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Opened 4 years ago
Closed 4 years ago
#5141 closed defect (fixed)
Hand-drawn regions can include headers
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.4.0-81-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-view/seq_canvas.py", line 1714, in _box_corners
uly = self.bottom_ruler_y + self.letter_gaps[1] + self.line_index[line1] * (
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol1/80s_vol1_full_mask_rfn179_pp192.mrc
Opened 80s_vol1_full_mask_rfn179_pp192.mrc as #1, grid size 360,360,360, pixel
1.38, shown at level 0.0387, step 2, values float32
> volume #1 step 1
> volume #1 level 0.05015
> open
> /home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol1/phenix/RealSpaceRefine_1/80s_vol1FM_r1_real_space_refined.pdb
Summary of feedback from opening
/home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol1/phenix/RealSpaceRefine_1/80s_vol1FM_r1_real_space_refined.pdb
---
warnings | Ignored bad PDB record found on line 432
LINK C7 3HE A54277 O2' A B6 76
Ignored bad PDB record found on line 433
SSBOND 1 CYS AV 17 CYS AV 56
Ignored bad PDB record found on line 434
SSBOND 2 CYS Aa 23 CYS Aa 74
Ignored bad PDB record found on line 435
SSBOND 3 CYS Ad 21 CYS Ad 24
Ignored bad PDB record found on line 436
SSBOND 4 CYS Ad 24 CYS Ad 39
7 messages similar to the above omitted
Chain information for 80s_vol1FM_r1_real_space_refined.pdb #2
---
Chain | Description
A5 | No description available
A7 | No description available
A8 | No description available
AA | No description available
AB | No description available
AC | No description available
AD | No description available
AE | No description available
AF | No description available
AG | No description available
AH | No description available
AI | No description available
AJ | No description available
AK | No description available
AL | No description available
AN | No description available
AO | No description available
AP | No description available
AQ | No description available
AR | No description available
AS | No description available
AT | No description available
AU | No description available
AV | No description available
AW | No description available
AX | No description available
AY | No description available
AZ | No description available
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Ag | No description available
B2 | No description available
B3 | No description available
B4 | No description available
B6 | No description available
CA | No description available
CB | No description available
CC | No description available
CD | No description available
CE | No description available
CF | No description available
CG | No description available
CH | No description available
CI | No description available
CJ | No description available
CL | No description available
CM | No description available
CN | No description available
CO | No description available
CP | No description available
CQ | No description available
CR | No description available
CS | No description available
CT | No description available
CU | No description available
CV | No description available
CW | No description available
CX | No description available
CY | No description available
CZ | No description available
Ca | No description available
Cb | No description available
Cc | No description available
Cd | No description available
Ce | No description available
Cf | No description available
Cg | No description available
Ch | No description available
Ci | No description available
Cj | No description available
Ck | No description available
Cl | No description available
Cm | No description available
Cn | No description available
Co | No description available
Cp | No description available
Cr | No description available
Cz | No description available
> show cartoons
> hide atoms
> open
> /home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol2/80s_vol2SM.pdb
Summary of feedback from opening
/home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol2/80s_vol2SM.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLN A 8
GLY A 11 1 4
Start residue of secondary structure not found: HELIX 2 2 TYR A 34 HIS A 38 1
5
Start residue of secondary structure not found: HELIX 3 3 ILE A 104 LEU A 106
1 3
Start residue of secondary structure not found: HELIX 4 4 ARG A 174 ASP A 176
1 3
Start residue of secondary structure not found: HELIX 5 5 ALA A 182 LYS A 188
1 7
433 messages similar to the above omitted
PDB SEQRES record for chain 6 is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for 80s_vol2SM.pdb #3
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
AA | No description available
AB | No description available
AC | No description available
AD | No description available
AE | No description available
AF | No description available
AG | No description available
AH | No description available
AI | No description available
AJ | No description available
AK | No description available
AL | No description available
AN | No description available
AO | No description available
AP | No description available
AQ | No description available
AR | No description available
AS | No description available
AT | No description available
AU | No description available
AV | No description available
AW | No description available
AX | No description available
AY | No description available
AZ | No description available
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Ag | No description available
CA | No description available
CB | No description available
CC | No description available
CD | No description available
CE | No description available
CF | No description available
CG | No description available
CH | No description available
CI | No description available
CJ | No description available
CL | No description available
CM | No description available
CN | No description available
CO | No description available
CP | No description available
CQ | No description available
CR | No description available
CS | No description available
CT | No description available
CU | No description available
CV | No description available
CW | No description available
CX | No description available
CY | No description available
CZ | No description available
Ca | No description available
Cb | No description available
Cc | No description available
Cd | No description available
Ce | No description available
Cf | No description available
Cg | No description available
Ch | No description available
Ci | No description available
Cj | No description available
Ck | No description available
Cl | No description available
Cm | No description available
Cn | No description available
Co | No description available
Cp | No description available
Cr | No description available
Cz | No description available
> show cartoons
> hide atoms
> open
> /home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol3/80s_vol3FM_PnAsite_tRNA.pdb
Summary of feedback from opening
/home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol3/80s_vol3FM_PnAsite_tRNA.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU A 12
LEU A 19 1 8
Start residue of secondary structure not found: HELIX 2 2 PHE A 32 MET A 34 1
3
Start residue of secondary structure not found: HELIX 3 3 LEU A 51 ILE A 65 1
15
Start residue of secondary structure not found: HELIX 4 4 TYR A 82 GLN A 84 1
3
Start residue of secondary structure not found: HELIX 5 5 ARG A 85 TYR A 93 1
9
295 messages similar to the above omitted
PDB SEQRES record for chain 6 is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for 80s_vol3FM_PnAsite_tRNA.pdb #4
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
AA | No description available
AB | No description available
AC | No description available
AD | No description available
AE | No description available
AF | No description available
AG | No description available
AH | No description available
AI | No description available
AJ | No description available
AK | No description available
AL | No description available
AN | No description available
AO | No description available
AP | No description available
AQ | No description available
AR | No description available
AS | No description available
AT | No description available
AU | No description available
AV | No description available
AW | No description available
AX | No description available
AY | No description available
AZ | No description available
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Ag | No description available
CA | No description available
CB | No description available
CC | No description available
CD | No description available
CE | No description available
CF | No description available
CG | No description available
CH | No description available
CI | No description available
CJ | No description available
CL | No description available
CM | No description available
CN | No description available
CO | No description available
CP | No description available
CQ | No description available
CR | No description available
CS | No description available
CT | No description available
CU | No description available
CV | No description available
CW | No description available
CX | No description available
CY | No description available
CZ | No description available
Ca | No description available
Cb | No description available
Cc | No description available
Cd | No description available
Ce | No description available
Cf | No description available
Cg | No description available
Ch | No description available
Ci | No description available
Cj | No description available
Ck | No description available
Cl | No description available
Cm | No description available
Cn | No description available
Co | No description available
Cp | No description available
Cr | No description available
Cz | No description available
> show cartoons
> hide atoms
> open
> /home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol4_IFRD1/80s_vol4FM_IFRD2.pdb
Summary of feedback from opening
/home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol4_IFRD1/80s_vol4FM_IFRD2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLN A 8
GLY A 11 1 4
Start residue of secondary structure not found: HELIX 2 2 TYR A 34 HIS A 38 1
5
Start residue of secondary structure not found: HELIX 3 3 ILE A 104 LEU A 106
1 3
Start residue of secondary structure not found: HELIX 4 4 ARG A 174 ASP A 176
1 3
Start residue of secondary structure not found: HELIX 5 5 ALA A 182 LYS A 188
1 7
433 messages similar to the above omitted
Chain information for 80s_vol4FM_IFRD2.pdb #5
---
Chain | Description
2 | No description available
5 | No description available
7 | No description available
8 | No description available
AA | No description available
AB | No description available
AC | No description available
AD | No description available
AE | No description available
AF | No description available
AG | No description available
AH | No description available
AI | No description available
AJ | No description available
AK | No description available
AL | No description available
AN | No description available
AO | No description available
AP | No description available
AQ | No description available
AR | No description available
AS | No description available
AT | No description available
AU | No description available
AV | No description available
AW | No description available
AX | No description available
AY | No description available
AZ | No description available
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Ag | No description available
CA | No description available
