![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 21 months ago
Closed 19 months ago
#14538 closed defect (fixed)
ISOLDE: ResidueStepper: self.positions is None
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.5.0-15-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session11_ISOLDE_head_good.cxs"
Opened Most_monomer_J590_class_8_00264_volume.mrc as #1.1.1.1, grid size
216,216,216, pixel 2.88, shown at level 0.427, step 1, values float32
Opened cryosparc_P1022_J624_map_sharp.mrc as #1.1.1.2, grid size 640,640,640,
pixel 0.97, shown at level 0.0637, step 1, values float32
Opened cryosparc_P1022_J625_map_sharp.mrc as #1.1.1.3, grid size 640,640,640,
pixel 0.97, shown at level 0.172, step 1, values float32
Opened cryosparc_P1022_J623_map_sharp(1).mrc as #1.1.1.4, grid size
640,640,640, pixel 0.97, shown at level 0.0312, step 1, values float32
Opened Most_full_J406_class_06_00267_volume.mrc as #5, grid size 128,128,128,
pixel 5.05, shown at level 0.493, step 1, values float32
Restoring stepper: all_ISOLDE.pdb
Log from Mon Feb 5 15:00:23 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session10_ISOLDE.cxs"
Opened Most_monomer_J590_class_8_00264_volume.mrc as #1.1.1.1, grid size
216,216,216, pixel 2.88, shown at level 0.427, step 1, values float32
Opened cryosparc_P1022_J624_map_sharp.mrc as #1.1.1.2, grid size 640,640,640,
pixel 0.97, shown at level 0.0522, step 1, values float32
Opened cryosparc_P1022_J625_map_sharp.mrc as #1.1.1.3, grid size 640,640,640,
pixel 0.97, shown at level 0.172, step 1, values float32
Opened cryosparc_P1022_J623_map_sharp(1).mrc as #1.1.1.4, grid size
640,640,640, pixel 0.97, shown at level 0.0312, step 1, values float32
Opened Most_full_J406_class_06_00267_volume.mrc as #5, grid size 128,128,128,
pixel 5.05, shown at level 0.493, step 1, values float32
Restoring stepper: all_ISOLDE.pdb
Log from Fri Feb 2 09:56:15 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session8_ISOLDE.cxs"
Opened cryosparc_P1022_J623_map_sharp(1).mrc as #2, grid size 640,640,640,
pixel 0.97, shown at level 0.0125, step 1, values float32
Opened cryosparc_P1022_J625_map_sharp.mrc as #4, grid size 640,640,640, pixel
0.97, shown at level 0.158, step 1, values float32
Opened Most_monomer_J590_class_8_00264_volume.mrc as #1.1.1.1, grid size
216,216,216, pixel 2.88, shown at level 0.298, step 1, values float32
Opened cryosparc_P1022_J624_map_sharp.mrc as #1.1.1.2, grid size 640,640,640,
pixel 0.97, shown at level 0.00621, step 1, values float32
Restoring stepper: all_ISOLDE.pdb
Log from Thu Feb 1 18:15:35 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session6_ISOLDE.cxs"
Opened cryosparc_P1022_J623_map_sharp(1).mrc as #4, grid size 640,640,640,
pixel 0.97, shown at level 8.17e-05, step 4, values float32
Opened cryosparc_P1022_J624_map_sharp.mrc as #5, grid size 640,640,640, pixel
0.97, shown at level 7.95e-05, step 4, values float32
Opened cryosparc_P1022_J625_map_sharp.mrc as #6, grid size 640,640,640, pixel
0.97, shown at level 1.79e-05, step 4, values float32
Opened Most_monomer_J590_class_8_00264_volume.mrc as #7.1.1.1, grid size
216,216,216, pixel 2.88, shown at level 0.503, step 1, values float32
Log from Thu Feb 1 17:30:20 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session5_ISOLDE.cxs"
Opened cryosparc_P1022_J623_map_sharp(1).mrc as #2, grid size 640,640,640,
pixel 0.97, shown at level 8.17e-05, step 4, values float32
Opened cryosparc_P1022_J624_map_sharp.mrc as #3, grid size 640,640,640, pixel
0.97, shown at level 7.95e-05, step 4, values float32
Opened cryosparc_P1022_J625_map_sharp.mrc as #4, grid size 640,640,640, pixel
0.97, shown at level 1.79e-05, step 4, values float32
Opened Most_monomer_J590_class_8_00264_volume.mrc as #6, grid size
216,216,216, pixel 2.88, shown at level 0.308, step 1, values float32
Log from Thu Feb 1 17:15:39 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session4_ISOLDE.cxs"
Opened cryosparc_P1022_J623_map_sharp(1).mrc as #2, grid size 640,640,640,
pixel 0.97, shown at level 8.17e-05, step 4, values float32
Opened cryosparc_P1022_J624_map_sharp.mrc as #3, grid size 640,640,640, pixel
0.97, shown at level 7.95e-05, step 4, values float32
Opened cryosparc_P1022_J625_map_sharp.mrc as #4, grid size 640,640,640, pixel
0.97, shown at level 1.79e-05, step 4, values float32
Opened Most_monomer_J590_class_8_00264_volume.mrc as #6, grid size
216,216,216, pixel 2.88, shown at level 0.308, step 1, values float32
Log from Thu Feb 1 16:46:20 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session2.cxs" format session
Opened Most_monomer_J590_class_8_00264_volume.mrc as #4, grid size
216,216,216, pixel 2.88, shown at level 0.0298, step 1, values float32
Log from Thu Feb 1 15:28:33 2024
> remotecontrol rest start port 50804
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
REST server started on host 127.0.0.1 port 50804
Visit http://127.0.0.1:50804/cmdline.html for CLI interface
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/6vxx.pdb"
> "/home/carl/Documents/Phenix/2F PXT-apt and Spike/7jji.pdb"
> "/home/carl/Documents/Phenix/2F PXT-apt and Spike/spike_monomer.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/spike_monomer.pdb
---
warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence
records as basis for sequence.
6vxx.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 6vxx.pdb #1
---
Chain | Description | UniProt
A B C | spike glycoprotein | SPIKE_SARS2 14-1211
Non-standard residues in 6vxx.pdb #1
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
7jji.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 7jji.pdb #2
---
Chain | Description | UniProt
A B C | spike glycoprotein | SPIKE_SARS2 1-1273
Non-standard residues in 7jji.pdb #2
---
EIC — linoleic acid (9,12-linoleic acid)
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
VCG — 2-hydroxyethyl
2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-α-L-
xylo-hexofuranoside (polysorbate 80)
Chain information for spike_monomer.pdb #3
---
Chain | Description
A | No description available
> select #1/A
7758 atoms, 7949 bonds, 983 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/B
7758 atoms, 7949 bonds, 983 residues, 1 model selected
> select #1/B
7758 atoms, 7949 bonds, 983 residues, 1 model selected
> select #1/C
7758 atoms, 7949 bonds, 983 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/A
8733 atoms, 8950 bonds, 1112 residues, 1 model selected
> select #2/B
8733 atoms, 8950 bonds, 1112 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/C
8733 atoms, 8950 bonds, 1112 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 112 atoms, 116 bonds
[Repeated 1 time(s)]Drag select of 84 atoms, 87 bonds
Drag select of 27 atoms, 29 bonds
Drag select of 28 atoms, 29 bonds
[Repeated 4 time(s)]Drag select of 139 atoms, 145 bonds
> select add #2/b:2@O4
615 atoms, 638 bonds, 44 residues, 2 models selected
Drag select of 28 atoms, 29 bonds
[Repeated 2 time(s)]Drag select of 140 atoms, 145 bonds
Drag select of 27 atoms, 29 bonds
> delete atoms sel
> delete bonds sel
> select clear
Drag select of 1 atoms
> delete atoms sel
> delete bonds sel
Drag select of 13 atoms, 13 bonds
Drag select of 5 atoms, 4 bonds
> delete atoms sel
> delete bonds sel
Drag select of 2 atoms
> delete atoms sel
> delete bonds sel
Drag select of 28 atoms, 29 bonds
[Repeated 1 time(s)]
> delete atoms sel
> delete bonds sel
Drag select of 56 atoms, 58 bonds
> delete atoms sel
> delete bonds sel
Drag select of 54 atoms, 57 bonds
> delete atoms sel
> delete bonds sel
Drag select of 1 atoms
[Repeated 1 time(s)]
> delete atoms sel
> delete bonds sel
Drag select of 1 atoms
> delete atoms sel
> delete bonds sel
> color #1 #33d17aff
Drag select of 28 atoms, 29 bonds
> delete atoms sel
> delete bonds sel
> hide #3 models
Alignment identifier is 1/B
Alignment identifier is 2/A
Alignment identifier is 3/A
> select #2/A:14
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:14-26
101 atoms, 102 bonds, 13 residues, 1 model selected
> open "/home/carl/Documents/Phenix/2F PXT-apt and
> Spike/Most_monomer_J590_class_8_00264_volume.mrc"
Opened Most_monomer_J590_class_8_00264_volume.mrc as #4, grid size
216,216,216, pixel 2.88, shown at level 0.0298, step 1, values float32
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/1.pdb"
> models #2 selectedOnly true relModel #4
> select #1/B:27
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/B:27
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/B:27-28
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #1/B:27-69
364 atoms, 379 bonds, 43 residues, 1 model selected
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/2.pdb"
> models #1 selectedOnly true relModel #4
> select #2/A:70
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:70-79
74 atoms, 74 bonds, 10 residues, 1 model selected
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/2-2.pdb"
> models #2 selectedOnly true relModel #4
> select #1/B:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:80,140
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #1/B:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:80-140
482 atoms, 493 bonds, 61 residues, 1 model selected
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/2-3.pdb"
> models #1 selectedOnly true relModel #4
> select #2/A:141
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:141-170
258 atoms, 266 bonds, 30 residues, 1 model selected
> select #2/A:164-165
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/A:141-164
205 atoms, 211 bonds, 24 residues, 1 model selected
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/3.pdb"
> models #2 selectedOnly true relModel #4
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session.cxs" includeMaps true
> select #1/B:165
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:165
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:165-167
21 atoms, 20 bonds, 3 residues, 1 model selected
> select #1/B:165-172
66 atoms, 67 bonds, 8 residues, 1 model selected
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/4.pdb"
> models #1 selectedOnly true relModel #1
> select #2/A:173
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:173-185
102 atoms, 103 bonds, 13 residues, 1 model selected
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/5.pdb"
> models #2 selectedOnly true relModel #4
> select #1/B:186
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:186-245
495 atoms, 508 bonds, 60 residues, 1 model selected
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/6.pdb"
> models #1 selectedOnly true relModel #4
> select #2/A:246
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:246
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:262
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:246-262
120 atoms, 123 bonds, 17 residues, 1 model selected
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/7.pdb"
> models #2 selectedOnly true relModel #4
> select #1/B:263
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/B:263
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/B:328
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/B:263-328
525 atoms, 536 bonds, 66 residues, 1 model selected
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/8.pdb"
> models #1 selectedOnly true relModel #4
> select #3/A:329
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #3/A:329
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #3/A:530
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:329-530
3126 atoms, 3176 bonds, 202 residues, 1 model selected
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/9_rbd.pdb"
> models #3 selectedOnly true relModel #4
> select #1/B:531
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:531
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:531
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/B:531-620
683 atoms, 694 bonds, 90 residues, 1 model selected
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/10.pdb"
> models #1 selectedOnly true relModel #4
> select #1/B:641
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/B:641-676
265 atoms, 270 bonds, 36 residues, 1 model selected
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/11.pdb"
> models #1 selectedOnly true relModel #4
> select #1/B:689
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:689
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:689
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/B:689-827
1070 atoms, 1091 bonds, 139 residues, 1 model selected
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/14.pdb"
> models #1 selectedOnly true relModel #4
> select #2/A:828
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:828
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:853-854
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #2/A:828-853
190 atoms, 192 bonds, 26 residues, 1 model selected
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/15.pdb"
> models #2 selectedOnly true relModel #4
> select #1/B:854
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:854
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:854
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/B:854-1147
2253 atoms, 2300 bonds, 294 residues, 1 model selected
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/16.pdb"
> models #1 selectedOnly true relModel #4
> ui tool show "Build Structure"
> select clear
[Repeated 1 time(s)]
> build start peptide "custom built" PVAIHADQLTPTWRVYSTGS -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 rotLib Dunbrack
Chain information for custom built #5
---
Chain | Description
A | No description available
> select clear
[Repeated 1 time(s)]
> build start peptide "custom built" QTNSPSGAGSVA -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0
> -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 -57.0,-47.0 rotLib Dunbrack
Chain information for custom built #6
---
Chain | Description
A | No description available
> hide #5 models
> show #5 models
> select add #5
156 atoms, 161 bonds, 20 residues, 1 model selected
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/11.pdb"
> models #5 selectedOnly true relModel #4
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/13.pdb"
> models #6 selectedOnly true relModel #4
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session2.cxs" includeMaps true
——— End of log from Thu Feb 1 15:28:33 2024 ———
opened ChimeraX session
> hide #1 models
> hide #2 models
> select subtract #5
Nothing selected
> hide #5 models
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/13.pdb"
> models #6 relModel #4
> close session
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/1.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
78 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (136 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
43 messages similar to the above omitted
1.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 1.pdb #1
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/2.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
68 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
28 messages similar to the above omitted
2.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 2.pdb #2
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/2-2.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/2-2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
77 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
43 messages similar to the above omitted
2-2.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 2-2.pdb #3
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/2-3.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/2-3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
67 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (166 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
28 messages similar to the above omitted
2-3.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 2-3.pdb #4
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/3.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
31 messages similar to the above omitted
End residue of secondary structure not found: SHEET 11 11 1 TRP A 152 VAL A
171 0
Start residue of secondary structure not found: SHEET 12 12 1 ASN A 188 ILE A
197 0
Start residue of secondary structure not found: SHEET 13 13 1 TYR A 200 PRO A
209 0
Start residue of secondary structure not found: SHEET 14 14 1 ALA A 222 LEU A
229 0
Start residue of secondary structure not found: SHEET 15 15 1 ARG A 237 SER A
247 0
Start residue of secondary structure not found: SHEET 16 16 1 ALA A 263 TYR A
269 0
41 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
43 messages similar to the above omitted
3.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 3.pdb #5
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/4.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
71 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
28 messages similar to the above omitted
4.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 4.pdb #6
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/5.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/5.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
78 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
43 messages similar to the above omitted
5.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 5.pdb #7
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/6.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/6.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
68 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
28 messages similar to the above omitted
6.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 6.pdb #8
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/7.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/7.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
78 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
43 messages similar to the above omitted
7.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 7.pdb #9
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/8.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/8.pdb
---
warnings | Start residue of secondary structure not found: HELIX 2 2 PHE B 338
ASN B 343 1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
Start residue of secondary structure not found: HELIX 6 6 ASP B 737 CYS B 743
1 7
66 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (538 )
27 messages similar to the above omitted
8.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 8.pdb #10
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/9_rbd.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/9_rbd.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 295
LEU A 303 1 9
Start residue of secondary structure not found: HELIX 9 9 LEU A 849 PHE A 855
1 7
Start residue of secondary structure not found: HELIX 10 10 ASP A 867 THR A
883 1 17
Start residue of secondary structure not found: HELIX 11 11 PHE A 898 ILE A
909 1 12
Start residue of secondary structure not found: HELIX 12 12 GLN A 913 GLU A
918 1 6
52 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (538 )
Cannot find LINK/SSBOND residue CYS (617 )
Cannot find LINK/SSBOND residue CYS (662 )
Cannot find LINK/SSBOND residue CYS (1032 )
4 messages similar to the above omitted
Chain information for 9_rbd.pdb #11
---
Chain | Description
A | No description available
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/10.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/10.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
65 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
27 messages similar to the above omitted
10.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 10.pdb #12
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/11.pdb"
Chain information for 11.pdb #13
---
Chain | Description
A | No description available
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/12.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/12.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
