,0.46637,0.10091,-183.86,-0.37764,0.55051,0.74453,-4.1224,0.29168,-0.69241,0.65992,308.12
> view matrix models
> #5,0.73626,0.63472,0.23462,-257.04,-0.50846,0.29012,0.81074,125.52,0.44652,-0.71622,0.53633,312.16
> view matrix models
> #5,0.73626,0.63472,0.23462,-256.59,-0.50846,0.29012,0.81074,126.89,0.44652,-0.71622,0.53633,312.21
> view matrix models
> #5,0.85016,0.1051,0.51594,-212.85,-0.52062,0.31422,0.79387,129.57,-0.078685,-0.94352,0.32185,715.3
> view matrix models
> #5,0.85016,0.1051,0.51594,-212.58,-0.52062,0.31422,0.79387,130.54,-0.078685,-0.94352,0.32185,716.6
> fitmap #6 inMap #2
Fit molecule 21-84.pdb (#6) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 471 atoms
average map value = 0.1695, steps = 48
shifted from previous position = 0.0106
rotated from previous position = 0.0166 degrees
atoms outside contour = 302, contour level = 0.225
Position of 21-84.pdb (#6) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.59362229 -0.80430148 0.02667789 462.09852598
0.78351977 0.57008534 -0.24718308 -102.48691655
0.18360104 0.16763604 0.96860147 -187.39412123
Axis 0.25161929 -0.09518581 0.96313415
Axis point 361.72894028 408.80504316 0.00000000
Rotation angle (degrees) 55.51749600
Shift along axis -54.45747392
> fitmap #5 inMap #2
Fit molecule 41-60.pdb (#5) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 144 atoms
average map value = 0.1773, steps = 108
shifted from previous position = 3.13
rotated from previous position = 21.6 degrees
atoms outside contour = 88, contour level = 0.225
Position of 41-60.pdb (#5) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.77858060 0.43899655 0.44843537 -288.00824292
-0.61692120 0.40450448 0.67511804 186.94276761
0.11498037 -0.80228309 0.58576562 461.37586501
Axis -0.80019032 0.18060597 -0.57190640
Axis point 0.00000000 493.50291757 158.49248135
Rotation angle (degrees) 67.39193036
Shift along axis 0.36057820
> view matrix models
> #5,0.77858,0.439,0.44844,-288.91,-0.61692,0.4045,0.67512,187.47,0.11498,-0.80228,0.58577,459.02
> view matrix models
> #5,0.77858,0.439,0.44844,-290.26,-0.61692,0.4045,0.67512,186.28,0.11498,-0.80228,0.58577,460.41
> view matrix models
> #5,0.80945,0.20071,0.55182,-251.78,-0.58694,0.30416,0.75033,181.16,-0.017244,-0.93124,0.364,668.19
> view matrix models
> #5,0.80945,0.20071,0.55182,-251.97,-0.58694,0.30416,0.75033,181.17,-0.017244,-0.93124,0.364,667.85
> view matrix models
> #5,0.7916,-0.14955,0.59246,-119.04,-0.60802,-0.28913,0.73941,439.13,0.060719,-0.94554,-0.3198,955.19
> view matrix models
> #5,0.7916,-0.14955,0.59246,-117.3,-0.60802,-0.28913,0.73941,441.4,0.060719,-0.94554,-0.3198,954.73
> view matrix models
> #5,0.7916,-0.14955,0.59246,-117.59,-0.60802,-0.28913,0.73941,441.4,0.060719,-0.94554,-0.3198,953.95
> view matrix models
> #5,0.78468,-0.40204,0.47185,44.412,-0.60988,-0.36435,0.70377,489.45,-0.11103,-0.84001,-0.53109,1076.2
> view matrix models
> #5,0.78468,-0.40204,0.47185,44.084,-0.60988,-0.36435,0.70377,489.59,-0.11103,-0.84001,-0.53109,1075.4
> view matrix models
> #5,0.66179,-0.47609,0.57911,74.976,-0.73911,-0.28502,0.61032,551.64,-0.12551,-0.83192,-0.54051,1082.2
> view matrix models
> #5,0.66179,-0.47609,0.57911,75.911,-0.73911,-0.28502,0.61032,551.74,-0.12551,-0.83192,-0.54051,1083.1
> view matrix models
> #5,0.66179,-0.47609,0.57911,76.828,-0.73911,-0.28502,0.61032,550.42,-0.12551,-0.83192,-0.54051,1081.8
> view matrix models
> #5,0.68599,-0.36377,0.63015,-2.5449,-0.67618,0.0010995,0.73674,349.37,-0.26869,-0.93149,-0.24522,1045.3
> fitmap #5 inMap #2
Fit molecule 41-60.pdb (#5) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 144 atoms
average map value = 0.1768, steps = 80
shifted from previous position = 1.52
rotated from previous position = 16.2 degrees
atoms outside contour = 83, contour level = 0.225
Position of 41-60.pdb (#5) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.60180845 -0.58986929 0.53840581 166.60232079
-0.61562487 0.08682221 0.78324193 267.79967354
-0.50875594 -0.80281762 -0.31088786 1117.71761967
Axis -0.83444510 0.55092446 -0.01355032
Axis point 0.00000000 674.31562156 439.60689230
Rotation angle (degrees) 108.12725837
Shift along axis -6.62853735
> view matrix models
> #5,0.60181,-0.58987,0.53841,167.56,-0.61562,0.086822,0.78324,268.7,-0.50876,-0.80282,-0.31089,1118.6
> volume zone #2 nearAtoms sel & #5 range 6.48
> view matrix models
> #5,0.60754,-0.49734,0.61931,90.119,-0.68411,0.068535,0.72615,329.91,-0.40359,-0.86484,-0.2986,1096.2
> view matrix models
> #5,0.60754,-0.49734,0.61931,89.816,-0.68411,0.068535,0.72615,329.75,-0.40359,-0.86484,-0.2986,1096.4
> view matrix models
> #5,0.66108,-0.37172,0.65177,1.6635,-0.69904,0.010502,0.71501,364.76,-0.27263,-0.92828,-0.2529,1049
> view matrix models
> #5,0.66108,-0.37172,0.65177,1.0117,-0.69904,0.010502,0.71501,364.27,-0.27263,-0.92828,-0.2529,1049.7
> view matrix models
> #5,0.66108,-0.37172,0.65177,0.7172,-0.69904,0.010502,0.71501,363.67,-0.27263,-0.92828,-0.2529,1050.1
> view matrix models
> #5,0.66108,-0.37172,0.65177,0.83227,-0.69904,0.010502,0.71501,363.84,-0.27263,-0.92828,-0.2529,1049.9
> select #5:41-50
75 atoms, 75 bonds, 10 residues, 1 model selected
> save /Users/egelmanlab01/Desktop/41-50_MFZ0_RBF_j257.pdb models #5
> selectedOnly true
> close #4-6
> open /Users/egelmanlab01/Desktop/1-20_MFZ0_RBF_j257.pdb
Summary of feedback from opening
/Users/egelmanlab01/Desktop/1-20_MFZ0_RBF_j257.pdb
---
warnings | Start residue of secondary structure not found: HELIX 3 3 ARG A 86
LYS A 88 1 3
Start residue of secondary structure not found: SHEET 1 1 1 HIS A 21 THR A 29
0
Start residue of secondary structure not found: SHEET 2 2 1 GLY A 32 GLY A 39
0
Start residue of secondary structure not found: SHEET 3 3 1 GLU A 45 PRO A 48
0
Start residue of secondary structure not found: SHEET 4 4 1 VAL A 66 GLY A 70
0
7 messages similar to the above omitted
Chain information for 1-20_MFZ0_RBF_j257.pdb #4
---
Chain | Description
A | No description available
> open /Users/egelmanlab01/Desktop/21-40_MFZ0_RBF_j257.pdb
Summary of feedback from opening
/Users/egelmanlab01/Desktop/21-40_MFZ0_RBF_j257.pdb
---
warnings | Start residue of secondary structure not found: SHEET 3 3 1 GLU A
45 PRO A 48 0
Start residue of secondary structure not found: SHEET 4 4 1 VAL A 66 GLY A 70
0
Start residue of secondary structure not found: SHEET 5 5 1 LYS A 78 MET A 82
0
Chain information for 21-40_MFZ0_RBF_j257.pdb #5
---
Chain | Description
A | No description available
> open /Users/egelmanlab01/Desktop/41-50_MFZ0_RBF_j257.pdb
Chain information for 41-50_MFZ0_RBF_j257.pdb #6
---
Chain | Description
A | No description available
> combine #4-6
Remapping chain ID 'A' in 21-40_MFZ0_RBF_j257.pdb #5 to 'B'
Remapping chain ID 'A' in 41-50_MFZ0_RBF_j257.pdb #6 to 'C'
> close #4-6
> color #7 #ff40ff transparency 0
> color #7 #ff9300 transparency 0
> volume zone #2 nearAtoms #7 range 6.48
> hide #7 atoms
> show #7 cartoons
> sym #7 C3
> view clip false
> close #7
> hide #4.3 models
> hide #4.2 models
> hide #4.1 models
> show #4.1 models
> select add #4.1
392 atoms, 395 bonds, 50 residues, 1 model selected
> save /Users/egelmanlab01/Desktop/1-50_MFZ0_RBF_j257.pdb models #4.1
> selectedOnly true
> select add #4
1176 atoms, 1185 bonds, 150 residues, 4 models selected
> select subtract #4
Nothing selected
> hide #!4 models
> hide #4.1 models
> open /Users/egelmanlab01/Desktop/1-50_MFZ0_RBF_j257.pdb
Chain information for 1-50_MFZ0_RBF_j257.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open /Users/egelmanlab01/Downloads/rotation_axis_Base.pdb
Summary of feedback from opening
/Users/egelmanlab01/Downloads/rotation_axis_Base.pdb
---
warning | Cannot find LINK/SSBOND residue mar (1 )
Chain information for rotation_axis_Base.pdb #6
---
Chain | Description
kM | No description available
> color #6 #00fdff transparency 0
> color #6 #aa7942 transparency 0
> view clip false
> hide #!6 models
> view #6 clip false
No displayed objects specified.
> select add #5
392 atoms, 395 bonds, 50 residues, 1 model selected
> view #6 clip false
No displayed objects specified.
> close #4
> select add #2
392 atoms, 395 bonds, 50 residues, 4 models selected
> select clear
> show #3 models
> select #5:95-120
Nothing selected
> select #3:95-120
206 atoms, 212 bonds, 26 residues, 1 model selected
> save /Users/egelmanlab01/Desktop/95-120.pdb models #3 selectedOnly true
> open /Users/egelmanlab01/Desktop/95-120.pdb
Summary of feedback from opening /Users/egelmanlab01/Desktop/95-120.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR A 7
GLN A 15 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP A 16 PHE A 18 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 86 LYS A 88 1
3
Start residue of secondary structure not found: SHEET 1 1 1 HIS A 21 THR A 29
0
Start residue of secondary structure not found: SHEET 2 2 1 GLY A 32 GLY A 39
0
6 messages similar to the above omitted
Chain information for 95-120.pdb #4
---
Chain | Description
A | No description available
> hide #3 models
> select add #3
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #4
206 atoms, 212 bonds, 26 residues, 1 model selected
> show #3 models
> select add #3
1663 atoms, 1701 bonds, 214 residues, 2 models selected
> select subtract #4
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> volume zone #2 nearAtoms sel & #3 range 6.48
> hide #3 models
> select subtract #3
Nothing selected
> select #2
3 models selected
> select clear
> select #4/A:113
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:114
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #4
206 atoms, 212 bonds, 26 residues, 1 model selected
> view matrix models
> #4,0.60631,-0.66217,0.44036,217.54,0.75464,0.65375,-0.055988,-133.91,-0.25081,0.36626,0.89607,0.49314
> view matrix models
> #4,0.99353,-0.077704,-0.082778,75.319,0.030045,0.88305,-0.46831,265.6,0.10949,0.46279,0.87968,-176.93
> view matrix models
> #4,0.99353,-0.077704,-0.082778,86.699,0.030045,0.88305,-0.46831,267.62,0.10949,0.46279,0.87968,-178.61
> view matrix models
> #4,0.99353,-0.077704,-0.082778,81.219,0.030045,0.88305,-0.46831,271.65,0.10949,0.46279,0.87968,-182.73
> view matrix models
> #4,0.99353,-0.077704,-0.082778,81.353,0.030045,0.88305,-0.46831,271.39,0.10949,0.46279,0.87968,-183.56
> view matrix models
> #4,0.99353,-0.077704,-0.082778,81.228,0.030045,0.88305,-0.46831,271.54,0.10949,0.46279,0.87968,-182.5
> volume zone #2 nearAtoms sel & #4 range 6.48
> view matrix models
> #4,0.99353,-0.077704,-0.082778,79.3,0.030045,0.88305,-0.46831,267.7,0.10949,0.46279,0.87968,-183.17
> volume zone #2 nearAtoms sel & #4 range 6.48
> volume zone #2 nearAtoms sel & #4 range 10
> volume zone #2 nearAtoms sel & #4 range 15
> view matrix models
> #4,0.99353,-0.077704,-0.082778,81.613,0.030045,0.88305,-0.46831,270.43,0.10949,0.46279,0.87968,-183.67
> view matrix models
> #4,0.95642,-0.19273,-0.21937,211.11,0.064549,0.8722,-0.48487,269.1,0.28478,0.44958,0.84663,-232.8
> view matrix models
> #4,0.95642,-0.19273,-0.21937,211.08,0.064549,0.8722,-0.48487,271.17,0.28478,0.44958,0.84663,-231.79
> fitmap #4 inMap #2
Fit molecule 95-120.pdb (#4) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 206 atoms
average map value = 0.239, steps = 72
shifted from previous position = 1.33
rotated from previous position = 6.11 degrees
atoms outside contour = 96, contour level = 0.225
Position of 95-120.pdb (#4) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.97013700 -0.15492526 -0.18663428 172.92631914
0.02488360 0.82895148 -0.55876672 340.54239292
0.24127784 0.53743613 0.80805160 -232.42737335
Axis 0.92085356 -0.35946303 0.15104653
Axis point 0.00000000 586.86039339 430.91165566
Rotation angle (degrees) 36.52761818
Shift along axis 1.72006687
> select add #3
1663 atoms, 1701 bonds, 214 residues, 2 models selected
> select subtract #4
1457 atoms, 1489 bonds, 188 residues, 1 model selected
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 1 maps.