CB | No description available
CC | No description available
CD | No description available
CE | No description available
CF | No description available
CG | No description available
CH | No description available
CI | No description available
CJ | No description available
CL | No description available
CM | No description available
CN | No description available
CO | No description available
CP | No description available
CQ | No description available
CR | No description available
CS | No description available
CT | No description available
CU | No description available
CV | No description available
CW | No description available
CX | No description available
CY | No description available
CZ | No description available
Ca | No description available
Cb | No description available
Cc | No description available
Cd | No description available
Ce | No description available
Cf | No description available
Cg | No description available
Ch | No description available
Ci | No description available
Cj | No description available
Ck | No description available
Cl | No description available
Cm | No description available
Cn | No description available
Co | No description available
Cp | No description available
Cr | No description available
Cz | No description available
DA | No description available
> show cartoons
> hide atoms
> ui tool show "Fit in Map"
Fit molecule 80s_vol2SM.pdb (#3) to map 80s_vol1_full_mask_rfn179_pp192.mrc
(#1) using 211555 atoms
average map value = 0.05401, steps = 92
shifted from previous position = 2.7
rotated from previous position = 0.647 degrees
atoms outside contour = 103242, contour level = 0.050155
Position of 80s_vol2SM.pdb (#3) relative to
80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates:
Matrix rotation and translation
0.99994351 0.00250712 0.01032935 -2.98360347
-0.00254656 0.99998951 0.00380694 0.83808567
-0.01031970 -0.00383303 0.99993940 1.00963281
Axis -0.33820695 0.91409350 -0.22371663
Axis point 130.01960104 0.00000000 238.83078316
Rotation angle (degrees) 0.64715949
Shift along axis 1.54929245
Fit molecule 80s_vol3FM_PnAsite_tRNA.pdb (#4) to map
80s_vol1_full_mask_rfn179_pp192.mrc (#1) using 211558 atoms
average map value = 0.05323, steps = 124
shifted from previous position = 0.639
rotated from previous position = 0.408 degrees
atoms outside contour = 103826, contour level = 0.050155
Position of 80s_vol3FM_PnAsite_tRNA.pdb (#4) relative to
80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates:
Matrix rotation and translation
0.99997858 -0.00201416 -0.00622815 2.32784426
0.00199679 0.99999410 -0.00279416 0.46569521
0.00623375 0.00278166 0.99997670 -2.71682833
Axis 0.39185138 -0.87578390 0.28187774
Axis point 425.45473115 0.00000000 388.75009135
Rotation angle (degrees) 0.40764643
Shift along axis -0.26149281
Fit molecule 80s_vol4FM_IFRD2.pdb (#5) to map
80s_vol1_full_mask_rfn179_pp192.mrc (#1) using 211125 atoms
average map value = 0.05337, steps = 136
shifted from previous position = 4.42
rotated from previous position = 0.506 degrees
atoms outside contour = 103503, contour level = 0.050155
Position of 80s_vol4FM_IFRD2.pdb (#5) relative to
80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates:
Matrix rotation and translation
0.99998491 0.00072174 -0.00544533 3.01915752
-0.00075936 0.99997584 -0.00691020 2.84754223
0.00544021 0.00691423 0.99996130 -6.92503617
Axis 0.78290108 -0.61646610 -0.08387755
Axis point 0.00000000 990.01759835 514.70061596
Rotation angle (degrees) 0.50586993
Shift along axis 1.18914353
> save 80s_vol2SM_fitvol1.pdb format pdb models #3 relModel #1
> save 80s_vol2SM_fitvol1.cif format mmcif models #3 relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> save 80s_vol3FM_PnAsite_tRNA_fitvol1.cif format mmcif models #4 relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> save 80s_vol4FM_IFRD2_fitvol1.cif format mmcif models #5 relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> save 80s_vol4FM_IFRD2_fitvol1.pdb format pdb models #5 relModel #1
> save 80s_vol3FM_PnAsite_tRNA_fitvol1.pdb format pdb models #4 relModel #1
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> help help:user
> select #2/4,6,3
Nothing selected
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> select #2/4,6,3
Nothing selected
> select #2/AA
1622 atoms, 1663 bonds, 202 residues, 1 model selected
> hide #!3 models
> hide #!4 models
> hide #!5 models
> select clear
> select #2/B4,B6,B3
3465 atoms, 3864 bonds, 165 residues, 1 model selected
> select ~sel
842262 atoms, 905734 bonds, 85 pseudobonds, 67257 residues, 10 models selected
> select clear
> hide #!2 models
> select #2/B4,B6,B3
3465 atoms, 3864 bonds, 165 residues, 1 model selected
> show #2/B4,B6,B3
> show #!2 models
> select clear
> hide #!2 atoms
> select #2/B4,B6,B3
3465 atoms, 3864 bonds, 165 residues, 1 model selected
> select ~sel
842262 atoms, 905734 bonds, 85 pseudobonds, 67257 residues, 10 models selected
> cartoon hide (#!2 & sel)
> select #3/3,4,6
3336 atoms, 3715 bonds, 159 residues, 1 model selected
> show #!3 models
> hide #!2 models
> select ~sel
842391 atoms, 905883 bonds, 85 pseudobonds, 67263 residues, 10 models selected
> cartoon hide (#!3 & sel)
> show #!2 models
> select clear
> select clear
> select #4/3,4,6
3315 atoms, 3693 bonds, 158 residues, 1 model selected
> show #!4 models
> select ~sel
842412 atoms, 905905 bonds, 85 pseudobonds, 67264 residues, 10 models selected
> cartoon hide (#!2-4 & sel)
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!4 models
> select #3/3,4,6
3336 atoms, 3715 bonds, 159 residues, 1 model selected
> select ~sel
842391 atoms, 905883 bonds, 85 pseudobonds, 67263 residues, 10 models selected
> cartoon hide (#!2-3 & sel)
> hide #!3 models
> show #!3 models
> show sel & #!2-3 atoms
> hide sel & #!2-3 atoms
> show sel & #!2-3 cartoons
> hide #!3 models
> show sel & #!2 cartoons
> show #!3 models
> hide sel & #!2-3 cartoons
> show #!4 models
> select clear
> hide #!4 models
> hide #!3 models
> show #!2 atoms
> show #!2 atoms
> show #!2 cartoons
> select clear
> hide #!2 atoms
> select #2/B4,B6,B3
3465 atoms, 3864 bonds, 165 residues, 1 model selected
> select ~sel
842262 atoms, 905734 bonds, 85 pseudobonds, 67257 residues, 10 models selected
> hide sel & #!2 cartoons
> hide #!2 models
> show #!3 models
> show sel & #!3 cartoons
> select clear
> select #3/3,4,6
3336 atoms, 3715 bonds, 159 residues, 1 model selected
> select ~sel
842391 atoms, 905883 bonds, 85 pseudobonds, 67263 residues, 10 models selected
> hide sel & #!3 cartoons
> show #!2 models
> show #!4 models
> select clear
> set bgColor white
> ui tool show "Color Actions"
> select #2/B6
1595 atoms, 1779 bonds, 76 residues, 1 model selected
> color sel forest green
> select clear
> select #3/6
1551 atoms, 1726 bonds, 74 residues, 1 model selected
> color sel forest green
> select clear
> select #4/6
1550 atoms, 1725 bonds, 74 residues, 1 model selected
> color sel forest green
> select clear
> select #4/4
1487 atoms, 1658 bonds, 71 residues, 1 model selected
> color sel hot pink
> select clear
> select #3/4
1487 atoms, 1658 bonds, 71 residues, 1 model selected
> color sel hot pink
> select #2/B4
1592 atoms, 1775 bonds, 76 residues, 1 model selected
> color sel hot pink
> select clear
> select #2/B3
278 atoms, 310 bonds, 13 residues, 1 model selected
> color sel magenta
> select clear
> select #3,4/3
576 atoms, 641 bonds, 27 residues, 2 models selected
> color sel magenta
> select clear
> toolshed show
> show #!1 models
> volume style surface
> volume style image
> volume style mesh
> volume style mesh
> volume style surface
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> ui tool show "Side View"
> set bgColor gray
> set bgColor white
> set bgColor black
> set bgColor white
> nucleotides #!2-4 fill
> style nucleic & #!2-4 stick
Changed 365108 atom styles
> hide #!1 models
> rainbow #!2-4
> rainbow #!2-4
> undo
> undo
> select #4/3,4,6
3315 atoms, 3693 bonds, 158 residues, 1 model selected
> cartoon style width 1 thickness 0.5
> select clear
> cartoon style #3/3,4,6 width 2 thickness 1
> cartoon style #2/B3,B4,B6 width 3 thickness 1.5
> cartoon style #2/B3,B4,B6 width 2 thickness 1
> cartoon style #3/3,4,6 width 1.5 thickness 0.75
> cartoon style #4/3,4,6 width 1 thickness 0.5
> volume show
> transparency 50
> volume showOutlineBox true
> volume showOutlineBox false
> volume step 1
> vop gaussian #1 sdev 4.14
Opened 80s_vol1_full_mask_rfn179_pp192.mrc gaussian as #6, grid size
360,360,360, pixel 1.38, shown at step 1, values float32
> vop gaussian #6 sdev 4.14
Opened 80s_vol1_full_mask_rfn179_pp192.mrc gaussian as #7, grid size
360,360,360, pixel 1.38, shown at step 1, values float32
> volume #!7 style surface
> volume show
> hide #!7 models
> hide #!6 models
> lighting flat
> surface dust #1 size 13.8
> lighting full
> lighting soft
> lighting simple
> nucleotides #!2-4 atoms
> style nucleic & #!2-4 stick
Changed 365108 atom styles
> nucleotides #!2-4 fill
> style nucleic & #!2-4 stick
Changed 365108 atom styles
> nucleotides #!2-4 slab
> style nucleic & #!2-4 stick
Changed 365108 atom styles
> nucleotides #!2-4 ladder
> volume #1 change image level -0.01395,0 level 0.03873,0.8 level 0.314,1
> volume #1 level 0.01505
> volume #1 level 0.02508
> transparency #1.1 0
> transparency #1.1 50
> transparency #1.1 0
> transparency #1.1 50
> close #7
> close #6
> save 80s_vol1_threestates_tRNA.jpg format jpeg
> select #2,3,4/B3,3
854 atoms, 951 bonds, 40 residues, 3 models selected
> color sel red
> select clear
> select #2,3,4/B3,3,3
854 atoms, 951 bonds, 40 residues, 3 models selected
> color sel dark red
> color sel crimson
> color sel red
> select clear
> transparency #1.1 80
> save 80s_vol1_threestates_tRNA_2.jpg format jpeg
> hide #!1 models
> save 80s_vol1_threestates_tRNA_only.jpg format jpeg
> save 80s_vol1_threestates_tRNA_only_3.jpg format jpeg
> show #!1 models
> save 80s_vol1_threestates_tRNA_3.jpg format jpeg
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!5 models
> select #5/DA
2882 atoms, 2930 bonds, 370 residues, 1 model selected
> select ~sel
842845 atoms, 906668 bonds, 85 pseudobonds, 67052 residues, 12 models selected
> cartoon hide (#!5 & sel)
> cartoon style (#!5 & sel) modeHelix tube sides 20
> cartoon style (#!5 & sel & coil) xsection oval
> cartoon style (#!5 & sel) xsection barbell modeHelix default
> cartoon style (#!5 & sel) xsection oval modeHelix default
> color (#!5 & sel) cornflower blue
> select #5/DA
2882 atoms, 2930 bonds, 370 residues, 1 model selected
> color sel cornflower blue
> select clear
> cartoon style #5/DA helix width 2 thick 0.5
Expected a keyword
> cartoon style helix #5/DA width 2 thick 0.5
Expected a keyword
> cartoon style helix width 2 thickness 0.5
> cartoon style helix width 23 thickness 1
> cartoon style helix width 3 thickness 1
> undo
> undo
> undo
> cartoon style width 3 thickness 1
> cartoon style width 3 thickness 0.5
> cartoon style width 1 thickness 0.5
> cartoon style width 2 thickness 2
> cartoon style width 1.5 thickness 1.5
> cartoon style width 1.5 thickness 0.5
> show #!4 models
> show #!3 models
> show #!2 models
> save 80s_vol1_threestates_tRNA_IFRD2_1.jpg format jpeg
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> save 80s_vol3_tRNA_IFRD2_1.jpg format jpeg
> hide #!5 models
> hide #!4 models
> open /home/dell/Droso_80s_new/6xu6.cif
6xu6.cif title:
Drosophila melanogaster Testis 80S ribosome [more info...]