67 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
27 messages similar to the above omitted
12.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 12.pdb #14
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/13.pdb"
Chain information for 13.pdb #15
---
Chain | Description
A | No description available
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/14.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/14.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
62 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
26 messages similar to the above omitted
14.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 14.pdb #16
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/15.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/15.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 15 15 ASP A 848 PHE A 855
1 8
Start residue of secondary structure not found: HELIX 16 16 THR A 866 SER A
884 1 19
Start residue of secondary structure not found: HELIX 17 17 GLY A 885 GLY A
889 1 5
Start residue of secondary structure not found: HELIX 18 18 PRO A 897 GLY A
910 1 14
Start residue of secondary structure not found: HELIX 19 19 GLN A 913 GLU A
918 1 6
Start residue of secondary structure not found: HELIX 20 20 ASN A 919 THR A
941 1 23
63 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
42 messages similar to the above omitted
15.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 15.pdb #17
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/16.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/16.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
51 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
26 messages similar to the above omitted
16.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 16.pdb #18
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> select add #13
156 atoms, 161 bonds, 20 residues, 1 model selected
> select add #15
231 atoms, 236 bonds, 32 residues, 2 models selected
> view matrix models
> #13,1,0,0,-7.469,0,1,0,-50.801,0,0,1,-4.5191,#15,1,0,0,-7.469,0,1,0,-50.801,0,0,1,-4.5191
> select subtract #15
156 atoms, 161 bonds, 20 residues, 1 model selected
> view matrix models #13,1,0,0,-32.215,0,1,0,-44.929,0,0,1,-7.2571
> combine
Remapping chain ID 'A' in 2-2.pdb #3 to 'C'
Remapping chain ID 'B' in 2-3.pdb #4 to 'D'
Remapping chain ID 'A' in 3.pdb #5 to 'E'
Remapping chain ID 'B' in 4.pdb #6 to 'F'
Remapping chain ID 'A' in 5.pdb #7 to 'G'
Remapping chain ID 'B' in 6.pdb #8 to 'H'
Remapping chain ID 'A' in 7.pdb #9 to 'I'
Remapping chain ID 'B' in 8.pdb #10 to 'J'
Remapping chain ID 'A' in 9_rbd.pdb #11 to 'K'
Remapping chain ID 'B' in 10.pdb #12 to 'L'
Remapping chain ID 'A' in 11.pdb #13 to 'M'
Remapping chain ID 'B' in 12.pdb #14 to 'N'
Remapping chain ID 'A' in 13.pdb #15 to 'O'
Remapping chain ID 'B' in 14.pdb #16 to 'P'
Remapping chain ID 'A' in 15.pdb #17 to 'Q'
Remapping chain ID 'B' in 16.pdb #18 to 'R'
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> hide #12 models
> show #12 models
> hide #12 models
> select subtract #13
Nothing selected
> hide #13 models
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> select #19/J:328
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #19/K:530
22 atoms, 20 bonds, 2 residues, 1 model selected
> select add #19/L:531
29 atoms, 26 bonds, 3 residues, 1 model selected
> select add #19/K:329
49 atoms, 46 bonds, 4 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> show sel cartoons
> select #19/K:329
20 atoms, 20 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected atoms"
> select #19/K:530
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #19/J:328
22 atoms, 20 bonds, 2 residues, 1 model selected
> select add #19/L:531@CA
23 atoms, 20 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select #19/K:329
20 atoms, 20 bonds, 1 residue, 1 model selected
> hide sel cartoons
> delete H
Alignment identifier is 19/K
> select clear
Drag select of 175 atoms, 1112 residues, 173 bonds
> ui tool show "Change Chain IDs"
> select clear
> select #19/L:561
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #19/L:560
15 atoms, 14 bonds, 2 residues, 1 model selected
> hide sel cartoons
> style sel stick
Changed 15 atom styles
> show sel atoms
> select #19/J:328@C
1 atom, 1 residue, 1 model selected
> select add #19/K:329@N
2 atoms, 2 residues, 1 model selected
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> hide sel cartoons
> style sel stick
Changed 9 atom styles
> show sel atoms
> select clear
> show sel cartoons
> select clear
> close session
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/1.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
78 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (136 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
43 messages similar to the above omitted
1.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 1.pdb #1
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/2.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
68 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
28 messages similar to the above omitted
2.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 2.pdb #2
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/2-2.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/2-2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
77 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
43 messages similar to the above omitted
2-2.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 2-2.pdb #3
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/2-3.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/2-3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
67 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (166 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
28 messages similar to the above omitted
2-3.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 2-3.pdb #4
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/3.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
31 messages similar to the above omitted
End residue of secondary structure not found: SHEET 11 11 1 TRP A 152 VAL A
171 0
Start residue of secondary structure not found: SHEET 12 12 1 ASN A 188 ILE A
197 0
Start residue of secondary structure not found: SHEET 13 13 1 TYR A 200 PRO A
209 0
Start residue of secondary structure not found: SHEET 14 14 1 ALA A 222 LEU A
229 0
Start residue of secondary structure not found: SHEET 15 15 1 ARG A 237 SER A
247 0
Start residue of secondary structure not found: SHEET 16 16 1 ALA A 263 TYR A
269 0
41 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
43 messages similar to the above omitted
3.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 3.pdb #5
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/4.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
71 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
28 messages similar to the above omitted
4.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 4.pdb #6
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/5.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/5.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
78 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
43 messages similar to the above omitted
5.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 5.pdb #7
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/6.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/6.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
68 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
28 messages similar to the above omitted
6.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 6.pdb #8
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/7.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/7.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
78 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
43 messages similar to the above omitted
7.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 7.pdb #9
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/8.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/8.pdb
---
warnings | Start residue of secondary structure not found: HELIX 2 2 PHE B 338
ASN B 343 1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
Start residue of secondary structure not found: HELIX 6 6 ASP B 737 CYS B 743
1 7
66 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (538 )
27 messages similar to the above omitted
8.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 8.pdb #10
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/9_rbd.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/9_rbd.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 295
LEU A 303 1 9
Start residue of secondary structure not found: HELIX 9 9 LEU A 849 PHE A 855
1 7
Start residue of secondary structure not found: HELIX 10 10 ASP A 867 THR A
883 1 17
Start residue of secondary structure not found: HELIX 11 11 PHE A 898 ILE A
909 1 12
Start residue of secondary structure not found: HELIX 12 12 GLN A 913 GLU A
918 1 6
52 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (538 )
Cannot find LINK/SSBOND residue CYS (617 )
Cannot find LINK/SSBOND residue CYS (662 )
Cannot find LINK/SSBOND residue CYS (1032 )
4 messages similar to the above omitted
Chain information for 9_rbd.pdb #11
---
Chain | Description
A | No description available
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/10.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/10.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
65 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
27 messages similar to the above omitted
10.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 10.pdb #12
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/11.pdb"
Chain information for 11.pdb #13
---
Chain | Description
A | No description available
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/12.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/12.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
67 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
27 messages similar to the above omitted
12.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 12.pdb #14
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/13.pdb"
Chain information for 13.pdb #15
---
Chain | Description
A | No description available
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/14.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/14.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
62 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
26 messages similar to the above omitted
14.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 14.pdb #16
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/15.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/15.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 15 15 ASP A 848 PHE A 855
1 8
Start residue of secondary structure not found: HELIX 16 16 THR A 866 SER A
884 1 19
Start residue of secondary structure not found: HELIX 17 17 GLY A 885 GLY A
889 1 5
Start residue of secondary structure not found: HELIX 18 18 PRO A 897 GLY A
910 1 14
Start residue of secondary structure not found: HELIX 19 19 GLN A 913 GLU A
918 1 6
Start residue of secondary structure not found: HELIX 20 20 ASN A 919 THR A
941 1 23
63 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
42 messages similar to the above omitted
15.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 15.pdb #17
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/16.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/16.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
51 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
26 messages similar to the above omitted
16.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 16.pdb #18
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> delete H
> combine
Remapping chain ID 'A' in 2-2.pdb #3 to 'C'
Remapping chain ID 'B' in 2-3.pdb #4 to 'D'
Remapping chain ID 'A' in 3.pdb #5 to 'E'
Remapping chain ID 'B' in 4.pdb #6 to 'F'
Remapping chain ID 'A' in 5.pdb #7 to 'G'
Remapping chain ID 'B' in 6.pdb #8 to 'H'
Remapping chain ID 'A' in 7.pdb #9 to 'I'
Remapping chain ID 'B' in 8.pdb #10 to 'J'
Remapping chain ID 'A' in 9_rbd.pdb #11 to 'K'
Remapping chain ID 'B' in 10.pdb #12 to 'L'
Remapping chain ID 'A' in 11.pdb #13 to 'M'
Remapping chain ID 'B' in 12.pdb #14 to 'N'
Remapping chain ID 'A' in 13.pdb #15 to 'O'
Remapping chain ID 'B' in 14.pdb #16 to 'P'
Remapping chain ID 'A' in 15.pdb #17 to 'Q'
Remapping chain ID 'B' in 16.pdb #18 to 'R'
> close #1-18
> close session
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/1.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
78 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (136 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
43 messages similar to the above omitted
1.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 1.pdb #1
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/2.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
68 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
28 messages similar to the above omitted
2.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 2.pdb #2
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/2-2.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/2-2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
77 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
43 messages similar to the above omitted
2-2.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 2-2.pdb #3
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/2-3.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/2-3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
67 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (166 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
28 messages similar to the above omitted
2-3.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 2-3.pdb #4
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/3.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
31 messages similar to the above omitted
End residue of secondary structure not found: SHEET 11 11 1 TRP A 152 VAL A
171 0
Start residue of secondary structure not found: SHEET 12 12 1 ASN A 188 ILE A
197 0
Start residue of secondary structure not found: SHEET 13 13 1 TYR A 200 PRO A
209 0
Start residue of secondary structure not found: SHEET 14 14 1 ALA A 222 LEU A
229 0
Start residue of secondary structure not found: SHEET 15 15 1 ARG A 237 SER A
247 0
Start residue of secondary structure not found: SHEET 16 16 1 ALA A 263 TYR A
269 0
41 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
43 messages similar to the above omitted
3.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 3.pdb #5
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/4.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
71 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
28 messages similar to the above omitted
4.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 4.pdb #6
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/5.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/5.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
78 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
43 messages similar to the above omitted
5.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 5.pdb #7
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/6.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/6.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
68 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
28 messages similar to the above omitted
6.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 6.pdb #8
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/7.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/7.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
78 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
43 messages similar to the above omitted
7.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 7.pdb #9
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/8.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/8.pdb
---
warnings | Start residue of secondary structure not found: HELIX 2 2 PHE B 338
ASN B 343 1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
Start residue of secondary structure not found: HELIX 6 6 ASP B 737 CYS B 743
1 7
66 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (538 )
27 messages similar to the above omitted
8.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 8.pdb #10
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/9_rbd.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/9_rbd.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 295
LEU A 303 1 9
Start residue of secondary structure not found: HELIX 9 9 LEU A 849 PHE A 855
1 7
Start residue of secondary structure not found: HELIX 10 10 ASP A 867 THR A
883 1 17
Start residue of secondary structure not found: HELIX 11 11 PHE A 898 ILE A
909 1 12
Start residue of secondary structure not found: HELIX 12 12 GLN A 913 GLU A
918 1 6
52 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (538 )
Cannot find LINK/SSBOND residue CYS (617 )
Cannot find LINK/SSBOND residue CYS (662 )
Cannot find LINK/SSBOND residue CYS (1032 )
4 messages similar to the above omitted
Chain information for 9_rbd.pdb #11
---
Chain | Description
A | No description available
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/10.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/10.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
65 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
27 messages similar to the above omitted
10.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 10.pdb #12
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/11.pdb"
Chain information for 11.pdb #13
---
Chain | Description
A | No description available
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/12.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/12.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
67 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
27 messages similar to the above omitted
12.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 12.pdb #14
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/13.pdb"
Chain information for 13.pdb #15
---
Chain | Description
A | No description available
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/14.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/14.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
62 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
26 messages similar to the above omitted
14.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 14.pdb #16
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/15.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/15.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 PHE A 342
1 6
Start residue of secondary structure not found: HELIX 3 3 SER A 349 TRP A 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP A 364 TYR A 369
1 6
Start residue of secondary structure not found: HELIX 5 5 SER A 383 ASP A 389
1 7
7 messages similar to the above omitted
End residue of secondary structure not found: HELIX 15 15 ASP A 848 PHE A 855
1 8
Start residue of secondary structure not found: HELIX 16 16 THR A 866 SER A
884 1 19
Start residue of secondary structure not found: HELIX 17 17 GLY A 885 GLY A
889 1 5
Start residue of secondary structure not found: HELIX 18 18 PRO A 897 GLY A
910 1 14
Start residue of secondary structure not found: HELIX 19 19 GLN A 913 GLU A
918 1 6
Start residue of secondary structure not found: HELIX 20 20 ASN A 919 THR A
941 1 23
63 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (15 )
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
42 messages similar to the above omitted
15.pdb title:
Structure of sars-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
[more info...]
