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Opened 2 months ago
Closed 2 months ago
#18714 closed defect (duplicate)
'ArrayGridData' object has no attribute 'dicom_data'
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | DICOM | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/guynovoa/Downloads/PlosPathogens2025/FiguraLlenasVaciasNTARNA.cxs
Opened cryosparc_P12_J11_008_volume_map_en1-37.mrc as #1, grid size
330,330,330, pixel 1.37, shown at level 0.214, step 1, values float32
Opened cryosparc_P12_J11_008_volume_map_sharp_en1-37.mrc as #2, grid size
330,330,330, pixel 1.37, shown at level 0.46, step 1, values float32
Opened cryosparc_P12_J9_008_volume_map_1_37.mrc as #18, grid size 330,330,330,
pixel 1.37, shown at level 0.13, step 1, values float32
Log from Thu Sep 4 16:20:59 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/guynovoa/Desktop/NTA_15Ene-v2.cxs format session
Opened RHDVv_Llenas.mrc as #1, grid size 330,330,330, pixel 1.37, shown at
level 0.4, step 1, values float32
Opened RHDVv_Llenas_sharp_en0.ccp4 as #3, grid size 330,330,330, pixel 1.37,
shown at level 0.9, step 1, values float32
Opened RHDVv_Llenas.mrc copy as #6, grid size 330,330,330, pixel 1.37, shown
at level 0.2, step 1, values float32
Opened cryosparc_P12_J11_008_volume_map.mrc as #7, grid size 330,330,330,
pixel 1.37, shown at level 0.3, step 1, values float32
Log from Wed Jan 15 09:26:31 2025UCSF ChimeraX version: 1.9rc202412041747
(2024-12-04)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/guynovoa/Downloads/NTA_14Ene.cxs
Opened RHDVv_Llenas.mrc as #1, grid size 330,330,330, pixel 1.37, shown at
level 0.4, step 1, values float32
Opened RHDVv_Llenas_sharp_en0.ccp4 as #3, grid size 330,330,330, pixel 1.37,
shown at level 0.9, step 1, values float32
Opened RHDVv_Llenas.mrc copy as #6, grid size 330,330,330, pixel 1.37, shown
at level 0.2, step 1, values float32
Opened cryosparc_P12_J11_008_volume_map.mrc as #7, grid size 330,330,330,
pixel 1.37, shown at level 0.3, step 1, values float32
Log from Tue Jan 14 16:48:39 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /media/data5/RHDV/13Ene/NTA.cxs
Opened RHDVv_Llenas.mrc as #1, grid size 330,330,330, pixel 1.37, shown at
level 0.22, step 1, values float32
Opened RHDVv_Llenas_sharp.mrc as #3, grid size 330,330,330, pixel 1.37, shown
at level 0.42, step 1, values float32
Opened RHDVv_Llenas.mrc copy as #6, grid size 330,330,330, pixel 1.37, shown
at level 0.195, step 1, values float32
Log from Mon Jan 13 16:03:47 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/guynovoa/Downloads/Capsid_from_5cp6cp6cp_fromLlenas_NTAadaptado_real_space_refined_010.pdb
Chain information for
Capsid_from_5cp6cp6cp_fromLlenas_NTAadaptado_real_space_refined_010.pdb #1
---
Chain | Description
0 1 4 7 A2 A5 A8 AC AF AI AL AO AR AU AX Aa Ad Ag Aj Am Ap As Av Ay B B3 BA BD BG BJ BM BP BS BV BY Bb Be Bh Bk Bn Bq Bt Bw Bz E H K N Q T W Z c f i l o r u x | No description available
2 5 8 A3 A6 A9 AA AD AG AJ AM AP AS AV AY Ab Ae Ah Ak An Aq At Aw Az B1 B4 BB BE BH BK BN BQ BT BW BZ Bc Bf Bi Bl Bo Br Bu Bx C F I L O R U X a d g j m p s v y | No description available
3 6 9 A A0 A1 A4 A7 AB AE AH AK AN AQ AT AW AZ Ac Af Ai Al Ao Ar Au Ax B2 BC BF BI BL BO BR BU BX Ba Bd Bg Bj Bm Bp Bs Bv By D G J M P S V Y b e h k n q t w z | No description available
> select #1/A,B,C
12059 atoms, 12402 bonds, 1634 residues, 1 model selected
> select ~sel & ##selected
711481 atoms, 731718 bonds, 96406 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #1
12059 atoms, 12402 bonds, 1634 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> ui mousemode right select
> select clear
> select #1:230-999
7469 atoms, 7679 bonds, 1024 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/C
1567 atoms, 1611 bonds, 209 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show Contacts
> contacts resSeparation 1 intraModel false intraMol false ignoreHiddenModels
> true color #000000 radius 0.05 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 1 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> contacts resSeparation 1 interModel false intraMol false ignoreHiddenModels
> true color #000000 radius 0.05 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 1 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
69 contacts
atom1 atom2 overlap distance
/B ARG 227 CA /A PHE 153 CE2 0.112 3.528
/B MET 177 CE /A ARG 174 NH1 0.097 3.423
/B MET 177 CE /A THR 52 OG1 0.091 3.249
/A ILE 142 CD1 /B ARG 227 CB 0.074 3.686
/B MET 225 CB /A PRO 139 CG 0.069 3.691
/B MET 177 CG /A ASN 176 O 0.057 3.243
/B ILE 55 CD1 /A ARG 174 NH1 0.050 3.470
/A ILE 142 CD1 /B ARG 227 CD 0.047 3.713
/A THR 52 CB /B MET 177 CE 0.046 3.714
/A PRO 139 CB /B MET 225 CE 0.042 3.718
/B MET 225 CG /A LEU 173 CD1 0.018 3.742
/B ALA 228 CB /A PHE 153 CE1 0.012 3.628
/B ILE 55 CD1 /A SER 49 CA 0.009 3.751
/B ALA 111 CB /A PRO 139 CG 0.006 3.754
/B GLY 182 CA /A GLY 141 O -0.009 3.309
/A ARG 174 O /B ILE 55 CG2 -0.049 3.349
/B ILE 226 CB /A PRO 154 CD -0.055 3.815
/B MET 177 CG /A PRO 175 C -0.057 3.547
/B MET 177 CE /A THR 52 CG2 -0.060 3.820
/B ALA 228 N /A PHE 153 CE1 -0.081 3.481
/B MET 177 CE /A ASN 176 O -0.094 3.394
/A PRO 139 CB /B ALA 111 CB -0.110 3.870
/A PRO 154 CG /B ILE 226 CB -0.111 3.871
/B TYR 178 OH /A PRO 140 CD -0.113 3.453
/A ALA 48 CB /B GLY 54 C -0.115 3.605
/B MET 177 CG /A PRO 175 O -0.123 3.423
/A PHE 153 CD2 /B ARG 227 CA -0.129 3.769
/A ARG 174 CG /B ILE 55 CG1 -0.140 3.900
/B MET 177 CB /A PRO 175 CA -0.147 3.907
/A PRO 175 CB /B ASN 176 ND2 -0.150 3.670
/A PRO 175 O /B ASN 176 CA -0.166 3.466
/A PRO 154 CD /B ILE 226 CG2 -0.168 3.928
/A ASN 45 CB /B GLY 57 CA -0.191 3.951
/B MET 177 CG /A ASN 176 C -0.201 3.691
/A ASN 45 CB /B GLY 54 O -0.211 3.511
/B ILE 55 CG1 /A ARG 174 NH1 -0.212 3.732
/B MET 225 CE /A LEU 173 CB -0.213 3.973
/B ARG 227 CA /A PHE 153 CZ -0.224 3.864
/A PRO 154 CG /B ILE 226 CG1 -0.232 3.992
/A GLN 152 OE1 /B PRO 229 CD -0.242 3.542
/A LEU 173 CD2 /B MET 225 SD -0.242 3.892
/B ALA 228 CB /A PHE 153 CD1 -0.244 3.884
/B ARG 227 CB /A PHE 153 CE2 -0.245 3.885
/B ILE 55 CD1 /A ARG 174 CZ -0.256 3.746
/A GLU 149 O /B ALA 228 CB -0.269 3.569
/A ARG 174 O /B MET 177 CB -0.269 3.569
/A PRO 140 CG /B TYR 178 OH -0.269 3.609
/B ALA 228 N /A PHE 153 CZ -0.271 3.671
/A ALA 48 CB /B GLY 54 CA -0.277 4.037
/A ASN 45 CB /B GLY 57 N -0.278 3.798
/A ASN 45 ND2 /B ILE 55 O -0.286 2.946
/A ARG 174 C /B TYR 178 CE1 -0.290 3.660
/B TYR 178 CE1 /A ARG 174 O -0.300 3.480
/B ALA 228 CB /A GLN 152 CB -0.304 4.064
/A GLY 141 CA /B GLY 182 CA -0.307 4.067
/A PRO 175 O /B MET 177 N -0.315 2.975
/B ILE 55 CD1 /A SER 49 CB -0.335 4.095
/A PRO 139 CG /B MET 225 CG -0.342 4.102
/A PRO 175 CA /B MET 177 CG -0.344 4.104
/B GLY 54 O /A ALA 48 CB -0.349 3.649
/A PRO 139 CB /B MET 225 CB -0.351 4.111
/B MET 225 CG /A LEU 173 CD2 -0.353 4.113
/A PHE 153 CD1 /B ALA 228 N -0.357 3.757
/B MET 177 CG /A ASN 176 CA -0.359 4.119
/A ASN 45 ND2 /B ILE 55 CD1 -0.377 3.897
/B MET 177 CB /A PRO 175 C -0.378 3.868
/A ALA 48 CB /B ILE 55 N -0.381 3.901
/A LEU 186 CD1 /B ASP 183 CB -0.383 4.143
/B ARG 227 CB /A PHE 153 CZ -0.387 4.027
69 contacts
> close #1
> open
> /Users/guynovoa/Downloads/Capsid_from_5cp6cp6cp_fromLlenas_NTAadaptado_real_space_refined_010.pdb
> format pdb
Chain information for
Capsid_from_5cp6cp6cp_fromLlenas_NTAadaptado_real_space_refined_010.pdb #1
---
Chain | Description
0 1 4 7 A2 A5 A8 AC AF AI AL AO AR AU AX Aa Ad Ag Aj Am Ap As Av Ay B B3 BA BD BG BJ BM BP BS BV BY Bb Be Bh Bk Bn Bq Bt Bw Bz E H K N Q T W Z c f i l o r u x | No description available
2 5 8 A3 A6 A9 AA AD AG AJ AM AP AS AV AY Ab Ae Ah Ak An Aq At Aw Az B1 B4 BB BE BH BK BN BQ BT BW BZ Bc Bf Bi Bl Bo Br Bu Bx C F I L O R U X a d g j m p s v y | No description available
3 6 9 A A0 A1 A4 A7 AB AE AH AK AN AQ AT AW AZ Ac Af Ai Al Ao Ar Au Ax B2 BC BF BI BL BO BR BU BX Ba Bd Bg Bj Bm Bp Bs Bv By D G J M P S V Y b e h k n q t w z | No description available
> select #1/A,B,C
12059 atoms, 12402 bonds, 1634 residues, 1 model selected
> select ~sel & ##selected
711481 atoms, 731718 bonds, 96406 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1:230-999
7469 atoms, 7679 bonds, 1024 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/B
1566 atoms, 1610 bonds, 209 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show Contacts
> contacts resSeparation 1 interModel false intraMol false ignoreHiddenModels
> true color #000000 radius 0.05 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 1 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
61 contacts
atom1 atom2 overlap distance
/A MET 177 CE /C THR 52 CG2 0.147 3.613
/A MET 177 CE /C THR 52 OG1 0.100 3.240
/A MET 177 CE /C MET 177 CA 0.071 3.689
/A ALA 111 CB /C ILE 142 CD1 0.065 3.695
/C ILE 142 CD1 /A ARG 227 CB 0.055 3.705
/A MET 177 CE /C MET 177 SD 0.047 3.603
/A ALA 228 CB /C GLN 152 CB 0.042 3.718
/A ARG 227 CA /C PHE 153 CE2 0.042 3.598
/A TYR 178 OH /C PRO 140 CG 0.033 3.307
/A ILE 226 CG2 /C PRO 154 CG 0.032 3.728
/A MET 225 SD /C LEU 173 CD2 0.029 3.621
/A MET 225 SD /C LEU 173 CB 0.029 3.621
/C PHE 153 CE2 /A ARG 227 CB 0.019 3.621