Chain information for 6xu6.cif #6
---
Chain | Description
A5 | 28S ribosomal RNA
A7 | 5S ribosomal RNA
A8 | 5.8S ribosomal RNA
A9 | 2S ribosomal RNA
AA | 40S ribosomal protein SA
AB | 40S ribosomal protein S3a
AC | 40S ribosomal protein S2
AD | 40S ribosomal protein S3
AE | 40S ribosomal protein S4
AF | 40S ribosomal protein S5a
AG | 40S ribosomal protein S6
AH | 40S ribosomal protein S7
AI | 40S ribosomal protein S8
AJ | 40S ribosomal protein S9
AK | 40S ribosomal protein S10b
AL | 40S ribosomal protein S11
AM | 40S ribosomal protein S12
AN | 40S ribosomal protein S13
AO | 40S ribosomal protein S14a
AP | GEO07301p1
AQ | 40S ribosomal protein S16
AR | 40S ribosomal protein S17
AS | 40S ribosomal protein S18
AT | 40S ribosomal protein S19a
AU | 40S ribosomal protein S20
AV | 40S ribosomal protein S21
AW | 40S ribosomal protein S15Aa
AX | 40S ribosomal protein S23
AY | 40S ribosomal protein S24
AZ | 40S ribosomal protein S25
Aa | 40S ribosomal protein S26
Ab | 40S ribosomal protein S27
Ac | 40S ribosomal protein S28
Ad | 40S ribosomal protein S29
Ae | 40S ribosomal protein S30
Af | Ubiquitin-40S ribosomal protein S27a
Ag | Guanine nucleotide-binding protein subunit beta-like protein
B2 | 18S ribosomal RNA
CA | 60S ribosomal protein L8
CB | 60S ribosomal protein L3
CC | 60S ribosomal protein L4
CD | 60S ribosomal protein L5
CE | Ribosomal protein L6, isoform A
CF | 60S ribosomal protein L7
CG | 60S ribosomal protein L7a
CH | 60S ribosomal protein L9
CI | 60S ribosomal protein L10
CJ | 60S ribosomal protein L11
CL | 60S ribosomal protein L13
CM | 60S ribosomal protein L14
CN | 60S ribosomal protein L15
CO | 60S ribosomal protein L13a
CP | 60S ribosomal protein L17
CQ | 60S ribosomal protein L18
CR | 60S ribosomal protein L19
CS | 60S ribosomal protein L18a
CT | RE62581p
CU | Ribosomal protein L22-like protein
CV | 60S ribosomal protein L23
CW | 60S ribosomal protein L24
CX | IP17216p
CY | GEO07453p1
CZ | 60S ribosomal protein L27
Ca | 60S ribosomal protein L27a
Cb | 60S ribosomal protein L29
Cc | RE25263p
Cd | 60S ribosomal protein L31
Ce | 60S ribosomal protein L32
Cf | GEO07455p1
Cg | RH48056p
Ch | FI02809p
Ci | 60S ribosomal protein L36
Cj | Probable 60S ribosomal protein L37-B
Ck | 60S ribosomal protein L38
Cl | 60S ribosomal protein L39
Cm | Ubiquitin-60S ribosomal protein L40
Cn | 60S ribosomal protein L41
Co | TA01007p
Cp | 60S ribosomal protein L37a
Cr | 60S ribosomal protein L28
Cz | 60S ribosomal protein L10a-2
DA | LP04564p
> show #!6 cartoons
> hide #!6 atoms
> show #!1 models
Fit molecule 6xu6.cif (#6) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1)
using 219765 atoms
average map value = 0.006181, steps = 176
shifted from previous position = 24.7
rotated from previous position = 9.35 degrees
atoms outside contour = 186849, contour level = 0.02508
Position of 6xu6.cif (#6) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1)
coordinates:
Matrix rotation and translation
0.98986152 -0.11989035 -0.07616079 59.78309359
0.12557242 0.98926096 0.07479522 -44.23003341
0.06637567 -0.08360061 0.99428628 23.99399532
Axis -0.48729600 -0.43850554 0.75515263
Axis point 365.86868120 501.77803488 0.00000000
Rotation angle (degrees) 9.35350262
Shift along axis 8.38218078
> ui tool show "Basic Actions"
> ui mousemode right rotate
> ui mousemode right rotate
> ui mousemode right select
> select #6
219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models
selected
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.037876,0.38773,-0.921,344.47,0.32506,0.87631,0.35555,-122.43,0.94494,-0.28591,-0.15922,149.08
> view matrix models
> #6,-0.10774,0.59164,-0.79897,288.2,0.3905,0.76424,0.51327,-146.87,0.91428,-0.2567,-0.31338,183.29
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.10774,0.59164,-0.79897,313.18,0.3905,0.76424,0.51327,-115.67,0.91428,-0.2567,-0.31338,189.55
> select clear
> ui mousemode right "rotate selected models"
> ui mousemode right select
> ui mousemode right "rotate selected models"
> select #6
219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models
selected
> view matrix models
> #6,0.59678,0.37943,-0.70703,197.8,0.41694,0.60621,0.67725,-124.08,0.68558,-0.69896,0.20357,213.09
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.59678,0.37943,-0.70703,194.24,0.41694,0.60621,0.67725,-129.18,0.68558,-0.69896,0.20357,215.4
> select clear
> lighting full
> lighting simple
> transparency #1.1 0
Fit molecule 6xu6.cif (#6) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1)
using 219765 atoms
average map value = 0.03966, steps = 112
shifted from previous position = 13.9
rotated from previous position = 2.87 degrees
atoms outside contour = 101230, contour level = 0.02508
Position of 6xu6.cif (#6) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1)
coordinates:
Matrix rotation and translation
0.57245378 0.41325506 -0.70817859 184.69259361
0.43079560 0.58329287 0.68861062 -120.52118635
0.69764735 -0.69927797 0.15587975 230.56955503
Axis -0.70252455 -0.71160412 0.00887871
Axis point -38.03310429 0.00000000 242.15535371
Rotation angle (degrees) 81.03603790
Shift along axis -41.94054939
> volume style mesh
> hide #!1 models
> select #6/DA
2756 atoms, 2800 bonds, 1 pseudobond, 350 residues, 2 models selected
> select ~sel
1062736 atoms, 1142576 bonds, 4465 pseudobonds, 85085 residues, 14 models
selected
> cartoon hide (#!6 & sel)
> show #!5 models
> select clear
> save 80s_vol4_IFRD2_dro80s.jpg format jpeg
> show #!4 models
> save 80s_vol3_tRNA_IFRD2_dro80s_1.jpg format jpeg
> open /home/dell/Anoribo/h80s_snapshots_vols/5aj0.cif
5aj0.cif title:
Cryo electron microscopy of actively translating human polysomes (POST state).
[more info...]
Chain information for 5aj0.cif #7
---
Chain | Description
A2 | 28S ribosomal RNA
A3 | 5.8S ribosomal RNA
A4 | 5S ribosomal RNA
AA | 60S ribosomal protein L8
AB | 60S ribosomal protein L3
AC | 60S ribosomal protein L4
AD | 60S ribosomal protein L5
AE | 60S ribosomal protein L6
AF | 60S ribosomal protein L7
AG | 60S ribosomal protein L7a
AH | 60S ribosomal protein L9
AI | 60S ribosomal protein L10
AJ | 60S ribosomal protein L11
AK | 60S acidic ribosomal protein P0
AL | 60S ribosomal protein L13
AM | 60S ribosomal protein L14
AN | 60S ribosomal protein L15
AO | 60S ribosomal protein L13a
AP | 60S ribosomal protein L17
AQ | 60S ribosomal protein L18
AR | 60S ribosomal protein L19
AS | 60S ribosomal protein L18a
AT | 60S ribosomal protein L21
AU | 60S ribosomal protein L22
AV | 60S ribosomal protein L23
AW | 60S ribosomal protein L24
AX | 60S ribosomal protein L23a
AY | 60S ribosomal protein L26
AZ | 60S ribosomal protein L27
Aa | 60S ribosomal protein L27a
Ab | 60S ribosomal protein L29
Ac | 60S ribosomal protein L30
Ad | 60S ribosomal protein L31
Ae | 60S ribosomal protein L32
Af | 60S ribosomal protein L35a
Ag | 60S ribosomal protein L34
Ah | 60S ribosomal protein L35
Ai | 60S ribosomal protein L36
Aj | 60S ribosomal protein L37
Ak | 60S ribosomal protein L38
Al | 60S ribosomal protein L39
Am | Ubiquitin-60S ribosomal protein L40
An | 60S ribosomal protein L41
Ao | 60S ribosomal protein L36a
Ap | 60S ribosomal protein L37a
Aq | 60S ribosomal protein L12
At | 60S ribosomal protein L28
Au | 60S ribosomal protein L10a
B1 | 18S ribosomal RNA
BA | 40S ribosomal protein SA
BB | 40S ribosomal protein S3a
BC | 40S ribosomal protein S2
BD | 40S ribosomal protein S3
BE | 40S ribosomal protein S4, Y isoform 1
BF | 40S ribosomal protein S5
BG | 40S ribosomal protein S6
BH | 40S ribosomal protein S7
BI | 40S ribosomal protein S8
BJ | 40S ribosomal protein S9
BK | 40S ribosomal protein S10
BL | 40S ribosomal protein S11
BM | 40S ribosomal protein S12
BN | 40S ribosomal protein S13
BO | 40S ribosomal protein S14
BP | 40S ribosomal protein S15
BQ | 40S ribosomal protein S16
BR | 40S ribosomal protein S17-like
BS | 40S ribosomal protein S18
BT | 40S ribosomal protein S19
BU | 40S ribosomal protein S20
BV | 40S ribosomal protein S21
BW | 40S ribosomal protein S15a
BX | 40S ribosomal protein S23
BY | 40S ribosomal protein S24
BZ | 40S ribosomal protein S25
Ba | 40S ribosomal protein S26
Bb | 40S ribosomal protein S27
Bc | 40S ribosomal protein S28
Bd | 40S ribosomal protein S29
Be | 40S ribosomal protein S30
Bf | Ubiquitin-40S ribosomal protein S27a
Bg | Guanine nucleotide-binding protein subunit beta-2-like 1
Bv Bw | tRNA
Bx | mRNA
By | Nascent protein chain
Non-standard residues in 5aj0.cif #7
---
MG — magnesium ion
ZN — zinc ion
> hide #!6 models
> hide #!5 models
> hide #!4 models
> show #!7 cartoons
> hide #!7 atoms
> show #!1 models
> select #7
218559 atoms, 234515 bonds, 5450 pseudobonds, 17869 residues, 4 models
selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,291.04,0,1,0,164.21,0,0,1,289.43