Chain information for 15.pdb #17
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 1-1273
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/16.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/16.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP B 294
LEU B 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PHE B 338 ASN B 343
1 6
Start residue of secondary structure not found: HELIX 3 3 SER B 349 TRP B 353
1 5
Start residue of secondary structure not found: HELIX 4 4 ASP B 364 SER B 371
1 8
Start residue of secondary structure not found: HELIX 5 5 ASP B 405 ILE B 410
1 6
51 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (131 )
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
26 messages similar to the above omitted
16.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 16.pdb #18
---
Chain | Description | UniProt
B | spike glycoprotein | SPIKE_SARS2 14-1211
> select add #13
156 atoms, 161 bonds, 20 residues, 1 model selected
> select add #15
231 atoms, 236 bonds, 32 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #13,1,0,0,22.525,0,1,0,-16.013,0,0,1,-3.2658,#15,1,0,0,22.525,0,1,0,-16.013,0,0,1,-3.2658
> select subtract #13
75 atoms, 75 bonds, 12 residues, 1 model selected
> view matrix models #15,1,0,0,-44.51,0,1,0,32.553,0,0,1,1.3388
> select clear
> ui tool show "Renumber Residues"
> renumber #15/A seqStart 677
12 residues renumbered
> renumber #15/A seqStart 677
0 residues renumbered
> ui tool show "Renumber Residues"
> renumber #15/A seqStart 677
0 residues renumbered
> ui tool show "Renumber Residues"
> renumber #13/A seqStart 621
20 residues renumbered
> view matrix models #15,1,0,0,-19.551,0,1,0,16.349,0,0,1,0.2611
> view matrix models #15,1,0,0,-43.564,0,1,0,-5.9248,0,0,1,-11.008
> view matrix models #15,1,0,0,-42.605,0,1,0,-17.953,0,0,1,-14.426
> view matrix models #15,1,0,0,-35.316,0,1,0,-16.522,0,0,1,-11.566
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.45759,-0.74875,-0.47956,482.71,0.6457,0.65062,-0.39971,11.065,0.6113,-0.12675,0.78119,-91.387
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.45759,-0.74875,-0.47956,489.96,0.6457,0.65062,-0.39971,12.724,0.6113,-0.12675,0.78119,-92.84
> view matrix models
> #15,0.45759,-0.74875,-0.47956,489.67,0.6457,0.65062,-0.39971,12.391,0.6113,-0.12675,0.78119,-91.079
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.0014991,-0.92219,-0.38673,649.12,0.71942,0.26961,-0.64012,172.34,0.69458,-0.27726,0.66384,-37.476
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.0014991,-0.92219,-0.38673,650.05,0.71942,0.26961,-0.64012,172.86,0.69458,-0.27726,0.66384,-37.731
> select clear
> view matrix models #13,1,0,0,-35.656,0,1,0,8.2111,0,0,1,-3.2928
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.17804,-0.80086,0.57177,282.73,-0.66235,0.33218,0.67153,212.21,-0.72773,-0.49827,-0.47131,771.73
> view matrix models
> #13,0.15488,-0.97248,0.17407,452.55,-0.62376,0.040373,0.78057,257.38,-0.76612,-0.22947,-0.60034,738.99
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.15488,-0.97248,0.17407,476.08,-0.62376,0.040373,0.78057,248.46,-0.76612,-0.22947,-0.60034,736.1
> view matrix models
> #13,0.15488,-0.97248,0.17407,464.39,-0.62376,0.040373,0.78057,247.01,-0.76612,-0.22947,-0.60034,750.81
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.47528,-0.84786,0.23504,594.13,-0.44627,0.46254,0.76609,73.212,-0.75826,0.25922,-0.59821,602.04
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.47528,-0.84786,0.23504,594.61,-0.44627,0.46254,0.76609,69.39,-0.75826,0.25922,-0.59821,599.56
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.3086,-0.87385,0.3757,514.12,-0.65173,0.48195,0.58564,174.36,-0.69283,-0.064125,-0.71824,710.72
> view matrix models
> #13,-0.084482,-0.99001,0.11286,557.24,-0.41462,0.13792,0.89948,119.54,-0.90607,0.029197,-0.42213,661.89
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.084482,-0.99001,0.11286,560.55,-0.41462,0.13792,0.89948,116.98,-0.90607,0.029197,-0.42213,661.82
> view matrix models
> #13,-0.084482,-0.99001,0.11286,558.31,-0.41462,0.13792,0.89948,115.69,-0.90607,0.029197,-0.42213,661.84
> view matrix models
> #13,-0.084482,-0.99001,0.11286,562.86,-0.41462,0.13792,0.89948,113.44,-0.90607,0.029197,-0.42213,666.57
> select clear
> combine
Remapping chain ID 'A' in 2-2.pdb #3 to 'C'
Remapping chain ID 'B' in 2-3.pdb #4 to 'D'
Remapping chain ID 'A' in 3.pdb #5 to 'E'
Remapping chain ID 'B' in 4.pdb #6 to 'F'
Remapping chain ID 'A' in 5.pdb #7 to 'G'
Remapping chain ID 'B' in 6.pdb #8 to 'H'
Remapping chain ID 'A' in 7.pdb #9 to 'I'
Remapping chain ID 'B' in 8.pdb #10 to 'J'
Remapping chain ID 'A' in 9_rbd.pdb #11 to 'K'
Remapping chain ID 'B' in 10.pdb #12 to 'L'
Remapping chain ID 'A' in 11.pdb #13 to 'M'
Remapping chain ID 'B' in 12.pdb #14 to 'N'
Remapping chain ID 'A' in 13.pdb #15 to 'O'
Remapping chain ID 'B' in 14.pdb #16 to 'P'
Remapping chain ID 'A' in 15.pdb #17 to 'Q'
Remapping chain ID 'B' in 16.pdb #18 to 'R'
> close #1-18
> select clear
> ui mousemode right "translate selected atoms"
> show sel atoms
> hide sel cartoons
> delete H
> select clear
> ui tool show "Build Structure"
> show sel atoms
> hide sel cartoons
> select clear
[Repeated 1 time(s)]
> show sel atoms
> hide sel cartoons
> select clear
> hide sel cartoons
> show sel atoms
> select clear
> show sel atoms
> hide sel cartoons
> select clear
> show sel cartoons
> hide sel surfaces
> show sel cartoons
> show sel atoms
> hide sel cartoons
> select clear
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/spike_monomer.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/spike_monomer.pdb
---
warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for spike_monomer.pdb #1
---
Chain | Description
A | No description available
> hide #1 models
> show sel atoms
> hide sel cartoons
> select clear
> show sel atoms
> hide sel cartoons
> select clear
> show sel atoms
> hide sel cartoons
> select clear
> show #1 models
> hide #1 models
> show sel atoms
> hide sel cartoons
> select clear
> show sel atoms
> hide sel cartoons
> select clear
Select exactly one bond first!
> show sel atoms
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> select clear
[Repeated 1 time(s)]
> show sel atoms
> hide sel cartoons
> show sel cartoons
> style sel stick
Changed 2 atom styles
> show sel atoms
> select add #19
8827 atoms, 9037 bonds, 1 pseudobond, 1134 residues, 2 models selected
> select subtract #19
Nothing selected
> select add #19
8827 atoms, 9037 bonds, 1 pseudobond, 1134 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select clear
> select add #19
8827 atoms, 9037 bonds, 1 pseudobond, 1134 residues, 2 models selected
> show sel atoms
> select clear
> show sel atoms
> hide sel cartoons
> select clear
> show sel atoms
> hide sel cartoons
Created disulphide bond between N649 and J617.
> select clear
> show sel atoms
> hide sel cartoons
> select clear
> show sel atoms
> hide sel cartoons
> select clear
[Repeated 1 time(s)]Created disulphide bond between D166 and D131.
> show sel atoms
> hide sel cartoons
> select clear
> show sel atoms
> hide sel cartoons
> show sel cartoons
> show sel atoms
> hide sel cartoons
[Repeated 1 time(s)]
> select clear
[Repeated 1 time(s)]
> show sel atoms
> hide sel cartoons
> select clear
> ui tool show "Side View"
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session3_ISOLDE.cxs" includeMaps true
> open "/home/carl/Documents/Phenix/2F PXT-apt and
> Spike/cryosparc_P1022_J623_map_sharp(1).mrc"
Opened cryosparc_P1022_J623_map_sharp(1).mrc as #2, grid size 640,640,640,
pixel 0.97, shown at level 8.17e-05, step 4, values float32
> open "/home/carl/Documents/Phenix/2F PXT-apt and
> Spike/cryosparc_P1022_J624_map_sharp.mrc"
Opened cryosparc_P1022_J624_map_sharp.mrc as #3, grid size 640,640,640, pixel
0.97, shown at level 7.95e-05, step 4, values float32
> open "/home/carl/Documents/Phenix/2F PXT-apt and
> Spike/cryosparc_P1022_J625_map_sharp.mrc"
Opened cryosparc_P1022_J625_map_sharp.mrc as #4, grid size 640,640,640, pixel
0.97, shown at level 1.79e-05, step 4, values float32
> open "/home/carl/Documents/Phenix/2F PXT-apt and
> Spike/Most_full_J406_class_06_00267_volume.mrc"
Opened Most_full_J406_class_06_00267_volume.mrc as #5, grid size 128,128,128,
pixel 5.05, shown at level 0.043, step 1, values float32
> open "/home/carl/Documents/Phenix/2F PXT-apt and
> Spike/Most_monomer_J590_class_8_00264_volume.mrc"
Opened Most_monomer_J590_class_8_00264_volume.mrc as #6, grid size
216,216,216, pixel 2.88, shown at level 0.0298, step 1, values float32
> close #5
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!6 models
> show #!6 models
> volume #6 level 0.3081
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/PXTaptamer.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/PXTaptamer.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 295
LEU A 303 1 9
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
66 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
Chain information for PXTaptamer.pdb #5
---
Chain | Description
B | No description available
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session4_ISOLDE.cxs" includeMaps true
——— End of log from Thu Feb 1 16:46:20 2024 ———
opened ChimeraX session
> hide #!6 models
> close #1
> select add #19
8827 atoms, 9045 bonds, 1 pseudobond, 1134 residues, 2 models selected
> show sel cartoons
> select clear
> color byhetero
> select #19/H:245
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #19
8827 atoms, 9045 bonds, 1 pseudobond, 1134 residues, 2 models selected
> hide sel atoms
> select subtract #19
Nothing selected
> select #19/H:245
10 atoms, 10 bonds, 1 residue, 1 model selected
> select add #19/I:246
21 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select clear
> select #19/I:246@N
1 atom, 1 residue, 1 model selected
> select add #19/H:245@C
2 atoms, 2 residues, 1 model selected
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> select clear
> show sel atoms
> hide sel cartoons
> select clear
[Repeated 1 time(s)]
> show sel atoms
> hide sel cartoons
> select clear
[Repeated 1 time(s)]
> select add #19
8827 atoms, 9048 bonds, 1 pseudobond, 1134 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select clear
> select ::name="CYS"
180 atoms, 164 bonds, 30 residues, 1 model selected
> show sel atoms
> select clear
Created disulphide bond between A136 and A15.