> show #3 models
> volume zone #2 nearAtoms sel & #3 range 6.48
> volume zone #2 nearAtoms sel & #3 range 10
> hide #3 models
> select subtract #3
Nothing selected
> show #3 models
> select #3/A:142
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models
> #3,0.24647,-0.65888,0.71073,433.7,0.34908,0.74448,0.56912,458.65,-0.9041,0.10783,0.41349,490.17
> view matrix models
> #3,-0.29604,-0.77185,-0.56268,436.47,-0.24708,-0.50715,0.82568,459.4,-0.92267,0.38346,-0.040574,490.84
> view matrix models
> #3,-0.29604,-0.77185,-0.56268,435.11,-0.24708,-0.50715,0.82568,457.72,-0.92267,0.38346,-0.040574,490.48
> view matrix models
> #3,-0.22427,-0.55481,-0.80118,435.52,-0.35896,-0.71729,0.5972,458.71,-0.90601,0.42152,-0.038289,490.42
> view matrix models
> #3,-0.22427,-0.55481,-0.80118,401.51,-0.35896,-0.71729,0.5972,416.21,-0.90601,0.42152,-0.038289,479.61
> view matrix models
> #3,-0.22427,-0.55481,-0.80118,392.03,-0.35896,-0.71729,0.5972,414.97,-0.90601,0.42152,-0.038289,478.8
> view matrix models
> #3,-0.22427,-0.55481,-0.80118,393.99,-0.35896,-0.71729,0.5972,422.75,-0.90601,0.42152,-0.038289,475.18
> view matrix models
> #3,-0.22427,-0.55481,-0.80118,392.87,-0.35896,-0.71729,0.5972,424.13,-0.90601,0.42152,-0.038289,477.63
> view matrix models
> #3,-0.22427,-0.55481,-0.80118,392.32,-0.35896,-0.71729,0.5972,423.8,-0.90601,0.42152,-0.038289,477.79
> view matrix models
> #3,-0.22427,-0.55481,-0.80118,428.8,-0.35896,-0.71729,0.5972,391.24,-0.90601,0.42152,-0.038289,492.64
> view matrix models
> #3,-0.4283,-0.84922,0.30884,425.23,0.72217,-0.11624,0.68188,392.87,-0.54316,0.51509,0.66307,491.24
> view matrix models
> #3,-0.4283,-0.84922,0.30884,374.37,0.72217,-0.11624,0.68188,355.63,-0.54316,0.51509,0.66307,502.22
> view matrix models
> #3,-0.4283,-0.84922,0.30884,385.33,0.72217,-0.11624,0.68188,363.63,-0.54316,0.51509,0.66307,500.28
> select #4:107-120
124 atoms, 127 bonds, 14 residues, 1 model selected
> save /Users/egelmanlab01/Desktop/108-120_MFZ0_RBF_j257.pdb models #4
> selectedOnly true
> hide #4 models
> show #4 models
> select #3:120-121
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #3:120-130
85 atoms, 85 bonds, 11 residues, 1 model selected
> select #3:121-130
77 atoms, 77 bonds, 10 residues, 1 model selected
> save /Users/egelmanlab01/Desktop/121-130.pdb models #3 selectedOnly true
> open /Users/egelmanlab01/Desktop/121-130.pdb
Summary of feedback from opening /Users/egelmanlab01/Desktop/121-130.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR A 7
GLN A 15 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP A 16 PHE A 18 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 86 LYS A 88 1
3
Start residue of secondary structure not found: SHEET 1 1 1 HIS A 21 THR A 29
0
Start residue of secondary structure not found: SHEET 2 2 1 GLY A 32 GLY A 39
0
8 messages similar to the above omitted
Chain information for 121-130.pdb #7
---
Chain | Description
A | No description available
> hide #3 models
> select add #3
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #4-5,7 atoms
> show #4-5,7 cartoons
Drag select of 3 residues
> view matrix models #7,1,0,0,30.52,0,1,0,50.979,0,0,1,-12.729
> view matrix models
> #7,0.85887,-0.49902,0.11538,208.94,0.50713,0.86011,-0.055001,-63.31,-0.071789,0.10575,0.9918,-19.974
> view matrix models
> #7,0.85887,-0.49902,0.11538,206.05,0.50713,0.86011,-0.055001,-58.439,-0.071789,0.10575,0.9918,-20.217
> view matrix models
> #7,0.57703,-0.81581,0.038621,469.27,0.81672,0.57641,-0.026695,-86.914,-0.00048396,0.046946,0.9989,-29.473
> view matrix models
> #7,0.88211,-0.43812,-0.17301,321.9,0.45241,0.89028,0.052175,-103.29,0.13117,-0.1243,0.98354,-9.0159
> view matrix models
> #7,0.88211,-0.43812,-0.17301,320.97,0.45241,0.89028,0.052175,-103.64,0.13117,-0.1243,0.98354,-10.002
> view matrix models
> #7,0.93198,-0.3439,-0.11465,237.53,0.35977,0.91626,0.17618,-141.04,0.044459,-0.20545,0.97766,55.94
> view matrix models
> #7,0.9444,-0.31328,0.099797,112.15,0.317,0.94813,-0.02354,-34.543,-0.087246,0.053867,0.99473,2.2702
> view matrix models
> #7,0.9444,-0.31328,0.099797,112.08,0.317,0.94813,-0.02354,-34.839,-0.087246,0.053867,0.99473,2.6388
> fitmap #4 inMap #2
Fit molecule 95-120.pdb (#4) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 206 atoms
average map value = 0.2391, steps = 40
shifted from previous position = 0.0217
rotated from previous position = 0.0789 degrees
atoms outside contour = 96, contour level = 0.225
Position of 95-120.pdb (#4) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.97015147 -0.15455301 -0.18686757 172.87702333
0.02414274 0.82831780 -0.55973810 341.59125672
0.24129495 0.53851925 0.80732506 -232.50989825
Axis 0.92117516 -0.35912591 0.14988298
Axis point 0.00000000 586.60681827 431.45414650
Rotation angle (degrees) 36.59234104
Shift along axis 1.72647089
> fitmap #7 inMap #2
Fit molecule 121-130.pdb (#7) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 77 atoms
average map value = 0.2449, steps = 144
shifted from previous position = 3.8
rotated from previous position = 73.4 degrees
atoms outside contour = 35, contour level = 0.225
Position of 121-130.pdb (#7) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.79990806 -0.09000129 0.59333537 -163.02588007
0.59599108 0.23495114 -0.76784933 498.97396824
-0.07029739 0.96783146 0.24157928 45.17433391
Axis 0.87625095 0.33503213 0.34632029
Axis point 0.00000000 260.10547188 373.23838106
Rotation angle (degrees) 82.05518551
Shift along axis 39.96551801
> view matrix models
> #7,0.79991,-0.090001,0.59334,-166.24,0.59599,0.23495,-0.76785,496,-0.070297,0.96783,0.24158,45.606
> view matrix models
> #7,0.79991,-0.090001,0.59334,-166.71,0.59599,0.23495,-0.76785,495.74,-0.070297,0.96783,0.24158,45.566
> view matrix models
> #7,0.83687,-0.54675,0.026492,276.12,0.54699,0.83714,-0.0020198,-97.428,-0.021073,0.016181,0.99965,-10.251
> view matrix models
> #7,0.83687,-0.54675,0.026492,276.15,0.54699,0.83714,-0.0020198,-97.093,-0.021073,0.016181,0.99965,-9.3525
> view matrix models
> #7,0.83687,-0.54675,0.026492,273.17,0.54699,0.83714,-0.0020198,-94.159,-0.021073,0.016181,0.99965,-9.9622
> view matrix models
> #7,0.83687,-0.54675,0.026492,273.23,0.54699,0.83714,-0.0020198,-93.982,-0.021073,0.016181,0.99965,-11.035
> view matrix models
> #7,0.8402,-0.5422,-0.0087778,288.27,0.53624,0.82833,0.16221,-170.41,-0.080681,-0.141,0.98672,76.083
> view matrix models
> #7,0.8402,-0.5422,-0.0087778,288.23,0.53624,0.82833,0.16221,-170.51,-0.080681,-0.141,0.98672,75.589
> fitmap #7 inMap #2
Fit molecule 121-130.pdb (#7) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 77 atoms
average map value = 0.2668, steps = 108
shifted from previous position = 6.97
rotated from previous position = 56.5 degrees
atoms outside contour = 30, contour level = 0.225
Position of 121-130.pdb (#7) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.46916229 -0.28089056 -0.83724981 759.59158735
0.68117845 0.71847754 0.14066254 -174.34080171
0.56203440 -0.63631008 0.52841916 242.79014489
Axis -0.41606729 -0.74931392 0.51518605
Axis point 162.40499609 0.00000000 774.29985900
Rotation angle (degrees) 69.02077031
Shift along axis -60.32313354
> view matrix models
> #7,0.72438,-0.67847,0.12232,315.68,0.68718,0.72482,-0.049165,-82.33,-0.055303,0.11967,0.99127,-32.204
> view matrix models
> #7,0.71944,-0.67979,0.14247,307.77,0.69363,0.71378,-0.096867,-56.409,-0.035843,0.16851,0.98505,-54.409
> view matrix models
> #7,0.71944,-0.67979,0.14247,308.21,0.69363,0.71378,-0.096867,-56.284,-0.035843,0.16851,0.98505,-53.886
> view matrix models
> #7,0.78094,-0.62448,0.012662,330.61,0.62316,0.78034,0.052427,-129.96,-0.042621,-0.033051,0.99854,15.877
> view matrix models
> #7,0.73465,-0.57945,0.35288,158.2,0.64484,0.75805,-0.097715,-53.473,-0.21088,0.29934,0.93055,-7.2868
> view matrix models
> #7,0.84759,-0.50886,0.1505,192.35,0.52979,0.79533,-0.29457,77.193,0.030203,0.32941,0.9437,-117.15
> view matrix models
> #7,0.83388,-0.51715,0.19289,179.02,0.55187,0.78696,-0.27592,62.317,-0.0091029,0.33653,0.94163,-103.69
> view matrix models
> #7,0.82,-0.53731,0.19721,189.52,0.57232,0.77389,-0.27119,56.894,-0.0069095,0.33524,0.94211,-104.3
> view matrix models
> #7,0.82,-0.53731,0.19721,189.82,0.57232,0.77389,-0.27119,56.374,-0.0069095,0.33524,0.94211,-104.42
> show #!1 models
> hide #!1 models
> show #!1 models
> view matrix models
> #7,0.82,-0.53731,0.19721,190.97,0.57232,0.77389,-0.27119,54.576,-0.0069095,0.33524,0.94211,-102.32
> view matrix models
> #7,0.82,-0.53731,0.19721,189.57,0.57232,0.77389,-0.27119,56.417,-0.0069095,0.33524,0.94211,-103.06
> view matrix models
> #7,0.82,-0.53731,0.19721,189.37,0.57232,0.77389,-0.27119,56.251,-0.0069095,0.33524,0.94211,-103.79
> view matrix models
> #7,0.82,-0.53731,0.19721,190.05,0.57232,0.77389,-0.27119,56.589,-0.0069095,0.33524,0.94211,-104.06
> view matrix models
> #7,0.82,-0.53731,0.19721,188.72,0.57232,0.77389,-0.27119,55.841,-0.0069095,0.33524,0.94211,-103.8
> select clear
Drag select of 17 residues
> view matrix models
> #1,0.70182,-0.71229,-0.0095731,434.78,-0.70344,-0.6951,0.14836,430.94,-0.11233,-0.097385,-0.98889,551.18
> view matrix models
> #1,0.088918,-0.98875,-0.12031,451.38,-0.97318,-0.060511,-0.22195,424.57,0.21217,0.13682,-0.96761,540.8
> view matrix models
> #1,0.088918,-0.98875,-0.12031,449.9,-0.97318,-0.060511,-0.22195,429.42,0.21217,0.13682,-0.96761,526.45
> view matrix models
> #1,-0.30944,-0.94977,0.046746,439.87,-0.94919,0.30554,-0.075363,407.44,0.057295,-0.067691,-0.99606,536.01
> view matrix models
> #1,-0.30944,-0.94977,0.046746,444.62,-0.94919,0.30554,-0.075363,401.96,0.057295,-0.067691,-0.99606,537.68