> select clear
> select #7
218559 atoms, 234515 bonds, 5450 pseudobonds, 17869 residues, 4 models
selected
> view matrix models #7,1,0,0,306.19,0,1,0,204.63,0,0,1,268.53
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.3923,-0.91193,0.12035,314.94,-0.88644,-0.33988,0.31418,219.01,-0.2456,-0.22994,-0.9417,248.98
> view matrix models
> #7,0.88584,-0.45936,0.065375,314.1,0.41166,0.7131,-0.56747,212.06,0.21405,0.5296,0.8208,259.84
> view matrix models
> #7,0.77049,-0.55823,0.30776,316.49,0.30879,0.74923,0.58593,221.23,-0.55767,-0.35642,0.74965,263.16
> view matrix models
> #7,0.43408,-0.72897,0.52932,316.16,0.45387,-0.33058,-0.82748,231.29,0.77819,0.59943,0.18736,262.12
> view matrix models
> #7,0.2026,-0.57808,0.79043,311.6,0.84568,0.51025,0.15641,231.35,-0.49374,0.63677,0.59224,242.61
> view matrix models
> #7,0.22953,-0.40124,0.88675,309.49,0.88009,0.47462,-0.013049,230.96,-0.41564,0.78342,0.46207,239.72
> view matrix models
> #7,0.31772,-0.61459,0.72204,313.71,0.90603,-0.027741,-0.4223,237.43,0.27957,0.78836,0.54802,253
> view matrix models
> #7,0.31995,-0.60493,0.72917,313.63,0.91298,-0.008812,-0.40791,237.31,0.25318,0.79623,0.54947,252.38
> view matrix models
> #7,-0.019164,-0.50623,0.86219,306.89,0.99884,0.028504,0.038938,242.66,-0.044287,0.86193,0.50509,245.25
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.019164,-0.50623,0.86219,236.9,0.99884,0.028504,0.038938,256.07,-0.044287,0.86193,0.50509,258.33
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.13352,-0.46236,0.87658,234.11,0.89273,-0.44019,-0.096211,262.27,0.43035,0.76971,0.47154,268.39
> view matrix models
> #7,0.41382,0.2562,0.87356,229.38,0.89674,0.050655,-0.43966,248.91,-0.15689,0.9653,-0.20878,246.94
> view matrix models
> #7,-0.33446,-0.55424,-0.76221,215.65,0.38626,-0.81835,0.42557,266.13,-0.85962,-0.15207,0.48779,264.01
> view matrix models
> #7,-0.47321,-0.76092,-0.44392,220.58,0.52212,-0.64812,0.55438,266.44,-0.70955,0.030563,0.70399,265.22
> view matrix models
> #7,-0.45331,-0.44799,-0.77059,211.28,0.5784,-0.80563,0.1281,266.3,-0.6782,-0.38764,0.62432,273.43
> view matrix models
> #7,-0.50016,-0.85616,-0.12975,225.23,0.73995,-0.5004,0.44952,266.3,-0.44979,0.12883,0.88379,269.73
> view matrix models
> #7,-0.46386,-0.1986,-0.86336,205.1,0.34318,-0.93874,0.031558,263.78,-0.81674,-0.28165,0.5036,267.57
> view matrix models
> #7,-0.75357,-0.56336,-0.33876,212.61,0.34727,-0.77872,0.5225,265.61,-0.55815,0.2761,0.78245,263.77
> view matrix models
> #7,-0.35476,0.18271,-0.91693,198.8,0.092636,-0.96902,-0.22893,257.23,-0.93036,-0.16616,0.32685,261.38
> view matrix models
> #7,-0.91737,-0.31618,-0.24178,205.65,0.032426,-0.6648,0.74632,259.93,-0.3967,0.67681,0.62012,256.91
> view matrix models
> #7,-0.90242,-0.17612,-0.3932,201.55,0.098754,-0.97289,0.20913,261.88,-0.41938,0.14989,0.89535,269.97
> view matrix models
> #7,-0.93493,-0.35204,-0.044479,208.07,0.13851,-0.47748,0.86765,259.28,-0.32668,0.80503,0.49518,254.3
> view matrix models
> #7,-0.9428,-0.23744,0.23398,208.45,0.31745,-0.85373,0.41276,265.48,0.10175,0.46342,0.88028,272.85
> view matrix models
> #7,-0.58501,0.042726,0.8099,215.08,0.78961,0.25798,0.55674,252.94,-0.18515,0.96521,-0.18465,246.68
> view matrix models
> #7,-0.76959,0.46921,-0.4331,190.47,-0.26383,-0.85132,-0.45349,246.15,-0.58148,-0.23474,0.77896,273.65
> view matrix models
> #7,-0.187,-0.98195,0.028296,235.02,0.96261,-0.17742,0.2047,261.27,-0.19599,0.065518,0.97841,276.54
> view matrix models
> #7,0.034468,-0.3254,-0.94495,215.79,0.2354,-0.91627,0.32411,264.36,-0.97129,-0.23361,0.045015,259.14
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.034468,-0.3254,-0.94495,227.53,0.2354,-0.91627,0.32411,263.98,-0.97129,-0.23361,0.045015,262.75
> select clear
> select #7
218559 atoms, 234515 bonds, 5450 pseudobonds, 17869 residues, 4 models
selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.86512,0.45133,0.21877,238.61,0.30366,-0.12417,-0.94465,236.25,-0.39919,0.88367,-0.24447,247.48
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.86512,0.45133,0.21877,251.11,0.30366,-0.12417,-0.94465,245.63,-0.39919,0.88367,-0.24447,257.24
> view matrix models
> #7,0.86512,0.45133,0.21877,237.37,0.30366,-0.12417,-0.94465,246.95,-0.39919,0.88367,-0.24447,257.47
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.8032,0.4696,-0.36653,229.92,-0.18219,-0.39216,-0.90167,244.07,-0.56717,0.791,-0.22942,256.48
> view matrix models
> #7,0.60888,0.39758,-0.68643,224.62,-0.45507,-0.53372,-0.71279,243.95,-0.64975,0.74638,-0.14404,256.77
> view matrix models
> #7,0.89202,0.3185,-0.3207,235.04,-0.34181,0.011114,-0.9397,232.65,-0.29573,0.94786,0.11878,261.74
> view matrix models
> #7,0.93012,0.33872,-0.14196,237.14,-0.092484,-0.15805,-0.98309,240.12,-0.35543,0.92752,-0.11568,258.69
> select clear
Fit molecule 5aj0.cif (#7) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1)
using 218559 atoms
average map value = 0.02062, steps = 2000
shifted from previous position = 3.43
rotated from previous position = 9.68 degrees
atoms outside contour = 138635, contour level = 0.02508
Position of 5aj0.cif (#7) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1)
coordinates:
Matrix rotation and translation
0.87063967 0.48416629 -0.08700314 236.59595549
-0.04131130 -0.10427594 -0.99369002 242.03573119
-0.49018356 0.86874018 -0.07078522 255.18283619
Axis 0.94219350 0.20396682 -0.26583631
Axis point 0.00000000 -45.49260849 252.16232888
Rotation angle (degrees) 98.75506440
Shift along axis 204.44956647
> hide #!1 models
> show #!1 models
> molmap #7 3.5
Opened 5aj0.cif map 3.5 as #8, grid size 258,256,241, pixel 1.17, shown at
level 0.116, step 1, values float32
> vop localCorrelation #0 #8 windowSize 5 model #9
volume local_correlation operation requires exactly two map arguments
> vop resample #8 onGrid #0
> vop localCorrelation #0 #8 windowSize 5 model #9
volume local_correlation operation requires exactly two map arguments
> vop localCorrelation #0 #8 windowSize 5
volume local_correlation operation requires exactly two map arguments
> hide #!7 models
> vop localCorrelation #0 #8 windowSize 5
volume local_correlation operation requires exactly two map arguments
> show #!6 models
> show #!7 models
> hide #!7 models
> show #!2 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!7 models
> hide #!8 models
> hide #!1 models
> hide #!6 models
> hide #!5 models
> hide #!2 models
> select #7/Bv,Bw,Bx
3810 atoms, 4242 bonds, 149 pseudobonds, 183 residues, 3 models selected
> select ~sel
1280241 atoms, 1375649 bonds, 9767 pseudobonds, 103121 residues, 20 models
selected
> cartoon hide (#!7 & sel)
> show #!4 models
> select clear
> show #!3 models
> show #!2 models
> hide #!3 models
> hide #!4 models
> vop localCorrelation #1 #8 windowSize 5
Opened local correlation as #9, grid size 356,356,356, pixel 1.38, shown at
step 1, values float32
> save local_corr_80s_vol1_5aj0_post.mrc format mrc relModel #1
Expected a keyword
> save local_corr_80s_vol1_5aj0_post.mrc format mrc models #9 relModel #1
Expected a keyword
> save local_corr_80s_vol1_5aj0_post.mrc format mrc models #9 relModel #1
Expected a keyword
> vop resample #9 onGrid #1
Opened local correlation resampled as #10, grid size 360,360,360, pixel 1.38,
shown at step 1, values float32
> save local_corr_80s_vol1_h80s_post.mrc format mrc models #10 relModel #1
Expected a keyword
> save local_corr_80s_vol1_h80s_post.mrc format mrc models #10
> save local_corr_80s_vol1_h80s_post.mrc format mrc models #10 relmodels #1
Expected a keyword
> hide #!10 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> select #7/Bv
1625 atoms, 1813 bonds, 76 pseudobonds, 78 residues, 3 models selected
> color sel hot pink
> cartoon style #7/Bv width 2.5 thickness 1.5
> select #7/Bw
1623 atoms, 1813 bonds, 62 pseudobonds, 76 residues, 2 models selected
> color sel forest green
> select clear
> select #7/Bx
562 atoms, 616 bonds, 29 residues, 1 model selected
> color sel red
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> show #!2 models
> hide #!4 models
> save 80s_vol1_h80s_post_tRNAs_mRNA.jpg format jpeg
> show #!3 models
> hide #!2 models
> save 80s_vol2_h80s_post_tRNAs_mRNA.jpg format jpeg
> show #!4 models
> hide #!3 models
> save 80s_vol3_h80s_post_tRNAs_mRNA.jpg format jpeg
> show #!5 models
> hide #!4 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!7 models
> save 80s_vol4_IFRD2_dro_IFRD2.jpg format jpeg
> show #!7 models
> hide #!6 models
> hide #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> hide #!3 models
> hide #!4 models
> hide #!7 models
> hide #!2 models
> open /home/dell/Anoribo/h80s_snapshots_vols/6mtc.cif
6mtc.cif title:
Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state) [more
info...]