> select clear
> show sel atoms
> hide sel cartoons
> select clear
> select add #19
8827 atoms, 9050 bonds, 1 pseudobond, 1134 residues, 2 models selected
> show sel cartoons
> select subtract #19
Nothing selected
> select clear
> ui tool show "Side View"
> rename #19 spike
> select clear
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 67 residues in model #19 to IUPAC-IUB
standards.
> show #!6 models
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session5_ISOLDE.cxs" includeMaps true
——— End of log from Thu Feb 1 17:15:39 2024 ———
opened ChimeraX session
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/combined.pdb" models #1 relModel #6
> close session
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/combined.pdb"
combined.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for combined.pdb #1
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 14-1211
N | No description available |
O | No description available |
R | No description available |
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
combined.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for combined.pdb
---
Chain | Description | UniProt
1.2/A | spike glycoprotein | SPIKE_SARS2 14-1211
1.2/N | No description available |
1.2/O | No description available |
1.2/R | No description available |
> isolde sim start /A-R
Sim termination reason: None
ISOLDE: stopped sim
> addh #1.2
Summary of feedback from adding hydrogens to combined.pdb #1.2
---
notes | Termini for combined.pdb (#1.2) chain A determined from SEQRES records
Termini for combined.pdb (#1.2) chain N determined from SEQRES records
Termini for combined.pdb (#1.2) chain O determined from SEQRES records
Termini for combined.pdb (#1.2) chain R determined from SEQRES records
Chain-initial residues that are actual N termini: /O GLN 677
Chain-initial residues that are not actual N termini: /A GLN 14, /N ASN 641,
/R SER 689
Chain-final residues that are actual C termini: /O ALA 688
Chain-final residues that are not actual C termini: /A SER 640, /N THR 676, /R
SER 1147
929 hydrogen bonds
Adding 'H' to /A GLN 14
Adding 'H' to /N ASN 641
Adding 'H' to /R SER 689
/N THR 676 is not terminus, removing H atom from 'C'
/R SER 1147 is not terminus, removing H atom from 'C'
8602 hydrogens added
> open "/home/carl/Documents/Phenix/2F PXT-apt and
> Spike/Most_monomer_J590_class_8_00264_volume.mrc"
> "/home/carl/Documents/Phenix/2F PXT-apt and Spike/PXTaptamer.pdb"
> "/home/carl/Documents/Phenix/2F PXT-apt and
> Spike/cryosparc_P1022_J623_map_sharp(1).mrc" "/home/carl/Documents/Phenix/2F
> PXT-apt and Spike/cryosparc_P1022_J624_map_sharp.mrc"
> "/home/carl/Documents/Phenix/2F PXT-apt and
> Spike/cryosparc_P1022_J625_map_sharp.mrc"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/PXTaptamer.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 295
LEU A 303 1 9
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
66 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
Opened Most_monomer_J590_class_8_00264_volume.mrc as #2, grid size
216,216,216, pixel 2.88, shown at level 0.0298, step 1, values float32
Chain information for PXTaptamer.pdb #3
---
Chain | Description
B | No description available
Opened cryosparc_P1022_J623_map_sharp(1).mrc as #4, grid size 640,640,640,
pixel 0.97, shown at level 8.17e-05, step 4, values float32
Opened cryosparc_P1022_J624_map_sharp.mrc as #5, grid size 640,640,640, pixel
0.97, shown at level 7.95e-05, step 4, values float32
Opened cryosparc_P1022_J625_map_sharp.mrc as #6, grid size 640,640,640, pixel
0.97, shown at level 1.79e-05, step 4, values float32
> hide #!5 models
> hide #!6 models
> hide #!4 models
> hide #!2 models
> select clear
> combine
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> clipper associate #2 toModel #7
Opened Most_monomer_J590_class_8_00264_volume.mrc as #7.1.1.1, grid size
216,216,216, pixel 2.88, shown at step 1, values float32
> hide #3 models
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session6_ISOLDE.cxs" includeMaps true
——— End of log from Thu Feb 1 17:30:20 2024 ———
opened ChimeraX session
> close #1.1,3#1#1.2
> close #3
> select clear
[Repeated 1 time(s)]
> clipper associate #5 toModel #7
Opened cryosparc_P1022_J624_map_sharp.mrc as #7.1.1.2, grid size 640,640,640,
pixel 0.97, shown at step 1, values float32
> clipper associate #6 toModel #7
Opened cryosparc_P1022_J625_map_sharp.mrc as #7.1.1.3, grid size 640,640,640,
pixel 0.97, shown at step 1, values float32
> clipper associate #4 toModel #7
Opened cryosparc_P1022_J623_map_sharp(1).mrc as #7.1.1.4, grid size
640,640,640, pixel 0.97, shown at step 1, values float32
> isolde sim start /A:14-445,447-475,489-640/B:94-95,103-122/N-R
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde stepto /R:1146
> volume #7.1.1.4 level 0.07358
> volume #7.1.1.2 level 0.04374
> volume #7.1.1.3 level 0.0908
> isolde stepto prev
[Repeated 145 time(s)]
> isolde stepto /R:1000
> isolde stepto prev
[Repeated 98 time(s)]
> isolde stepto next
> isolde stepto /R:902
> isolde stepto prev
[Repeated 47 time(s)]
> isolde stepto next
> isolde pepflip /R:855
> isolde stepto /R:855
> isolde pepflip /R:855
> isolde cisflip /R:855
[Repeated 1 time(s)]
> volume #7.1.1.1 level 0.3221
> isolde stepto /A:590
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 40 residues in model #7.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session7_ISOLDE.cxs" includeMaps true
Taking snapshot of stepper: combination
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/all_ISOLDE.pdb" relModel #7.1.1.1
> close session
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/all_ISOLDE.pdb"
all_ISOLDE.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for all_ISOLDE.pdb #1
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 14-1211
B | spike glycoprotein | SPIKE_SARS2 14-1211
N | No description available |
O | No description available |
R | No description available |
> open "/home/carl/Documents/Phenix/2F PXT-apt and
> Spike/cryosparc_P1022_J623_map_sharp(1).mrc"
Opened cryosparc_P1022_J623_map_sharp(1).mrc as #2, grid size 640,640,640,
pixel 0.97, shown at level 8.17e-05, step 4, values float32
> open "/home/carl/Documents/Phenix/2F PXT-apt and
> Spike/cryosparc_P1022_J624_map_sharp.mrc"
Opened cryosparc_P1022_J624_map_sharp.mrc as #3, grid size 640,640,640, pixel
0.97, shown at level 7.95e-05, step 4, values float32
> open "/home/carl/Documents/Phenix/2F PXT-apt and
> Spike/cryosparc_P1022_J625_map_sharp.mrc"
Opened cryosparc_P1022_J625_map_sharp.mrc as #4, grid size 640,640,640, pixel
0.97, shown at level 1.79e-05, step 4, values float32
> open "/home/carl/Documents/Phenix/2F PXT-apt and
> Spike/Most_monomer_J590_class_8_00264_volume.mrc"
Opened Most_monomer_J590_class_8_00264_volume.mrc as #5, grid size
216,216,216, pixel 2.88, shown at level 0.0298, step 1, values float32
> volume #2 step 1
> volume #2 level 0.01246
> volume #3 step 1
> volume #3 level 0.02762
> volume #4 step 1
> volume #4 level 0.03618
> volume #5 level 0.1553
> select add #5
4 models selected
> transparency #5.1 50
> hide #!4 models
> hide #!3 models
> hide #!2 models
> select clear
> lighting simple
> lighting flat
> lighting full
> graphics silhouettes false
> set bgColor white
> show #!3 models
> hide #!5 models
> hide #!3 models
> show #!4 models
> volume #4 level 0.1582
> select add #1
26034 atoms, 26919 bonds, 1403 residues, 1 model selected
> style sel stick
Changed 26034 atom styles
> hide sel atoms
> show sel cartoons
> select clear
> select add #4
3 models selected
> transparency #4.1 50
> select clear
[Repeated 1 time(s)]
> graphics silhouettes true
> select clear
> show #!5 models
> volume #5 level 0.3046
> hide #!5 models
> hide #!4 models
> show sel atoms
> hide sel cartoons
> color sel byhetero
> select clear
> delete H
> select clear
> show sel atoms
> hide sel cartoons
> color sel byhetero
> select clear
> show sel atoms
> hide sel cartoons
> color sel byhetero
> select clear
> ui mousemode right "translate selected atoms"
> select clear
> show #!5 models
> hide #!5 models
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
all_ISOLDE.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for all_ISOLDE.pdb
---
Chain | Description | UniProt
1.2/A | spike glycoprotein | SPIKE_SARS2 14-1211
1.2/B | spike glycoprotein | SPIKE_SARS2 14-1211
1.2/N | No description available |
1.2/R | No description available |
> select clear
> clipper associate #5 toModel #1
Opened Most_monomer_J590_class_8_00264_volume.mrc as #1.1.1.1, grid size
216,216,216, pixel 2.88, shown at step 1, values float32
> isolde sim start
> /A:294-300,304-313,315,595-612,616-622,625,627-640/N:641-645,648-664,670-688/R:689-698,932-933,935-937,939-942
Sim termination reason: None
ISOLDE: stopped sim
> addh #1.2
Summary of feedback from adding hydrogens to all_ISOLDE.pdb #1.2
---
warning | Not adding hydrogens to /B G 1 P because it is missing heavy-atom
bond partners
notes | Termini for all_ISOLDE.pdb (#1.2) chain A determined from SEQRES
records
Termini for all_ISOLDE.pdb (#1.2) chain B determined from SEQRES records
Termini for all_ISOLDE.pdb (#1.2) chain N determined from SEQRES records
Termini for all_ISOLDE.pdb (#1.2) chain R determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A GLN 14, /N ASN 641,
/N GLN 677, /R SER 689
Chain-final residues that are actual C termini: /N ALA 688
Chain-final residues that are not actual C termini: /A SER 640, /N THR 676, /R
SER 1147
1603 hydrogen bonds
Adding 'H' to /A GLN 14
Adding 'H' to /R SER 689
/R SER 1147 is not terminus, removing H atom from 'C'
11489 hydrogens added
Chain B, residue 251 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 252 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 253 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 254 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 255 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 256 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 257 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 258 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 263 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 264 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 265 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 266 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 267 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 268 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 269 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
> select clear
Fetching CCD SAC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/SAC/SAC.cif
Fetching CCD THC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/THC/THC.cif
Failed to add atoms ['HB3'] to atom CB because this will lead to having 5
atoms attached, which is more than its assigned geometry can support. This is
probably due to an error in the MD template (SER). If this template is built
into ISOLDE, please report this using Help/Report a bug
> select clear
[Repeated 1 time(s)]
Chain B, residue 251 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 252 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 253 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 254 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 255 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 256 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 257 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 258 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 263 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 264 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 265 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 266 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 267 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 268 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 269 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
> isolde sim start
> /A:293-301,305-320,535-538,550-555,590-592,594-622,624-688/R:689-699,940-941
ISOLDE: started sim
> select clear
> volume #1.1.1.1 level 0.2975
> clipper associate #3 toModel #1
Opened cryosparc_P1022_J624_map_sharp.mrc as #1.1.1.2, grid size 640,640,640,
pixel 0.97, shown at step 1, values float32
> volume #1.1.1.2 level 0.05221
> isolde stepto /A:655
> isolde stepto next
> isolde stepto /A:656
> isolde stepto next
[Repeated 3 time(s)]
> isolde stepto prev
[Repeated 9 time(s)]
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/spike_monomer.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/spike_monomer.pdb
---
warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for spike_monomer.pdb #3
---
Chain | Description
A | No description available
> select clear
[Repeated 2 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui mousemode right "translate selected atoms"
> select clear
> isolde sim start #1.2/A:636-640,654-657,673-686/R:689-691,693-694
ISOLDE: started sim