/A MET 177 CE /C ASN 176 O 0.007 3.293
/A PRO 180 CG /C LEU 186 CD1 -0.005 3.765
/C ILE 142 CD1 /A ARG 227 CD -0.007 3.767
/A ALA 111 CB /C PRO 139 CB -0.011 3.771
/C PHE 153 CE1 /A ALA 228 CB -0.011 3.651
/A ILE 55 CD1 /C SER 49 CA -0.012 3.772
/A GLY 54 CA /C GLU 44 OE1 -0.016 3.316
/A ASN 176 CA /C PRO 175 O -0.028 3.328
/C PRO 175 O /A MET 177 CG -0.029 3.329
/A ILE 55 CD1 /C ARG 174 NH1 -0.038 3.558
/C GLU 44 CD /A GLY 57 O -0.040 3.340
/A ASN 176 CB /C PRO 175 CB -0.042 3.802
/C PRO 139 CB /A MET 225 CE -0.044 3.804
/C PRO 139 CG /A MET 225 CB -0.047 3.807
/A GLY 54 O /C ASN 45 CA -0.049 3.349
/A ILE 55 CG2 /C ARG 174 O -0.051 3.351
/C PRO 139 CB /A MET 225 SD -0.069 3.719
/A GLY 54 CA /C GLU 44 CG -0.084 3.844
/A ILE 226 CG2 /C PRO 154 CD -0.101 3.861
/A PRO 58 CA /C GLU 44 OE2 -0.140 3.440
/C GLU 44 CG /A GLY 54 O -0.152 3.452
/C GLU 44 CD /A PRO 58 CA -0.164 3.924
/C PRO 175 O /A ASN 176 CB -0.172 3.472
/C LEU 186 CD1 /A ASP 183 CB -0.174 3.934
/A ILE 55 CD1 /C SER 49 CB -0.184 3.944
/A ALA 111 CB /C PRO 139 CG -0.191 3.951
/C THR 42 CG2 /A PRO 58 CD -0.196 3.956
/A MET 177 CE /C THR 52 CB -0.197 3.957
/A GLY 54 CA /C GLU 44 CD -0.211 3.971
/A MET 225 SD /C LEU 173 CG -0.255 3.905
/C PHE 153 CZ /A ALA 228 N -0.260 3.660
/A ARG 227 CA /C PHE 153 CD2 -0.271 3.911
/C PRO 139 CB /A MET 225 CB -0.275 4.035
/A MET 225 SD /C LEU 173 CD1 -0.275 3.925
/A ILE 55 O /C ASN 45 ND2 -0.286 2.946
/A ARG 227 CB /C PHE 153 CZ -0.309 3.949
/A ALA 228 CB /C PHE 153 CD1 -0.318 3.958
/A MET 177 CE /C ASN 176 C -0.337 3.827
/A ALA 228 CB /C GLU 149 O -0.338 3.638
/C ARG 174 O /A TYR 178 CE1 -0.358 3.538
/A ALA 228 N /C PHE 153 CE1 -0.358 3.758
/C GLU 44 CD /A GLY 57 C -0.358 3.848
/A TYR 178 CE1 /C PRO 175 CA -0.359 3.999
/A ILE 55 CG1 /C ASP 172 O -0.367 3.667
/C PRO 175 O /A MET 177 N -0.379 3.039
/A PRO 58 CG /C THR 42 CG2 -0.389 4.149
/A ILE 55 CD1 /C SER 49 N -0.399 3.919
/A TYR 178 CE1 /C ARG 174 C -0.400 3.770
61 contacts
> close #1
> open
> /Users/guynovoa/Downloads/Capsid_from_5cp6cp6cp_fromLlenas_NTAadaptado_real_space_refined_010.pdb
> format pdb
Chain information for
Capsid_from_5cp6cp6cp_fromLlenas_NTAadaptado_real_space_refined_010.pdb #1
---
Chain | Description
0 1 4 7 A2 A5 A8 AC AF AI AL AO AR AU AX Aa Ad Ag Aj Am Ap As Av Ay B B3 BA BD BG BJ BM BP BS BV BY Bb Be Bh Bk Bn Bq Bt Bw Bz E H K N Q T W Z c f i l o r u x | No description available
2 5 8 A3 A6 A9 AA AD AG AJ AM AP AS AV AY Ab Ae Ah Ak An Aq At Aw Az B1 B4 BB BE BH BK BN BQ BT BW BZ Bc Bf Bi Bl Bo Br Bu Bx C F I L O R U X a d g j m p s v y | No description available
3 6 9 A A0 A1 A4 A7 AB AE AH AK AN AQ AT AW AZ Ac Af Ai Al Ao Ar Au Ax B2 BC BF BI BL BO BR BU BX Ba Bd Bg Bj Bm Bp Bs Bv By D G J M P S V Y b e h k n q t w z | No description available
> select #1/A,B,C
12059 atoms, 12402 bonds, 1634 residues, 1 model selected
> select #1/A,B,C,BO,b
19957 atoms, 20526 bonds, 2702 residues, 1 model selected
> select #1/A,B,C,BO,b,Aa,c
28065 atoms, 28864 bonds, 3802 residues, 1 model selected
> select #1/A,B,C,BO,b,Aa,c,Ab,BQ
36177 atoms, 37206 bonds, 4902 residues, 1 model selected
> select ~sel & ##selected
687363 atoms, 706914 bonds, 93138 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save /Users/guynovoa/Desktop/12Ene/9cp.pdb relModel #1
> open /Users/guynovoa/Desktop/12Ene/9cp_vacias.pdb
Chain information for 9cp_vacias.pdb #2
---
Chain | Description
A BO b | No description available
Aa B c | No description available
Ab BQ C | No description available
> hide #1 models
> close #1
> select #1:230-999
Nothing selected
> select #2:230-999
22407 atoms, 23037 bonds, 3072 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save /Users/guynovoa/Desktop/12Ene/9cp_vacias_domS.pdb relModel #2
> select #2/A
1457 atoms, 1499 bonds, 192 residues, 1 model selected
> select ~sel & ##selected
12313 atoms, 12661 bonds, 1638 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> open /Users/guynovoa/Desktop/12Ene/9cp_vacias_domS.pdb
Chain information for 9cp_vacias_domS.pdb #1
---
Chain | Description
A BO b | No description available
Aa B c | No description available
Ab BQ C | No description available
> select #1/B
1566 atoms, 1610 bonds, 209 residues, 1 model selected
> select ~sel & ##selected
12204 atoms, 12550 bonds, 1621 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #1
1566 atoms, 1610 bonds, 209 residues, 1 model selected
> select add #2
3023 atoms, 3109 bonds, 401 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select clear
> ui mousemode right zoom
> ui mousemode right translate
> ui tool show Contacts
> contacts resSeparation 1 interModel false intraMol false ignoreHiddenModels
> true color #000000 radius 0.05 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 1 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> contacts resSeparation 1 intraModel false intraMol false ignoreHiddenModels
> true color #000000 radius 0.05 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 1 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
69 contacts
atom1 atom2 overlap distance
9cp_vacias_domS.pdb #1/B ARG 227 CA 9cp_vacias.pdb #2/A PHE 153 CE2 0.112 3.528
9cp_vacias_domS.pdb #1/B MET 177 CE 9cp_vacias.pdb #2/A ARG 174 NH1 0.097 3.423
9cp_vacias_domS.pdb #1/B MET 177 CE 9cp_vacias.pdb #2/A THR 52 OG1 0.091 3.249
9cp_vacias.pdb #2/A ILE 142 CD1 9cp_vacias_domS.pdb #1/B ARG 227 CB 0.074 3.686
9cp_vacias_domS.pdb #1/B MET 225 CB 9cp_vacias.pdb #2/A PRO 139 CG 0.069 3.691
9cp_vacias_domS.pdb #1/B MET 177 CG 9cp_vacias.pdb #2/A ASN 176 O 0.057 3.243
9cp_vacias_domS.pdb #1/B ILE 55 CD1 9cp_vacias.pdb #2/A ARG 174 NH1 0.050 3.470
9cp_vacias.pdb #2/A ILE 142 CD1 9cp_vacias_domS.pdb #1/B ARG 227 CD 0.047 3.713
9cp_vacias.pdb #2/A THR 52 CB 9cp_vacias_domS.pdb #1/B MET 177 CE 0.046 3.714
9cp_vacias.pdb #2/A PRO 139 CB 9cp_vacias_domS.pdb #1/B MET 225 CE 0.042 3.718
9cp_vacias_domS.pdb #1/B MET 225 CG 9cp_vacias.pdb #2/A LEU 173 CD1 0.018 3.742
9cp_vacias_domS.pdb #1/B ALA 228 CB 9cp_vacias.pdb #2/A PHE 153 CE1 0.012 3.628
9cp_vacias_domS.pdb #1/B ILE 55 CD1 9cp_vacias.pdb #2/A SER 49 CA 0.009 3.751
9cp_vacias_domS.pdb #1/B ALA 111 CB 9cp_vacias.pdb #2/A PRO 139 CG 0.006 3.754
9cp_vacias_domS.pdb #1/B GLY 182 CA 9cp_vacias.pdb #2/A GLY 141 O -0.009 3.309
9cp_vacias.pdb #2/A ARG 174 O 9cp_vacias_domS.pdb #1/B ILE 55 CG2 -0.049 3.349
9cp_vacias_domS.pdb #1/B ILE 226 CB 9cp_vacias.pdb #2/A PRO 154 CD -0.055 3.815
9cp_vacias_domS.pdb #1/B MET 177 CG 9cp_vacias.pdb #2/A PRO 175 C -0.057 3.547
9cp_vacias_domS.pdb #1/B MET 177 CE 9cp_vacias.pdb #2/A THR 52 CG2 -0.060 3.820
9cp_vacias_domS.pdb #1/B ALA 228 N 9cp_vacias.pdb #2/A PHE 153 CE1 -0.081 3.481
9cp_vacias_domS.pdb #1/B MET 177 CE 9cp_vacias.pdb #2/A ASN 176 O -0.094 3.394
9cp_vacias.pdb #2/A PRO 139 CB 9cp_vacias_domS.pdb #1/B ALA 111 CB -0.110 3.870
9cp_vacias.pdb #2/A PRO 154 CG 9cp_vacias_domS.pdb #1/B ILE 226 CB -0.111 3.871
9cp_vacias_domS.pdb #1/B TYR 178 OH 9cp_vacias.pdb #2/A PRO 140 CD -0.113 3.453
9cp_vacias.pdb #2/A ALA 48 CB 9cp_vacias_domS.pdb #1/B GLY 54 C -0.115 3.605
9cp_vacias_domS.pdb #1/B MET 177 CG 9cp_vacias.pdb #2/A PRO 175 O -0.123 3.423
9cp_vacias.pdb #2/A PHE 153 CD2 9cp_vacias_domS.pdb #1/B ARG 227 CA -0.129 3.769
9cp_vacias.pdb #2/A ARG 174 CG 9cp_vacias_domS.pdb #1/B ILE 55 CG1 -0.140 3.900
9cp_vacias_domS.pdb #1/B MET 177 CB 9cp_vacias.pdb #2/A PRO 175 CA -0.147 3.907
9cp_vacias.pdb #2/A PRO 175 CB 9cp_vacias_domS.pdb #1/B ASN 176 ND2 -0.150 3.670
9cp_vacias.pdb #2/A PRO 175 O 9cp_vacias_domS.pdb #1/B ASN 176 CA -0.166 3.466
9cp_vacias.pdb #2/A PRO 154 CD 9cp_vacias_domS.pdb #1/B ILE 226 CG2 -0.168 3.928
9cp_vacias.pdb #2/A ASN 45 CB 9cp_vacias_domS.pdb #1/B GLY 57 CA -0.191 3.951
9cp_vacias_domS.pdb #1/B MET 177 CG 9cp_vacias.pdb #2/A ASN 176 C -0.201 3.691
9cp_vacias.pdb #2/A ASN 45 CB 9cp_vacias_domS.pdb #1/B GLY 54 O -0.211 3.511
9cp_vacias_domS.pdb #1/B ILE 55 CG1 9cp_vacias.pdb #2/A ARG 174 NH1 -0.212 3.732
9cp_vacias_domS.pdb #1/B MET 225 CE 9cp_vacias.pdb #2/A LEU 173 CB -0.213 3.973
9cp_vacias_domS.pdb #1/B ARG 227 CA 9cp_vacias.pdb #2/A PHE 153 CZ -0.224 3.864
9cp_vacias.pdb #2/A PRO 154 CG 9cp_vacias_domS.pdb #1/B ILE 226 CG1 -0.232 3.992
9cp_vacias.pdb #2/A GLN 152 OE1 9cp_vacias_domS.pdb #1/B PRO 229 CD -0.242 3.542
9cp_vacias.pdb #2/A LEU 173 CD2 9cp_vacias_domS.pdb #1/B MET 225 SD -0.242 3.892
9cp_vacias_domS.pdb #1/B ALA 228 CB 9cp_vacias.pdb #2/A PHE 153 CD1 -0.244 3.884
9cp_vacias_domS.pdb #1/B ARG 227 CB 9cp_vacias.pdb #2/A PHE 153 CE2 -0.245 3.885
9cp_vacias_domS.pdb #1/B ILE 55 CD1 9cp_vacias.pdb #2/A ARG 174 CZ -0.256 3.746
9cp_vacias.pdb #2/A GLU 149 O 9cp_vacias_domS.pdb #1/B ALA 228 CB -0.269 3.569
9cp_vacias.pdb #2/A ARG 174 O 9cp_vacias_domS.pdb #1/B MET 177 CB -0.269 3.569
9cp_vacias.pdb #2/A PRO 140 CG 9cp_vacias_domS.pdb #1/B TYR 178 OH -0.269 3.609
9cp_vacias_domS.pdb #1/B ALA 228 N 9cp_vacias.pdb #2/A PHE 153 CZ -0.271 3.671
9cp_vacias.pdb #2/A ALA 48 CB 9cp_vacias_domS.pdb #1/B GLY 54 CA -0.277 4.037
9cp_vacias.pdb #2/A ASN 45 CB 9cp_vacias_domS.pdb #1/B GLY 57 N -0.278 3.798
9cp_vacias.pdb #2/A ASN 45 ND2 9cp_vacias_domS.pdb #1/B ILE 55 O -0.286 2.946