Chain information for 6mtc.cif #11
---
Chain | Description
4 | Z-site tRNA
5 | 28S rRNA
7 | 5S rRNA
8 | 5.8S rRNA
9 | 18S rRNA
A | 60S ribosomal protein L8
AA | 40S ribosomal protein SA
B | 60S ribosomal protein L3
BB | 40S ribosomal protein S3a
C | 60S ribosomal protein L4
CC | 40S ribosomal protein S2
D | 60S ribosomal protein L5
DD | 40S ribosomal protein S3
E | 60S ribosomal protein L6
EE | 40S ribosomal protein S4, X isoform
F | 60S ribosomal protein L7
FF | 40S ribosomal protein S5
G | 60S ribosomal protein L7a
GG | 40S ribosomal protein S6
H | 60S ribosomal protein L9
HH | 40S ribosomal protein S7
I | 60S ribosomal protein L10
II | 40S ribosomal protein S8
J | 60S ribosomal protein L11
JJ | 40S ribosomal protein S9
KK | 40S ribosomal protein S10
L | 60S ribosomal protein L13
LL | 40S ribosomal protein S11
M | 60S ribosomal protein L14
MM | 40S ribosomal protein S12
N | 60S Ribosomal protein L15
NN | 40S ribosomal protein S13
O | 60S ribosomal protein L13a
OO | 40S ribosomal protein S14
P | 60S ribosomal protein L17
PP | 40S ribosomal protein S15
Q | 60S ribosomal protein L18
QQ | 40S ribosomal protein S16
R | 60S ribosomal protein L19
RR | 40S ribosomal protein S17
S | 60S ribosomal protein L18a
SS | 40S ribosomal protein S18
T | 60S ribosomal protein L21
TT | 40S ribosomal protein S19
U | 60S ribosomal protein L22
UU | 40S ribosomal protein S20
V | 60S ribosomal protein L23
VV | 40S ribosomal protein S21
W | 60S ribosomal protein L24
WW | 40S ribosomal protein S15a
X | 60S ribosomal protein L23a
XX | 40S ribosomal protein S23
Y | 60S ribosomal protein L26
YY | 40S ribosomal protein S24
Z | 60S ribosomal protein L27
ZZ | 40S ribosomal protein S25
a | 60S ribosomal protein L27a
aa | 40S ribosomal protein S26
b | 60S ribosomal protein L29
bb | 40S ribosomal protein S27
c | 60S ribosomal protein L30
cc | 40S ribosomal protein S28
d | 60S ribosomal protein L31
dd | 40S ribosomal protein S29
e | 60S ribosomal protein L32
ee | 40S ribosomal protein S30
f | 60S ribosomal protein L35a
ff | 40S ribosomal protein S27a
g | 60S ribosomal protein L34
gg | Receptor of activated protein C kinase 1
h | 60S ribosomal protein L35
i | 60S ribosomal protein L36
j | 60S ribosomal protein L37
k | 60S ribosomal protein L38
l | 60S ribosomal protein L39
m | 60S ribosomal protein L40
n | 60S ribosomal protein L41
o | 60S ribosomal protein L36a
p | 60S ribosomal protein L37a
r | 60S ribosomal protein L28
u | 60S ribosomal protein L10a
v | Interferon-related developmental regulator 2
Non-standard residues in 6mtc.cif #11
---
B8N —
(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid
MG — magnesium ion
ZN — zinc ion
> show #!11 cartoons
> hide #!11 atoms
> show #!1 models
> volume #1 style surface
> select #11
216975 atoms, 232683 bonds, 5820 pseudobonds, 17849 residues, 4 models
selected
> hide #!11 models
> show #!11 models
> view matrix models
> #11,0.15097,-0.57978,0.80066,149.17,0.98823,0.10867,-0.10765,35.123,-0.024598,0.80749,0.58937,-105.54
> view matrix models
> #11,0.62057,-0.35533,0.69903,-0.0010932,0.77573,0.40848,-0.48103,106.06,-0.11461,0.84077,0.52913,-76.297
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.62057,-0.35533,0.69903,-21.923,0.77573,0.40848,-0.48103,76.648,-0.11461,0.84077,0.52913,-73.929
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.78685,-0.29276,0.54328,-37.294,0.60434,0.54393,-0.58217,108.64,-0.12507,0.78641,0.60491,-77.035
> view matrix models
> #11,0.083985,-0.58394,0.80744,142.91,0.99642,0.057235,-0.062249,5.55,-0.0098651,0.80978,0.58665,-106.67
> view matrix models
> #11,0.85404,0.078418,0.51426,-148.69,0.51676,-0.01429,-0.85601,359.73,-0.059778,0.99682,-0.052727,28.581
> view matrix models
> #11,0.84778,-0.10912,0.519,-96.455,0.5283,0.087769,-0.84451,325.46,0.046602,0.99015,0.13206,-46.113
> view matrix models
> #11,0.026593,-0.80084,0.59829,274.29,0.99136,0.098023,0.087143,-45.392,-0.12843,0.59081,0.79653,-74.398
> view matrix models
> #11,-0.14388,-0.071769,-0.98699,547.48,-0.12921,-0.98747,0.090639,528.42,-0.98112,0.14057,0.1328,440.35
> view matrix models
> #11,0.392,0.67888,-0.62085,108.25,-0.046152,-0.65951,-0.75028,647.24,-0.9188,0.32277,-0.2272,473.09
> view matrix models
> #11,0.29009,-0.054372,-0.95545,427.99,-0.38904,-0.91887,-0.065829,615.69,-0.87436,0.3908,-0.28771,459.92
> view matrix models
> #11,0.69868,-0.50906,-0.5027,330.37,-0.62869,-0.77221,-0.09181,640.69,-0.34145,0.38019,-0.85957,489.1
> view matrix models
> #11,0.87724,-0.067609,0.47526,-103.2,0.18916,-0.86124,-0.47168,569.46,0.4412,0.50368,-0.74273,231.67
> view matrix models
> #11,0.91109,0.35217,-0.21421,-39.242,0.32918,-0.9344,-0.13613,463.74,-0.2481,0.053515,-0.96725,586.33
> view matrix models
> #11,0.81572,-0.052415,0.57606,-119.96,0.22847,-0.88572,-0.40411,548.16,0.53141,0.46126,-0.71052,212.57
> view matrix models
> #11,-0.92521,-0.27048,0.26612,450.67,0.27747,-0.0039151,0.96072,-81.683,-0.25882,0.96272,0.078675,50.722
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.92521,-0.27048,0.26612,400.26,0.27747,-0.0039151,0.96072,-256.49,-0.25882,0.96272,0.078675,-100.24
> view matrix models
> #11,-0.92521,-0.27048,0.26612,395.64,0.27747,-0.0039151,0.96072,-273.08,-0.25882,0.96272,0.078675,-115.75
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.84859,-0.49545,-0.18554,562.85,0.47329,-0.86765,0.15225,139.73,-0.23642,0.041383,0.97077,-109.81
> view matrix models
> #11,-0.94884,-0.10981,0.29606,348.67,0.23598,0.37638,0.89591,-350.66,-0.20981,0.91993,-0.33121,-3.7274
> view matrix models
> #11,-0.84325,-0.45973,-0.27853,577.08,0.49756,-0.86365,-0.08084,196.46,-0.20339,-0.20675,0.95702,-45.321
> view matrix models
> #11,-0.84531,-0.47974,-0.23514,571.27,0.48689,-0.87293,0.030641,171.14,-0.21996,-0.088587,0.97148,-77.992
> view matrix models
> #11,-0.84548,-0.31402,-0.43191,579.19,0.52061,-0.66473,-0.53582,260.14,-0.11884,-0.67789,0.7255,127.99
> view matrix models
> #11,-0.87138,-0.49009,0.022514,510.02,0.40231,-0.68755,0.6045,-16.588,-0.28078,0.53581,0.79628,-188.33
> view matrix models
> #11,-0.88225,-0.46191,0.09099,486.13,0.37378,-0.56975,0.7319,-77.13,-0.28623,0.67972,0.67531,-193.81
> view matrix models
> #11,-0.8438,-0.4666,-0.26512,575.45,0.49439,-0.86803,-0.045815,188.86,-0.20875,-0.16973,0.96313,-55.948
> view matrix models
> #11,-0.95555,-0.052184,0.29019,335.94,0.22668,0.49936,0.83622,-366.15,-0.18854,0.86482,-0.46533,43.046
> view matrix models
> #11,-0.91087,0.15771,-0.38137,450.54,0.41134,0.4216,-0.80812,60.123,0.033341,-0.89296,-0.44889,471.71
> view matrix models
> #11,-0.86177,-0.13935,-0.48779,550.02,0.50522,-0.32279,-0.80035,241.45,-0.045924,-0.93616,0.34857,284.89
> view matrix models
> #11,-0.84318,-0.45881,-0.28023,577.28,0.49795,-0.863,-0.085313,197.4,-0.2027,-0.21148,0.95613,-43.94
> view matrix models
> #11,-0.84409,-0.33807,-0.41619,581.21,0.52003,-0.70532,-0.48177,256.74,-0.13067,-0.62309,0.77116,103.19
> view matrix models
> #11,-0.87522,-0.48132,0.048148,501.51,0.39198,-0.64739,0.65364,-38.639,-0.28344,0.59095,0.75527,-191.75
> view matrix models
> #11,-0.84248,-0.44605,-0.30209,579.55,0.5028,-0.85238,-0.14366,209.23,-0.19342,-0.27292,0.94239,-25.411
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.84248,-0.44605,-0.30209,579.38,0.5028,-0.85238,-0.14366,217.18,-0.19342,-0.27292,0.94239,-0.68253
> ui mousemode right rotate
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.8871,-0.44627,0.1179,475.45,0.36168,-0.51333,0.77826,-94.55,-0.28679,0.73303,0.61678,-167.71
> view matrix models
> #11,-0.96722,0.080864,0.24074,315.27,0.21728,0.75424,0.6196,-367.32,-0.13147,0.6516,-0.74709,190.03
> view matrix models
> #11,-0.86027,-0.50592,-0.063099,534.95,0.43418,-0.79185,0.42948,60.374,-0.26725,0.34207,0.90087,-141.8
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.86027,-0.50592,-0.063099,596.48,0.43418,-0.79185,0.42948,255.36,-0.26725,0.34207,0.90087,-11.99
> view matrix models
> #11,-0.86027,-0.50592,-0.063099,592.36,0.43418,-0.79185,0.42948,237.22,-0.26725,0.34207,0.90087,-17.525
> transparency #1 80
> view matrix models
> #11,-0.86027,-0.50592,-0.063099,611.84,0.43418,-0.79185,0.42948,237.14,-0.26725,0.34207,0.90087,-12.398
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.18286,-0.11298,0.97663,-36.42,0.75346,-0.62202,-0.21303,287.81,0.63155,0.77481,-0.028615,-97.713
> view matrix models
> #11,0.43493,-0.16094,0.88596,-59.91,0.8903,0.22429,-0.39632,69.864,-0.13493,0.96114,0.24084,-35.813
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.43493,-0.16094,0.88596,-72.035,0.8903,0.22429,-0.39632,60.748,-0.13493,0.96114,0.24084,-25.412
> view matrix models
> #11,0.43493,-0.16094,0.88596,-66.786,0.8903,0.22429,-0.39632,77.071,-0.13493,0.96114,0.24084,-23.061
> ui mousemode right "translate selected models"
Fit molecule 6mtc.cif (#11) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1)
using 216975 atoms
average map value = 0.008739, steps = 180
shifted from previous position = 9.48
rotated from previous position = 2.04 degrees
atoms outside contour = 173984, contour level = 0.02508
Position of 6mtc.cif (#11) relative to 80s_vol1_full_mask_rfn179_pp192.mrc
(#1) coordinates:
Matrix rotation and translation
0.42405514 -0.17973943 0.88762024 -55.70253111
0.89259011 0.24870445 -0.37606821 57.77251395
-0.15316100 0.95175559 0.26589830 -16.73381131
Axis 0.66422480 0.52063588 0.53641747
Axis point 0.00000000 56.70758592 62.34194609
Rotation angle (degrees) 91.75759853
Shift along axis -15.89686784
> transparency #1 0
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.30169,-0.48375,0.82156,223.99,0.95306,-0.17611,0.24627,-9.4679,0.025552,0.8573,0.51418,-102.13
> view matrix models
> #11,0.53781,-0.39476,0.74493,15.155,0.75188,0.62428,-0.212,-56.865,-0.38136,0.67412,0.63256,15.697
> view matrix models
> #11,-0.64685,-0.72444,-0.23827,664.99,0.61818,-0.68105,0.39246,172.37,-0.44659,0.10656,0.88837,119.02
Fit molecule 6mtc.cif (#11) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1)
using 216975 atoms
average map value = 0.008184, steps = 268
shifted from previous position = 5.55
rotated from previous position = 5.01 degrees
atoms outside contour = 175992, contour level = 0.02508
Position of 6mtc.cif (#11) relative to 80s_vol1_full_mask_rfn179_pp192.mrc
(#1) coordinates:
Matrix rotation and translation
-0.59821467 -0.75745761 -0.26152558 664.76867012