Chain B, residue 251 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 252 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 253 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 254 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 255 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 256 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 257 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 258 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 263 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 264 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 265 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 266 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 267 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 268 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 269 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
> isolde cisflip #1.2/A:677
> isolde pepflip #1.2/A:677
> select clear
[Repeated 9 time(s)]
> delete atoms (#!1.2 & sel)
> delete bonds (#!1.2 & sel)
Sim termination reason: coord length mismatch
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> delete atoms (#!1.2 & sel)
> delete bonds (#!1.2 & sel)
> select clear
> isolde sim start #1.2/A:638,654,676-690
Sim termination reason: None
ISOLDE: stopped sim
Chain B, residue 251 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 252 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 253 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 254 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 255 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 256 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 257 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 258 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 263 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 264 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 265 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 266 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 267 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 268 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 269 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
> isolde cisflip #1.2/A:689
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #1.2/A:633-640,654,674-691
ISOLDE: started sim
> select clear
> isolde pepflip #1.2/A:689
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #1.1.1.2 level 0.006207
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session8_ISOLDE.cxs" includeMaps true
Taking snapshot of stepper: all_ISOLDE.pdb
——— End of log from Thu Feb 1 18:15:35 2024 ———
opened ChimeraX session
> volume #1.1.1.1 level 0.3019
> volume #1.1.1.2 level 0.05221
> volume #1.1.1.1 level 0.2531
> hide #3 models
Drag select of 631 atoms, 527 residues, 631 bonds
Drag select of 675 atoms, 664 residues, 676 bonds
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> select clear
> show #!4 models
> hide #!4 models
> show #3 models
> clipper associate #4 toModel #1
Opened cryosparc_P1022_J625_map_sharp.mrc as #1.1.1.3, grid size 640,640,640,
pixel 0.97, shown at step 1, values float32
> isolde stepto #1.2/A:293
> isolde stepto prev
> isolde sim start
> #1.2/A:14-46,48-294,297,300-301,306,321-324,539,621-634,842-847,973-982
ISOLDE: started sim
> select clear
> isolde stepto #1.2/A:289
> isolde stepto prev
[Repeated 5 time(s)]
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto #1.2/A:283
> isolde sim start #1.2/A:283
ISOLDE: started sim
> isolde stepto prev
[Repeated 6 time(s)]
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #1.2/A:14-46,51-290,293,842-844
ISOLDE: started sim
> select clear
> volume #1.1.1.3 level 0.06073
> isolde stepto prev
> isolde stepto next
> isolde stepto #1.2/A:276
> isolde stepto prev
[Repeated 12 time(s)]
> volume #1.1.1.1 level 0.3472
> isolde stepto #1.2/A:263
> isolde stepto prev
[Repeated 8 time(s)]
> volume #1.1.1.3 level 0.1721
> volume #1.1.1.1 level 0.1375
> isolde cisflip #1.2/A:70
> isolde pepflip #1.2/A:69
> isolde pepflip #1.2/A:137
[Repeated 1 time(s)]
> volume #1.1.1.1 level 0.2047
> volume #1.1.1.1 level 0.3526
> volume #1.1.1.1 level 0.1563
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/all_ISOLDE_DONE.pdb" models #1 relModel #1.1.1.1
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session9_ISOLDE.cxs" includeMaps true
Taking snapshot of stepper: all_ISOLDE.pdb
> isolde sim start #1.2/A:567,570-573
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #1.2/A:321-332,528-590
ISOLDE: started sim
> isolde pepflip #1.2/A:560
> isolde stepto #1.2/A:557
> isolde stepto next
> isolde pepflip #1.2/A:558
[Repeated 3 time(s)]
> isolde stepto next
> isolde stepto prev
> isolde stepto #1.2/A:560
> isolde stepto next
> isolde pepflip #1.2/A:564
[Repeated 1 time(s)]
> select clear
> isolde pepflip #1.2/A:561
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip #1.2/A:561
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde pepflip #1.2/A:560
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 7 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> clipper associate #2 toModel #1
Opened cryosparc_P1022_J623_map_sharp(1).mrc as #1.1.1.4, grid size
640,640,640, pixel 0.97, shown at step 1, values float32
> select clear
> volume #1.1.1.1 level 0.1233
> volume #1.1.1.1 level 0.4268
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/spike_monomer.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/spike_monomer.pdb
---
warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for spike_monomer.pdb #2
---
Chain | Description
A | No description available
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/spike_monomer.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/spike_monomer.pdb
---
warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for spike_monomer.pdb #4
---
Chain | Description
A | No description available
> select add #3
16512 atoms, 16717 bonds, 1068 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.99953,0.0064494,-0.029842,6.9443,-0.0062675,0.99996,0.0061857,-0.029367,0.029881,-0.0059958,0.99954,-6.514
> undo
> view matrix models
> #3,0.096041,-0.96157,-0.25723,615.26,0.99325,0.075682,0.087933,-31.782,-0.065086,-0.26394,0.96234,107.62
> open "/home/carl/Documents/Phenix/2F PXT-apt and
> Spike/Most_full_J406_class_06_00267_volume.mrc"
Opened Most_full_J406_class_06_00267_volume.mrc as #5, grid size 128,128,128,
pixel 5.05, shown at level 0.043, step 1, values float32
> select add #5
16512 atoms, 16717 bonds, 1068 residues, 3 models selected
> view matrix models
> #3,-0.25446,-0.82701,0.50131,454.37,0.44786,0.35866,0.81902,-160.45,-0.85713,0.43292,0.27911,393.41,#5,0.64183,-0.27125,0.71727,-26.34,-0.51254,0.54399,0.66436,100.68,-0.5704,-0.79404,0.21013,696.51
> undo
> select subtract #3
2 models selected
> view matrix models
> #5,-0.65347,0.75438,0.062383,268.75,0.74992,0.63398,0.18893,-183.89,0.10297,0.17024,-0.98001,547.28
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.65347,0.75438,0.062383,251.57,0.74992,0.63398,0.18893,-172.5,0.10297,0.17024,-0.98001,577.15
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.65347,0.75438,0.062383,259.03,0.74992,0.63398,0.18893,-169.95,0.10297,0.17024,-0.98001,569.32
> ui tool show "Fit in Map"
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 20802 points
correlation = 0.05547, correlation about mean = 0.03341, overlap = 13.65
steps = 524, shift = 27.5, angle = 7.9 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.66866301 0.74032594 -0.06933461 285.96968299
0.71294546 0.66481734 0.22299481 -166.23883163
0.21118369 0.09967659 -0.97235078 566.25013249
Axis -0.40084132 -0.91181433 -0.08899922
Axis point 155.55086373 0.00000000 303.14248387
Rotation angle (degrees) 171.15138763
Shift along axis -13.44533623
> volume #5 level 0.07726
> view matrix models
> #5,-0.66866,0.74033,-0.069335,299.45,0.71295,0.66482,0.22299,-167,0.21118,0.099677,-0.97235,559.91
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.69792,0.71144,0.082179,268.48,0.71579,0.68915,0.11277,-139.85,0.023593,0.13752,-0.99022,611.46
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.69792,0.71144,0.082179,279.6,0.71579,0.68915,0.11277,-169.65,0.023593,0.13752,-0.99022,597.34
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 15868 points
correlation = 0.07408, correlation about mean = 0.05154, overlap = 18.31
steps = 1604, shift = 18.2, angle = 20 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.79315950 0.58576733 -0.16665728 432.61548426
0.52975049 0.79859088 0.28568696 -206.95381765
0.30043707 0.13830855 -0.94372047 481.56455088
Axis -0.29895036 -0.94747952 -0.11362760
Axis point 217.05528559 0.00000000 282.00737454
Rotation angle (degrees) 165.72991079
Shift along axis 12.03492603
> view matrix models
> #5,-0.79316,0.58577,-0.16666,293.72,0.52975,0.79859,0.28569,-104.72,0.30044,0.13831,-0.94372,515.56
> view matrix models
> #5,-0.79316,0.58577,-0.16666,378.68,0.52975,0.79859,0.28569,-194.53,0.30044,0.13831,-0.94372,505.49
> view matrix models
> #5,-0.79316,0.58577,-0.16666,395.34,0.52975,0.79859,0.28569,-191.27,0.30044,0.13831,-0.94372,508.34
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 15868 points
correlation = 0.04237, correlation about mean = 0.0126, overlap = 8.74
steps = 64, shift = 6.33, angle = 2.8 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.78352990 0.59325283 -0.18474842 395.64951001
0.54774419 0.79984674 0.24540071 -191.93577361
0.29335508 0.09108392 -0.95165463 528.55840301
Axis -0.30591225 -0.94777581 -0.09021476
Axis point 192.97662616 0.00000000 300.44219388
Rotation angle (degrees) 165.39084736
Shift along axis 13.19428423
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 15868 points
correlation = 0.04238, correlation about mean = 0.01263, overlap = 8.767
steps = 80, shift = 0.858, angle = 0.629 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.78230969 0.59319857 -0.19001846 397.29606048
0.55003839 0.80104633 0.23618331 -189.69218495
0.29231719 0.08025104 -0.95294829 533.07045407
Axis -0.30650148 -0.94808212 -0.08483595
Axis point 192.88190948 0.00000000 302.38545600
Rotation angle (degrees) 165.26348115
Shift along axis 12.84839700
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.79661,0.60259,0.047955,321.09,0.60336,0.78773,0.12424,-165.36,0.037088,0.1279,-0.99109,608.97
> view matrix models
> #5,-0.88888,0.44452,0.11093,380.41,0.45786,0.87046,0.1807,-165.64,-0.016234,0.21141,-0.97726,593.84
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.88888,0.44452,0.11093,312.85,0.45786,0.87046,0.1807,-56.106,-0.016234,0.21141,-0.97726,611.04
> hide #4 models
> hide #3 models
> view matrix models
> #5,-0.88888,0.44452,0.11093,436.26,0.45786,0.87046,0.1807,-115.47,-0.016234,0.21141,-0.97726,580.62
> view matrix models
> #5,-0.88888,0.44452,0.11093,404.21,0.45786,0.87046,0.1807,-141.62,-0.016234,0.21141,-0.97726,591.26
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.91538,0.39965,-0.048592,478.98,0.39491,0.91481,0.084701,-105.25,0.078303,0.058344,-0.99522,617.58
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.91538,0.39965,-0.048592,448.6,0.39491,0.91481,0.084701,-121.23,0.078303,0.058344,-0.99522,609.37
> view matrix models
> #5,-0.91538,0.39965,-0.048592,452.8,0.39491,0.91481,0.084701,-121.67,0.078303,0.058344,-0.99522,610.74
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.95968,0.26362,0.097562,463.02,0.27929,0.93354,0.22474,-137.65,-0.03183,0.24293,-0.96952,576.49
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.95968,0.26362,0.097562,483.46,0.27929,0.93354,0.22474,-137.9,-0.03183,0.24293,-0.96952,577.79
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 15868 points
correlation = 0.08704, correlation about mean = 0.0707, overlap = 21.33
steps = 264, shift = 8.35, angle = 6.31 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.95596121 0.29337498 -0.00832596 504.37229053
0.28436320 0.93287138 0.22110764 -146.60353308
0.07263449 0.20900273 -0.97521388 556.64569982
Axis -0.14698465 -0.98306737 -0.10942607
Axis point 257.30406657 0.00000000 291.77997206
Rotation angle (degrees) 177.64003760
Shift along axis 9.07461187
> volume #5 level 0.4925
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.65298,0.68102,0.33139,173.8,0.72417,0.68955,0.0098827,-132.88,-0.22178,0.24644,-0.94344,624.28
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.65298,0.68102,0.33139,185.45,0.72417,0.68955,0.0098827,-143.77,-0.22178,0.24644,-0.94344,623.76
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.09882, correlation about mean = 0.06206, overlap = 26.06
steps = 100, shift = 5.42, angle = 4.04 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.69184583 0.66688561 0.27679047 222.16671073
0.69512984 0.71886317 0.00550297 -137.99016487
-0.19530463 0.19621252 -0.96091455 637.17248170
Axis 0.37398225 0.92578051 0.05538705
Axis point 183.59972167 0.00000000 306.91477506
Rotation angle (degrees) 165.22810984
Shift along axis -9.37109811
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.09358, correlation about mean = 0.06508, overlap = 23.53