9cp_vacias.pdb #2/A ARG 174 C 9cp_vacias_domS.pdb #1/B TYR 178 CE1 -0.290 3.660
9cp_vacias_domS.pdb #1/B TYR 178 CE1 9cp_vacias.pdb #2/A ARG 174 O -0.300 3.480
9cp_vacias_domS.pdb #1/B ALA 228 CB 9cp_vacias.pdb #2/A GLN 152 CB -0.304 4.064
9cp_vacias.pdb #2/A GLY 141 CA 9cp_vacias_domS.pdb #1/B GLY 182 CA -0.307 4.067
9cp_vacias.pdb #2/A PRO 175 O 9cp_vacias_domS.pdb #1/B MET 177 N -0.315 2.975
9cp_vacias_domS.pdb #1/B ILE 55 CD1 9cp_vacias.pdb #2/A SER 49 CB -0.335 4.095
9cp_vacias.pdb #2/A PRO 139 CG 9cp_vacias_domS.pdb #1/B MET 225 CG -0.342 4.102
9cp_vacias.pdb #2/A PRO 175 CA 9cp_vacias_domS.pdb #1/B MET 177 CG -0.344 4.104
9cp_vacias_domS.pdb #1/B GLY 54 O 9cp_vacias.pdb #2/A ALA 48 CB -0.349 3.649
9cp_vacias.pdb #2/A PRO 139 CB 9cp_vacias_domS.pdb #1/B MET 225 CB -0.351 4.111
9cp_vacias_domS.pdb #1/B MET 225 CG 9cp_vacias.pdb #2/A LEU 173 CD2 -0.353 4.113
9cp_vacias.pdb #2/A PHE 153 CD1 9cp_vacias_domS.pdb #1/B ALA 228 N -0.357 3.757
9cp_vacias_domS.pdb #1/B MET 177 CG 9cp_vacias.pdb #2/A ASN 176 CA -0.359 4.119
9cp_vacias.pdb #2/A ASN 45 ND2 9cp_vacias_domS.pdb #1/B ILE 55 CD1 -0.377 3.897
9cp_vacias_domS.pdb #1/B MET 177 CB 9cp_vacias.pdb #2/A PRO 175 C -0.378 3.868
9cp_vacias.pdb #2/A ALA 48 CB 9cp_vacias_domS.pdb #1/B ILE 55 N -0.381 3.901
9cp_vacias.pdb #2/A LEU 186 CD1 9cp_vacias_domS.pdb #1/B ASP 183 CB -0.383 4.143
9cp_vacias_domS.pdb #1/B ARG 227 CB 9cp_vacias.pdb #2/A PHE 153 CZ -0.387 4.027
69 contacts
> combine #1,2
> save /Users/guynovoa/Desktop/12Ene/AB_vacias.pdb models #4
> close
> open /Users/guynovoa/Desktop/12Ene/9cp_vacias_domS.pdb format pdb
Chain information for 9cp_vacias_domS.pdb #1
---
Chain | Description
A BO b | No description available
Aa B c | No description available
Ab BQ C | No description available
> select #1/A,C
3024 atoms, 3110 bonds, 401 residues, 1 model selected
> select ~sel & ##selected
10746 atoms, 11050 bonds, 1429 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save /Users/guynovoa/Desktop/12Ene/AC_vacias.pdb relModel #1
> close
> open /Users/guynovoa/Desktop/12Ene/9cp_vacias_domS.pdb format pdb
Chain information for 9cp_vacias_domS.pdb #1
---
Chain | Description
A BO b | No description available
Aa B c | No description available
Ab BQ C | No description available
> select #1/A,b
2914 atoms, 2998 bonds, 384 residues, 1 model selected
> select ~sel & ##selected
10856 atoms, 11162 bonds, 1446 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save /Users/guynovoa/Desktop/12Ene/AA5_vacias.pdb relModel #1
> close
> open /Users/guynovoa/Desktop/12Ene/9cp_vacias_domS.pdb format pdb
Chain information for 9cp_vacias_domS.pdb #1
---
Chain | Description
A BO b | No description available
Aa B c | No description available
Ab BQ C | No description available
> select #1/A,c
3023 atoms, 3109 bonds, 401 residues, 1 model selected
> save /Users/guynovoa/Desktop/12Ene/ABp2_vacias.pdb relModel #1
> save /Users/guynovoa/Desktop/12Ene/ABp2_vacias.pdb selectedOnly true
> relModel #1
> select #1/B,C
3133 atoms, 3221 bonds, 418 residues, 1 model selected
> save /Users/guynovoa/Desktop/12Ene/BC_vacias.pdb selectedOnly true relModel
> #1
> select #1/B,BO
3023 atoms, 3109 bonds, 401 residues, 1 model selected
> save /Users/guynovoa/Desktop/12Ene/BA5prima_vacias.pdb selectedOnly true
> relModel #1
> select #1/B,BQ
3133 atoms, 3221 bonds, 418 residues, 1 model selected
> save /Users/guynovoa/Desktop/12Ene/BC3_vacias.pdb selectedOnly true relModel
> #1
> select #1/B,Ab
3133 atoms, 3221 bonds, 418 residues, 1 model selected
> save /Users/guynovoa/Desktop/12Ene/BC2_vacias.pdb selectedOnly true relModel
> #1
> ui mousemode right select
> select clear
> select #1/C,Ab
3134 atoms, 3222 bonds, 418 residues, 1 model selected
> save /Users/guynovoa/Desktop/12Ene/CC2_vacias.pdb selectedOnly true relModel
> #1
> select #1/C,Aa
3133 atoms, 3221 bonds, 418 residues, 1 model selected
> save /Users/guynovoa/Desktop/12Ene/CB3_vacias.pdb selectedOnly true relModel
> #1
> select #1/C,c
3133 atoms, 3221 bonds, 418 residues, 1 model selected
> save /Users/guynovoa/Desktop/12Ene/CB2_vacias.pdb selectedOnly true relModel
> #1
> close
> open /Users/guynovoa/Desktop/12Ene/9cp_vacias.pdb format pdb
Chain information for 9cp_vacias.pdb #1
---
Chain | Description
A BO b | No description available
Aa B c | No description available
Ab BQ C | No description available
> select #1/C,Ab
8112 atoms, 8342 bonds, 1100 residues, 1 model selected
> select ~sel & ##selected
28065 atoms, 28864 bonds, 3802 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1:1-229
3134 atoms, 3222 bonds, 418 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save /Users/guynovoa/Desktop/12Ene/SpikeCC.pdb relModel #1
> close
> open /Users/guynovoa/Desktop/17Dic/NT15_Capsid.pdb format pdb
Chain information for NT15_Capsid.pdb #1
---
Chain | Description
0 2 6 A4 A8 AD AH AL AP AT AX Ab Af Aj An Ar Av Az B B0 B2 B6 BB BF BJ BN BR BV BZ Bd Bh Bl Bp Bt Bx CD CH CL CP CT CX Cb Cf Cj Cn Cr Cv Cz F J N R V Z d h l p t x | No description available
1 5 9 A A3 A7 AC AG AK AO AS AW Aa Ae Ai Am Aq Au Ay B1 B5 B9 BA BE BI BM BQ BU BY Bc Bg Bk Bo Bs Bw CC CG CK CO CS CW Ca Ce Ci Cm Cq Cu Cy E I M Q U Y c g k o s w | No description available
3 7 A1 A5 A9 AA AE AI AM AQ AU AY Ac Ag Ak Ao As Aw B3 B7 BC BG BK BO BS BW Ba Be Bi Bm Bq Bu By C C1 CA CE CI CM CQ CU CY Cc Cg Ck Co Cs Cw G K O S W a e i m q u y | No description available
4 8 A0 A2 A6 AB AF AJ AN AR AV AZ Ad Ah Al Ap At Ax B4 B8 BD BH BL BP BT BX Bb Bf Bj Bn Br Bv Bz C2 CB CF CJ CN CR CV CZ Cd Ch Cl Cp Ct Cx D H L P T X b f j n r v z | No description available
> close
> open "/Users/guynovoa/Desktop/RHDV 2024/Mapas/RHDVv_Llenas.mrc"
Opened RHDVv_Llenas.mrc as #1, grid size 330,330,330, pixel 1.42, shown at
level 0.86, step 2, values float32
> volume #1 step 1
> open /Users/guynovoa/Downloads/Capsid_Trimero_v4-coot-0_LLENAS.pdb format
> pdb
Chain information for Capsid_Trimero_v4-coot-0_LLENAS.pdb #2
---
Chain | Description
0 1 4 7 A2 A5 A8 AC AF AI AL AO AR AU AX Aa Ad Ag Aj Am Ap As Av Ay B B3 BA BD BG BJ BM BP BS BV BY Bb Be Bh Bk Bn Bq Bt Bw Bz E H K N Q T W Z c f i l o r u x | No description available
2 5 8 A3 A6 A9 AA AD AG AJ AM AP AS AV AY Ab Ae Ah Ak An Aq At Aw Az B1 B4 BB BE BH BK BN BQ BT BW BZ Bc Bf Bi Bl Bo Br Bu Bx C F I L O R U X a d g j m p s v y | No description available
3 6 9 A A0 A1 A4 A7 AB AE AH AK AN AQ AT AW AZ Ac Af Ai Al Ao Ar Au Ax B2 BC BF BI BL BO BR BU BX Ba Bd Bg Bj Bm Bp Bs Bv By D G J M P S V Y b e h k n q t w z | No description available
> ui tool show "Side View"
> select add #2
727740 atoms, 748380 bonds, 98700 residues, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> show sel cartoons
> select subtract #2
Nothing selected
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui tool show "Map Coordinates"
> close #1
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> open "/Users/guynovoa/Desktop/RHDV 2024/Mapas/RHDVv_Llenas.mrc" format mrc
Opened RHDVv_Llenas.mrc as #1, grid size 330,330,330, pixel 1.42, shown at
level 0.86, step 2, values float32
> ui mousemode right translate
> volume #1 step 1
> color #1 #b2b2b280 models
> volume #1 level 0.6
> view orient
> hide #2 models
> color #1 #b2b2b2b6 models
> color #1 #b2b2b200 models
> color #1 #b2b2b2ff models
> view orient
> volume #1 level 0.5
> volume #1 level 0.4
> volume #1 level 0.3
> volume #1 level 0.25
> view orient
[Repeated 4 time(s)]
> ui mousemode right zoom
> open "/Users/guynovoa/Desktop/RHDV 2024/Mapas/RHDVv_Llenas_sharp.mrc"
Opened RHDVv_Llenas_sharp.mrc as #3, grid size 330,330,330, pixel 1.42, shown
at level 2.02, step 2, values float32
> show #2 models
> volume #1-3 transparency 0.5
> hide #!3 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> volume #3 step 1
> hide #!1 models
> show #!3 models
> volume #3 color silver
> volume #3 color #c0c0c080
> show #2 models
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> view orient
> hide #2 models
> show #!1 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!3 models
> hide #2 models
> volume #1 level 0.1
> volume #1 level 0.15
> volume #1 level 0.18
> volume #1 level 0.19
> volume #1 level 0.2
> volume #1 level 0.22
> ui mousemode right "mark point"
> marker #4 position 225.6,227.3,45.57 color yellow radius 1
> marker change #4 radius 100
> marker change #4 radius 120
> marker change #4 radius 140
> ui mousemode right zoom
> turn y 90
> ui mousemode right "move markers"
> marker change #4:1 position 225.6,223.2,222.3
> marker change #4 radius 120
> marker change #4 radius 110
> view orient
> ui mousemode right zoom
> ui mousemode right "move markers"
> marker change #4:1 position 226.2,226.3,222.3
> turn y 90
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right "move markers"
> ui mousemode right "resize markers"
> ui mousemode right "move markers"
> view orient
> ui mousemode right zoom
> turn y 90
> ui mousemode right "move markers"
> marker change #4:1 position 226.2,226.1,224.5
> marker change #4:1 position 226.2,225.1,226
> marker change #4 radius 114
> marker change #4 radius 112
> marker change #4 radius 111
> turn y 90
[Repeated 2 time(s)]
> turn x 90
[Repeated 2 time(s)]