0.61536602 -0.64327875 0.45553898 149.73573493
-0.51328551 0.11157631 0.85093331 142.17278403
Axis -0.23928233 0.17514023 0.95502349
Axis point 317.07308855 209.54303229 0.00000000
Rotation angle (degrees) 134.04956933
Shift along axis 2.93570586
> hide #!11 models
> show #!11 models
> hide #!1 models
> show #!1 models
> select clear
> select #1
3 models selected
> view matrix models
> #1,0.90269,0.42052,-0.091165,-62.418,-0.37301,0.87038,0.32139,23.493,0.2145,-0.25611,0.94255,36.376
> view matrix models
> #1,-0.30675,-0.94947,-0.066459,534.61,0.72694,-0.18864,-0.66028,332.47,0.61438,-0.25085,0.74807,4.4567
> view matrix models
> #1,-0.96559,-0.18414,-0.18364,508.5,-0.085406,-0.44244,0.89272,143.47,-0.24564,0.87769,0.41149,-12.668
> undo
> undo
> undo
> undo
> hide #!11 models
> show #!11 models
> select #11
216975 atoms, 232683 bonds, 5820 pseudobonds, 17849 residues, 4 models
selected
> view matrix models
> #11,0.29957,-0.39982,0.86626,37.723,0.92563,-0.098252,-0.36545,147.4,0.23122,0.91131,0.34065,-121.88
> view matrix models
> #11,0.57179,-0.17635,0.80122,-72.957,0.79369,-0.12825,-0.59464,250.66,0.20762,0.97594,0.066642,-59.072
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.57179,-0.17635,0.80122,-78.117,0.79369,-0.12825,-0.59464,240.94,0.20762,0.97594,0.066642,-71.927
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.93489,0.18402,0.30351,-130.6,0.35202,-0.37135,-0.85917,488.62,-0.045395,0.91007,-0.41195,139.08
> view matrix models
> #11,0.72381,0.20899,-0.65758,176.97,0.023722,-0.96,-0.27899,573.34,-0.68959,0.18634,-0.69982,575.9
Fit molecule 6mtc.cif (#11) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1)
using 216975 atoms
average map value = 0.009215, steps = 112
shifted from previous position = 3.76
rotated from previous position = 5.48 degrees
atoms outside contour = 173830, contour level = 0.02508
Position of 6mtc.cif (#11) relative to 80s_vol1_full_mask_rfn179_pp192.mrc
(#1) coordinates:
Matrix rotation and translation
0.77546173 0.18022404 -0.60512554 157.16733277
-0.02100276 -0.95050310 -0.31000258 587.29865088
-0.63104371 0.25310475 -0.73329421 552.49036178
Axis 0.94079663 0.04330210 -0.33619433
Axis point 0.00000000 245.40513699 352.17197706
Rotation angle (degrees) 162.58614090
Shift along axis -12.45036786
> transparency #1 50
> transparency #1 0
> view matrix models
> #11,0.95724,-0.089419,-0.27514,97.243,0.023002,-0.9245,0.38048,380.44,-0.28839,-0.37054,-0.88291,682.61
Fit molecule 6mtc.cif (#11) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1)
using 216975 atoms
average map value = 0.00773, steps = 80
shifted from previous position = 2.73
rotated from previous position = 1.49 degrees
atoms outside contour = 177813, contour level = 0.02508
Position of 6mtc.cif (#11) relative to 80s_vol1_full_mask_rfn179_pp192.mrc
(#1) coordinates:
Matrix rotation and translation
0.95649366 -0.11384011 -0.26862356 101.38612454
0.00091086 -0.91956120 0.39294433 381.72307799
-0.29174856 -0.37609374 -0.87945156 681.49144584
Axis -0.98861303 0.02972762 0.14751455
Axis point 0.00000000 261.98654941 309.26139322
Rotation angle (degrees) 157.11094105
Shift along axis 11.64598214
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.95649,-0.11384,-0.26862,99.115,0.00091086,-0.91956,0.39294,377.25,-0.29175,-0.37609,-0.87945,670.75
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.92304,-0.28959,-0.25325,151.81,-0.17395,-0.90134,0.39664,413.91,-0.34313,-0.32206,-0.88235,669.12
> show #!8 models
Fit molecule 6mtc.cif (#11) to map 5aj0.cif map 3.5 (#8) using 216975 atoms
average map value = 0.1746, steps = 148
shifted from previous position = 8.04
rotated from previous position = 1.11 degrees
atoms outside contour = 142062, contour level = 0.11646
Position of 6mtc.cif (#11) relative to 5aj0.cif map 3.5 (#8) coordinates:
Matrix rotation and translation
0.98226435 -0.06116753 0.17723848 -274.83517518
0.14865067 -0.32205827 -0.93497615 301.91918715
0.11427123 0.94474119 -0.30725406 -199.05821020
Axis 0.99327757 0.03327306 0.11087184
Axis point 0.00000000 215.82804475 27.87773470
Rotation angle (degrees) 108.87618295
Shift along axis -285.01178949
> hide #!8 models
> select clear
> volume #1 style mesh
> select #11
216975 atoms, 232683 bonds, 5820 pseudobonds, 17849 residues, 4 models
selected
> view matrix models
> #11,0.95109,0.30871,0.010787,-91.111,0.19677,-0.57857,-0.79154,565.05,-0.23812,0.75496,-0.61102,266.4
> view matrix models
> #11,0.94695,0.32134,-0.0052805,-89.205,0.18774,-0.56642,-0.80245,566.88,-0.26085,0.75889,-0.59669,266.95
Fit molecule 6mtc.cif (#11) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1)
using 216975 atoms
average map value = 0.03599, steps = 180
shifted from previous position = 20.3
rotated from previous position = 14 degrees
atoms outside contour = 106897, contour level = 0.02508
Position of 6mtc.cif (#11) relative to 80s_vol1_full_mask_rfn179_pp192.mrc
(#1) coordinates:
Matrix rotation and translation
0.94548535 0.27462258 0.17503720 -135.84192386
0.27759275 -0.39857195 -0.87411760 514.52180374
-0.17028762 0.87505525 -0.45307760 189.76807173
Axis 0.98106272 0.19368315 0.00166588
Axis point 0.00000000 211.31745167 257.89255622
Rotation angle (degrees) 116.94161072
Shift along axis -33.29911263
> view matrix models
> #11,0.84252,-0.53863,-0.005861,164.29,0.056015,0.098429,-0.99357,463.54,0.53574,0.83677,0.1131,-127.01
> undo
> select clear
> hide #!1 models
> show #!6 models
> hide #!11 models
> show #!7 models
> show #!5 models
> show #!4 models
> show #!3 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!4 models
> hide #!3 models
> select #11/v
2737 atoms, 2779 bonds, 2 pseudobonds, 354 residues, 2 models selected
> show #!11 models
> select ~sel
1498289 atoms, 1609795 bonds, 15734 pseudobonds, 120799 residues, 28 models
selected
> cartoon hide (#!11 & sel)
> show #!6 models
> show #!5 models
> select clear
> hide #!11 models
> show #!11 models
> select down
Nothing selected
> save 80s_vol4_IFRD2_dro_IFRD2_rab_IFRD2.jpg format jpeg
> save 6xu6_alignedto_80s_vol1.cif format mmcif models #6 relmodels #1
Expected a keyword
> save 6xu6_alignedto_80s_vol1.cif format mmcif models #6 relModel #1
> save 5aj0_alignedto_80s_vol1.cif format mmcif models #7 relModel #1
> save 6mtc_alignedto_80s_vol1.cif format mmcif models #11 relModel #1
> show #!1 models
> volume #1 style surface
> transparency #1 50
> transparency #1 0
> lighting full
> transparency #1 30
> transparency #1 0
> volume #1 level 0.03101
> volume #1 level 0.04024
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting flat
> volume #1 level 0.07452
> volume #1 level 0.04485
> lighting soft
> lighting simple
> lighting soft
> lighting full
> transparency #1 10
> transparency #1 75
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting soft
> lighting simple
> lighting full
> lighting full
> lighting simple
> save 80svol1_map_80s_vol4_IFRD2_dro_IFRD2_rab_IFRD2.jpg format jpeg
> save 80svol1_map_80s_vol4_IFRD2_dro_IFRD2_rab_IFRD2_2.jpg format jpeg
> save 80svol1_map_80s_vol4_IFRD2_dro_IFRD2_rab_IFRD2_3.jpg format jpeg
> hide #!11 models
> hide #!6 models
> hide #!5 models
> hide #!1 models
> show #!2 models
> select #2/B5
Nothing selected
> select ~sel
1501026 atoms, 1612574 bonds, 15736 pseudobonds, 121153 residues, 29 models
selected
> select clear
> select #2
211489 atoms, 227564 bonds, 23 pseudobonds, 16795 residues, 2 models selected
> cartoon (#!2 & sel)
> select clear
> select #2/B5
Nothing selected
> select #2/A5
74437 atoms, 83252 bonds, 14 pseudobonds, 3486 residues, 2 models selected
> select #2/A5,A7,A8
80391 atoms, 89915 bonds, 14 pseudobonds, 3765 residues, 2 models selected
> select ~sel
1420635 atoms, 1522659 bonds, 15722 pseudobonds, 117388 residues, 29 models
selected
> cartoon hide (#!2 & sel)
> hide #!2 models
> show #!3 models
> select #3/5,7,8
80575 atoms, 90120 bonds, 14 pseudobonds, 3774 residues, 2 models selected
> hide #!3 models
> show #!6 models
> show #!5 models
> hide #!6 models
> select #5
211125 atoms, 226838 bonds, 21 pseudobonds, 17017 residues, 2 models selected
> cartoon (#!5 & sel)
> select clear
> select #5/5,7,8
80599 atoms, 90148 bonds, 13 pseudobonds, 3775 residues, 2 models selected
> select ~sel
1420427 atoms, 1522426 bonds, 15723 pseudobonds, 117378 residues, 29 models
selected
> cartoon hide (#!5 & sel)
> select #5/5,7,8
80599 atoms, 90148 bonds, 13 pseudobonds, 3775 residues, 2 models selected
> color sel bychain
> select clear
> show #!6 models
> hide #!5 models
> select #6/A5,A7,A8,A9
82989 atoms, 92737 bonds, 3034 pseudobonds, 3980 residues, 3 models selected
> select #6
219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models
selected
> cartoon (#!6 & sel)
> select #6/A5,A7,A8,A9
82989 atoms, 92737 bonds, 3034 pseudobonds, 3980 residues, 3 models selected
> select ~sel
1418037 atoms, 1519837 bonds, 12702 pseudobonds, 117173 residues, 29 models
selected
> cartoon hide (#!6 & sel)
> show #!5 models
> select clear
> show #!11 models
> hide #!6 models
> hide #!5 models
> select #11
216975 atoms, 232683 bonds, 5820 pseudobonds, 17849 residues, 4 models
selected
> show sel cartoons
> select #11/A5,A7,A8
Nothing selected
> select #11/5,7,8
83236 atoms, 92867 bonds, 4013 pseudobonds, 4083 residues, 3 models selected
> select ~sel
1417790 atoms, 1519707 bonds, 11723 pseudobonds, 117070 residues, 29 models
selected
> cartoon hide (#!11 & sel)
> show #!6 models
> show #!5 models
> select clear
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!11 models
> hide #!11 models
> show #!7 models
> hide #!6 models
> hide #!5 models
> select #7
218559 atoms, 234515 bonds, 5450 pseudobonds, 17869 residues, 4 models
selected
> select ~sel
1282467 atoms, 1378059 bonds, 10286 pseudobonds, 103284 residues, 25 models
selected
> cartoon #7
> show #!5 models
> hide #!5 models
> select #7/A2,A3,A4
83542 atoms, 93177 bonds, 3729 pseudobonds, 4125 residues, 4 models selected
> select ~sel
1417484 atoms, 1519397 bonds, 12007 pseudobonds, 117028 residues, 29 models
selected
> cartoon hide (#!7 & sel)
> select clear
> show #!6 models
Fit molecule 5aj0.cif (#7) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1)
using 218559 atoms
average map value = 0.02053, steps = 2000
shifted from previous position = 1.15