steps = 516, shift = 1.26, angle = 1.35 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.70466370 0.65171752 0.28055904 230.21370744
0.68366901 0.72943915 0.02269917 -144.31205326
-0.18985730 0.20780480 -0.95956834 631.03906855
Axis 0.36543587 0.92869678 0.06307868
Axis point 187.27984924 0.00000000 304.20934809
Rotation angle (degrees) 165.32908381
Shift along axis -10.08868296
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.09852, correlation about mean = 0.06151, overlap = 25.92
steps = 416, shift = 1.86, angle = 3.66 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.73259003 0.62459563 0.27054052 252.11795520
0.66384472 0.74344763 0.08121475 -161.95710425
-0.15040633 0.23909401 -0.95927682 607.32251921
Axis 0.34983998 0.93276366 0.08697090
Axis point 193.69331005 0.00000000 295.54968843
Rotation angle (degrees) 166.95919285
Shift along axis -10.04737873
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07852, correlation about mean = 0.03478, overlap = 17.33
steps = 536, shift = 8.05, angle = 17.5 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.68185526 0.73005554 0.04574209 271.71136828
0.71798180 0.65599565 0.23274853 -205.76454843
0.13991274 0.19154279 -0.97146066 533.34198569
Axis -0.39813142 -0.90988049 -0.11665700
Axis point 173.25692794 0.00000000 283.82292810
Rotation angle (degrees) 177.03368086
Shift along axis 16.82623886
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07838, correlation about mean = 0.03464, overlap = 17.18
steps = 44, shift = 0.675, angle = 0.417 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.68560617 0.72679483 0.04139432 275.69955382
0.71441670 0.66082812 0.23003262 -205.12482139
0.13983199 0.18728457 -0.97230218 534.50552099
Axis -0.39570351 -0.91120260 -0.11457990
Axis point 174.43386082 0.00000000 284.33559058
Rotation angle (degrees) 176.90364731
Shift along axis 16.57140068
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07879, correlation about mean = 0.03666, overlap = 17.33
steps = 236, shift = 2.96, angle = 3.08 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.66983939 0.74068838 0.05192255 261.77416490
0.72247062 0.63403417 0.27574792 -215.79425387
0.17132260 0.22221933 -0.95982663 508.48375025
Axis -0.40517594 -0.90377931 -0.13789639
Axis point 169.90996683 0.00000000 275.63264636
Rotation angle (degrees) 176.21251367
Shift along axis 18.84771400
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.0788, correlation about mean = 0.03677, overlap = 17.29
steps = 60, shift = 0.052, angle = 0.293 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.67359564 0.73725244 0.05222828 264.04534245
0.71917430 0.63749960 0.27637406 -216.03334696
0.17046194 0.22372559 -0.95962993 508.20756472
Axis -0.40287356 -0.90474080 -0.13833646
Axis point 170.88904162 0.00000000 275.52892339
Rotation angle (degrees) 176.25355695
Shift along axis 18.77366252
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.0787, correlation about mean = 0.03683, overlap = 17.28
steps = 96, shift = 0.359, angle = 0.409 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.67620992 0.73479393 0.05308544 265.40891068
0.71595959 0.63847487 0.28240351 -217.48715397
0.17361466 0.22897108 -0.95782578 504.73452775
Axis -0.40120305 -0.90500641 -0.14141964
Axis point 171.56784828 0.00000000 274.38766844
Rotation angle (degrees) 176.18183409
Shift along axis 18.96503053
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07845, correlation about mean = 0.03789, overlap = 16.88
steps = 76, shift = 1.49, angle = 1.44 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.68760979 0.72510675 0.03759008 278.20056776
0.70548444 0.65496573 0.27076121 -215.08917714
0.17171056 0.21269727 -0.96191236 512.29450911
Axis -0.39375781 -0.90953162 -0.13306775
Axis point 175.21415981 0.00000000 277.67029946
Rotation angle (degrees) 175.77171569
Shift along axis 17.91688635
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07637, correlation about mean = 0.03768, overlap = 16.21
steps = 180, shift = 2.14, angle = 2.12 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.70193390 0.71200668 0.01831183 294.41517587
0.69317901 0.67701238 0.24729968 -209.58873300
0.16368168 0.18628140 -0.96876601 526.27774735
Axis -0.38430197 -0.91556044 -0.11857938
Axis point 179.72598553 0.00000000 283.24001981
Rotation angle (degrees) 175.44658506
Shift along axis 16.34113070
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07441, correlation about mean = 0.03444, overlap = 15.67
steps = 212, shift = 2.55, angle = 2.44 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.71191982 0.70217541 -0.01094943 311.80698273
0.68320694 0.69612704 0.22053448 -202.68587278
0.16247608 0.14952215 -0.97531773 540.43471405
Axis -0.37700609 -0.92071988 -0.10070404
Axis point 183.51159875 0.00000000 289.43457641
Rotation angle (degrees) 174.59591472
Shift along axis 14.63982168
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07721, correlation about mean = 0.03344, overlap = 16.94
steps = 288, shift = 8.47, angle = 8.55 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.68220555 0.73098798 -0.01588031 293.98466491
0.67871434 0.64119915 0.35806497 -233.45888501
0.27192362 0.23349571 -0.93356163 461.24790882
Axis -0.39181026 -0.90523569 -0.16441737
Axis point 176.98917388 0.00000000 265.16614488
Rotation angle (degrees) 170.85309837
Shift along axis 20.31193920
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07712, correlation about mean = 0.03278, overlap = 17.15
steps = 188, shift = 1.27, angle = 1.26 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.67400734 0.73851754 -0.01749251 289.33587859
0.68004653 0.62954454 0.37577976 -236.60914631
0.28853225 0.24138259 -0.92654391 450.45472589
Axis -0.39608732 -0.90189793 -0.17232227
Axis point 175.11261605 0.00000000 261.93470563
Rotation angle (degrees) 170.23218227
Shift along axis 21.17164646
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07709, correlation about mean = 0.03269, overlap = 17.19
steps = 96, shift = 0.335, angle = 0.324 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.67285717 0.73949913 -0.02010701 289.58800375
0.67893288 0.62808684 0.38020665 -237.37726027
0.29379143 0.24217346 -0.92468299 447.72987197
Axis -0.39640224 -0.90145017 -0.17393351
Axis point 175.02037876 0.00000000 261.26733207
Rotation angle (degrees) 169.97327660
Shift along axis 21.31520838
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07704, correlation about mean = 0.03296, overlap = 17.42
steps = 104, shift = 0.598, angle = 0.464 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.67036529 0.74167309 -0.02305290 289.04110396
0.67820679 0.62501463 0.38651301 -238.42912790
0.30107469 0.24347027 -0.92199581 443.64789578
Axis -0.39742085 -0.90053547 -0.17633075
Axis point 174.59271066 0.00000000 260.15903949
Rotation angle (degrees) 169.63234830
Shift along axis 21.61416036
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07824, correlation about mean = 0.03204, overlap = 18.01
steps = 80, shift = 1.05, angle = 0.956 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.66696977 0.74453314 -0.02866626 289.05182718
0.67480794 0.61992502 0.40040884 -240.71240001
0.31588858 0.24771637 -0.91588811 434.93647657
Axis -0.39839572 -0.89899110 -0.18192266
Axis point 174.25118957 0.00000000 257.84591926
Rotation angle (degrees) 168.95183171
Shift along axis 22.11649473
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07725, correlation about mean = 0.03103, overlap = 17.67
steps = 64, shift = 0.407, angle = 0.362 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.66496070 0.74652236 -0.02305785 285.63937910
0.67780141 0.61613960 0.40119480 -240.76875824
0.31370774 0.25115013 -0.91570251 434.55913700
Axis -0.40008778 -0.89797122 -0.18324151
Axis point 173.35213113 0.00000000 257.36047307
Rotation angle (degrees) 169.19222035
Shift along axis 22.29332028
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07718, correlation about mean = 0.03082, overlap = 17.73
steps = 100, shift = 0.519, angle = 0.517 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.66087432 0.75028471 -0.01783309 281.09150456
0.68105406 0.60953772 0.40574519 -241.37365015
0.31529435 0.25600128 -0.91381226 431.74886030
Axis -0.40281984 -0.89613219 -0.18623446
Axis point 171.99043034 0.00000000 256.13684756
Rotation angle (degrees) 169.28816485
Shift along axis 22.66694452
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07716, correlation about mean = 0.03072, overlap = 17.73
steps = 56, shift = 0.332, angle = 0.36 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.65847662 0.75224067 -0.02329269 281.69865706
0.68137621 0.60901632 0.40598722 -241.39098006
0.31958572 0.25146201 -0.91358188 431.69774107
Axis -0.40376792 -0.89592693 -0.18516586
Axis point 171.75208893 0.00000000 256.46696947
Rotation angle (degrees) 168.96818750
Shift along axis 22.59211655
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07808, correlation about mean = 0.02985, overlap = 18.77
steps = 128, shift = 1.83, angle = 1.91 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.64617602 0.76272335 -0.02663956 275.37378581
0.68036562 0.59151509 0.43268066 -245.12926246
0.34577334 0.26146322 -0.90115360 415.14759202
Axis -0.40953425 -0.89077281 -0.19699110
Axis point 169.13015951 0.00000000 251.59277263
Rotation angle (degrees) 167.93394636
Shift along axis 23.79910421
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.0781, correlation about mean = 0.02983, overlap = 18.73
steps = 100, shift = 0.229, angle = 0.366 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.64241653 0.76587811 -0.02705082 273.24366920
0.68450884 0.58932092 0.42912531 -244.48121105
0.34459929 0.25716067 -0.90283982 417.60659768
Axis -0.41187913 -0.89015347 -0.19489066
Axis point 168.15281277 0.00000000 252.34380239
Rotation angle (degrees) 167.95052786
Shift along axis 23.69480725
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07712, correlation about mean = 0.02942, overlap = 18.32
steps = 84, shift = 0.977, angle = 0.903 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.63581939 0.77136867 -0.02690923 269.18932445
0.68485697 0.57990235 0.44123036 -245.97791196
0.35595599 0.26211384 -0.89699035 409.87757097
Axis -0.41514601 -0.88738310 -0.20051188
Axis point 166.62509531 0.00000000 249.90581575
Rotation angle (degrees) 167.54181017
Shift along axis 24.33844703
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07808, correlation about mean = 0.0301, overlap = 18.34
steps = 100, shift = 2.1, angle = 2.03 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.64006000 0.76743920 -0.03688247 275.62176186
0.69041816 0.59555834 0.41064957 -241.76006914
0.33711423 0.23737603 -0.91104700 429.42870843
Axis -0.41322480 -0.89191180 -0.18368069
Axis point 168.04551848 0.00000000 256.54924375
Rotation angle (degrees) 167.89756371
Shift along axis 22.85714856
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07888, correlation about mean = 0.03326, overlap = 18.16
steps = 112, shift = 0.824, angle = 0.716 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.63829416 0.76855637 -0.04360856 277.06468080
0.68629634 0.59380688 0.41998899 -243.21156193
0.34868027 0.23814812 -0.90648087 423.43334106
Axis -0.41314312 -0.89128166 -0.18689508
Axis point 168.16840593 0.00000000 255.12963958
Rotation angle (degrees) 167.28685160
Shift along axis 23.16502973
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07882, correlation about mean = 0.03309, overlap = 18.18
steps = 92, shift = 0.336, angle = 0.339 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.63583873 0.77079384 -0.03982459 274.12108877
0.68814661 0.58951670 0.42299449 -243.53647892
0.34951880 0.24155112 -0.90525670 421.59198201
Axis -0.41479891 -0.89008055 -0.18894040
Axis point 167.31650277 0.00000000 254.29362069
Rotation angle (degrees) 167.36657993
Shift along axis 23.40619456
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07605, correlation about mean = 0.02931, overlap = 17.39
steps = 548, shift = 0.999, angle = 1.03 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.63809997 0.76805558 -0.05402858 280.91272517
0.68602872 0.59900362 0.41298825 -242.28686493
0.34956124 0.22646263 -0.90913236 427.96053203
Axis -0.41256538 -0.89267730 -0.18143054
Axis point 168.73135783 0.00000000 257.22100016
Rotation angle (degrees) 166.93502763
Shift along axis 22.74400943
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07781, correlation about mean = 0.03137, overlap = 18.44
steps = 200, shift = 1.53, angle = 1.42 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.64258394 0.76358929 -0.06338223 287.35160828
0.68751488 0.61112308 0.39223959 -239.13156144
0.33824429 0.20847064 -0.91767686 440.85630041
Axis -0.41003699 -0.89613464 -0.16974206
Axis point 170.23678556 0.00000000 261.83280154
Rotation angle (degrees) 167.05072938
Shift along axis 21.63742986
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07677, correlation about mean = 0.0299, overlap = 17.49