> view matrix models
> #1,-0.30944,-0.94977,0.046746,447.29,-0.94919,0.30554,-0.075363,405.82,0.057295,-0.067691,-0.99606,534.67
> view matrix models
> #1,-0.30944,-0.94977,0.046746,448.75,-0.94919,0.30554,-0.075363,404.5,0.057295,-0.067691,-0.99606,535.01
> view matrix models
> #1,-0.056553,-0.99644,0.062572,449.8,-0.997,0.059677,0.049229,407.93,-0.052788,-0.0596,-0.99683,534.73
> view matrix models
> #1,-0.056553,-0.99644,0.062572,449.38,-0.997,0.059677,0.049229,408.41,-0.052788,-0.0596,-0.99683,535.06
> view matrix models
> #1,-0.056553,-0.99644,0.062572,453.48,-0.997,0.059677,0.049229,412.65,-0.052788,-0.0596,-0.99683,534.67
> view matrix models
> #1,-0.25013,-0.96241,-0.10581,460.69,-0.9626,0.25894,-0.079703,411.29,0.10411,0.081918,-0.99119,528.77
> view matrix models
> #1,-0.25013,-0.96241,-0.10581,456.41,-0.9626,0.25894,-0.079703,408.24,0.10411,0.081918,-0.99119,529.1
> select add #1
4216 atoms, 3611 bonds, 445 pseudobonds, 1147 residues, 2 models selected
> volume zone #2 nearAtoms sel & #1 range 6.48
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #1.1 models
> hide #7 models
> show #7 models
> save 121-130_MFZ0_RBF_j257.pdb #7
> show #1.1 models
> hide #1.1 models
> hide #!1 models
> show #3 models
> select #3:131-138
55 atoms, 54 bonds, 8 residues, 1 model selected
> save /Users/egelmanlab01/Desktop/131-138.pdb models #3 selectedOnly true
> select #3:139-146
58 atoms, 57 bonds, 8 residues, 1 model selected
> save /Users/egelmanlab01/Desktop/139-146.pdb models #3 selectedOnly true
> open /Users/egelmanlab01/Desktop/131-138.pdb
Summary of feedback from opening /Users/egelmanlab01/Desktop/131-138.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR A 7
GLN A 15 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP A 16 PHE A 18 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 86 LYS A 88 1
3
Start residue of secondary structure not found: SHEET 1 1 1 HIS A 21 THR A 29
0
Start residue of secondary structure not found: SHEET 2 2 1 GLY A 32 GLY A 39
0
8 messages similar to the above omitted
Chain information for 131-138.pdb #8
---
Chain | Description
A | No description available
> open /Users/egelmanlab01/Desktop/139-146.pdb
Summary of feedback from opening /Users/egelmanlab01/Desktop/139-146.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR A 7
GLN A 15 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP A 16 PHE A 18 1
3
Start residue of secondary structure not found: HELIX 3 3 ARG A 86 LYS A 88 1
3
Start residue of secondary structure not found: SHEET 1 1 1 HIS A 21 THR A 29
0
Start residue of secondary structure not found: SHEET 2 2 1 GLY A 32 GLY A 39
0
8 messages similar to the above omitted
Chain information for 139-146.pdb #9
---
Chain | Description
A | No description available
> hide #3 models
> select add #3
1457 atoms, 1489 bonds, 188 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #7 models
> show #7 models
> select add #8
55 atoms, 54 bonds, 8 residues, 1 model selected
> view matrix models #8,1,0,0,11.899,0,1,0,14.417,0,0,1,-1.97
> view matrix models
> #8,-0.19775,-0.90758,0.37039,619.36,0.97231,-0.13362,0.1917,-46.644,-0.12449,0.39804,0.90888,-52.571
> view matrix models
> #8,-0.19775,-0.90758,0.37039,617.29,0.97231,-0.13362,0.1917,-20.452,-0.12449,0.39804,0.90888,-55.782
> view matrix models
> #8,-0.57868,-0.81247,0.070857,884.86,0.79373,-0.54109,0.27786,153.97,-0.18742,0.21703,0.958,9.7297
> view matrix models
> #8,-0.57868,-0.81247,0.070857,890.41,0.79373,-0.54109,0.27786,150.06,-0.18742,0.21703,0.958,4.7379
> view matrix models
> #8,-0.57868,-0.81247,0.070857,892.4,0.79373,-0.54109,0.27786,152.07,-0.18742,0.21703,0.958,7.3805
> view matrix models
> #8,-0.57868,-0.81247,0.070857,894.63,0.79373,-0.54109,0.27786,153.09,-0.18742,0.21703,0.958,5.9245
> view matrix models
> #8,-0.57868,-0.81247,0.070857,894.42,0.79373,-0.54109,0.27786,153.42,-0.18742,0.21703,0.958,5.5167
> fitmap #8 inMap #2
Fit molecule 131-138.pdb (#8) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 55 atoms
average map value = 0.2539, steps = 80
shifted from previous position = 3.92
rotated from previous position = 14.7 degrees
atoms outside contour = 18, contour level = 0.225
Position of 131-138.pdb (#8) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.69428131 -0.67606831 0.24678958 799.13660688
0.71965920 -0.64833259 0.24850649 240.52386326
-0.00800564 0.35013781 0.93666399 -101.42036593
Axis 0.07144912 0.17912682 0.98122811
Axis point 352.10025112 299.57356053 0.00000000
Rotation angle (degrees) 134.66617544
Shift along axis 0.66536689
> view matrix models
> #8,-0.69428,-0.67607,0.24679,800.45,0.71966,-0.64833,0.24851,236.83,-0.0080056,0.35014,0.93666,-103.19
> view matrix models
> #8,-0.83486,-0.52155,0.17603,834.91,0.54769,-0.75504,0.36048,285.09,-0.055099,0.39736,0.91601,-91.549
> view matrix models
> #8,-0.83486,-0.52155,0.17603,834.9,0.54769,-0.75504,0.36048,285.03,-0.055099,0.39736,0.91601,-94.336
> fitmap #8 inMap #2
Fit molecule 131-138.pdb (#8) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 55 atoms
average map value = 0.2232, steps = 52
shifted from previous position = 1.1
rotated from previous position = 3.99 degrees
atoms outside contour = 28, contour level = 0.225
Position of 131-138.pdb (#8) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.84028128 -0.48780700 0.23658339 792.43370485
0.54213521 -0.75933002 0.35987128 289.05952418
0.00409713 0.43065329 0.90250815 -122.32443867
Axis 0.06688746 0.21969446 0.97327304
Axis point 357.83299834 274.88465677 0.00000000
Rotation angle (degrees) 148.05447819
Shift along axis -2.54642665
> view matrix models
> #8,-0.84028,-0.48781,0.23658,796.26,0.54214,-0.75933,0.35987,289.69,0.0040971,0.43065,0.90251,-122.63
> fitmap #8 inMap #2
Fit molecule 131-138.pdb (#8) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 55 atoms
average map value = 0.2471, steps = 212
shifted from previous position = 1.68
rotated from previous position = 39.4 degrees
atoms outside contour = 24, contour level = 0.225
Position of 131-138.pdb (#8) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.97736218 -0.14348042 0.15548805 765.10644266
0.20659937 -0.48881255 0.84757241 70.02966037
-0.04560554 0.86050895 0.50738987 -59.49275324
Axis 0.03202646 0.49783900 0.86667793
Axis point 379.75888417 97.12534371 0.00000000
Rotation angle (degrees) 168.34802254
Shift along axis 7.80609060
> view matrix models
> #8,-0.97736,-0.14348,0.15549,765.27,0.2066,-0.48881,0.84757,68.391,-0.045606,0.86051,0.50739,-57.611
> fitmap #8 inMap #2
Fit molecule 131-138.pdb (#8) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 55 atoms
average map value = 0.2469, steps = 56
shifted from previous position = 2.56
rotated from previous position = 1.32 degrees
atoms outside contour = 24, contour level = 0.225
Position of 131-138.pdb (#8) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.97986597 -0.12481617 0.15583197 759.05324074
0.19703744 -0.47852921 0.85567870 65.83548238
-0.03223239 0.86915518 0.49348794 -60.78185787
Axis 0.03612858 0.50417485 0.86284555
Axis point 377.43458225 92.04061480 0.00000000
Rotation angle (degrees) 169.25098869
Shift along axis 8.17075346
> view matrix models
> #8,-0.97987,-0.12482,0.15583,759,0.19704,-0.47853,0.85568,65.863,-0.032232,0.86916,0.49349,-60.347
> view matrix models
> #8,-0.97987,-0.12482,0.15583,758.74,0.19704,-0.47853,0.85568,63.878,-0.032232,0.86916,0.49349,-58.752
> fitmap #8 inMap #2
Fit molecule 131-138.pdb (#8) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 55 atoms
average map value = 0.2473, steps = 56
shifted from previous position = 2.83
rotated from previous position = 0.185 degrees
atoms outside contour = 25, contour level = 0.225
Position of 131-138.pdb (#8) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.97978825 -0.12754435 0.15410200 760.91775870
0.19687634 -0.47843047 0.85577099 65.82494144
-0.03542166 0.86881340 0.49387102 -59.58937529
Axis 0.03469190 0.50411986 0.86293664
Axis point 378.26578452 92.11333604 0.00000000
Rotation angle (degrees) 169.16538060
Shift along axis 8.15949146
> view matrix models
> #8,-0.97979,-0.12754,0.1541,761.33,0.19688,-0.47843,0.85577,64.234,-0.035422,0.86881,0.49387,-56.877
> view matrix models
> #8,-0.95927,-0.21884,-0.17861,958.32,0.028481,-0.70401,0.70962,287.74,-0.28104,0.67563,0.68157,12.688
> view matrix models
> #8,-0.95927,-0.21884,-0.17861,959.08,0.028481,-0.70401,0.70962,287.96,-0.28104,0.67563,0.68157,11.511
> fitmap #8 inMap #2
Fit molecule 131-138.pdb (#8) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 55 atoms
average map value = 0.2473, steps = 92
shifted from previous position = 2.32
rotated from previous position = 23.8 degrees
atoms outside contour = 25, contour level = 0.225
Position of 131-138.pdb (#8) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.97805658 -0.13894954 0.15523643 763.84132822
0.20387124 -0.48482467 0.85051841 68.12095686
-0.04291669 0.86350337 0.50251377 -59.13877153
Axis 0.03277533 0.50015811 0.86531361
Axis point 379.33236963 95.28953695 0.00000000
Rotation angle (degrees) 168.57468213
Shift along axis 7.93281658
> view matrix models
> #8,-0.97806,-0.13895,0.15524,766.21,0.20387,-0.48482,0.85052,67.889,-0.042917,0.8635,0.50251,-56.116
> view matrix models
> #8,-0.88527,-0.076469,-0.45874,1023.7,-0.17019,-0.8647,0.47258,547.37,-0.43281,0.49644,0.75248,101.2
> view matrix models
> #8,-0.88527,-0.076469,-0.45874,1024,-0.17019,-0.8647,0.47258,547.13,-0.43281,0.49644,0.75248,102.17
> hide sel cartoons
> show sel cartoons
> view matrix models
> #8,0.88621,-0.10487,0.45125,-122.04,-0.042729,-0.98839,-0.14578,860.98,0.4613,0.10991,-0.88041,735.84