> ui tool show "Map Eraser"
> select subtract #4
Nothing selected
> hide #4 models
> show #4 models
> hide #4 models
> hide #!1 models
> show #4 models
> hide #4 models
> show #4 models
> show #!1 models
> volume erase #1 center 226.05,226.05,226.05 radius 110.99 outside true
Opened RHDVv_Llenas.mrc copy as #6, grid size 330,330,330, pixel 1.37, shown
at step 1, values float32
> hide #4 models
> hide #5 models
> show #!3 models
> volume #6 level 0.1783
> volume #3 level 1.462
> view orient
> volume #3 level 1.6
> ui mousemode right zoom
> show #!6 models
> hide #!6 models
> show #!6 models
> ui tool show "Side View"
> volume #6 level 0.1857
> volume #6 level 0.1947
> show #2 models
> ui mousemode right translate
> ui mousemode right rotate
> volume #3 level 1.3
> volume #3 level 1.2
> volume #3 level 1.1
> volume #3 level 0.6
> volume #3 level 0.7
> ui mousemode right zoom
> ui mousemode right translate
> volume #3 level 0.6
> ui mousemode right rotate
> ui tool show "Hide Dust"
> surface dust #3 size 8.22
> volume #3 level 0.5
> volume #3 level 0.4
> volume #3 level 0.45
> volume #3 level 0.44
> volume #3 level 0.42
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> select #2/AV:19
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/K:20
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #3
4 models selected
> select clear
[Repeated 1 time(s)]
> save /Users/guynovoa/Desktop/13Ene/DetalleNTA_BC.cxs includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 922, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 651, in save
fserialize(stream, data)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 147, in write
self._f.write(buf)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 741, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
Out of disk space
Cannot save '/Users/guynovoa/Desktop/13Ene/DetalleNTA_BC.cxs': [Errno 28] No
space left on device
> save /Users/guynovoa/Desktop/13Ene/NTA.cxs includeMaps true
——— End of log from Mon Jan 13 16:03:47 2025 ———
opened ChimeraX session
> hide #2 models
> show #2 models
> hide #!3 models
> show #!3 models
> save /media/data5/RHDV/13Ene/RHDVv_Llenas_sharp_en0.ccp4 models #3
> hide #!3 models
> hide #2 models
> show #2 models
> select #2/A,B,C
12129 atoms, 12473 bonds, 1645 residues, 1 model selected
> ui mousemode right zoom
> save /media/data5/RHDV/13Ene/Trimero_Llenas_30Dic_toFixNt.pdb models #2
> selectedOnly true
> open /media/data5/RHDV/13Ene/Trimero_Llenas_30Dic_sin_19C.pdb
Summary of feedback from opening
/media/data5/RHDV/13Ene/Trimero_Llenas_30Dic_sin_19C.pdb
---
warnings | Start residue of secondary structure not found: HELIX 18 18 THR D 52 GLY D 56 1 5
Start residue of secondary structure not found: HELIX 19 19 LEU D 106 MET D
109 1 4
Start residue of secondary structure not found: HELIX 20 20 THR D 245 VAL D
247 1 3
Start residue of secondary structure not found: HELIX 21 21 LEU D 492 LEU D
500 1 9
Start residue of secondary structure not found: HELIX 22 22 ALA E 43 VAL E 50
1 8
329 messages similar to the above omitted
End residue of secondary structure not found: HELIX 362 362 ALA C 43 VAL C 50
1 8
Start residue of secondary structure not found: HELIX 369 369 ALA D 43 GLY D
56 1 14
Start residue of secondary structure not found: HELIX 370 370 LEU D 106 GLN D
108 1 3
Start residue of secondary structure not found: HELIX 371 371 VAL D 150 GLN D
152 1 3
Start residue of secondary structure not found: HELIX 372 372 VAL D 234 ILE D
237 1 4
Start residue of secondary structure not found: HELIX 373 373 PRO D 246 LEU D
248 1 3
328 messages similar to the above omitted
End residue of secondary structure not found: HELIX 702 702 ALA A 43 VAL A 50
1 8
Start residue of secondary structure not found: HELIX 719 719 ALA D 43 VAL D
50 1 8
Start residue of secondary structure not found: HELIX 720 720 THR D 52 GLY D
56 1 5
Start residue of secondary structure not found: HELIX 721 721 PRO D 97 ASN D
99 1 3
Start residue of secondary structure not found: HELIX 722 722 PRO D 101 GLN D
108 1 8
Start residue of secondary structure not found: HELIX 723 723 VAL D 150 GLN D
152 1 3
Start residue of secondary structure not found: HELIX 724 724 PRO D 440 ARG D
442 1 3
1217 messages similar to the above omitted
PDB SEQRES record for chain B is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for Trimero_Llenas_30Dic_sin_19C.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #2 models
> hide #5 models
> show #5 models
> ui tool show "Side View"
> select #5/A
4002 atoms, 4116 bonds, 542 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dodger blue
> select #5/B
4059 atoms, 4174 bonds, 551 residues, 1 model selected
> color sel red
> select #5/C
4061 atoms, 4176 bonds, 551 residues, 1 model selected
> color sel forest green
> select add #5
12122 atoms, 12466 bonds, 1644 residues, 1 model selected
> select subtract #5
Nothing selected
> select #5:206-216
249 atoms, 246 bonds, 33 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 2
Assigning ss_type attribute to 33 items
> select clear
> select #5/B:206
7 atoms, 6 bonds, 1 residue, 1 model selected
> setattr sel r ss_type 0
Assigning ss_type attribute to 1 item
> select #5:75-81
183 atoms, 189 bonds, 21 residues, 1 model selected
> setattr sel r ss_type 2
Assigning ss_type attribute to 21 items
> select #5:118-124
186 atoms, 189 bonds, 21 residues, 1 model selected
> setattr sel r ss_type 2
Assigning ss_type attribute to 21 items
> select clear
> select #5:187-193
150 atoms, 150 bonds, 21 residues, 1 model selected
> setattr sel r ss_type 2
Assigning ss_type attribute to 21 items
> select #5:134-139
117 atoms, 117 bonds, 18 residues, 1 model selected
> setattr sel r ss_type 2
Assigning ss_type attribute to 18 items
> select clear
> select #5:154-159
141 atoms, 144 bonds, 18 residues, 1 model selected
> setattr sel r ss_type 2
Assigning ss_type attribute to 18 items
> select #5:154
21 atoms, 21 bonds, 3 residues, 1 model selected
> setattr sel r ss_type 0
Assigning ss_type attribute to 3 items
> select clear
> select #5:44
27 atoms, 24 bonds, 3 residues, 1 model selected
> select #5/A:44
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:43-44
14 atoms, 13 bonds, 2 residues, 1 model selected
> setattr sel r ss_type 0
Assigning ss_type attribute to 2 items
> select clear
> select #5/B:132-134
26 atoms, 25 bonds, 3 residues, 1 model selected
> select #5:132-134
78 atoms, 75 bonds, 9 residues, 1 model selected
> setattr sel r ss_type 2
Assigning ss_type attribute to 9 items
> select clear
> select #5:79
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #5:194
21 atoms, 18 bonds, 3 residues, 1 model selected
> setattr sel r ss_type 2
Assigning ss_type attribute to 3 items
> select clear
> select #5:88-94
171 atoms, 171 bonds, 21 residues, 1 model selected
> setattr sel r ss_type 2
Assigning ss_type attribute to 21 items
> select #5:88-89
42 atoms, 39 bonds, 6 residues, 1 model selected
> setattr sel r ss_type 0
Assigning ss_type attribute to 6 items
> select clear
> view orient
> show #!3 models
> volume #1 level 0.3
> volume #1 level 0.4
> volume #3 level 0.49
> volume #3 level 0.6
> volume #3 level 0.9
> volume #3 level 1.3
> view orient
> ui mousemode right translate
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> open /home/virus/Downloads/cryosparc_P12_J11_008_volume_map.mrc
Opened cryosparc_P12_J11_008_volume_map.mrc as #7, grid size 330,330,330,
pixel 1.42, shown at level 0.862, step 2, values float32
> volume #7 step 1
> ui tool show "Map Coordinates"
> hide #!6 models
> volume #7 level 0.8
> volume #7 level 2
> volume #7 level 0.4
> volume #7 level 0.3
> volume #7 transparency 0.1
> show #4 models
> ui mousemode right zoom
> ui mousemode right translate
> volume #6 level 0.3
> hide #!6 models
> show #!6 models
> hide #5 models
> show #5 models
> hide #4 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> hide #!7 models
> volume #3 level 1
> volume #3 level 0.9
> sym #5 i,222r center 226.05,226.05,226.05
Made 60 graphical clones for Trimero_Llenas_30Dic_sin_19C.pdb symmetry i,222r
> ui mousemode right zoom
> ui tool show "Map Statistics"
> measure mapstats #!3,6
Map RHDVv_Llenas_sharp_en0.ccp4 #3, minimum -3.194, maximum 6.785, mean
0.08037, SD 0.4344, RMS 0.4418
Map RHDVv_Llenas.mrc copy #6, minimum -0.01633, maximum 0.3866, mean 0.01688,
SD 0.06725, RMS 0.06934
> hide #!3 models
> show #!3 models
> select add #3
4 models selected
> select subtract #3
Nothing selected
> select add #6
4 models selected
> select subtract #6
Nothing selected
> volume #6 level 0.2
> ui tool show "Map Statistics"
> measure mapstats #!3,6
Map RHDVv_Llenas_sharp_en0.ccp4 #3, minimum -3.194, maximum 6.785, mean
0.08037, SD 0.4344, RMS 0.4418
Map RHDVv_Llenas.mrc copy #6, minimum -0.01633, maximum 0.3866, mean 0.01688,
SD 0.06725, RMS 0.06934
> volume #6 level 0.4
> volume #6 level 0.3132
> volume #6 level 0.2
> save /media/data5/RHDV/13Ene/NTA_14Ene.cxs includeMaps true
——— End of log from Tue Jan 14 16:48:39 2025 ———
opened ChimeraX session
> ui mousemode right zoom
> hide #!3 models
> ui mousemode right rotate
> ui tool show "Side View"