rotated from previous position = 0.43 degrees
atoms outside contour = 172740, contour level = 0.044855
Position of 5aj0.cif (#7) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1)
coordinates:
Matrix rotation and translation
0.87248244 0.48097788 -0.08622443 237.60246905
-0.03769838 -0.10967539 -0.99325228 242.56671876
-0.48718909 0.86984571 -0.07755776 255.47263685
Axis 0.94330365 0.20301210 -0.26261056
Axis point 0.00000000 -44.32785130 251.57535803
Rotation angle (degrees) 99.05458525
Shift along axis 206.28544252
> select #7/A2,A3,A4
83542 atoms, 93177 bonds, 3729 pseudobonds, 4125 residues, 4 models selected
> view matrix models
> #7,0.87146,0.48168,-0.092412,237.56,-0.045967,-0.10737,-0.99316,242.73,-0.48831,0.86974,-0.071431,255.56
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.87146,0.48168,-0.092412,236.1,-0.045967,-0.10737,-0.99316,251.79,-0.48831,0.86974,-0.071431,253.39
> select clear
> hide #!7 models
> show #!11 models
> ui tool show Matchmaker
> matchmaker #!7 to #11
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 6mtc.cif, chain B (#11) with 5aj0.cif, chain AB (#7), sequence
alignment score = 1897.7
RMSD between 391 pruned atom pairs is 0.713 angstroms; (across all 394 pairs:
0.792)
> show #!7 models
> show #!5 models
> matchmaker #!7 to #11
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 6mtc.cif, chain B (#11) with 5aj0.cif, chain AB (#7), sequence
alignment score = 1897.7
RMSD between 391 pruned atom pairs is 0.713 angstroms; (across all 394 pairs:
0.792)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 2149, in <lambda>
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 620, in close_request
all_windows = self.tool_instance_to_windows[tool_instance]
KeyError: <chimerax.match_maker.tool.MatchMakerTool object at 0x7f76f24efdf0>
KeyError:
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py",
line 620, in close_request
all_windows = self.tool_instance_to_windows[tool_instance]
See log for complete Python traceback.
> open /media/dell/DATA/kmani/Human_80s/h80s_6ek0.cif
h80s_6ek0.cif title:
High-resolution cryo-EM structure of the human 80S ribosome [more info...]
Chain information for h80s_6ek0.cif #12
---
Chain | Description
L5 | 28S ribosomal RNA
L7 | 5S ribosomal RNA
L8 | 5.8S ribosomal RNA
LA | 60S ribosomal protein L8
LB | 60S ribosomal protein L3
LC | 60S ribosomal protein L4
LD | 60S ribosomal protein L5
LE | 60S ribosomal protein L6
LF | 60S ribosomal protein L7
LG | 60S ribosomal protein L7a
LH | 60S ribosomal protein L9
LI | 60S ribosomal protein L10-like
LJ | 60S ribosomal protein L11
LL | 60S ribosomal protein L13
LM | 60S ribosomal protein L14
LN | 60S ribosomal protein L15
LO | 60S ribosomal protein L13a
LP | 60S ribosomal protein L17
LQ | 60S ribosomal protein L18
LR | 60S ribosomal protein L19
LS | 60S ribosomal protein L18a
LT | 60S ribosomal protein L21
LU | 60S ribosomal protein L22
LV | 60S ribosomal protein L23
LW | 60S ribosomal protein L24
LX | 60S ribosomal protein L23a
LY | 60S ribosomal protein L26
LZ | 60S ribosomal protein L27
La | 60S ribosomal protein L27a
Lb | 60S ribosomal protein L29
Lc | 60S ribosomal protein L30
Ld | 60S ribosomal protein L31
Le | 60S ribosomal protein L32
Lf | 60S ribosomal protein L35a
Lg | 60S ribosomal protein L34
Lh | 60S ribosomal protein L35
Li | 60S ribosomal protein L36
Lj | 60S ribosomal protein L37
Lk | 60S ribosomal protein L38
Ll | 60S ribosomal protein L39
Lm | Ubiquitin-60S ribosomal protein L40
Ln | 60S ribosomal protein L41
Lo | 60S ribosomal protein L36a
Lp | 60S ribosomal protein L37a
Lr | 60S ribosomal protein L28
Lz | 60S ribosomal protein L10a
S2 | 18S ribosomal RNA
S6 | Human initiator Met-tRNA-i
SA | 40S ribosomal protein SA
SB | 40S ribosomal protein S3a
SC | 40S ribosomal protein S2
SD | 40S ribosomal protein S3
SE | 40S ribosomal protein S4, X isoform
SF | 40S ribosomal protein S5
SG | 40S ribosomal protein S6
SH | 40S ribosomal protein S7
SI | 40S ribosomal protein S8
SJ | 40S ribosomal protein S9
SK | 40S ribosomal protein S10
SL | 40S ribosomal protein S11
SM | 40S ribosomal protein S12
SN | 40S ribosomal protein S13
SO | 40S ribosomal protein S14
SP | 40S ribosomal protein S15
SQ | 40S ribosomal protein S16
SR | 40S ribosomal protein S17
SS | 40S ribosomal protein S18
ST | 40S ribosomal protein S19
SU | 40S ribosomal protein S20
SV | 40S ribosomal protein S21
SW | 40S ribosomal protein S15a
SX | 40S ribosomal protein S23
SY | 40S ribosomal protein S24
SZ | 40S ribosomal protein S25
Sa | 40S ribosomal protein S26
Sb | 40S ribosomal protein S27
Sc | 40S ribosomal protein S28
Sd | 40S ribosomal protein S29
Se | 40S ribosomal protein S30
Sf | Ubiquitin-40S ribosomal protein S27a
Sg | Receptor of activated protein C kinase 1
Non-standard residues in h80s_6ek0.cif #12
---
B8N —
(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid
HMT —
(3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine
(Homoharringtonine, Cephalotaxine, [3(R)]-4-methyl
2-hydroxy-2-(4-hydroxy-4-methylpentyl)butanedioate)
HYG — hygromycin B (hygromix, antihelmycin, hydromycin B, destomysin,
antibiotic A-396-II)
MG — magnesium ion
ZN — zinc ion
> show #!5-7,11-12 cartoons
> hide #!5-7,11-12 atoms
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!11 models
> show #!1 models
> lighting full
> lighting full
> lighting soft
> lighting simple
> lighting full
> hide #!12 models
> show #!12 models
> select #12
219534 atoms, 235413 bonds, 5578 pseudobonds, 18056 residues, 4 models
selected
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.99724,-0.072923,-0.013941,593.56,0.049236,-0.50903,-0.85934,628.35,0.05557,-0.85765,0.51121,349.35
> view matrix models
> #12,-0.9876,-0.022197,0.15539,531.26,-0.11428,-0.57694,-0.80875,679.8,0.1076,-0.81649,0.56725,308.17
> view matrix models
> #12,-0.97174,-0.17017,0.16362,564.72,-0.066132,-0.46913,-0.88065,656.19,0.22662,-0.86658,0.44462,320.97
> view matrix models
> #12,-0.8701,0.40221,-0.28488,501.39,-0.16254,-0.77981,-0.60455,693.5,-0.46531,-0.47971,0.74389,332.39
> view matrix models
> #12,-0.98365,0.085414,0.15856,500.02,-0.17833,-0.58519,-0.79105,695.53,0.025224,-0.80639,0.59085,322.55
> view matrix models
> #12,-0.88086,0.44075,0.17269,370.3,-0.46017,-0.71172,-0.53074,739.99,-0.11102,-0.54698,0.82975,226.36
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.88086,0.44075,0.17269,343.91,-0.46017,-0.71172,-0.53074,704,-0.11102,-0.54698,0.82975,233.27
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.92011,-0.35969,-0.155,661.23,0.22727,-0.16802,-0.95923,475.88,0.31898,-0.91782,0.23634,371.75
> view matrix models
> #12,-0.96162,-0.26963,-0.050816,620.44,0.12526,-0.26662,-0.95563,530.81,0.24412,-0.92532,0.29016,380.6
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.96162,-0.26963,-0.050816,581.07,0.12526,-0.26662,-0.95563,542.82,0.24412,-0.92532,0.29016,360.03
> view matrix models
> #12,-0.96162,-0.26963,-0.050816,596.19,0.12526,-0.26662,-0.95563,550.59,0.24412,-0.92532,0.29016,370.37
Fit molecule h80s_6ek0.cif (#12) to map 80s_vol1_full_mask_rfn179_pp192.mrc
(#1) using 219534 atoms
average map value = 0.02188, steps = 292
shifted from previous position = 17.8
rotated from previous position = 17.1 degrees
atoms outside contour = 169312, contour level = 0.044855
Position of h80s_6ek0.cif (#12) relative to
80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates:
Matrix rotation and translation
-0.85240763 -0.52232920 0.02394720 600.11165791
0.08982797 -0.19140393 -0.97739220 538.19145832
0.51510406 -0.83098542 0.21007394 289.86377693
Axis 0.18338042 -0.61519388 0.76675166
Axis point 192.20541738 466.84534439 0.00000000
Rotation angle (degrees) 156.47253128
Shift along axis 1.21017408
> ui mousemode right "translate selected models"
> volume #1 style mesh
> lighting simple
> volume #1 style surface
> lighting full
> select clear
> select #12/L5,L7,L8
86445 atoms, 96316 bonds, 3878 pseudobonds, 4326 residues, 4 models selected
> select ~sel
1634115 atoms, 1751671 bonds, 17436 pseudobonds, 134883 residues, 32 models
selected
> cartoon hide (#!12 & sel)
> hide #!1 models
> show #!7 models
> hide #!7 models
> show #!11 models
> hide #!11 models
> show #!5 models
> select clear
> select #5/5,7,8
80599 atoms, 90148 bonds, 13 pseudobonds, 3775 residues, 2 models selected
> select ~sel
1639961 atoms, 1757839 bonds, 21301 pseudobonds, 135434 residues, 32 models
selected
> cartoon hide (#!5,12 & sel)
> select clear
> hide #!12 models
> show #!12 models
> hide #!5 models
> cartoon #12
> select #!12/L5,L7,L8
86445 atoms, 96316 bonds, 3878 pseudobonds, 4326 residues, 4 models selected
> cartoon hide (#!12 & sel)
> undo
> select ~sel
1634115 atoms, 1751671 bonds, 17436 pseudobonds, 134883 residues, 32 models
selected
> cartoon hide (#!12 & sel)
> show #!5 models
> select clear
> hide #!12 models
> hide #!5 models
> show #!6 models
> select #6/A5,A7,A8,A9
82989 atoms, 92737 bonds, 3034 pseudobonds, 3980 residues, 3 models selected
> select ~sel
1637571 atoms, 1755250 bonds, 18280 pseudobonds, 135229 residues, 32 models
selected
> cartoon hide (#!6 & sel)
> show #!12 models
> show #!5 models
> select clear
> hide #!12 models
> show #!12 models
> select #6/A5,A7,A8,A9
82989 atoms, 92737 bonds, 3034 pseudobonds, 3980 residues, 3 models selected
> color (#!6 & sel) blue
> color (#!6 & sel) light sea green
> select clear
> select #12/L5,L7,L8
86445 atoms, 96316 bonds, 3878 pseudobonds, 4326 residues, 4 models selected
> color (#!12 & sel) orange
> ui tool show "Color Actions"
> color sel burly wood
> select clear
> select #5/5,7,8
80599 atoms, 90148 bonds, 13 pseudobonds, 3775 residues, 2 models selected
> color sel olive drab
> select clear
> hide #!6 models
> hide #!5 models
> show #!5 models
> select #12
219534 atoms, 235413 bonds, 5578 pseudobonds, 18056 residues, 4 models
selected
> view matrix models
> #12,-0.85241,-0.52233,0.023947,600.95,0.089828,-0.1914,-0.97739,544.77,0.5151,-0.83099,0.21007,290.52
> view matrix models
> #12,-0.85241,-0.52233,0.023947,602.59,0.089828,-0.1914,-0.97739,550.35,0.5151,-0.83099,0.21007,290.96
> view matrix models
> #12,-0.85241,-0.52233,0.023947,602.44,0.089828,-0.1914,-0.97739,551.17,0.5151,-0.83099,0.21007,290.96
> ~select #12
Nothing selected
Fit molecule h80s_6ek0.cif (#12) to map 80s_vol1_full_mask_rfn179_pp192.mrc