steps = 1220, shift = 1.61, angle = 1.54 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.64078929 0.76614531 -0.04909666 280.65888581
0.68528085 0.59964144 0.41330417 -242.34763554
0.34609144 0.23119589 -0.90926850 427.61768416
Axis -0.41147074 -0.89292114 -0.18271196
Axis point 169.08062877 0.00000000 256.79880501
Rotation angle (degrees) 167.21521900
Shift along axis 22.78354223
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07808, correlation about mean = 0.03249, overlap = 18.1
steps = 392, shift = 0.811, angle = 0.809 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.63479535 0.77140068 -0.04445081 275.18849547
0.68740660 0.59007449 0.42341976 -243.63721973
0.35285557 0.23822911 -0.90484245 421.40973245
Axis -0.41492650 -0.89017966 -0.18819185
Axis point 167.34809343 0.00000000 254.54159184
Rotation angle (degrees) 167.10525090
Shift along axis 23.39202030
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07603, correlation about mean = 0.0303, overlap = 17.95
steps = 152, shift = 1.56, angle = 1.49 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.64113957 0.76544095 -0.05513831 283.21890864
0.68716471 0.60459254 0.40283069 -240.77280548
0.34167931 0.22038159 -0.91361219 434.26440664
Axis -0.41118943 -0.89431636 -0.17641285
Axis point 169.44210342 0.00000000 259.24078621
Rotation angle (degrees) 167.18197405
Shift along axis 22.26061496
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07736, correlation about mean = 0.03187, overlap = 18.14
steps = 548, shift = 1.44, angle = 1.45 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.65277954 0.75443572 -0.06859774 295.68132235
0.67906523 0.62288410 0.38844028 -238.73676496
0.33578166 0.20698352 -0.91891704 442.63503101
Axis -0.40360617 -0.89944306 -0.16764322
Axis point 173.16489537 0.00000000 262.82137296
Rotation angle (degrees) 167.00921580
Shift along axis 21.18655956
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07633, correlation about mean = 0.03112, overlap = 18.06
steps = 88, shift = 1.15, angle = 1.35 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.65772173 0.74795866 -0.08921882 306.73979516
0.67168435 0.63597356 0.37997079 -237.41877842
0.34094325 0.18998815 -0.92068574 447.15851922
Axis -0.39879367 -0.90295575 -0.16010787
Axis point 175.65882304 0.00000000 265.69879414
Rotation angle (degrees) 166.21987035
Shift along axis 20.45916585
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07764, correlation about mean = 0.03316, overlap = 18.37
steps = 80, shift = 0.62, angle = 0.608 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.66105466 0.74457038 -0.09285318 310.32418641
0.67084977 0.64191402 0.37135833 -235.93805995
0.33610616 0.18319761 -0.92383511 452.15676997
Axis -0.39681405 -0.90463675 -0.15547015
Axis point 176.64787074 0.00000000 267.50664210
Rotation angle (degrees) 166.28518949
Shift along axis 20.00036162
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07635, correlation about mean = 0.03128, overlap = 17.99
steps = 100, shift = 0.454, angle = 0.451 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.66078740 0.74555634 -0.08663593 307.62991784
0.67133797 0.63869887 0.37599085 -236.73860314
0.33565663 0.19028803 -0.92256443 449.50890065
Axis -0.39743569 -0.90377804 -0.15883996
Axis point 176.19944813 0.00000000 266.24607946
Rotation angle (degrees) 166.48934119
Shift along axis 20.29606434
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07642, correlation about mean = 0.03137, overlap = 17.93
steps = 76, shift = 0.317, angle = 0.394 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.66176280 0.74544529 -0.07988329 305.58615638
0.67224020 0.63717216 0.37696787 -236.91310681
0.33190833 0.19576256 -0.92277511 449.04466352
Axis -0.39754196 -0.90341967 -0.16060288
Axis point 176.01122219 0.00000000 265.62934658
Rotation angle (degrees) 166.82611163
Shift along axis 20.43077293
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07635, correlation about mean = 0.03165, overlap = 17.81
steps = 76, shift = 1.01, angle = 0.972 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.66631085 0.74105561 -0.08286410 309.64017873
0.67266116 0.64530356 0.36209157 -234.26307568
0.32180248 0.18552608 -0.92845208 457.89621987
Axis -0.39519971 -0.90574957 -0.15308465
Axis point 177.14446161 0.00000000 268.56780014
Rotation angle (degrees) 167.09191441
Shift along axis 19.71708861
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07469, correlation about mean = 0.02943, overlap = 17.03
steps = 180, shift = 0.777, angle = 0.791 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.67163551 0.73492494 -0.09376084 317.42716490
0.66576128 0.65420942 0.35884814 -233.64072013
0.32506567 0.17859282 -0.92867483 459.16524189
Axis -0.39085287 -0.90815371 -0.14996959
Axis point 179.25999667 0.00000000 269.78314460
Rotation angle (degrees) 166.66805471
Shift along axis 19.25354660
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07643, correlation about mean = 0.03166, overlap = 17.84
steps = 72, shift = 0.94, angle = 0.882 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.66834001 0.73929299 -0.08226498 310.66753347
0.66912156 0.64581794 0.36768949 -235.29079282
0.32495845 0.19069632 -0.92630283 454.33334511
Axis -0.39372517 -0.90587744 -0.15609789
Axis point 177.72354501 0.00000000 267.45196660
Rotation angle (degrees) 167.01079936
Shift along axis 19.90651752
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07651, correlation about mean = 0.03153, overlap = 17.84
steps = 96, shift = 0.789, angle = 0.8 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.66536325 0.74278816 -0.07454880 305.73565626
0.67037256 0.63844689 0.37813521 -237.10230275
0.32846981 0.20162180 -0.92274388 448.25949315
Axis -0.39586054 -0.90383593 -0.16240398
Axis point 176.58766872 0.00000000 265.03178132
Rotation angle (degrees) 167.11769959
Shift along axis 20.47377208
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07895, correlation about mean = 0.03336, overlap = 18.08
steps = 328, shift = 3.7, angle = 3.75 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.64342923 0.76459953 -0.03723457 277.75773371
0.68392300 0.59602606 0.42071641 -243.37671836
0.34387234 0.24523566 -0.90642778 422.72670986
Axis -0.41071911 -0.89199463 -0.18882636
Axis point 169.03953716 0.00000000 254.52488348
Rotation angle (degrees) 167.66505622
Shift along axis 23.18836749
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.0768, correlation about mean = 0.02995, overlap = 17.48
steps = 140, shift = 0.788, angle = 0.873 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.64332756 0.76390069 -0.05084689 282.86191104
0.68240077 0.60226510 0.41425351 -242.57160132
0.34707185 0.23180274 -0.90874014 426.91384375
Axis -0.40974850 -0.89364712 -0.18303278
Axis point 169.85202495 0.00000000 256.72713695
Rotation angle (degrees) 167.13600608
Shift along axis 22.73194298
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07806, correlation about mean = 0.03377, overlap = 18.14
steps = 792, shift = 2.87, angle = 3.14 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.64393255 0.75812200 -0.10296574 303.69852465
0.66001086 0.61851301 0.42641219 -244.74662828
0.38695810 0.20662218 -0.89864939 418.08786093
Axis -0.40265197 -0.89753306 -0.17973812
Axis point 174.03996975 0.00000000 257.77844431
Rotation angle (degrees) 164.16142439
Shift along axis 22.23705544
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07667, correlation about mean = 0.03029, overlap = 17.81
steps = 60, shift = 0.208, angle = 0.242 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.64545161 0.75643121 -0.10584932 305.79899967
0.65871196 0.62142578 0.42417990 -244.48896446
0.38664040 0.20406338 -0.89937054 419.30987342
Axis -0.40151042 -0.89834130 -0.17824785
Axis point 174.61921029 0.00000000 258.38356328
Rotation angle (degrees) 164.09098209
Shift along axis 22.11196693
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07585, correlation about mean = 0.0303, overlap = 17.44
steps = 28, shift = 0.0607, angle = 0.032 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.64552059 0.75630174 -0.10635264 306.04936305
0.65841755 0.62164280 0.42431898 -244.45977622
0.38702653 0.20388219 -0.89924554 419.18627235
Axis -0.40139392 -0.89839540 -0.17823757
Axis point 174.67131970 0.00000000 258.37665394
Rotation angle (degrees) 164.06247149
Shift along axis 22.06044222
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07677, correlation about mean = 0.03066, overlap = 17.67
steps = 40, shift = 0.827, angle = 0.839 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.64865841 0.75409940 -0.10284155 306.61419040
0.66235202 0.62589398 0.41176031 -242.62445198
0.37487611 0.19897448 -0.90547064 427.17569648
Axis -0.40076318 -0.89973869 -0.17279803
Axis point 174.97564995 0.00000000 260.56711346
Rotation angle (degrees) 164.60477462
Shift along axis 21.60381095
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07677, correlation about mean = 0.03054, overlap = 17.73
steps = 76, shift = 0.404, angle = 0.407 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.64807421 0.75431391 -0.10493036 307.07666134
0.65957509 0.62480198 0.41783158 -243.54650455
0.38073686 0.20157642 -0.90244469 423.24148998
Axis -0.40046264 -0.89936155 -0.17543793
Axis point 175.10068745 0.00000000 259.52673505
Rotation angle (degrees) 164.33533674
Shift along axis 21.81101883
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07681, correlation about mean = 0.03056, overlap = 17.72
steps = 28, shift = 0.0199, angle = 0.0127 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.64813845 0.75426678 -0.10487232 307.07944434
0.65946857 0.62479776 0.41800598 -243.55889807
0.38081201 0.20176574 -0.90237067 423.14430692
Axis -0.40042029 -0.89936021 -0.17554146
Axis point 175.10520444 0.00000000 259.49438194
Rotation angle (degrees) 164.33474676
Shift along axis 21.80696924
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07684, correlation about mean = 0.02988, overlap = 17.71
steps = 124, shift = 0.879, angle = 1.01 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.65424482 0.74677768 -0.11952757 316.84653418
0.64972384 0.63588744 0.41654066 -243.36821868
0.38706934 0.19485966 -0.90122531 422.89037770
Axis -0.39485147 -0.90233503 -0.17286935
Axis point 177.81252509 0.00000000 260.57585472
Rotation angle (degrees) 163.69715199
Shift along axis 21.38756223
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07662, correlation about mean = 0.02957, overlap = 17.74
steps = 96, shift = 0.59, angle = 0.588 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.65407959 0.74636343 -0.12296972 318.14227757
0.64489734 0.63518576 0.42502529 -244.61345177
0.39533195 0.19869752 -0.89678982 417.20799002
Axis -0.39389284 -0.90203387 -0.17658800
Axis point 178.23259159 0.00000000 259.11897372
Rotation angle (degrees) 163.30385229
Shift along axis 21.66173020
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.08036, correlation about mean = 0.03747, overlap = 19.41
steps = 68, shift = 0.96, angle = 0.967 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.65588174 0.74212823 -0.13807558 325.62144092
0.63574820 0.64168638 0.42902546 -245.13717044
0.40699312 0.19360866 -0.89267705 413.41731615
Axis -0.39028658 -0.90364409 -0.17636251
Axis point 180.10707137 0.00000000 259.16462373
Rotation angle (degrees) 162.44658526
Shift along axis 21.51976255
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07779, correlation about mean = 0.03475, overlap = 18.4
steps = 60, shift = 0.718, angle = 0.687 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.65974756 0.73828452 -0.14024681 328.95132141
0.63611505 0.64801301 0.41885177 -243.60581582
0.40011353 0.18712333 -0.89715888 419.53614170
Axis -0.38830907 -0.90548580 -0.17120613
Axis point 181.03870397 0.00000000 261.21738194
Rotation angle (degrees) 162.63958467
Shift along axis 21.01966916
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07794, correlation about mean = 0.03511, overlap = 18.28
steps = 64, shift = 0.668, angle = 0.606 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.66324441 0.73485613 -0.14175101 331.80910703
0.63643034 0.65346120 0.40981083 -242.15678736
0.39378078 0.18159010 -0.90108921 424.96366161
Axis -0.38655579 -0.90707323 -0.16671167
Axis point 181.85500246 0.00000000 263.00697784
Rotation angle (degrees) 162.83060968
Shift along axis 20.54480476
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07792, correlation about mean = 0.0352, overlap = 18.27
steps = 48, shift = 0.329, angle = 0.369 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.66561142 0.73179673 -0.14640706 335.28901751
0.63369540 0.65782181 0.40706344 -241.68427324
0.39419744 0.17816859 -0.90158991 426.09336113
Axis -0.38456421 -0.90826483 -0.16481918
Axis point 182.81606148 0.00000000 263.73310062
Rotation angle (degrees) 162.68631566
Shift along axis 20.34481375