> sym clear
> sym #5 i,222r center 226.05,226.05,226.05 newModel true copies true
Made 60 copies for Trimero_Llenas_30Dic_sin_19C.pdb symmetry i,222r
> select #8.1
12122 atoms, 12466 bonds, 1644 residues, 1 model selected
> ui mousemode right zoom
> ui mousemode right translate
> select #8.1, 8.10/B
Nothing selected
> select #8.1, 8.10
Nothing selected
> select #8.1,8.10
Nothing selected
> select #8.1,8.10/B, 8.45/C, 8.51/B
Expected an objects specifier or a keyword
> select #8.1,8.10/B, 8.45/C, 8.51/B, 8.4/C
Expected an objects specifier or a keyword
> select #8.1,8.10/B, 8.45/C, 8.51/B, 8.4/C, 8.30/B
Expected an objects specifier or a keyword
> select #8.1,8.10/B, 8.45/C, 8.51/B, 8.4/C, 8.30/B, 8.10/A
Expected an objects specifier or a keyword
> select #8.1,8.10/B, 8.45/C, 8.51/B, 8.4/C, 8.30/B, 8.10/A, 8.6/A, 8.26/A,
> 8.47/A
Expected an objects specifier or a keyword
> select #8.1 #8.10/B, 8.45/C, 8.51/B, 8.4/C, 8.30/B, 8.10/A, 8.6/A, 8.26/A,
> 8.47/A
Expected a keyword
> select #8.1 #8.10/B, 8.45/C, 8.51/B, 8.4/C, 8.30/B, 8.10/A, 8.6/A, 8.26/A,
> 8.47/A
Expected a keyword
> select #8.1 #8.10/B, 8.45/C, 8.51/B, 8.4/C, 8.30/B, 8.10/A, 8.6/A, 8.26/A,
> 8.47/A
Expected a keyword
> select #8.1 #8.10/B
16181 atoms, 16640 bonds, 2195 residues, 2 models selected
> select #8.1 #8.10/B #8.45/C #8.51/B #8.4/C #8.30/B #8.10/A #8.6/A #8.26/A
> #8.47/A
48429 atoms, 49804 bonds, 6567 residues, 9 models selected
> select ~sel & ##selected
60669 atoms, 62390 bonds, 8229 residues, 8 models selected
> select ~sel
1406514 atoms, 1446416 bonds, 190756 residues, 74 models selected
> select subtract #1
1406514 atoms, 1446416 bonds, 190756 residues, 72 models selected
> select subtract #2
678774 atoms, 698036 bonds, 92056 residues, 71 models selected
> select subtract #3
678774 atoms, 698036 bonds, 92056 residues, 69 models selected
> select subtract #4
678773 atoms, 698036 bonds, 92055 residues, 68 models selected
> select subtract #5
666651 atoms, 685570 bonds, 90411 residues, 67 models selected
> select subtract #6
666651 atoms, 685570 bonds, 90411 residues, 63 models selected
> select subtract #7
666651 atoms, 685570 bonds, 90411 residues, 61 models selected
> delete atoms sel
> delete bonds sel
> sym clear
> show #5 models
> close #8
> sym #5 i,222r center 226.05,226.05,226.05 newModel true copies true
Made 60 copies for Trimero_Llenas_30Dic_sin_19C.pdb symmetry i,222r
> select #8.1 #8.10/B #8.45/C #8.51/B #8.4/C #8.30/B #8.10/A #8.6/A #8.26/A
> #8.47/A
48429 atoms, 49804 bonds, 6567 residues, 9 models selected
> select ~sel
1418754 atoms, 1459002 bonds, 192418 residues, 73 models selected
> select subtract #1
1418754 atoms, 1459002 bonds, 192418 residues, 71 models selected
> select subtract #2
691014 atoms, 710622 bonds, 93718 residues, 70 models selected
> select subtract #3
691014 atoms, 710622 bonds, 93718 residues, 68 models selected
> select subtract #4
691013 atoms, 710622 bonds, 93717 residues, 67 models selected
> select subtract #5
678891 atoms, 698156 bonds, 92073 residues, 66 models selected
> select subtract #6
678891 atoms, 698156 bonds, 92073 residues, 62 models selected
> select subtract #7
678891 atoms, 698156 bonds, 92073 residues, 60 models selected
> delete atoms sel
> delete bonds sel
> save /Users/guynovoa/Desktop/NTA_15Ene.cxs includeMaps true
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right zoom
> select #8.1/B
4059 atoms, 4174 bonds, 551 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!6 models
> ui mousemode right select
Drag select of 94 residues
> select up
2060 atoms, 2101 bonds, 279 residues, 5 models selected
> select up
20010 atoms, 20580 bonds, 2710 residues, 5 models selected
> delete atoms sel
> delete bonds sel
> show #!6 models
> select #8:40-999
23592 atoms, 24270 bonds, 3186 residues, 6 models selected
> select #8:45-999
23382 atoms, 24060 bonds, 3156 residues, 6 models selected
> delete atoms sel
> delete bonds sel
> select #8:40-45
210 atoms, 204 bonds, 30 residues, 6 models selected
> delete atoms sel
> delete bonds sel
> select #8:20-21
66 atoms, 60 bonds, 12 residues, 6 models selected
> show sel atoms
> select clear
> show #!3 models
> show #!7 models
> ui mousemode right translate
> ui mousemode right zoom
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> show #!6 models
> open /Users/guynovoa/Downloads/Llenas_9cp_domS_B.pdb format pdb
Summary of feedback from opening
/Users/guynovoa/Downloads/Llenas_9cp_domS_B.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 52 GLY A 56 1 5
Start residue of secondary structure not found: HELIX 2 2 LEU A 106 MET A 109
1 4
Start residue of secondary structure not found: HELIX 8 8 ALA C 43 GLY C 56 1
14
Start residue of secondary structure not found: HELIX 9 9 LEU C 106 GLN C 108
1 3
Start residue of secondary structure not found: HELIX 10 10 VAL C 150 GLN C
152 1 3
20 messages similar to the above omitted
Chain information for Llenas_9cp_domS_B.pdb #9
---
Chain | Description
B | No description available
> select #9/B:48@CA
1 atom, 1 residue, 1 model selected
> select ~sel & ##selected
1570 atoms, 1615 bonds, 210 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #9
1 atom, 1 residue, 1 model selected
> select subtract #9
Nothing selected
> select add #9
1 atom, 1 residue, 1 model selected
> select #9/B:48@CA
1 atom, 1 residue, 1 model selected
> close #9
> select #8:33-45
258 atoms, 252 bonds, 42 residues, 6 models selected
> delete atoms sel
> delete bonds sel
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right rotate
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> graphics silhouettes true
> open /Users/guynovoa/Downloads/Llenas_9cp_domS_B.pdb format pdb
Summary of feedback from opening
/Users/guynovoa/Downloads/Llenas_9cp_domS_B.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 52 GLY A 56 1 5
Start residue of secondary structure not found: HELIX 2 2 LEU A 106 MET A 109
1 4
Start residue of secondary structure not found: HELIX 8 8 ALA C 43 GLY C 56 1
14
Start residue of secondary structure not found: HELIX 9 9 LEU C 106 GLN C 108
1 3
Start residue of secondary structure not found: HELIX 10 10 VAL C 150 GLN C
152 1 3
20 messages similar to the above omitted
Chain information for Llenas_9cp_domS_B.pdb #9
---
Chain | Description
B | No description available
> select add #9
1571 atoms, 1615 bonds, 210 residues, 1 model selected
> select #9/B:48
5 atoms, 4 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
1566 atoms, 1611 bonds, 209 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #9/B:48
5 atoms, 4 bonds, 1 residue, 1 model selected
> select subtract #9
Nothing selected
> color #9 black
> close #9
> open /Users/guynovoa/Downloads/Llenas_9cp_domS_B.pdb format pdb
Summary of feedback from opening
/Users/guynovoa/Downloads/Llenas_9cp_domS_B.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A 52 GLY A 56 1 5
Start residue of secondary structure not found: HELIX 2 2 LEU A 106 MET A 109
1 4
Start residue of secondary structure not found: HELIX 8 8 ALA C 43 GLY C 56 1
14
Start residue of secondary structure not found: HELIX 9 9 LEU C 106 GLN C 108
1 3
Start residue of secondary structure not found: HELIX 10 10 VAL C 150 GLN C
152 1 3
20 messages similar to the above omitted
Chain information for Llenas_9cp_domS_B.pdb #9
---
Chain | Description
B | No description available
> select #9/B:48-49
11 atoms, 10 bonds, 2 residues, 1 model selected
> select ~sel & ##selected
1560 atoms, 1605 bonds, 208 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #9
11 atoms, 10 bonds, 2 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,-15.851,0,1,0,8.1329,0,0,1,-14.973
> view matrix models #9,1,0,0,-30.875,0,1,0,12.885,0,0,1,-28.191
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,-27.807,0,1,0,10.574,0,0,1,-38.116
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models #9,1,0,0,-28.879,0,1,0,8.0447,0,0,1,-39.102
> ui mousemode right select
> select clear
> select #9/B:49
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #9/B:48@C
1 atom, 1 residue, 1 model selected
> select ~sel & ##selected
10 atoms, 10 bonds, 2 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> select #9/B:48@C
1 atom, 1 residue, 1 model selected
> select #9/B:49
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #9/B:48@CA
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #9/B:48@CB
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!6 models
> select #9/B:48@N
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!6 models
> color #9 black
> ui mousemode right "translate selected models"
> select add #9
8 atoms, 7 bonds, 2 residues, 1 model selected
> view matrix models #9,1,0,0,-30.074,0,1,0,6.2681,0,0,1,-39.204
> view matrix models #9,1,0,0,-28.506,0,1,0,5.8282,0,0,1,-38.231
> view matrix models #9,1,0,0,-29.184,0,1,0,6.7784,0,0,1,-38.023
> view matrix models #9,1,0,0,-29.234,0,1,0,6.8071,0,0,1,-38.009
> view matrix models #9,1,0,0,-29.193,0,1,0,6.701,0,0,1,-37.634
> select subtract #9
Nothing selected
> select #9/B:48@CA
Nothing selected
> select #9/B:48@O
1 atom, 1 residue, 1 model selected
> ui tool show Distances
Exactly two atoms must be selected!