> view matrix models
> #8,0.88621,-0.10487,0.45125,-121.61,-0.042729,-0.98839,-0.14578,861.65,0.4613,0.10991,-0.88041,735.16
> fitmap #8 inMap #2
Fit molecule 131-138.pdb (#8) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 55 atoms
average map value = 0.2198, steps = 80
shifted from previous position = 2.71
rotated from previous position = 37.6 degrees
atoms outside contour = 33, contour level = 0.225
Position of 131-138.pdb (#8) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.90743411 0.11896601 0.40300173 -187.07789014
-0.10111455 -0.86907825 0.48423012 515.04838718
0.40784697 -0.48015628 -0.77660207 916.88984498
Axis -0.97492375 -0.00489818 -0.22248527
Axis point 0.00000000 381.69669136 409.91006461
Rotation angle (degrees) 150.35689883
Shift along axis -24.13060581
> view matrix models
> #8,0.90743,0.11897,0.403,-186.64,-0.10111,-0.86908,0.48423,516.55,0.40785,-0.48016,-0.7766,918.57
> view matrix models
> #8,0.83834,0.41931,0.34836,-241.88,0.19552,-0.82779,0.52586,364.68,0.50887,-0.37274,-0.77596,839.56
> view matrix models
> #8,0.89536,0.42641,0.12847,-153.58,0.31583,-0.81136,0.49189,329.31,0.31398,-0.39984,-0.86113,969.04
> view matrix models
> #8,0.8797,0.38435,0.28002,-210.02,0.28718,-0.89873,0.33138,455.07,0.37903,-0.2111,-0.90099,895
> view matrix models
> #8,0.8797,0.38435,0.28002,-210.28,0.28718,-0.89873,0.33138,454.34,0.37903,-0.2111,-0.90099,896.18
> fitmap #8 inMap #2
Fit molecule 131-138.pdb (#8) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 55 atoms
average map value = 0.2616, steps = 128
shifted from previous position = 3.53
rotated from previous position = 31.1 degrees
atoms outside contour = 22, contour level = 0.225
Position of 131-138.pdb (#8) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.77326284 0.54004425 0.33229016 -254.22489792
0.12962286 -0.64760967 0.75086590 206.95426659
0.62069514 -0.53754431 -0.57077459 755.25672488
Axis -0.93186482 -0.20859386 -0.29684432
Axis point 0.00000000 292.61657719 374.92363314
Rotation angle (degrees) 136.26630438
Shift along axis -30.45981993
> view matrix models
> #8,0.94169,0.27985,0.18684,-149.24,0.2458,-0.95131,0.18601,563.82,0.22979,-0.12924,-0.96462,959.93
> view matrix models
> #8,0.94169,0.27985,0.18684,-147.78,0.2458,-0.95131,0.18601,566.14,0.22979,-0.12924,-0.96462,957.15
> view matrix models
> #8,0.91663,0.15056,0.3703,-184.97,0.14048,-0.9886,0.05422,688.61,0.37424,0.0023207,-0.92733,833.57
> view matrix models
> #8,0.8899,0.38476,0.24501,-195.98,0.32784,-0.91296,0.24297,490.91,0.31717,-0.13589,-0.93858,912.22
> view matrix models
> #8,0.8899,0.38476,0.24501,-196.16,0.32784,-0.91296,0.24297,490.77,0.31717,-0.13589,-0.93858,912.39
> view matrix models
> #8,0.75132,-0.47684,0.45622,65.108,-0.60453,-0.77457,0.18598,831.7,0.26469,-0.41552,-0.87022,1000.2
> view matrix models
> #8,0.75132,-0.47684,0.45622,65.438,-0.60453,-0.77457,0.18598,831.99,0.26469,-0.41552,-0.87022,998.56
> view matrix models
> #8,0.94885,-0.15208,0.27668,-38.127,-0.25246,-0.89171,0.37566,640.46,0.18959,-0.42629,-0.88449,1039.1
> view matrix models
> #8,0.91103,-0.12446,0.3931,-93.451,-0.21399,-0.95763,0.19275,743.79,0.35246,-0.25973,-0.89906,922.09
> view matrix models
> #8,0.91103,-0.12446,0.3931,-93.229,-0.21399,-0.95763,0.19275,741.92,0.35246,-0.25973,-0.89906,924.21
> view matrix models
> #8,0.91103,-0.12446,0.3931,-92.1,-0.21399,-0.95763,0.19275,742.04,0.35246,-0.25973,-0.89906,921.9
> view matrix models
> #8,0.88858,0.013497,0.45852,-167.65,-0.095498,-0.97222,0.21369,690.58,0.44867,-0.23367,-0.86261,856.2
> view matrix models
> #8,0.88858,0.013497,0.45852,-168.39,-0.095498,-0.97222,0.21369,689.63,0.44867,-0.23367,-0.86261,856.32
> view matrix models
> #8,0.88858,0.013497,0.45852,-168.84,-0.095498,-0.97222,0.21369,689.56,0.44867,-0.23367,-0.86261,856.47
> view matrix models
> #8,0.87244,-0.18413,0.45271,-87.067,-0.19171,-0.98101,-0.029551,855.32,0.44956,-0.061009,-0.89117,807.48
> view matrix models
> #8,0.87244,-0.18413,0.45271,-86.663,-0.19171,-0.98101,-0.029551,855.49,0.44956,-0.061009,-0.89117,806.95
> view matrix models
> #8,0.92823,0.050514,0.36855,-151.21,0.034789,-0.99818,0.049193,733.25,0.37037,-0.032841,-0.9283,846.51
> view matrix models
> #8,0.92823,0.050514,0.36855,-151.48,0.034789,-0.99818,0.049193,733.31,0.37037,-0.032841,-0.9283,846.2
> view matrix models
> #8,0.92823,0.050514,0.36855,-154.31,0.034789,-0.99818,0.049193,731.83,0.37037,-0.032841,-0.9283,845.42
> view matrix models
> #8,0.92019,-0.37238,0.12074,131.24,-0.38049,-0.92332,0.052114,864.37,0.092079,-0.093897,-0.99131,1008.5
> fitmap #8 inMap #2
Fit molecule 131-138.pdb (#8) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 55 atoms
average map value = 0.2156, steps = 72
shifted from previous position = 2.04
rotated from previous position = 11 degrees
atoms outside contour = 31, contour level = 0.225
Position of 131-138.pdb (#8) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.84176148 -0.53204942 0.09143853 233.50158879
-0.53924755 -0.83667087 0.09588481 872.35779794
0.02548850 -0.13002015 -0.99118367 1047.04022730
Axis -0.95948147 0.28010824 -0.03057246
Axis point 0.00000000 502.48016322 492.84760045
Rotation angle (degrees) 173.23932506
Shift along axis -11.69643637
Drag select of 58 atoms, 57 bonds
> hide sel atoms
> show sel cartoons
> view matrix models
> #9,0.5368,-0.58636,0.60665,80.443,-0.53002,0.32508,0.7832,47.424,-0.65645,-0.74196,-0.13628,1114.4
> view matrix models
> #9,0.5368,-0.58636,0.60665,114.13,-0.53002,0.32508,0.7832,88.195,-0.65645,-0.74196,-0.13628,1112.3
> view matrix models
> #9,-0.29866,0.62509,0.72115,-71.811,-0.70105,0.36903,-0.61021,859,-0.64756,-0.68781,0.328,848.52
> view matrix models
> #9,-0.29866,0.62509,0.72115,-68.745,-0.70105,0.36903,-0.61021,863.1,-0.64756,-0.68781,0.328,839.52
> view matrix models
> #9,-0.64683,-0.65688,0.38746,711.29,-0.66067,0.73642,0.14556,320.62,-0.38095,-0.16183,-0.91032,1183.9
> view matrix models
> #9,-0.64683,-0.65688,0.38746,711.69,-0.66067,0.73642,0.14556,321.36,-0.38095,-0.16183,-0.91032,1185
> fitmap #8 inMap #2
Fit molecule 131-138.pdb (#8) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 55 atoms
average map value = 0.2158, steps = 48
shifted from previous position = 0.0234
rotated from previous position = 0.236 degrees
atoms outside contour = 31, contour level = 0.225
Position of 131-138.pdb (#8) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.84043988 -0.53462736 0.08851195 236.45759545
-0.54142771 -0.83527545 0.09576488 872.74485001
0.02273333 -0.12840745 -0.99146089 1047.64454806
Axis -0.95913799 0.28143872 -0.02909581
Axis point 0.00000000 503.07474636 493.46032566
Rotation angle (degrees) 173.28900299
Shift along axis -11.65333124
> fitmap #8 inMap #2
Fit molecule 131-138.pdb (#8) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 55 atoms
average map value = 0.2157, steps = 40
shifted from previous position = 0.0219
rotated from previous position = 0.314 degrees
atoms outside contour = 31, contour level = 0.225
Position of 131-138.pdb (#8) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.84045650 -0.53450971 0.08906298 236.12659669
-0.54124756 -0.83599289 0.09037104 875.70729677
0.02615181 -0.12415806 -0.99191776 1045.01160892
Axis -0.95915445 0.28127432 -0.03012475
Axis point 0.00000000 503.02229534 493.09587499
Rotation angle (degrees) 173.57904348
Shift along axis -11.64861718
> fitmap #9 inMap #2
Fit molecule 139-146.pdb (#9) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 58 atoms
average map value = 0.2548, steps = 96
shifted from previous position = 5.08
rotated from previous position = 15.5 degrees
atoms outside contour = 25, contour level = 0.225
Position of 139-146.pdb (#9) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.59554815 -0.77073784 0.22646321 817.15008946
-0.68578855 0.63460626 0.35632701 254.59775307
-0.41834967 0.05690401 -0.90650177 1115.10212708
Axis -0.41818930 0.90057826 0.11864447
Axis point 582.06250652 0.00000000 455.93447361
Rotation angle (degrees) 159.02261926
Shift along axis 19.86248216
> view matrix models
> #9,-0.59555,-0.77074,0.22646,818.97,-0.68579,0.63461,0.35633,256.39,-0.41835,0.056904,-0.9065,1115.3
> view matrix models
> #9,-0.59555,-0.77074,0.22646,818.8,-0.68579,0.63461,0.35633,258.28,-0.41835,0.056904,-0.9065,1116.4
> view matrix models
> #9,-0.38276,-0.87608,-0.29321,1045,-0.92343,0.35334,0.14974,560.4,-0.027583,0.32807,-0.94425,885.66
> view matrix models
> #9,-0.38276,-0.87608,-0.29321,1043.5,-0.92343,0.35334,0.14974,563.42,-0.027583,0.32807,-0.94425,884.64
> view matrix models
> #9,-0.43904,-0.88634,0.14712,840.94,-0.88368,0.45557,0.10755,532.23,-0.16235,-0.082787,-0.98325,1108.4
> view matrix models
> #9,-0.43904,-0.88634,0.14712,840.77,-0.88368,0.45557,0.10755,532.15,-0.16235,-0.082787,-0.98325,1107.4
> view matrix models
> #9,0.43638,-0.13176,-0.89006,762.75,-0.83542,0.30803,-0.45519,859.45,0.33414,0.94221,0.024341,16.441
> view matrix models
> #9,0.46755,0.81879,0.33312,-233.6,-0.79985,0.55231,-0.23493,641.52,-0.37635,-0.1566,0.91315,235.09
> view matrix models
> #9,0.45504,0.84829,-0.27081,72.956,-0.86609,0.35094,-0.35598,804.02,-0.20694,0.39653,0.89439,-24.594
> view matrix models
> #9,0.45504,0.84829,-0.27081,73.069,-0.86609,0.35094,-0.35598,803.88,-0.20694,0.39653,0.89439,-24.24
> view matrix models
> #9,0.20965,0.92298,-0.32274,166.61,-0.96203,0.13572,-0.2368,858.53,-0.17476,0.36013,0.91639,-34.538
> view matrix models
> #9,0.19957,0.94273,-0.26727,134.46,-0.95922,0.13224,-0.24981,865.48,-0.20016,0.30622,0.93068,-12.266
> view matrix models
> #9,0.19957,0.94273,-0.26727,134.55,-0.95922,0.13224,-0.24981,865.67,-0.20016,0.30622,0.93068,-12.892