(#1) using 219534 atoms
average map value = 0.02188, steps = 652
shifted from previous position = 13.2
rotated from previous position = 0.00856 degrees
atoms outside contour = 169339, contour level = 0.044855
Position of h80s_6ek0.cif (#12) relative to
80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates:
Matrix rotation and translation
-0.85244625 -0.52227199 0.02382009 600.14096309
0.08994099 -0.19137788 -0.97738690 538.14209034
0.51502043 -0.83102738 0.21011302 289.90403899
Axis 0.18330726 -0.61520143 0.76676310
Axis point 192.22947706 466.84550915 0.00000000
Rotation angle (degrees) 156.47062941
Shift along axis 1.23213638
> show #!6 models
> hide #!12 models
> hide #!5 models
> show #!12 models
> ui tool show Matchmaker
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 277, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 277, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
> select #12
219534 atoms, 235413 bonds, 5578 pseudobonds, 18056 residues, 4 models
selected
> select #6
219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models
selected
> select #12
219534 atoms, 235413 bonds, 5578 pseudobonds, 18056 residues, 4 models
selected
No reference and/or match structure/chain chosen
> matchmaker #12/L5 to #6/A5 pairing ss
Reference chain (6xu6.cif (#6) chain A5) not compatible with BLOSUM-62
similarity matrix
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and setattr(pself, "value", pself.get_attribute()))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 281, in set_value
self.widget.setText(value)
RuntimeError: wrapped C/C++ object of type QPushButton has been deleted
Error processing trigger "setting changed":
RuntimeError: wrapped C/C++ object of type QPushButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/ui/options/options.py", line 281, in set_value
self.widget.setText(value)
See log for complete Python traceback.
> matchmaker #12/L5 to #6/A5 pairing ss matrix Nucleic
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 6xu6.cif, chain A5 (#6) with h80s_6ek0.cif, chain L5 (#12),
sequence alignment score = 6666.6
RMSD between 2273 pruned atom pairs is 0.766 angstroms; (across all 3479
pairs: 15.075)
> select clear
> show #!5 models
> select #5
211125 atoms, 226838 bonds, 21 pseudobonds, 17017 residues, 2 models selected
> color sel green
> select #6
219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models
selected
> color sel blue
> select #12
219534 atoms, 235413 bonds, 5578 pseudobonds, 18056 residues, 4 models
selected
> color sel red
> select clear
> select #5
211125 atoms, 226838 bonds, 21 pseudobonds, 17017 residues, 2 models selected
> color sel light gray
> select #6
219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models
selected
> color sel dim gray
> select #12
219534 atoms, 235413 bonds, 5578 pseudobonds, 18056 residues, 4 models
selected
> color sel black
> select #5
211125 atoms, 226838 bonds, 21 pseudobonds, 17017 residues, 2 models selected
> color sel purple
> select #6
219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models
selected
> color sel hot pink
> select #12
219534 atoms, 235413 bonds, 5578 pseudobonds, 18056 residues, 4 models
selected
> color sel gray
> ~select #12
Nothing selected
> hide #!12 models
> select #5
211125 atoms, 226838 bonds, 21 pseudobonds, 17017 residues, 2 models selected
> color sel light gray
> select #6
219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models
selected
> color sel dim gray
> ~select #6
Nothing selected
> select #6
219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models
selected
> color sel black
> ~select #6
Nothing selected
> select #6
219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models
selected
> color sel maroon
> select clear
> mmaker #6 to #5 showAlignment true
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 80s_vol4FM_IFRD2.pdb, chain CB (#5) with 6xu6.cif, chain CB (#6),
sequence alignment score = 1649.6
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 80s_vol4FM_IFRD2.pdb #5/CB,
6xu6.cif #6/CB
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 376 pruned atom pairs is 0.703 angstroms; (across all 403 pairs:
1.197)
> mmaker #6/A5,A7,A8,A9 to #5/5,7,8 showAlignment true
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 80s_vol4FM_IFRD2.pdb, chain AA (#5) with 6xu6.cif, chain AA (#6),
sequence alignment score = 0
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 80s_vol4FM_IFRD2.pdb #5/AA,
6xu6.cif #6/AA
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Fewer than 3 residues aligned; cannot match 80s_vol4FM_IFRD2.pdb, chain AA
with 6xu6.cif, chain AA
> mmaker #6/A5,A7,A8,A9 to #5/5,7,8 matrix Nucleic showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 80s_vol4FM_IFRD2.pdb, chain 5 (#5) with 6xu6.cif, chain A5 (#6),
sequence alignment score = 8439.6
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 80s_vol4FM_IFRD2.pdb #5/5,
6xu6.cif #6/A5
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 2222 pruned atom pairs is 0.860 angstroms; (across all 3329
pairs: 14.753)
> show #!12 models
> hide #!6 models
> toolshed show
> ui tool show "Show Sequence Viewer"
> show #!6 models
> hide #!12 models
> mmaker #6/A5,A7,A8,A9 to #5/5,7,8 matrix Nucleic showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 80s_vol4FM_IFRD2.pdb, chain 5 (#5) with 6xu6.cif, chain A5 (#6),
sequence alignment score = 8439.6
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 80s_vol4FM_IFRD2.pdb #5/5,
6xu6.cif #6/A5
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 2222 pruned atom pairs is 0.860 angstroms; (across all 3329
pairs: 14.753)
> ui tool show Matchmaker
> sequence header conservation show
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
> sequence header consensus show
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
> sequence header rmsd hide
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/tool.py", line 553, in <lambda>
action.triggered.connect(lambda *, action=action, hdr=hdr,
align_arg=align_arg, self=self: run(
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/cmd.py", line 221, in seqalign_header
alignment._dispatch_header_command(subcommand_text)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 623, in
_dispatch_header_command
header.process_command(remainder)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/alignment_headers/header_sequence.py", line 188, in
process_command
self._command_runner.run(command_text, log=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/alignment_headers/header_sequence.py", line 313, in <lambda>
lambda session, hdr=self: setattr(hdr, "shown", False), registry=registry)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/alignment_headers/header_sequence.py", line 277, in shown
self.notify_alignment(self.alignment.NOTE_HDR_SHOWN)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/alignment_headers/header_sequence.py", line 152, in
notify_alignment
self.alignment.notify(note_name, note_data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 517, in notify
self._notify_observers(note_name, note_data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 652, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/tool.py", line 478, in alignment_notification
self.seq_canvas.alignment_notification(note_name, note_data)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/seq_canvas.py", line 1021, in alignment_notification
self.hide_header(hdr)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/seq_canvas.py", line 657, in hide_header
self.sv.region_browser.redraw_regions()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/region_browser.py", line 1032, in redraw_regions
region.redraw()
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/region_browser.py", line 289, in redraw
self.add_blocks(blocks, make_cb=False)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/region_browser.py", line 77, in add_blocks
for x1, y1, x2, y2 in self.seq_canvas.bbox_list(cover_gaps=self.cover_gaps,
*block):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/seq_canvas.py", line 424, in bbox_list
return self.lead_block.bbox_list(line1, line2, pos1, pos2, cover_gaps)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/seq_canvas.py", line 1686, in bbox_list
bboxes.append(self._box_corners(left,right,line1,line2))
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/seq_canvas.py", line 1714, in _box_corners
uly = self.bottom_ruler_y + self.letter_gaps[1] + self.line_index[line1] * (
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File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-
view/seq_canvas.py", line 1714, in _box_corners
uly = self.bottom_ruler_y + self.letter_gaps[1] + self.line_index[line1] * (
See log for complete Python traceback.
> sequence header rmsd show
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
OpenGL version: 3.3.0 NVIDIA 470.42.01
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 5820 Tower
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 Intel(R) Xeon(R) W-2145 CPU @ 3.70GHz
Cache Size: 11264 KB
Memory:
total used free shared buff/cache available
Mem: 125G 35G 72G 335M 17G 88G
Swap: 2.0G 0B 2.0G
Graphics:
65:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1)
Subsystem: Dell Device [1028:12a0]
Kernel driver in use: nvidia
Locale: ('en_IN', 'ISO8859-1')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
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: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
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: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 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: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
distro: 1.5.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
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-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.2.0
Change History (3)
comment:1 by , 4 years ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Hand-drawn regions can include headers |
comment:2 by , 4 years ago
comment:3 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
Until I have time to fix this (should be soon though), the way to avoid the problem is when you draw regions on the sequence with the mouse, avoid including header lines in the region.