> select #9/B:48@O #8.45/C:20@C
2 atoms, 2 residues, 2 models selected
> distance #9/B:48@O #8.45/C:20@C
Distance between Llenas_9cp_domS_B.pdb #9/B ALA 48 O and
Trimero_Llenas_30Dic_sin_19C.pdb #8.45/C ALA 20 C: 8.338Å
> distance style color black
[Repeated 2 time(s)]
> select add #9
9 atoms, 7 bonds, 3 residues, 2 models selected
> select subtract #9
1 atom, 1 residue, 1 model selected
> select add #8
510 atoms, 516 bonds, 78 residues, 7 models selected
> select subtract #8
Nothing selected
> select add #9
8 atoms, 7 bonds, 2 residues, 1 model selected
> view matrix models #9,1,0,0,-28.671,0,1,0,7.081,0,0,1,-36.613
> select #9/B:48@O #8.45/C:20@CB
2 atoms, 2 residues, 2 models selected
> distance #8.45/C:20@CB #9/B:48@O
Distance between Trimero_Llenas_30Dic_sin_19C.pdb #8.45/C ALA 20 CB and
Llenas_9cp_domS_B.pdb #9/B ALA 48 O: 6.122Å
> ~distance #9/B:48@O #8.45/C:20@C
> ~distance #8.45/C:20@CB #9/B:48@O
> select #9/B:48@O #8.45/C:20@N
2 atoms, 2 residues, 2 models selected
> distance #8.45/C:20@N #9/B:48@O
Distance between Trimero_Llenas_30Dic_sin_19C.pdb #8.45/C ALA 20 N and
Llenas_9cp_domS_B.pdb #9/B ALA 48 O: 6.405Å
> ui mousemode right translate
> select add #8
511 atoms, 516 bonds, 79 residues, 8 models selected
> select add #9
518 atoms, 523 bonds, 80 residues, 8 models selected
> select subtract #9
510 atoms, 516 bonds, 78 residues, 7 models selected
> select subtract #8
Nothing selected
> save /Users/guynovoa/Desktop/Atomo.pdb models #9
> open /Users/guynovoa/Desktop/Atomo.pdb
Chain information for Atomo.pdb #11
---
Chain | Description
B | No description available
> select add #11
8 atoms, 7 bonds, 2 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,-6.0435,0,1,0,2.4805,0,0,1,-14.219
> view matrix models #11,1,0,0,11.942,0,1,0,-3.8264,0,0,1,-2.2726
> view matrix models #11,1,0,0,-0.39949,0,1,0,3.7583,0,0,1,12.197
> view matrix models #11,1,0,0,-1.969,0,1,0,4.6458,0,0,1,13.247
> view matrix models #11,1,0,0,6.1481,0,1,0,-0.034614,0,0,1,5.6021
> view matrix models #11,1,0,0,6.0819,0,1,0,-0.011205,0,0,1,3.8511
> view matrix models #11,1,0,0,4.4515,0,1,0,-3.4844,0,0,1,4.2603
> open /Users/guynovoa/Desktop/Atomo.pdb
Chain information for Atomo.pdb #12
---
Chain | Description
B | No description available
> select subtract #11
Nothing selected
> select add #12
8 atoms, 7 bonds, 2 residues, 1 model selected
> view matrix models #12,1,0,0,-11.223,0,1,0,5.9478,0,0,1,-1.2931
> view matrix models #12,1,0,0,-18.615,0,1,0,8.8062,0,0,1,-2.2358
> view matrix models #12,1,0,0,-16.27,0,1,0,6.6649,0,0,1,-6.798
> view matrix models #12,1,0,0,-17.264,0,1,0,6.0982,0,0,1,-9.8934
> ui mousemode right translate
> select subtract #12
Nothing selected
> select add #12
8 atoms, 7 bonds, 2 residues, 1 model selected
> select subtract #12
Nothing selected
> select #11/B:49#OG
Expected an objects specifier or a keyword
> select #11/B:49@OG
1 atom, 1 residue, 1 model selected
> select ~sel & ##selected
7 atoms, 7 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> color #11 black
> select #11/B:49@OG
1 atom, 1 residue, 1 model selected
> select #11/B:49@OG #8.10/B:20@N
2 atoms, 2 residues, 2 models selected
> distance #11/B:49@OG #8.10/B:20@N
Distance between Atomo.pdb #11/B SER 49 OG and
Trimero_Llenas_30Dic_sin_19C.pdb #8.10/B ALA 20 N: 13.698Å
> ~distance #11/B:49@OG #8.10/B:20@N
> select #11/B:49@OG #8.10/B:30@N
2 atoms, 2 residues, 2 models selected
> distance #8.10/B:30@N #11/B:49@OG
Distance between Trimero_Llenas_30Dic_sin_19C.pdb #8.10/B MET 30 N and
Atomo.pdb #11/B SER 49 OG: 16.698Å
> select #12/B:49@OG
1 atom, 1 residue, 1 model selected
> select ~sel & ##selected
7 atoms, 7 bonds, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> color #12 black
> save /Users/guynovoa/Desktop/Atomo.pdb models #12
> hide #!6 models
> select add #12
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #12,1,0,0,-16.884,0,1,0,6.9536,0,0,1,-9.8838
> show #!6 models
> view matrix models #12,1,0,0,-19.65,0,1,0,6.4844,0,0,1,-11.894
> select #12/B:49@OG 8.51/B:20@N
Expected a keyword
> select #12/B:49@OG #8.51/B:20@N
2 atoms, 2 residues, 2 models selected
> distance #12/B:49@OG #8.51/B:20@N
Distance between Atomo.pdb #12/B SER 49 OG and
Trimero_Llenas_30Dic_sin_19C.pdb #8.51/B ALA 20 N: 8.028Å
> open /Users/guynovoa/Desktop/Atomo.pdb
> color #13 black
> select add #13
3 atoms, 3 residues, 3 models selected
> select subtract #12
2 atoms, 2 residues, 2 models selected
> select add #8
511 atoms, 516 bonds, 79 residues, 8 models selected
> select subtract #8
1 atom, 1 residue, 1 model selected
> view matrix models #13,1,0,0,11.943,0,1,0,-5.7096,0,0,1,-5.6807
> view matrix models #13,1,0,0,11.089,0,1,0,-6.7264,0,0,1,-5.981
> select #13/B:49@OG #8.45/C:20@N
2 atoms, 2 residues, 2 models selected
> select #13/B:49@OG #8.45/C:30@N
2 atoms, 2 residues, 2 models selected
> distance #8.45/C:30@N #13/B:49@OG
Distance between Trimero_Llenas_30Dic_sin_19C.pdb #8.45/C MET 30 N and
Atomo.pdb #13/B SER 49 OG: 17.495Å
> ui mousemode right select
> select clear
> save /Users/guynovoa/Desktop/NTA_15Ene-v2.cxs includeMaps true
——— End of log from Wed Jan 15 09:26:31 2025 ———
> view name session-start
opened ChimeraX session
> close #2,4-5,8-13#1,3,6-7
> open
> /Users/guynovoa/Documents/DepositoRHDV/Llenas/cryosparc_P12_J11_008_volume_map_en1-37.mrc
Opened cryosparc_P12_J11_008_volume_map_en1-37.mrc as #1, grid size
330,330,330, pixel 1.37, shown at level 0.862, step 2, values float32
> open
> /Users/guynovoa/Documents/DepositoRHDV/Llenas/cryosparc_P12_J11_008_volume_map_sharp_en1-37.mrc
Opened cryosparc_P12_J11_008_volume_map_sharp_en1-37.mrc as #2, grid size
330,330,330, pixel 1.37, shown at level 1.97, step 2, values float32
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> volume #1 step 1
> volume #2 step 1
> ui tool show "Surface Color"
> open /Users/guynovoa/Documents/DepositoRHDV/Llenas/D_1292144900_model_P1.cif
Summary of feedback from opening
/Users/guynovoa/Documents/DepositoRHDV/Llenas/D_1292144900_model_P1.cif
---
warning | Missing or incorrect sequence information. Inferred polymer connectivity.
D_1292144900_model_P1.cif title:
CP of empty RHDV virion [more info...]