> fitmap #9 inMap #2
Fit molecule 139-146.pdb (#9) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 58 atoms
average map value = 0.2407, steps = 80
shifted from previous position = 3.67
rotated from previous position = 16 degrees
atoms outside contour = 31, contour level = 0.225
Position of 139-146.pdb (#9) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.37228839 0.84324245 -0.38774155 168.39901980
-0.92808910 0.33498894 -0.16258226 730.05819965
-0.00720714 0.42038621 0.90731663 -117.01299238
Axis 0.30630523 -0.19994166 -0.93069890
Axis point 605.89165092 256.59598578 0.00000000
Rotation angle (degrees) 72.10359034
Shift along axis 14.51631758
> show sel atoms
> view matrix models
> #9,0.37229,0.84324,-0.38774,168.67,-0.92809,0.33499,-0.16258,731.81,-0.0072071,0.42039,0.90732,-117.28
> view matrix models
> #9,0.35069,0.82039,-0.45164,218.37,-0.93572,0.28743,-0.20445,773.9,-0.037915,0.49431,0.86846,-112.72
> view matrix models
> #9,0.35069,0.82039,-0.45164,217.96,-0.93572,0.28743,-0.20445,774.48,-0.037915,0.49431,0.86846,-112.21
> fitmap #9 inMap #2
Fit molecule 139-146.pdb (#9) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 58 atoms
average map value = 0.2408, steps = 52
shifted from previous position = 2.26
rotated from previous position = 5.27 degrees
atoms outside contour = 31, contour level = 0.225
Position of 139-146.pdb (#9) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.37149192 0.84334759 -0.38827643 168.94234385
-0.92841159 0.33439349 -0.16196567 730.08615150
-0.00675625 0.42064929 0.90719816 -117.22498505
Axis 0.30604116 -0.20040831 -0.93068540
Axis point 605.72315605 256.35141421 0.00000000
Rotation angle (degrees) 72.14905431
Shift along axis 14.48755899
> view matrix models
> #9,0.37149,0.84335,-0.38828,169.19,-0.92841,0.33439,-0.16197,730.92,-0.0067562,0.42065,0.9072,-117.3
> view matrix models
> #9,0.37149,0.84335,-0.38828,169.31,-0.92841,0.33439,-0.16197,732.19,-0.0067562,0.42065,0.9072,-116.86
> view matrix models
> #9,0.38128,0.78685,-0.48528,236.54,-0.92445,0.32745,-0.19538,750.51,0.0051757,0.52311,0.85225,-130.8
> view matrix models
> #9,0.38128,0.78685,-0.48528,236.16,-0.92445,0.32745,-0.19538,751.84,0.0051757,0.52311,0.85225,-131.14
> view matrix models
> #9,0.34363,0.77266,-0.53378,280.84,-0.9391,0.28189,-0.19652,774.83,-0.0013747,0.5688,0.82247,-130.1
> view matrix models
> #9,0.34363,0.77266,-0.53378,281.35,-0.9391,0.28189,-0.19652,775.03,-0.0013747,0.5688,0.82247,-129.52
> view matrix models
> #9,-0.16742,0.30018,0.93908,-110.32,-0.96759,0.1326,-0.21489,850.46,-0.18903,-0.94462,0.26825,786.64
> view matrix models
> #9,-0.53142,-0.82052,0.21056,818.5,-0.84109,0.54065,-0.01594,548.84,-0.10076,-0.18557,-0.97745,1116.8
> view matrix models
> #9,-0.53142,-0.82052,0.21056,818.76,-0.84109,0.54065,-0.01594,548.36,-0.10076,-0.18557,-0.97745,1118.4
> view matrix models
> #9,-0.53142,-0.82052,0.21056,818.96,-0.84109,0.54065,-0.01594,548.94,-0.10076,-0.18557,-0.97745,1118.9
> fitmap #9 inMap #2
Fit molecule 139-146.pdb (#9) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 58 atoms
average map value = 0.2303, steps = 76
shifted from previous position = 2.71
rotated from previous position = 20.8 degrees
atoms outside contour = 24, contour level = 0.225
Position of 139-146.pdb (#9) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.28344679 -0.95895613 -0.00781239 889.06992244
-0.95837973 0.28354771 -0.03330086 695.37211175
0.03414925 -0.00195179 -0.99941482 1010.11007047
Axis 0.59847006 -0.80106960 0.01100379
Axis point 696.02823005 0.00000000 517.16700846
Rotation angle (degrees) 178.49919420
Shift along axis -13.84469145
> view matrix models
> #9,-0.28345,-0.95896,-0.0078124,888.97,-0.95838,0.28355,-0.033301,695.48,0.034149,-0.0019518,-0.99941,1010.1
> view matrix models
> #9,-0.24729,-0.96562,0.08011,832.18,-0.95659,0.25646,0.13844,616.03,-0.15423,-0.042396,-0.98713,1090.7
> view matrix models
> #9,-0.24729,-0.96562,0.08011,831.45,-0.95659,0.25646,0.13844,617.37,-0.15423,-0.042396,-0.98713,1091.9
> fitmap #9 inMap #2
Fit molecule 139-146.pdb (#9) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 58 atoms
average map value = 0.2384, steps = 164
shifted from previous position = 1.98
rotated from previous position = 29.4 degrees
atoms outside contour = 28, contour level = 0.225
Position of 139-146.pdb (#9) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.21223699 -0.88263485 -0.41941764 1046.26170764
-0.97532272 0.16460383 0.14714325 652.48868121
-0.06083600 0.44029681 -0.89578885 831.68856536
Axis 0.62063294 -0.75915021 -0.19622872
Axis point 724.37677627 0.00000000 414.50625008
Rotation angle (degrees) 166.33921956
Shift along axis -9.19361504
> view matrix models
> #9,0.15179,0.18885,0.9702,-206.06,-0.73633,0.67642,-0.016465,456.98,-0.65938,-0.71189,0.24173,897.42
> view matrix models
> #9,0.66016,0.56911,0.49021,-292.46,-0.44809,0.82217,-0.35107,466.03,-0.60283,0.012104,0.79777,321.5
> view matrix models
> #9,0.66016,0.56911,0.49021,-292.82,-0.44809,0.82217,-0.35107,467.79,-0.60283,0.012104,0.79777,317.61
> view matrix models
> #9,0.46282,0.88342,0.073266,-117.84,-0.8398,0.46342,-0.28281,714.46,-0.28379,0.069361,0.95637,92.631
> view matrix models
> #9,0.46282,0.88342,0.073266,-118.49,-0.8398,0.46342,-0.28281,713.27,-0.28379,0.069361,0.95637,93.656
> view matrix models
> #9,0.46282,0.88342,0.073266,-118.16,-0.8398,0.46342,-0.28281,712.76,-0.28379,0.069361,0.95637,92.966
> view matrix models
> #9,0.37381,0.86036,-0.34648,141.28,-0.92545,0.32113,-0.20104,755.69,-0.061697,0.3958,0.91626,-91.533
> fitmap #9 inMap #2
Fit molecule 139-146.pdb (#9) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 58 atoms
average map value = 0.2407, steps = 64
shifted from previous position = 1.99
rotated from previous position = 3.46 degrees
atoms outside contour = 31, contour level = 0.225
Position of 139-146.pdb (#9) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.37255567 0.84316406 -0.38765529 168.28133919
-0.92798032 0.33515189 -0.16286711 730.10177481
-0.00740029 0.42041355 0.90730240 -116.94164412
Axis 0.30649090 -0.19980895 -0.93066627
Axis point 606.00814213 256.66201195 0.00000000
Rotation angle (degrees) 72.09106622
Shift along axis 14.52947241
> view matrix models
> #9,0.37256,0.84316,-0.38766,168.67,-0.92798,0.33515,-0.16287,732.15,-0.0074003,0.42041,0.9073,-117.32
> view matrix models
> #9,0.33616,0.79556,-0.50408,260.3,-0.94155,0.27148,-0.19944,779.71,-0.021817,0.54166,0.84032,-121.89
> view matrix models
> #9,0.33616,0.79556,-0.50408,260.32,-0.94155,0.27148,-0.19944,779.86,-0.021817,0.54166,0.84032,-121.51
> view matrix models
> #9,0.33616,0.79556,-0.50408,260.63,-0.94155,0.27148,-0.19944,779.93,-0.021817,0.54166,0.84032,-121.08
> save 131-138_MFZ0_RBF_j257 #8
Cannot determine format for '131-138_MFZ0_RBF_j257'
> save 131-138_MFZ0_RBF_j257.pdb #8
> save 139-146_MFZ0_RBF_j257.pdb #9
> hide #7 models
> hide #8 models
> hide #9 models
> open /Users/egelmanlab01/Desktop/108-120_MFZ0_RBF_j257.pdb
Summary of feedback from opening
/Users/egelmanlab01/Desktop/108-120_MFZ0_RBF_j257.pdb
---
warning | Start residue of secondary structure not found: SHEET 1 1 1 GLY A 97
GLN A 100 0
Chain information for 108-120_MFZ0_RBF_j257.pdb #10
---
Chain | Description
A | No description available
> open /Users/egelmanlab01/Desktop/121-130_MFZ0_RBF_j257.pdb
Chain information for 121-130_MFZ0_RBF_j257.pdb #11
---
Chain | Description
A | No description available
> open /Users/egelmanlab01/Desktop/131-138_MFZ0_RBF_j257.pdb
Chain information for 131-138_MFZ0_RBF_j257.pdb #12
---
Chain | Description
A | No description available
> open /Users/egelmanlab01/Desktop/139-146_MFZ0_RBF_j257.pdb
Chain information for 139-146_MFZ0_RBF_j257.pdb #13
---
Chain | Description
A | No description available
> hide #!2 models
> select subtract #9
Nothing selected
> hide #4 models
> show #5,10-13 cartoons
> hide #5,10-13 atoms
> hide #12 models
> show #12 models
> hide #11 models
> show #11 models
> show #9 models
> show #8 models
> hide #8 models
> hide #9 models
> hide #10 models
> show #10 models
> show #3 models
Drag select of 25 residues
> view matrix models
> #3,-0.4283,-0.84922,0.30884,416.25,0.72217,-0.11624,0.68188,384.59,-0.54316,0.51509,0.66307,498.74
> view matrix models
> #3,-0.4283,-0.84922,0.30884,397.7,0.72217,-0.11624,0.68188,397.19,-0.54316,0.51509,0.66307,500.12
> view matrix models
> #3,-0.4283,-0.84922,0.30884,398.75,0.72217,-0.11624,0.68188,405.95,-0.54316,0.51509,0.66307,492.5
> view matrix models
> #3,-0.47748,0.80572,-0.35046,396,-0.82531,-0.54812,-0.13572,404.71,-0.30145,0.22443,0.92669,493.28
> view matrix models
> #3,-0.47748,0.80572,-0.35046,398.28,-0.82531,-0.54812,-0.13572,413.7,-0.30145,0.22443,0.92669,491.59
> view matrix models
> #3,-0.85402,0.2218,-0.47059,399.1,-0.42533,-0.81856,0.38607,414.08,-0.29958,0.52987,0.79341,491.16
> view matrix models
> #3,-0.85402,0.2218,-0.47059,398.6,-0.42533,-0.81856,0.38607,411.79,-0.29958,0.52987,0.79341,492.02
> view matrix models
> #3,-0.62077,0.59305,-0.51277,398.46,-0.71643,-0.69473,0.06384,411.52,-0.31838,0.407,0.85615,492.1
> view matrix models
> #3,-0.6762,0.51293,-0.52882,398.55,-0.66397,-0.73532,0.13579,411.58,-0.3192,0.44295,0.8378,492.05
> view matrix models
> #3,-0.6762,0.51293,-0.52882,399.79,-0.66397,-0.73532,0.13579,416.5,-0.3192,0.44295,0.8378,491.06
> view matrix models
> #3,-0.6762,0.51293,-0.52882,400.55,-0.66397,-0.73532,0.13579,415.55,-0.3192,0.44295,0.8378,492.97
> select add #3
1457 atoms, 1489 bonds, 188 residues, 1 model selected
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 6 atomic
models, 0 maps.