Chain information for D_1292144900_model_P1.cif #3
---
Chain | Description
A | Capsid protein (A)
B | Capsid protein (B)
C | Capsid protein (C)
D_1292144900_model_P1.cif mmCIF Assemblies
---
1| author_defined_assembly
> view orient
> sym #3 assembly 1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 316, in interceptRequest
self._callback(info)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept
return interceptor(request_info, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/log/tool.py", line 222, in link_intercept
chimerax_intercept(request_info, *args, session=self.session, view=self, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 455, in chimerax_intercept
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 479, in thread_safe
func(*args, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 442, in defer
cxcmd(session, topic)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 464, in cxcmd
run(session, cmd)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/sym.py", line 122, in sym
assem = pdb_assemblies(m)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/sym.py", line 251, in pdb_assemblies
m.assemblies = alist = mmcif_assemblies(m)
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/sym.py", line 282, in mmcif_assemblies
alist = [Assembly(id, name[id], chain_ops[id], ops, True) for id in ids]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/sym.py", line 282, in <listcomp>
alist = [Assembly(id, name[id], chain_ops[id], ops, True) for id in ids]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/sym.py", line 363, in __init__
ops = operator_products(products, operator_table)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/sym.py", line 562, in operator_products
p = Places(tuple(oper_table[e] for e in products[0]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/sym.py", line 562, in <genexpr>
p = Places(tuple(oper_table[e] for e in products[0]))
~~~~~~~~~~^^^
KeyError: '?'
KeyError: '?'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/sym.py", line 562, in
p = Places(tuple(oper_table[e] for e in products[0]))
~~~~~~~~~~^^^
See log for complete Python traceback.
> hide #!2 models
> save /Users/guynovoa/Desktop/PlosPathogens2025/Trimero_Llenas.pdb
> open /Users/guynovoa/Desktop/PlosPathogens2025/Trimero_Llenas.pdb
Chain information for Trimero_Llenas.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select #4/A
4002 atoms, 4116 bonds, 2 pseudobonds, 542 residues, 2 models selected
> color sel red
> hide #!1 models
> ui mousemode right zoom
> ui mousemode right translate
> show #!1 models
> select #4/C
4061 atoms, 4176 bonds, 551 residues, 1 model selected
> color sel dodgerblue
> select #4/B
4060 atoms, 4177 bonds, 1 pseudobond, 551 residues, 2 models selected
> color sel forest green
> sym #4 i,222r center 226.05,226.05,226.05 newModel true copies true
Made 60 copies for Trimero_Llenas.pdb symmetry i,222r
> view orient
[Repeated 1 time(s)]
> hide #!5 models
> show #!4 models
> select #4/A
4002 atoms, 4116 bonds, 2 pseudobonds, 542 residues, 2 models selected
> color sel dodgerblue
> select #4/C
4061 atoms, 4176 bonds, 551 residues, 1 model selected
> color sel forest green
> select #4/B
4060 atoms, 4177 bonds, 1 pseudobond, 551 residues, 2 models selected
> color sel red
> close #5
> sym #4 i,222r center 226.05,226.05,226.05 newModel true copies true
Made 60 copies for Trimero_Llenas.pdb symmetry i,222r
> view orient
> ui mousemode right zoom
> hide #!1 models
> hide #3 models
> select add #4
12123 atoms, 12470 bonds, 3 pseudobonds, 1644 residues, 3 models selected
> select subtract #4
Nothing selected
> show #!1 models
> color #1 white models
> color #1 #ffffff7f models
> color #1 #ffffff22 models
> color #1 #ffffff1a models
> clip near 10
> ui tool show "Side View"
> view orient
> clip near -10
> clip far 10
> color #1 silver models
> show #!2 models
> hide #!2 models
> volume #1 level 0.3088
> ui mousemode right translate
> ui mousemode right rotate
> volume #1 level 0.2
> volume #1 level 0.1
> volume #1 level 0.12
> volume #1 level 0.13
> volume #1 level 0.127
> clip near 10
> clip near -15
> volume #1 level 0.2143
> open /Users/guynovoa/Downloads/Trimero_Llenas_30Dic_sin_19C-coot-0.pdb
Chain information for Trimero_Llenas_30Dic_sin_19C-coot-0.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select #6/A:30-571
4002 atoms, 4116 bonds, 542 residues, 1 model selected
> color sel dodgerblue
> select #6/B:20-570
4059 atoms, 4174 bonds, 551 residues, 1 model selected
> color sel red
> select #6/C:20-570
4061 atoms, 4176 bonds, 551 residues, 1 model selected
> color sel forest green
> hide #!5 models
> sym #6 i,222r center 226.05,226.05,226.05 newModel true copies true
Made 60 copies for Trimero_Llenas_30Dic_sin_19C-coot-0.pdb symmetry i,222r
> ui mousemode right zoom
> clip near 5
> clip near -5
[Repeated 1 time(s)]
> select #7.37/C
4061 atoms, 4176 bonds, 551 residues, 1 model selected
> select #7.37/C #7.4/B
8120 atoms, 8350 bonds, 1102 residues, 2 models selected
> select #7.37/C #7.4/B #7.51/C
12181 atoms, 12526 bonds, 1653 residues, 3 models selected
> select #7.37/C #7.4/B #7.51/C #7.24/B
16240 atoms, 16700 bonds, 2204 residues, 4 models selected
> clip far -10
> clip far 15
> clip far 5
> select #7.37/C #7.4/B #7.51/C #7.24/B #7.28/C
20301 atoms, 20876 bonds, 2755 residues, 5 models selected
> select #7.37/C #7.4/B #7.51/C #7.24/B #7.28/C #7.57/B
24360 atoms, 25050 bonds, 3306 residues, 6 models selected
> select ~sel
1466708 atoms, 1508520 bonds, 183 pseudobonds, 198906 residues, 253 models
selected
> select subtract #1
1466708 atoms, 1508520 bonds, 183 pseudobonds, 198906 residues, 249 models
selected
> select subtract #2
1466708 atoms, 1508520 bonds, 183 pseudobonds, 198906 residues, 247 models
selected
> select subtract #3
1454585 atoms, 1496046 bonds, 183 pseudobonds, 197262 residues, 246 models
selected
> select subtract #4
1442462 atoms, 1483576 bonds, 180 pseudobonds, 195618 residues, 243 models
selected
> select subtract #5
715082 atoms, 735376 bonds, 96978 residues, 62 models selected
> select subtract #6
702960 atoms, 722910 bonds, 95334 residues, 61 models selected
> delete atoms sel
> delete bonds sel
> show #6 models
> hide #6 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> delete atoms #1
> delete bonds #1
> show #6 models
> hide #6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> combine #7-8
Remapping chain ID 'B' in Trimero_Llenas_30Dic_sin_19C-coot-0.pdb #7.24 to 'C'
Remapping chain ID 'C' in Trimero_Llenas_30Dic_sin_19C-coot-0.pdb #7.28 to 'D'
Remapping chain ID 'C' in Trimero_Llenas_30Dic_sin_19C-coot-0.pdb #7.37 to 'E'
Remapping chain ID 'C' in Trimero_Llenas_30Dic_sin_19C-coot-0.pdb #7.51 to 'F'
Remapping chain ID 'B' in Trimero_Llenas_30Dic_sin_19C-coot-0.pdb #7.57 to 'G'
> hide #!7 models
> hide #7.4 models
> hide #7.24 models
> hide #7.37 models
> hide #7.28 models
> hide #7.51 models
> hide #7.57 models
> save /Users/guynovoa/Desktop/PlosPathogens2025/HexameroCterminal.pdb models
> #8
> open /Users/guynovoa/Desktop/PlosPathogens2025/HexameroCterminal-coot-0.pdb
Chain information for HexameroCterminal-coot-0.pdb #9
---
Chain | Description
B C G | No description available
D E F | No description available
> select #9
24360 atoms, 25050 bonds, 3306 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> hide #8 models
> select #9/C,E
8120 atoms, 8350 bonds, 1102 residues, 1 model selected
> hide #!1 models
> view orient
> save /Users/guynovoa/Desktop/PlosPathogens2025/9c-oseac-ye-oseab.pdb models
> #9 selectedOnly true
> show #6 models
> open /Users/guynovoa/Desktop/PlosPathogens2025/9c-oseac-ye-oseab.pdb
Summary of feedback from opening
/Users/guynovoa/Desktop/PlosPathogens2025/9c-oseac-ye-oseab.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA B 43 GLY B 56 1 14
Start residue of secondary structure not found: HELIX 2 2 PRO B 97 ASN B 99 1
3
Start residue of secondary structure not found: HELIX 3 3 PRO B 101 VAL B 105
1 5
Start residue of secondary structure not found: HELIX 4 4 LEU B 106 GLN B 108
1 3
Start residue of secondary structure not found: HELIX 5 5 MET B 109 MET B 109
1 1
131 messages similar to the above omitted
Chain information for 9c-oseac-ye-oseab.pdb #10
---
Chain | Description
C | No description available
E | No description available
> hide #9 models
> select #910C
Expected an objects specifier or a keyword
> matchmaker #10/C to #6/C
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 Trimero_Llenas_30Dic_sin_19C-coot-0.pdb, chain C (#6) with
9c-oseac-ye-oseab.pdb, chain C (#10), sequence alignment score = 2674.2
RMSD between 275 pruned atom pairs is 0.858 angstroms; (across all 551 pairs:
3.865)
> select #10/E
4061 atoms, 4176 bonds, 551 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> matchmaker #10 to #6
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 Trimero_Llenas_30Dic_sin_19C-coot-0.pdb, chain B (#6) with
9c-oseac-ye-oseab.pdb, chain C (#10), sequence alignment score = 2795.2
RMSD between 551 pruned atom pairs is 0.000 angstroms; (across all 551 pairs:
0.000)
> matchmaker #10 to #6/C
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 Trimero_Llenas_30Dic_sin_19C-coot-0.pdb, chain C (#6) with
9c-oseac-ye-oseab.pdb, chain C (#10), sequence alignment score = 2674.2
RMSD between 275 pruned atom pairs is 0.858 angstroms; (across all 551 pairs:
3.865)
> open /Users/guynovoa/Desktop/PlosPathogens2025/9c-oseac-ye-oseab.pdb
Summary of feedback from opening
/Users/guynovoa/Desktop/PlosPathogens2025/9c-oseac-ye-oseab.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA B 43 GLY B 56 1 14
Start residue of secondary structure not found: HELIX 2 2 PRO B 97 ASN B 99 1
3
Start residue of secondary structure not found: HELIX 3 3 PRO B 101 VAL B 105
1 5
Start residue of secondary structure not found: HELIX 4 4 LEU B 106 GLN B 108
1 3
Start residue of secondary structure not found: HELIX 5 5 MET B 109 MET B 109
1 1
131 messages similar to the above omitted
Chain information for 9c-oseac-ye-oseab.pdb #11
---
Chain | Description
C | No description available
E | No description available
> matchmaker #11 to #6
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 Trimero_Llenas_30Dic_sin_19C-coot-0.pdb, chain C (#6) with
9c-oseac-ye-oseab.pdb, chain E (#11), sequence alignment score = 2803
RMSD between 550 pruned atom pairs is 0.040 angstroms; (across all 551 pairs:
0.133)
> matchmaker #10 to #6
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 Trimero_Llenas_30Dic_sin_19C-coot-0.pdb, chain B (#6) with
9c-oseac-ye-oseab.pdb, chain C (#10), sequence alignment score = 2795.2
RMSD between 551 pruned atom pairs is 0.000 angstroms; (across all 551 pairs:
0.000)
> select #11/C
4059 atoms, 4174 bonds, 551 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #6/C
4061 atoms, 4176 bonds, 551 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #10 models
> show #10 models
> close #10
> combine #6,11
> hide #11 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> select #10/E
4061 atoms, 4176 bonds, 551 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel C
Chain IDs of 551 residues changed
> color sel forest green
> view orient
> sym #10 i,222r center 226.05,226.05,226.05 newModel true copies true
Made 60 copies for combination symmetry i,222r
> view orient
> show #!1 models
> view orient
[Repeated 1 time(s)]
> clip near 10
[Repeated 1 time(s)]
> view orient
> clip near -15
> clip far 15
> ui mousemode right translate
> volume #1 level 0.127
> clip near -1
[Repeated 1 time(s)]
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right zoom
> clip near -1
[Repeated 2 time(s)]
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> color #1 white models
> color #1 #ffffff00 models
> color #1 #ffffff0f models
> color #1 #ffffff0c models
> color #1 #ffffff13 models
> color #1 #ffffff10 models
> color #1 #ffffff0c models
> color #1 #ffffff0e models
> color #1 #ffffff0f models
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> graphics silhouettes true
> open /Users/guynovoa/Desktop/PlosPathogens2025/HexameroCterminal-coot-1.pdb
Chain information for HexameroCterminal-coot-1.pdb #13
---
Chain | Description
B C G | No description available
D E F | No description available
> select #13
24360 atoms, 25050 bonds, 3306 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> select clear
> select #13/B
4059 atoms, 4174 bonds, 551 residues, 1 model selected
> hide #!1 models
> show #!1 models
> select #13/F
4061 atoms, 4176 bonds, 551 residues, 1 model selected
> color sel red
> hide #!1 models
> show #!1 models
> show #!12 models
> color sel forest green
> select #12.51/C
4061 atoms, 4176 bonds, 551 residues, 1 model selected
> hide sel cartoons
> select add #12
727320 atoms, 747960 bonds, 98640 residues, 61 models selected
> select subtract #12
Nothing selected
> select add #12
727320 atoms, 747960 bonds, 98640 residues, 61 models selected
> select subtract #12
Nothing selected
> select #13/A,B,C,D,E
16240 atoms, 16700 bonds, 2204 residues, 1 model selected
> hide sel cartoons
> view name 1
> hide #!1 models
> hide #!12 models
> show #6 models
> view orient
> show #!5 models
> hide #!5 models
> hide #6 models
> show #6 models
> show #10 models
> combine #13
> select add #13
24360 atoms, 25050 bonds, 3306 residues, 1 model selected
> select subtract #13
Nothing selected
> hide #14 models
> hide #13 models
> show #14 models
> select add #14
24360 atoms, 25050 bonds, 3306 residues, 1 model selected
> show sel cartoons
> combine #14/A,B,C,D,E
> select #14/A,B,C,D,E
16240 atoms, 16700 bonds, 2204 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #15 models
> select #14/G
4059 atoms, 4174 bonds, 551 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> matchmaker #14 to #10
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 combination, chain C (#10) with copy of HexameroCterminal-
coot-1.pdb, chain F (#14), sequence alignment score = 2803
RMSD between 550 pruned atom pairs is 0.040 angstroms; (across all 551 pairs:
0.133)
> select #10/C
4061 atoms, 4176 bonds, 551 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> combine #10,14
> hide #14 models
> hide #10 models
> hide #6 models
> show #!1 models
> view 1
> save /Users/guynovoa/Desktop/PlosPathogens2025/Trimero_good_4sept.pdb models
> #16
> sym #16 i,222r center 226.05,226.05,226.05 newModel true copies true
Made 60 copies for combination symmetry i,222r
> save /Users/guynovoa/Desktop/PlosPathogens2025/LlenasUnsharpSigma06.png
> width 2000 height 1344 supersample 3 transparentBackground true
> save /Users/guynovoa/Desktop/PlosPathogens2025/LlenasUnsharpSigma06.cxs
> volume #1 level 0.15
> save /Users/guynovoa/Desktop/PlosPathogens2025/LlenasUnsharpSigma07.png
> width 2000 height 1344 supersample 3 transparentBackground true
> volume #1 level 0.171
> save /Users/guynovoa/Desktop/PlosPathogens2025/LlenasUnsharpSigma08.png
> width 2000 height 1344 supersample 3 transparentBackground true
> volume #1 level 0.193
> save /Users/guynovoa/Desktop/PlosPathogens2025/LlenasUnsharpSigma09.png
> width 2000 height 1344 supersample 3 transparentBackground true
> volume #1 level 0.2143
> save /Users/guynovoa/Desktop/PlosPathogens2025/LlenasUnsharpSigma1.png width
> 2000 height 1344 supersample 3 transparentBackground true
> show #!2 models
> hide #!1 models
> volume #2 color white
> volume #2 color #ffffff0b
> volume #2 color #ffffff1e
> volume #2 color #ffffff1f
> ui tool show "Map Coordinates"
> ui tool show "Map Statistics"
> measure mapstats #!2
Map cryosparc_P12_J11_008_volume_map_sharp_en1-37.mrc #2, minimum -3, maximum
6.345, mean 0.08058, SD 0.4233, RMS 0.4309
> volume #2 level 0.4233
> save /Users/guynovoa/Desktop/PlosPathogens2025/LlenasSharpSigma1.png width
> 2000 height 1344 supersample 3 transparentBackground true
> volume #2 level 0.38
> save /Users/guynovoa/Desktop/PlosPathogens2025/LlenasSharpSigma09.png width
> 2000 height 1344 supersample 3 transparentBackground true
> volume #2 level 0.339
> save /Users/guynovoa/Desktop/PlosPathogens2025/LlenasSharpSigma08.png width
> 2000 height 1344 supersample 3 transparentBackground true
> volume #2 level 0.8466
> volume #2 level 0.63
> volume #2 level 0.5
> volume #2 level 0.46
> hide #!2 models
> open
> /Users/guynovoa/Documents/DepositoRHDV/Vacias/cryosparc_P12_J9_008_volume_map_1_37.mrc
Opened cryosparc_P12_J9_008_volume_map_1_37.mrc as #18, grid size 330,330,330,
pixel 1.37, shown at level 0.869, step 2, values float32
> ui tool show "Map Statistics"
> measure mapstats #!18
Map cryosparc_P12_J9_008_volume_map_1_37.mrc #18, step 2, minimum -0.3434,
maximum 1.453, mean 0.06121, SD 0.2127, RMS 0.2213
> volume #18 level 0.2127
> volume #18 step 1
> volume #18 color white
> volume #18 color #ffffff2c
> volume #18 color #ffffff18
> volume #18 color #ffffff1a
> save /Users/guynovoa/Desktop/PlosPathogens2025/VaciasUnsharpSigma1.png width
> 2000 height 1368 supersample 3 transparentBackground true
> volume #18 level 0.217
> save /Users/guynovoa/Desktop/PlosPathogens2025/VaciasUnsharpSigma1.png width
> 2000 height 1368 supersample 3 transparentBackground true
> volume #18 level 0.195
> save /Users/guynovoa/Desktop/PlosPathogens2025/VaciasUnsharpSigma09.png
> width 2000 height 1368 supersample 3 transparentBackground true
> volume #18 level 0.174
> save /Users/guynovoa/Desktop/PlosPathogens2025/VaciasUnsharpSigma08.png
> width 2000 height 1368 supersample 3 transparentBackground true
> volume #18 level 0.152
> save /Users/guynovoa/Desktop/PlosPathogens2025/VaciasUnsharpSigma07.png
> width 2000 height 1368 supersample 3 transparentBackground true
> volume #18 level 0.13
> view 1
> save /Users/guynovoa/Desktop/PlosPathogens2025/VaciasUnsharpSigma06.png
> width 2000 height 1368 supersample 3 transparentBackground true
> open /Users/guynovoa/Downloads/cryosparc_P18_J16_010_volume_map.mrc
Opened cryosparc_P18_J16_010_volume_map.mrc as #19, grid size 440,440,440,
pixel 1.06, shown at level 0.517, step 2, values float32
> volume #19 step 1
> volume #19 level 0.2
> volume #19 level 0.1
> volume #19 level 0.05
> view orient
> ui tool show "Side View"
> view 1
> ui tool show "Map Statistics"
> measure mapstats #!18-19
Map cryosparc_P12_J9_008_volume_map_1_37.mrc #18, minimum -0.4121, maximum
1.474, mean 0.06121, SD 0.2127, RMS 0.2214
Map cryosparc_P18_J16_010_volume_map.mrc #19, minimum -1.215, maximum 1.406,
mean -0.1392, SD 0.3085, RMS 0.3384
> volume #19 level 0.3085
> view orient
[Repeated 4 time(s)]
> view 1
> volume #19 level 0.1
> volume #19 level 0.03
> close #19
> view 1
> open /Users/guynovoa/Documents/PhenixNT15/NT15_centered0.mrc
Opened NT15_centered0.mrc as #19, grid size 440,440,440, pixel 1.08, shown at
level 0.136, step 2, values float32
> volume #19 step 1
> volume #19 level 0.07602
> volume #19 level 0.05
> close #19
> save /Users/guynovoa/Desktop/PlosPathogens2025/Figura_NTA-Genome.cxs
> includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1058, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 746, in save
fserialize(stream, data)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 151, in write
self._f.write(buf)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 741, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
Out of disk space
Cannot save '/Users/guynovoa/Desktop/PlosPathogens2025/Figura_NTA-Genome.cxs':
[Errno 28] No space left on device
> save /Users/guynovoa/Desktop/PlosPathogens2025/FiguraLlenasVaciasNTARNA.cxs
> includeMaps true
——— End of log from Thu Sep 4 16:20:59 2025 ———
opened ChimeraX session
> view orient
> hide #!17 models
> view orient
[Repeated 1 time(s)]
> color #18 silver models
> lighting soft
[Repeated 1 time(s)]
> view orient
> hide #!18 models
> show #!18 models
> color #18.1 black
> color #18.1 #212121ff
> color #18.1 #919191ff
> color #18.1 darkgrey
> color #18.1 silver
> clip near -10
> clip far 10
> ui tool show Orthoplanes
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 742, in
_onSliderMoved
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> hide #!18 models
> hide #18.1 models
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 742, in
_onSliderMoved
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> ui tool show Orthoplanes
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen
self._update_position_label_text()
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'
AttributeError: 'ArrayGridData' object has no attribute 'dicom_data'
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text
dicom_data = self.view.drawing.parent.data.dicom_data
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGN63Y/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 6 hours, 38 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
narwhals: 1.33.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 2.2.4
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
plotly: 6.0.1
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pyKVFinder: 0.7.3
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
toml: 0.10.2
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 2 months ago
| Component: | Unassigned → DICOM |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → 'ArrayGridData' object has no attribute 'dicom_data' |
comment:2 by , 2 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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