> hide #5 models
> hide #10 models
> hide #13 models
> hide #12 models
> hide #11 models
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> show #!2 models
> show #5 models
> show #13 models
> show #12 models
> show #11 models
> show #10 models
> select clear
Drag select of 5 residues
> view matrix models
> #3,-0.6762,0.51293,-0.52882,377.4,-0.66397,-0.73532,0.13579,398.67,-0.3192,0.44295,0.8378,515.26
> select #3-51-100
Expected an objects specifier or a keyword
> select #3:51-100
377 atoms, 386 bonds, 50 residues, 1 model selected
> save /Users/egelmanlab01/Desktop/51-100.pdb models #3 selectedOnly true
> open /Users/egelmanlab01/Desktop/51-100.pdb
Summary of feedback from opening /Users/egelmanlab01/Desktop/51-100.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR A 7
GLN A 15 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP A 16 PHE A 18 1
3
Start residue of secondary structure not found: SHEET 1 1 1 HIS A 21 THR A 29
0
Start residue of secondary structure not found: SHEET 2 2 1 GLY A 32 GLY A 39
0
Start residue of secondary structure not found: SHEET 3 3 1 GLU A 45 PRO A 48
0
5 messages similar to the above omitted
Chain information for 51-100.pdb #14
---
Chain | Description
A | No description available
> hide #5 models
> show #5 models
> hide #3 models
Drag select of 46 residues
> view matrix models
> #14,-0.19628,0.64492,-0.73862,553.62,-0.97846,-0.17789,0.10469,785.25,-0.063877,0.74326,0.66595,-108.61
> view matrix models
> #14,0.56292,0.81253,-0.1514,-87.874,-0.68693,0.5618,0.46099,203.72,0.45962,-0.1555,0.8744,-46.322
> view matrix models
> #14,0.56292,0.81253,-0.1514,-54.92,-0.68693,0.5618,0.46099,217.59,0.45962,-0.1555,0.8744,-76.101
> view matrix models
> #14,0.56292,0.81253,-0.1514,-56.627,-0.68693,0.5618,0.46099,221.9,0.45962,-0.1555,0.8744,-75.372
> view matrix models
> #14,0.63843,0.72183,-0.26715,8.7464,-0.57027,0.67672,0.46567,130.01,0.51692,-0.14495,0.84367,-85.791
> view matrix models
> #14,0.63843,0.72183,-0.26715,8.3931,-0.57027,0.67672,0.46567,130.45,0.51692,-0.14495,0.84367,-86.604
> view matrix models
> #14,0.56995,0.79371,-0.21254,-21.833,-0.75167,0.60813,0.25529,329.69,0.33188,0.014259,0.94321,-130.51
> view matrix models
> #14,0.56995,0.79371,-0.21254,-21.446,-0.75167,0.60813,0.25529,329.64,0.33188,0.014259,0.94321,-131.71
> view matrix models
> #14,0.56995,0.79371,-0.21254,-20.873,-0.75167,0.60813,0.25529,331.04,0.33188,0.014259,0.94321,-131.07
> view matrix models
> #14,0.58719,0.80523,-0.082539,-96.216,-0.78002,0.59014,0.20811,372.16,0.21628,-0.057817,0.97462,-74.582
> view matrix models
> #14,0.58719,0.80523,-0.082539,-95.946,-0.78002,0.59014,0.20811,372.61,0.21628,-0.057817,0.97462,-74.499
> view matrix models
> #14,0.58719,0.80523,-0.082539,-96.116,-0.78002,0.59014,0.20811,373.03,0.21628,-0.057817,0.97462,-75.042
> view matrix models
> #14,0.57546,0.81437,-0.075119,-99.067,-0.79673,0.57897,0.17324,400.98,0.18458,-0.039845,0.98201,-74.059
> view matrix models
> #14,0.57546,0.81437,-0.075119,-98.842,-0.79673,0.57897,0.17324,401.22,0.18458,-0.039845,0.98201,-72.947
> view matrix models
> #14,0.57546,0.81437,-0.075119,-99.861,-0.79673,0.57897,0.17324,401.32,0.18458,-0.039845,0.98201,-73.363
> view matrix models
> #14,0.62455,0.77912,-0.05395,-114.54,-0.69826,0.588,0.40827,244.71,0.34982,-0.21732,0.91126,-28.992
> view matrix models
> #14,0.79873,0.56559,-0.20529,-19.204,-0.47465,0.80196,0.36272,98.068,0.36978,-0.19228,0.909,-45.357
> view matrix models
> #14,0.79873,0.56559,-0.20529,-18.935,-0.47465,0.80196,0.36272,97.435,0.36978,-0.19228,0.909,-44.638
> view matrix models
> #14,0.79617,0.58276,-0.16282,-45.861,-0.56548,0.81237,0.14246,236.11,0.21528,-0.021349,0.97632,-88.701
> view matrix models
> #14,0.79617,0.58276,-0.16282,-46.817,-0.56548,0.81237,0.14246,239.14,0.21528,-0.021349,0.97632,-92.122
> view matrix models
> #14,0.79617,0.58276,-0.16282,-46.732,-0.56548,0.81237,0.14246,237.85,0.21528,-0.021349,0.97632,-93.184
> view matrix models
> #14,0.79617,0.58276,-0.16282,-46.44,-0.56548,0.81237,0.14246,237.48,0.21528,-0.021349,0.97632,-93.979
> view matrix models
> #14,0.82393,0.5538,-0.12019,-66.291,-0.54999,0.83257,0.065877,261.49,0.13655,0.011823,0.99056,-84.913
> view matrix models
> #14,0.82393,0.5538,-0.12019,-66.86,-0.54999,0.83257,0.065877,261.11,0.13655,0.011823,0.99056,-85.188
> fitmap #9 inMap #2
Fit molecule 139-146.pdb (#9) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 58 atoms
average map value = 0.2409, steps = 68
shifted from previous position = 2.27
rotated from previous position = 8.34 degrees
atoms outside contour = 30, contour level = 0.225
Position of 139-146.pdb (#9) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.37155989 0.84366815 -0.38751425 168.40768422
-0.92838291 0.33450892 -0.16189166 729.98734153
-0.00695587 0.41991406 0.90753720 -117.06588752
Axis 0.30564310 -0.19992076 -0.93092104
Axis point 605.45644706 256.64233443 -0.00000000
Rotation angle (degrees) 72.13332978
Shift along axis 14.51211848
> fitmap #14 inMap #2
Fit molecule 51-100.pdb (#14) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 377 atoms
average map value = 0.1758, steps = 144
shifted from previous position = 2.35
rotated from previous position = 31.3 degrees
atoms outside contour = 247, contour level = 0.225
Position of 51-100.pdb (#14) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.44602991 0.86424483 -0.23267615 6.66280045
-0.79321488 0.50212142 0.34450578 345.00198038
0.41456902 0.03090230 0.90949303 -154.05532324
Axis -0.17357058 -0.35823174 -0.91735668
Axis point 320.43553307 194.35661266 0.00000000
Rotation angle (degrees) 64.60716404
Shift along axis 16.57655488
> view matrix models
> #14,0.76048,0.54248,-0.35692,78.442,-0.27819,0.76882,0.57579,-67.008,0.58676,-0.33858,0.73558,13.168
> view matrix models
> #14,0.76048,0.54248,-0.35692,80.106,-0.27819,0.76882,0.57579,-68.067,0.58676,-0.33858,0.73558,21.725
> view matrix models
> #14,0.76048,0.54248,-0.35692,81.593,-0.27819,0.76882,0.57579,-72.595,0.58676,-0.33858,0.73558,21.599
> view matrix models
> #14,0.76048,0.54248,-0.35692,81.273,-0.27819,0.76882,0.57579,-72.74,0.58676,-0.33858,0.73558,20.666
> view matrix models
> #14,0.76048,0.54248,-0.35692,81.892,-0.27819,0.76882,0.57579,-74.55,0.58676,-0.33858,0.73558,20.322
> view matrix models
> #14,0.87642,0.40971,-0.25304,40.402,-0.3267,0.89193,0.31262,24.411,0.35378,-0.19132,0.91555,-40.683
> view matrix models
> #14,0.87642,0.40971,-0.25304,41.958,-0.3267,0.89193,0.31262,26.557,0.35378,-0.19132,0.91555,-43.251
> select #14:85-100
127 atoms, 130 bonds, 16 residues, 1 model selected
> fitmap sel inMap #2 moveWholeMolecules false
Fit molecule 51-100.pdb (#14) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 127 atoms
average map value = 0.2442, steps = 108
shifted from previous position = 1.98
rotated from previous position = 22.8 degrees
atoms outside contour = 64, contour level = 0.225
> volume #2 level 0.25
> view matrix models
> #14,0.91586,0.39541,-0.069649,-57.851,-0.37158,0.90047,0.22601,82.769,0.15208,-0.18111,0.97163,0.1034
> view matrix models
> #14,0.94793,0.31836,-0.0089696,-69.089,-0.3122,0.9344,0.17157,74.037,0.063003,-0.15984,0.98513,18.137
> view matrix models
> #14,0.8406,0.50296,-0.20105,-7.6649,-0.46391,0.86012,0.2121,140.19,0.27961,-0.085022,0.95634,-78.24
> view matrix models
> #14,0.8406,0.50296,-0.20105,-7.1078,-0.46391,0.86012,0.2121,140.78,0.27961,-0.085022,0.95634,-79.437
> view matrix models
> #14,0.85638,0.50779,-0.093596,-68.132,-0.48522,0.85341,0.19041,162.15,0.17656,-0.11765,0.97723,-38.335
> view matrix models
> #14,0.85638,0.50779,-0.093596,-67.607,-0.48522,0.85341,0.19041,164.23,0.17656,-0.11765,0.97723,-37.677
> view matrix models
> #14,0.85638,0.50779,-0.093596,-68.037,-0.48522,0.85341,0.19041,164.45,0.17656,-0.11765,0.97723,-37.496
> view matrix models
> #14,0.82699,0.55502,-0.089663,-77.885,-0.53608,0.82651,0.17175,203.39,0.16943,-0.093972,0.98105,-46.183
> view matrix models
> #14,0.83364,0.53711,-0.12867,-53.896,-0.51265,0.83918,0.18157,184.74,0.2055,-0.085404,0.97492,-60.017
> view matrix models
> #14,0.83364,0.53711,-0.12867,-54.492,-0.51265,0.83918,0.18157,185.16,0.2055,-0.085404,0.97492,-61.15
> view matrix models
> #14,0.84717,0.52551,-0.078311,-79.845,-0.51567,0.84875,0.11705,214.41,0.12798,-0.058777,0.99003,-50.361
> fitmap sel inMap #2 moveWholeMolecules false
Fit molecule 51-100.pdb (#14) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 127 atoms
average map value = 0.2452, steps = 72
shifted from previous position = 2.64
rotated from previous position = 9.3 degrees
atoms outside contour = 63, contour level = 0.25
> save /Users/egelmanlab01/Desktop/85-100_MFZ0_RBF_j257.pdb models #14
> selectedOnly true
> open /Users/egelmanlab01/Desktop/85-100_MFZ0_RBF_j257.pdb
Summary of feedback from opening
/Users/egelmanlab01/Desktop/85-100_MFZ0_RBF_j257.pdb
---
warnings | Start residue of secondary structure not found: SHEET 1 1 1 VAL A
66 GLY A 70 0
Start residue of secondary structure not found: SHEET 2 2 1 LYS A 78 MET A 82
0
Chain information for 85-100_MFZ0_RBF_j257.pdb #15
---
Chain | Description
A | No description available
> select add #15
254 atoms, 260 bonds, 32 residues, 2 models selected
> select add #14
504 atoms, 516 bonds, 66 residues, 2 models selected
> select subtract #15
377 atoms, 386 bonds, 50 residues, 1 model selected
> select subtract #14
Nothing selected
> hide #15 models
> show #15 models
Drag select of 1 residues
[Repeated 1 time(s)]
> view matrix models
> #14,0.96487,0.13938,-0.22272,101.9,-0.23593,0.83264,-0.50105,422.88,0.11561,0.53599,0.83627,-206.83
> view matrix models
> #14,0.96487,0.13938,-0.22272,142.87,-0.23593,0.83264,-0.50105,421.69,0.11561,0.53599,0.83627,-190.53
> view matrix models
> #14,0.294,-0.89836,0.32637,534.26,0.95518,0.28853,-0.066227,-19.414,-0.034671,0.33121,0.94292,-105.79
> view matrix models
> #14,0.43007,-0.88456,-0.18055,729.16,0.90064,0.43419,0.018151,-99.007,0.062339,-0.17042,0.9834,38.154
> view matrix models
> #14,0.43007,-0.88456,-0.18055,706.13,0.90064,0.43419,0.018151,-112.45,0.062339,-0.17042,0.9834,18.652
> view matrix models
> #14,0.71725,-0.6472,-0.25824,543.18,0.50437,0.7379,-0.44846,144.78,0.4808,0.19141,0.85568,-217.98
> view matrix models
> #14,0.71725,-0.6472,-0.25824,522.99,0.50437,0.7379,-0.44846,171.81,0.4808,0.19141,0.85568,-208.78
> view matrix models
> #14,0.71725,-0.6472,-0.25824,529.48,0.50437,0.7379,-0.44846,174.22,0.4808,0.19141,0.85568,-210.29
> view matrix models
> #14,0.65625,-0.72832,-0.19722,554.3,0.68033,0.68417,-0.2628,38.307,0.32633,0.038294,0.94448,-135.77
> view matrix models
> #14,-0.35011,-0.64589,-0.67842,1133.8,0.53603,-0.7321,0.42037,318.51,-0.76818,-0.21648,0.60253,542.05
> view matrix models
> #14,-0.21532,-0.21458,-0.95268,1047.5,-0.50547,-0.81021,0.29673,798.07,-0.83555,0.54544,0.065989,528.88
> view matrix models
> #14,-0.033606,-0.034329,-0.99885,930.9,-0.81506,-0.57745,0.047269,943.85,-0.57841,0.8157,-0.0085743,362.43
> view matrix models
> #14,-0.033606,-0.034329,-0.99885,930,-0.81506,-0.57745,0.047269,942.14,-0.57841,0.8157,-0.0085743,360.94
> view matrix models
> #14,-0.033606,-0.034329,-0.99885,929.58,-0.81506,-0.57745,0.047269,942.24,-0.57841,0.8157,-0.0085743,360.73
> view matrix models
> #14,-0.2846,-0.17329,-0.94285,1050.6,-0.7982,-0.50186,0.33317,764.27,-0.53092,0.84741,0.0045093,323.95
> view matrix models
> #14,-0.2846,-0.17329,-0.94285,1051.4,-0.7982,-0.50186,0.33317,765.23,-0.53092,0.84741,0.0045093,323.84
> view matrix models
> #14,0.67479,-0.3564,-0.64625,620.95,-0.41248,0.544,-0.7307,731.49,0.61198,0.75963,0.22008,-172.77
> view matrix models
> #14,0.61889,-0.67085,-0.40857,649.45,0.64806,0.73002,-0.21699,8.6847,0.44384,-0.13048,0.88656,-85.27
> view matrix models
> #14,0.61889,-0.67085,-0.40857,647.86,0.64806,0.73002,-0.21699,8.4784,0.44384,-0.13048,0.88656,-89.836
> view matrix models
> #14,0.61889,-0.67085,-0.40857,652.02,0.64806,0.73002,-0.21699,6.886,0.44384,-0.13048,0.88656,-88.545
> view matrix models
> #14,0.64619,-0.65807,-0.38651,625.85,0.5581,0.7529,-0.34882,96.481,0.52055,0.009699,0.85378,-156.74
> view matrix models
> #14,0.67508,-0.70282,-0.22429,552.64,0.64533,0.70989,-0.28215,48.19,0.35752,0.045732,0.93278,-149.62
> view matrix models
> #14,0.67508,-0.70282,-0.22429,551.41,0.64533,0.70989,-0.28215,49.712,0.35752,0.045732,0.93278,-153.25
> volume zone #2 nearAtoms sel & #14 range 6.48
> select add #14
377 atoms, 386 bonds, 50 residues, 1 model selected
> show #!1 models
> volume zone #2 nearAtoms sel & #14 range 6.48
> select clear
> select add #1
4216 atoms, 3611 bonds, 445 pseudobonds, 1147 residues, 2 models selected
> volume zone #2 nearAtoms sel & #1 range 6.48
> select subtract #1
Nothing selected
> hide #!1 models
> volume #2 level 0.22
> select #14/A:57
7 atoms, 6 bonds, 1 residue, 1 model selected
> view matrix models
> #14,0.67508,-0.70282,-0.22429,552.1,0.64533,0.70989,-0.28215,49.76,0.35752,0.045732,0.93278,-151.74
> open /Users/egelmanlab01/Desktop/85-100_MFZ0_RBF_j257.pdb
Summary of feedback from opening
/Users/egelmanlab01/Desktop/85-100_MFZ0_RBF_j257.pdb
---
warnings | Start residue of secondary structure not found: SHEET 1 1 1 VAL A
66 GLY A 70 0
Start residue of secondary structure not found: SHEET 2 2 1 LYS A 78 MET A 82
0
Chain information for 85-100_MFZ0_RBF_j257.pdb #16
---
Chain | Description
A | No description available
> hide #15 models
> select add #14
377 atoms, 386 bonds, 50 residues, 1 model selected
> hide #14 models
> hide #16 models
> show #16 models
> select subtract #14
Nothing selected
> hide #5 models
> show #5 models
> combine #5 #510-13 #16
Remapping chain ID 'A' in 85-100_MFZ0_RBF_j257.pdb #16 to 'D'
> hide #16 models
> hide #13 models
> hide #12 models
> hide #11 models
> hide #10 models
> hide #5 models
> hide #17 models
> show #17 models
> view #10 clip false
> close #17
> combine #5 #10-13 #16
Remapping chain ID 'A' in 108-120_MFZ0_RBF_j257.pdb #10 to 'D'
Remapping chain ID 'A' in 121-130_MFZ0_RBF_j257.pdb #11 to 'E'
Remapping chain ID 'A' in 131-138_MFZ0_RBF_j257.pdb #12 to 'F'
Remapping chain ID 'A' in 139-146_MFZ0_RBF_j257.pdb #13 to 'G'
Remapping chain ID 'A' in 85-100_MFZ0_RBF_j257.pdb #16 to 'H'
> hide #17 models
> show #17 models
Drag select of 2 residues
> close #17
> show #10 models
> show #11 models
> show #12 models
> show #13 models
Drag select of 2 cryosparc_P101_J257_005_volume_map_sharp.mrc , 3 residues
> select clear
> combine #10-13
Remapping chain ID 'A' in 121-130_MFZ0_RBF_j257.pdb #11 to 'B'
Remapping chain ID 'A' in 131-138_MFZ0_RBF_j257.pdb #12 to 'C'
Remapping chain ID 'A' in 139-146_MFZ0_RBF_j257.pdb #13 to 'D'
> hide #13 models
> hide #12 models
> hide #11 models
> hide #10 models
> select #17/A:118
8 atoms, 7 bonds, 1 residue, 1 model selected
> view matrix models #17,1,0,0,1.1654,0,1,0,5.0514,0,0,1,5.315
> view matrix models
> #17,0.96495,0.24489,0.094342,-132.6,-0.23787,0.96801,-0.079808,155.41,-0.11087,0.054569,0.99234,31.993
> view matrix models
> #17,0.96495,0.24489,0.094342,-132.04,-0.23787,0.96801,-0.079808,153.66,-0.11087,0.054569,0.99234,32.93
> view matrix models
> #17,0.96495,0.24489,0.094342,-131.72,-0.23787,0.96801,-0.079808,152.7,-0.11087,0.054569,0.99234,30.862
> view matrix models
> #17,0.96495,0.24489,0.094342,-131.13,-0.23787,0.96801,-0.079808,152.4,-0.11087,0.054569,0.99234,31.578
> view matrix models
> #17,0.92725,0.35991,0.10333,-167.71,-0.35073,0.93144,-0.096973,222.31,-0.13115,0.053678,0.98991,41.464
> view matrix models
> #17,0.93514,0.35146,0.044562,-138.27,-0.34973,0.9359,-0.042165,192.85,-0.056525,0.023845,0.99812,19.141
> volume #2 level 0.2
> ui tool show "Fit in Map"
> fitmap #17 inMap #2
Fit molecule combination (#17) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 314 atoms
average map value = 0.1958, steps = 56
shifted from previous position = 2.07
rotated from previous position = 8.07 degrees
atoms outside contour = 160, contour level = 0.2
Position of combination (#17) relative to
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.97304088 0.23031615 -0.01207954 -77.02963512
-0.23051137 0.97289284 -0.01854812 115.81143979
0.00748017 0.02083255 0.99975500 -6.99256997
Axis 0.08507005 -0.04225284 -0.99547867
Axis point 456.17431872 386.19143893 0.00000000
Rotation angle (degrees) 13.38305925
Shift along axis -4.48532344
> show #16 models
> select #16/A:97
4 atoms, 3 bonds, 1 residue, 1 model selected
> view matrix models #16,1,0,0,2.6732,0,1,0,0.44577,0,0,1,4.6563
> view matrix models #16,1,0,0,2.2708,0,1,0,-0.30838,0,0,1,6.6919
> select #17/A
124 atoms, 127 bonds, 14 residues, 1 model selected
> fitmap sel inMap #2 moveWholeMolecules false
Fit molecule combination (#17) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 124 atoms
average map value = 0.2397, steps = 80
shifted from previous position = 0.254
rotated from previous position = 10.6 degrees
atoms outside contour = 48, contour level = 0.2
> select #16/A:91
9 atoms, 8 bonds, 1 residue, 1 model selected
> view matrix models #16,1,0,0,3.7762,0,1,0,-0.082777,0,0,1,6.419
> view matrix models
> #16,-0.93723,-0.34724,-0.032051,962.59,0.34298,-0.93451,0.095115,638.24,-0.062979,0.078151,0.99495,1.3801
> view matrix models
> #16,-0.93723,-0.34724,-0.032051,961.21,0.34298,-0.93451,0.095115,637.91,-0.062979,0.078151,0.99495,1.4427
> view matrix models
> #16,-0.93723,-0.34724,-0.032051,961.69,0.34298,-0.93451,0.095115,635.64,-0.062979,0.078151,0.99495,1.1754
> view matrix models
> #16,-0.93723,-0.34724,-0.032051,961.46,0.34298,-0.93451,0.095115,635.58,-0.062979,0.078151,0.99495,0.70171
> fitmap #16 inMap #2 moveWholeMolecules false
Fit molecule 85-100_MFZ0_RBF_j257.pdb (#16) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 127 atoms
average map value = 0.2115, steps = 64
shifted from previous position = 2.14
rotated from previous position = 13 degrees
atoms outside contour = 66, contour level = 0.2
> view matrix models
> #16,-0.93723,-0.34724,-0.032051,961.35,0.34298,-0.93451,0.095115,634.28,-0.062979,0.078151,0.99495,0.3629
> view matrix models
> #16,-0.79265,0.60545,-0.071665,515.04,-0.60874,-0.79245,0.0381,993.04,-0.033724,0.073826,0.9967,-10.682
> view matrix models
> #16,-0.79265,0.60545,-0.071665,515.13,-0.60874,-0.79245,0.0381,993.51,-0.033724,0.073826,0.9967,-11.62
> view matrix models
> #16,-0.88215,0.47086,0.010111,570.48,-0.46841,-0.8749,-0.12308,1047.3,-0.049107,-0.11331,0.99235,76.446
> view matrix models
> #16,-0.79711,0.27919,0.53541,367.64,-0.51487,-0.7775,-0.36111,1138,0.31546,-0.56351,0.7635,226.51
> view matrix models
> #16,-0.79711,0.27919,0.53541,367.59,-0.51487,-0.7775,-0.36111,1138.5,0.31546,-0.56351,0.7635,223.79
> view matrix models
> #16,-0.77608,0.57491,0.25919,364.17,-0.63059,-0.70254,-0.32983,1139.5,-0.0075357,-0.41942,0.90776,227.07
> view matrix models
> #16,-0.77608,0.57491,0.25919,364.89,-0.63059,-0.70254,-0.32983,1141.4,-0.0075357,-0.41942,0.90776,228.11
> view matrix models
> #16,-0.77608,0.57491,0.25919,362.83,-0.63059,-0.70254,-0.32983,1143,-0.0075357,-0.41942,0.90776,228.5
> view matrix models
> #16,-0.77608,0.57491,0.25919,360.6,-0.63059,-0.70254,-0.32983,1140.1,-0.0075357,-0.41942,0.90776,229.4
> view matrix models
> #16,-0.93471,0.35524,0.010732,637.43,-0.33042,-0.85751,-0.39433,1113,-0.13088,-0.37214,0.9189,254.8
> fitmap #16 inMap #2 moveWholeMolecules false
Fit molecule 85-100_MFZ0_RBF_j257.pdb (#16) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 127 atoms
average map value = 0.2154, steps = 80
shifted from previous position = 4.13
rotated from previous position = 7.97 degrees
atoms outside contour = 70, contour level = 0.2
> view matrix models
> #16,-0.84272,0.53438,0.065317,497.45,-0.4207,-0.57798,-0.69925,1175.2,-0.33591,-0.61675,0.71188,541.29
> view matrix models
> #16,-0.84272,0.53438,0.065317,494.9,-0.4207,-0.57798,-0.69925,1179.4,-0.33591,-0.61675,0.71188,542.34
> view matrix models
> #16,-0.96236,0.1748,-0.20809,827.14,-0.015716,-0.80022,-0.5995,1061.6,-0.27131,-0.57367,0.77285,468.61
> view matrix models
> #16,-0.95768,0.14565,-0.24826,856.74,0.0046848,-0.85452,-0.5194,1038.4,-0.2878,-0.49858,0.81767,422
> view matrix models
> #16,-0.95768,0.14565,-0.24826,856.71,0.0046848,-0.85452,-0.5194,1038.5,-0.2878,-0.49858,0.81767,421.07
> fitmap #16 inMap #2 moveWholeMolecules false
Fit molecule 85-100_MFZ0_RBF_j257.pdb (#16) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 127 atoms
average map value = 0.2164, steps = 68
shifted from previous position = 3.52
rotated from previous position = 15.6 degrees
atoms outside contour = 69, contour level = 0.2
> hide #16 models
> select add #16
127 atoms, 130 bonds, 16 residues, 1 model selected
> save 108-146_MFZ0_RBF_j257.pdb #17
> select subtract #16
Nothing selected
> hide #17 models
> show #17 models
> show #10 models
> hide #10 models
> transparency 0
> transparency 50
> ui tool show AlphaFold
> open /Users/egelmanlab01/Documents/milano/ravi2/A0A482MFZ0.fasta
Summary of feedback from opening
/Users/egelmanlab01/Documents/milano/ravi2/A0A482MFZ0.fasta
---
notes | Alignment identifier is A0A482MFZ0.fasta
Associated A0A482MFZ0_unrelaxed_rank_1_model_3.pdb chain A to
A0A482MFZ0|A0A482MFZ0_9CAUD Baseplate protein OS=Agrobacterium phage Milano
OX=2557550 GN=Milano_027 PE=4 SV=1 with 0 mismatches
Associated 1-50_MFZ0_RBF_j257.pdb chain A to A0A482MFZ0|A0A482MFZ0_9CAUD
Baseplate protein OS=Agrobacterium phage Milano OX=2557550 GN=Milano_027 PE=4
SV=1 with 0 mismatches
Associated 1-50_MFZ0_RBF_j257.pdb chain B to A0A482MFZ0|A0A482MFZ0_9CAUD
Baseplate protein OS=Agrobacterium phage Milano OX=2557550 GN=Milano_027 PE=4
SV=1 with 0 mismatches
Associated 1-50_MFZ0_RBF_j257.pdb chain C to A0A482MFZ0|A0A482MFZ0_9CAUD
Baseplate protein OS=Agrobacterium phage Milano OX=2557550 GN=Milano_027 PE=4
SV=1 with 0 mismatches
Associated 95-120.pdb chain A to A0A482MFZ0|A0A482MFZ0_9CAUD Baseplate protein
OS=Agrobacterium phage Milano OX=2557550 GN=Milano_027 PE=4 SV=1 with 0
mismatches
8 messages similar to the above omitted
Opened 1 sequences from A0A482MFZ0.fasta
> ui tool show AlphaFold
> close all
> ui tool show AlphaFold
> alphafold predict
> MTTSKTYDERNRDIQDGFERHVFKGIEHTDTGALVSVKGSGTQEEDVPVINSGYGFTPAADTELEVFLHGDGSDASNKFATMTIPRNKQRKWPEGAGGVQHPFNADKFVQFDDDSIWLKDGKFTLGNNQELTITVSNGLVTLSSNNEVDFRCPKLMHNGVNIGDSHVHPQKPDSGGDSEEDTDPPKRD,MTTSKTYDERNRDIQDGFERHVFKGIEHTDTGALVSVKGSGTQEEDVPVINSGYGFTPAADTELEVFLHGDGSDASNKFATMTIPRNKQRKWPEGAGGVQHPFNADKFVQFDDDSIWLKDGKFTLGNNQELTITVSNGLVTLSSNNEVDFRCPKLMHNGVNIGDSHVHPQKPDSGGDSEEDTDPPKRD,MTTSKTYDERNRDIQDGFERHVFKGIEHTDTGALVSVKGSGTQEEDVPVINSGYGFTPAADTELEVFLHGDGSDASNKFATMTIPRNKQRKWPEGAGGVQHPFNADKFVQFDDDSIWLKDGKFTLGNNQELTITVSNGLVTLSSNNEVDFRCPKLMHNGVNIGDSHVHPQKPDSGGDSEEDTDPPKRD
Running AlphaFold prediction
> alphafold predict
> MTTSKTYDERNRDIQDGFERHVFKGIEHTDTGALVSVKGSGTQEEDVPVINSGYGFTPAADTELEVFLHGDGSDASNKFATMTIPRNKQRKWPEGAGGVQHPFNADKFVQFDDDSIWLKDGKFTLGNNQELTITVSNGLVTLSSNNEVDFRCPKLMHNGVNIGDSHVHPQKPDSGGDSEEDTDPPKRD,MTTSKTYDERNRDIQDGFERHVFKGIEHTDTGALVSVKGSGTQEEDVPVINSGYGFTPAADTELEVFLHGDGSDASNKFATMTIPRNKQRKWPEGAGGVQHPFNADKFVQFDDDSIWLKDGKFTLGNNQELTITVSNGLVTLSSNNEVDFRCPKLMHNGVNIGDSHVHPQKPDSGGDSEEDTDPPKRD,MTTSKTYDERNRDIQDGFERHVFKGIEHTDTGALVSVKGSGTQEEDVPVINSGYGFTPAADTELEVFLHGDGSDASNKFATMTIPRNKQRKWPEGAGGVQHPFNADKFVQFDDDSIWLKDGKFTLGNNQELTITVSNGLVTLSSNNEVDFRCPKLMHNGVNIGDSHVHPQKPDSGGDSEEDTDPPKRD
> prokaryote true
Running AlphaFold prediction
[Repeated 2 time(s)]
> open /Users/egelmanlab01/Downloads/model_1.pdb
Summary of feedback from opening /Users/egelmanlab01/Downloads/model_1.pdb
---
warnings | Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
3553 messages similar to the above omitted
Chain information for model_1.pdb #1
---
Chain | Description
A B C | No description available
> open
> /Users/egelmanlab01/Documents/milano/base_plate/cryosparc_P101_J257_005_volume_map_sharp.mrc
Opened cryosparc_P101_J257_005_volume_map_sharp.mrc as #2, grid size
768,768,768, pixel 1.08, shown at step 1, values float32
> volume #2 region 0,0,0,767,767,767 step 4
[Repeated 1 time(s)]
> volume #2 change image level -0.055,0 level 0.2541,0.8 level 0.9056,1
> volume #2 step 1
> volume #2 level 0.2
> volume #2 level 0.23
Drag select of 564 residues
> view matrix models #1,1,0,0,-17.085,0,1,0,42.126,0,0,1,146.77
> view matrix models #1,1,0,0,-46.537,0,1,0,116.12,0,0,1,281.62
> view matrix models
> #1,-0.99947,-0.026685,0.018493,-49.288,-0.030103,0.97503,-0.22001,126.29,-0.01216,-0.22045,-0.97532,373.19
> view matrix models
> #1,-0.99947,-0.026685,0.018493,-84.54,-0.030103,0.97503,-0.22001,214.8,-0.01216,-0.22045,-0.97532,538.28
> view matrix models
> #1,-0.99947,-0.026685,0.018493,77.542,-0.030103,0.97503,-0.22001,445,-0.01216,-0.22045,-0.97532,691.85
> view matrix models
> #1,-0.99947,-0.026685,0.018493,373.2,-0.030103,0.97503,-0.22001,532.99,-0.01216,-0.22045,-0.97532,676.78
> view matrix models
> #1,-0.99947,-0.026685,0.018493,435.61,-0.030103,0.97503,-0.22001,397.82,-0.01216,-0.22045,-0.97532,563.08
> view matrix models
> #1,-0.99622,-0.018041,-0.084957,439.71,-0.0074283,0.9923,-0.12361,393.16,0.086533,-0.12252,-0.98869,560.39
> view matrix models
> #1,-0.99622,-0.018041,-0.084957,415.96,-0.0074283,0.9923,-0.12361,383.95,0.086533,-0.12252,-0.98869,568.7
> view matrix models
> #1,-0.99622,-0.018041,-0.084957,421.74,-0.0074283,0.9923,-0.12361,381.31,0.086533,-0.12252,-0.98869,530.97
> view matrix models
> #1,-0.99208,0.079256,0.097451,410.61,0.07341,0.99536,-0.062185,378.71,-0.10193,-0.054538,-0.9933,528.54
> view matrix models
> #1,-0.99208,0.079256,0.097451,419.33,0.07341,0.99536,-0.062185,364.74,-0.10193,-0.054538,-0.9933,521.49
> ui tool show "Side View"
> view matrix models
> #1,-0.99208,0.079256,0.097451,414.6,0.07341,0.99536,-0.062185,374.54,-0.10193,-0.054538,-0.9933,521.63
> view matrix models
> #1,-0.99208,0.079256,0.097451,411.05,0.07341,0.99536,-0.062185,377.16,-0.10193,-0.054538,-0.9933,526.39
> volume zone #2 nearAtoms sel & #1 range 6.48
> view matrix models
> #1,-0.99208,0.079256,0.097451,410.59,0.07341,0.99536,-0.062185,375.39,-0.10193,-0.054538,-0.9933,522.69
> view matrix models
> #1,-0.37427,0.91546,-0.14783,392.87,0.92689,0.36447,-0.089624,399.7,-0.028169,-0.17056,-0.98494,526.47
> view matrix models
> #1,0.19975,0.97542,-0.092988,389.29,0.97617,-0.18989,0.10502,410.75,0.08478,-0.11175,-0.99011,524.81
> view matrix models
> #1,0.19975,0.97542,-0.092988,389.1,0.97617,-0.18989,0.10502,410.82,0.08478,-0.11175,-0.99011,525.75
> view matrix models
> #1,0.19975,0.97542,-0.092988,383.51,0.97617,-0.18989,0.10502,410.92,0.08478,-0.11175,-0.99011,523.92
> view matrix models
> #1,0.2508,0.96434,-0.084565,383.61,0.9672,-0.25325,-0.019474,418.4,-0.040196,-0.076907,-0.99623,522.79
> view matrix models
> #1,0.2508,0.96434,-0.084565,383.25,0.9672,-0.25325,-0.019474,416.3,-0.040196,-0.076907,-0.99623,520.29
> view matrix models
> #1,0.2508,0.96434,-0.084565,381.75,0.9672,-0.25325,-0.019474,418.71,-0.040196,-0.076907,-0.99623,519.51
> view matrix models
> #1,-0.12197,0.99247,0.011629,376.15,0.98337,0.12242,-0.13414,410.56,-0.13455,-0.004925,-0.99089,516.65
> fitmap #1 inMap #2 moveWholeMolecules false
Fit molecule model_1.pdb (#1) to map
cryosparc_P101_J257_005_volume_map_sharp.mrc (#2) using 5337 atoms
average map value = 0.1321, steps = 172
shifted from previous position = 5.49
rotated from previous position = 7.56 degrees
atoms outside contour = 3976, contour level = 0.23
> view clip false
> volume #2 level 0.2
> transparency 50
> color #1 #ff9300 transparency 0
> color #2 black models transparency 0
> color #2 white models transparency 0
> transparency 50
> select add #1
5337 atoms, 5433 bonds, 564 residues, 1 model selected
> volume zone #2 nearAtoms sel & #1 range 6.48
> color zone #2 near sel & #1 distance 6.48
> close all
> open /Users/egelmanlab01/Downloads/tube-sheath_C3_j450.pdb
Chain information for tube-sheath_C3_j450.pdb #1
---
Chain | Description
C D E F G H I L O T U V a b c e i j | No description available
J M P R W Y | No description available
K N Q S X Z d f g h k l | No description available
> coulombic
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 1334, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 390, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 408, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 327, in run
f(s)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 61, in func_plus_tip
func(cmd + " %s")(session)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 569, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 512, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX_Daily.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
"/Applications/ChimeraX_Daily.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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/coulombic/coulombic.py", line 84, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 62, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 168, in hbond_add_hydrogens
_make_shared_data(session, structures, in_isolation)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 365, in _make_shared_data
from chimerax.atom_search import AtomSearchTree
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atom_search/__init__.py", line 15, in <module>
import chimerax.atom_search_lib
ModuleNotFoundError: No module named 'chimerax.atom_search_lib'
ModuleNotFoundError: No module named 'chimerax.atom_search_lib'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atom_search/__init__.py", line 15, in
import chimerax.atom_search_lib
See log for complete Python traceback.
> hide atoms
> show cartoons
> coulombic
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1286, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 1334, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 390, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 408, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 327, in run
f(s)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 61, in func_plus_tip
func(cmd + " %s")(session)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 569, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 512, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX_Daily.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
"/Applications/ChimeraX_Daily.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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic
assign_charges(session, needs_assignment, his_scheme, charge_method,
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/coulombic/coulombic.py", line 84, in assign_charges
cmd_addh(session, addh_structures, hbond=hbond)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 62, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 168, in hbond_add_hydrogens
_make_shared_data(session, structures, in_isolation)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 365, in _make_shared_data
from chimerax.atom_search import AtomSearchTree
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atom_search/__init__.py", line 15, in <module>
import chimerax.atom_search_lib
ModuleNotFoundError: No module named 'chimerax.atom_search_lib'
ModuleNotFoundError: No module named 'chimerax.atom_search_lib'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atom_search/__init__.py", line 15, in
import chimerax.atom_search_lib
See log for complete Python traceback.
OpenGL version: 4.1 ATI-4.8.15
OpenGL renderer: AMD Radeon Pro 5300 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Locale: UTF-8
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac20,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3.3 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: 8 GB
System Firmware Version: 1731.100.130.0.0 (iBridge: 19.16.14243.0.0,0)
OS Loader Version: 540.100.7~23
Software:
System Software Overview:
System Version: macOS 12.3.1 (21E258)
Kernel Version: Darwin 21.4.0
Time since boot: 41 days 20:46
Graphics/Displays:
AMD Radeon Pro 5300:
Chipset Model: AMD Radeon Pro 5300
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0047
ROM Revision: 113-D3220I-231
VBIOS Version: 113-D322A1XL-012
Option ROM Version: 113-D322A1XL-012
EFI Driver Version: 01.01.231
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
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: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.5.30
cftime: 1.5.2
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: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.36.2
ChimeraX-AtomicLibrary: 6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
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: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.1
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4.dev202203030220
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: 1.0
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: 1.1
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-ItemsInspection: 1.0
ChimeraX-Label: 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: 1.5.2
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: 1.8
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
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
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: 1.7.7
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
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.16.2
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: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.5.1
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.29.1
funcparserlib: 1.0.0a0
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.26
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: 4.9.2
kiwisolver: 1.3.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.0
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.4
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: 9.0.0
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.28
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: 3.0.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.2.2
QtPy: 2.0.1
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.1
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: 1.26.8
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
| Component: | Unassigned → Surface/Binding Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Coulombic: No module named 'chimerax.atom_search_lib' |
comment:2 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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Fixed a week after this build.