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07835, correlation about mean = 0.03548, overlap = 19.05
steps = 48, shift = 0.303, angle = 0.26 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.66758956 0.73032599 -0.14473477 335.81456012
0.63400503 0.65955870 0.40375733 -241.11712046
0.39033554 0.17778161 -0.90334484 428.20811021
Axis -0.38381379 -0.90880277 -0.16359861
Axis point 183.08690226 0.00000000 264.25868987
Rotation angle (degrees) 162.87951857
Shift along axis 20.18339500
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.0783, correlation about mean = 0.03541, overlap = 19.02
steps = 44, shift = 0.267, angle = 0.281 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.66865514 0.72852355 -0.14884142 338.25268657
0.63098958 0.66183124 0.40476116 -241.21218144
0.39338593 0.17672824 -0.90222761 427.11085845
Axis -0.38244066 -0.90938533 -0.16357708
Axis point 183.75100396 0.00000000 264.26298602
Rotation angle (degrees) 162.65476970
Shift along axis 20.12768971
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07788, correlation about mean = 0.03524, overlap = 18.18
steps = 76, shift = 0.125, angle = 0.164 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.66970946 0.72764908 -0.14837820 338.72720033
0.62931135 0.66216051 0.40683009 -241.51552991
0.39427972 0.17908187 -0.90137296 425.71172781
Axis -0.38169767 -0.90947480 -0.16481043
Axis point 184.03998625 0.00000000 263.81147160
Rotation angle (degrees) 162.64232067
Shift along axis 20.19917117
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07787, correlation about mean = 0.03531, overlap = 18.13
steps = 72, shift = 0.24, angle = 0.274 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.67184927 0.72503991 -0.15144543 341.40478233
0.62697177 0.66555155 0.40490439 -241.13712755
0.39436658 0.17708271 -0.90172986 426.48457952
Axis -0.38000332 -0.91040666 -0.16357627
Axis point 184.81899187 0.00000000 264.31108779
Rotation angle (degrees) 162.55664610
Shift along axis 20.03513693
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07794, correlation about mean = 0.03352, overlap = 18.23
steps = 44, shift = 0.233, angle = 0.334 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.67338546 0.72272219 -0.15564284 344.06818260
0.62530196 0.66910600 0.40161505 -240.54296523
0.39439766 0.17311796 -0.90248584 428.03607264
Axis -0.37860224 -0.91137512 -0.16141788
Axis point 185.44814687 0.00000000 265.11803826
Rotation angle (degrees) 162.43641332
Shift along axis 19.86721552
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.0785, correlation about mean = 0.03409, overlap = 19.05
steps = 52, shift = 0.457, angle = 0.431 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.67522167 0.72131844 -0.15419286 344.65397165
0.62702925 0.67140289 0.39503483 -239.48662845
0.38847143 0.17005264 -0.90563352 432.23240102
Axis -0.37813896 -0.91208338 -0.15847662
Axis point 185.65127379 0.00000000 266.29448819
Rotation angle (degrees) 162.69332408
Shift along axis 19.60594526
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.0785, correlation about mean = 0.03431, overlap = 19.41
steps = 60, shift = 0.476, angle = 0.619 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.67544604 0.72314991 -0.14431524 340.70123646
0.63192144 0.66849651 0.39215781 -239.11018419
0.38006312 0.17368555 -0.90850723 434.91044828
Axis -0.37972189 -0.91141061 -0.15856221
Axis point 184.85113890 0.00000000 266.31947980
Rotation angle (degrees) 163.28124441
Shift along axis 19.59547720
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07836, correlation about mean = 0.03584, overlap = 19.02
steps = 68, shift = 0.48, angle = 0.451 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.67480384 0.72442266 -0.14089574 338.81257017
0.63103375 0.66538124 0.39882860 -240.23999564
0.38266985 0.18022110 -0.90613694 430.98195249
Axis -0.38018312 -0.91053969 -0.16241387
Axis point 184.54525638 0.00000000 264.84999366
Rotation angle (degrees) 163.29148325
Shift along axis 19.93978179
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07853, correlation about mean = 0.03442, overlap = 19.48
steps = 44, shift = 0.307, angle = 0.324 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.67624035 0.72354432 -0.13850139 338.78071366
0.63250254 0.66664172 0.39437215 -239.52716215
0.37767653 0.17908788 -0.90845363 433.88462117
Axis -0.37993445 -0.91095263 -0.16067086
Axis point 184.64696383 0.00000000 265.55428684
Rotation angle (degrees) 163.54168721
Shift along axis 19.77081675
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07854, correlation about mean = 0.03449, overlap = 19.46
steps = 48, shift = 0.18, angle = 0.165 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.67711710 0.72304351 -0.13682303 338.60730147
0.63314175 0.66718480 0.39242324 -239.19914947
0.37502532 0.17908811 -0.90955125 435.18128427
Axis -0.37975685 -0.91113882 -0.16003370
Axis point 184.67571897 0.00000000 265.81840252
Rotation angle (degrees) 163.68703766
Shift along axis 19.71151540
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07675, correlation about mean = 0.0309, overlap = 18.44
steps = 48, shift = 0.317, angle = 0.323 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.67859447 0.72222083 -0.13381576 338.30438791
0.63458903 0.66820656 0.38832563 -238.51646755
0.36987342 0.17859761 -0.91175467 437.88086367
Axis -0.37952879 -0.91148785 -0.15858057
Axis point 184.72696852 0.00000000 266.40957969
Rotation angle (degrees) 163.96046699
Shift along axis 19.56920990
> fitmap #5 inMap #1.1.1.2
Fit map Most_full_J406_class_06_00267_volume.mrc in map
cryosparc_P1022_J624_map_sharp.mrc using 7868 points
correlation = -0.005114, correlation about mean = 0.0137, overlap = -8.165e-06
steps = 24, shift = 0, angle = 0 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
cryosparc_P1022_J624_map_sharp.mrc (#1.1.1.2) coordinates:
Matrix rotation and translation
-0.67859447 0.72222083 -0.13381576 338.30438791
0.63458903 0.66820656 0.38832563 -238.51646755
0.36987342 0.17859761 -0.91175467 437.88086367
Axis -0.37952879 -0.91148785 -0.15858057
Axis point 184.72696852 0.00000000 266.40957969
Rotation angle (degrees) 163.96046699
Shift along axis 19.56920990
> fitmap #5 inMap #1.1.1.2
Fit map Most_full_J406_class_06_00267_volume.mrc in map
cryosparc_P1022_J624_map_sharp.mrc using 7868 points
correlation = -0.005114, correlation about mean = 0.0137, overlap = -8.165e-06
steps = 24, shift = 0, angle = 0 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
cryosparc_P1022_J624_map_sharp.mrc (#1.1.1.2) coordinates:
Matrix rotation and translation
-0.67859447 0.72222083 -0.13381576 338.30438791
0.63458903 0.66820656 0.38832563 -238.51646755
0.36987342 0.17859761 -0.91175467 437.88086367
Axis -0.37952879 -0.91148785 -0.15858057
Axis point 184.72696852 0.00000000 266.40957969
Rotation angle (degrees) 163.96046699
Shift along axis 19.56920990
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07891, correlation about mean = 0.03509, overlap = 19.47
steps = 48, shift = 0.355, angle = 0.328 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.68077513 0.71985991 -0.13545097 340.40227734
0.63377974 0.67158444 0.38379371 -237.67149471
0.36724446 0.17543113 -0.91343059 440.44723341
Axis -0.37819931 -0.91244343 -0.15624428
Axis point 185.32680506 0.00000000 267.33329254
Rotation angle (degrees) 164.01017592
Shift along axis 19.30452496
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07886, correlation about mean = 0.03525, overlap = 19.4
steps = 48, shift = 0.448, angle = 0.425 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.68351626 0.71708650 -0.13635435 342.57641188
0.63336351 0.67550424 0.37755095 -236.52755398
0.36284462 0.17170033 -0.91589453 444.08322939
Axis -0.37672042 -0.91356760 -0.15321868
Axis point 185.98790420 0.00000000 268.53097856
Rotation angle (degrees) 164.14438963
Shift along axis 18.98653249
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07716, correlation about mean = 0.03308, overlap = 18.57
steps = 60, shift = 0.43, angle = 0.442 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.68625484 0.71381454 -0.13972522 345.80924590
0.63177593 0.68016229 0.37180434 -235.42768158
0.36043516 0.16687750 -0.91773549 447.11809623
Axis -0.37484027 -0.91486430 -0.15006025
Axis point 186.87435837 0.00000000 269.73234307
Rotation angle (degrees) 164.13615886
Shift along axis 18.66649427
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.07848, correlation about mean = 0.03472, overlap = 19.3
steps = 40, shift = 0.777, angle = 0.779 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.68334114 0.71583330 -0.14362316 345.55047940
0.62837741 0.67680183 0.38351161 -237.45421525
0.37173479 0.17181970 -0.91229998 439.71267313
Axis -0.37536396 -0.91381296 -0.15507343
Axis point 186.68734274 0.00000000 267.77796356
Rotation angle (degrees) 163.62145656
Shift along axis 19.09379096
> view matrix models
> #5,-0.68334,0.71583,-0.14362,350.42,0.62838,0.6768,0.38351,-248.37,0.37173,0.17182,-0.9123,438.74
> transparency #5.1 50
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.78253,0.62199,-0.02779,374.42,0.6206,0.77565,-0.11499,-117.69,-0.049969,-0.10723,-0.99298,686.21
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.78253,0.62199,-0.02779,360,0.6206,0.77565,-0.11499,-110.4,-0.049969,-0.10723,-0.99298,688.81
> fitmap #5 inMap #1.1.1.1
Fit map Most_full_J406_class_06_00267_volume.mrc in map
Most_monomer_J590_class_8_00264_volume.mrc using 7868 points
correlation = 0.0687, correlation about mean = 0.02727, overlap = 13.9
steps = 404, shift = 7.33, angle = 17.5 degrees
Position of Most_full_J406_class_06_00267_volume.mrc (#5) relative to
Most_monomer_J590_class_8_00264_volume.mrc (#1.1.1.1) coordinates:
Matrix rotation and translation
-0.71336388 0.67644044 -0.18314023 373.10451376
0.66232658 0.73616893 0.13920794 -194.50421843
0.22898802 -0.02199273 -0.97318078 563.20781250
Axis -0.36408310 -0.93082079 -0.03187715
Axis point 190.63146651 0.00000000 307.99454619
Rotation angle (degrees) 167.20996226
Shift along axis 27.25406460
> undo
> view matrix models
> #5,-0.78253,0.62199,-0.02779,352.31,0.6206,0.77565,-0.11499,-115.07,-0.049969,-0.10723,-0.99298,684.35
> view matrix models
> #5,-0.78253,0.62199,-0.02779,352.04,0.6206,0.77565,-0.11499,-113.64,-0.049969,-0.10723,-0.99298,684.79
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.78153,0.62315,-0.030054,352.09,0.62237,0.77541,-0.10671,-116.78,-0.043191,-0.1021,-0.99384,681.29
> view matrix models
> #5,-0.76214,0.64403,-0.066064,350.87,0.64336,0.76482,0.033831,-165.09,0.072316,-0.016718,-0.99724,618.79
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.76214,0.64403,-0.066064,348.77,0.64336,0.76482,0.033831,-155.47,0.072316,-0.016718,-0.99724,620.24
> view matrix models
> #5,-0.76214,0.64403,-0.066064,348.02,0.64336,0.76482,0.033831,-155.42,0.072316,-0.016718,-0.99724,620.31
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.73895,0.67327,0.025767,301.6,0.67376,0.73851,0.025321,-153.31,-0.0019817,0.036072,-0.99935,626.33
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.73895,0.67327,0.025767,317.57,0.67376,0.73851,0.025321,-153.04,-0.0019817,0.036072,-0.99935,622
> view matrix models
> #5,-0.73895,0.67327,0.025767,316.13,0.67376,0.73851,0.025321,-152.24,-0.0019817,0.036072,-0.99935,624.81
> show #4 models
> hide #4 models
> show #3 models
> fitmap #3 inMap #5
Fit molecule spike_monomer.pdb (#3) to map
Most_full_J406_class_06_00267_volume.mrc (#5) using 16512 atoms
average map value = 0.9921, steps = 116
shifted from previous position = 31
rotated from previous position = 39.6 degrees
atoms outside contour = 3362, contour level = 0.49251
Position of spike_monomer.pdb (#3) relative to
Most_full_J406_class_06_00267_volume.mrc (#5) coordinates:
Matrix rotation and translation
0.05062524 0.79072783 0.61007094 -98.10682988
0.91462270 -0.28205149 0.28967609 58.68501194
0.40112637 0.54331982 -0.73749657 297.57304261
Axis 0.72221587 0.59494112 0.35277373
Axis point 0.00000000 53.01352886 173.82614913
Rotation angle (degrees) 169.88636252
Shift along axis 69.03576823
> select subtract #5
Nothing selected
> select add #3
16512 atoms, 16717 bonds, 1068 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.4429,0.86814,0.22399,98.128,-0.82828,-0.30055,-0.47289,774.06,-0.34321,-0.39497,0.85218,244.43
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.4429,0.86814,0.22399,123.43,-0.82828,-0.30055,-0.47289,786.15,-0.34321,-0.39497,0.85218,256.34
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.90198,-0.42549,-0.073448,723.43,0.4317,-0.88517,-0.17355,516.61,0.0088306,-0.18825,0.98208,57.78
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.90198,-0.42549,-0.073448,703.26,0.4317,-0.88517,-0.17355,501.25,0.0088306,-0.18825,0.98208,61.91
> view matrix models
> #3,-0.90198,-0.42549,-0.073448,715.72,0.4317,-0.88517,-0.17355,492.02,0.0088306,-0.18825,0.98208,60.208
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.56899,-0.7894,-0.23041,775.6,0.82187,-0.53635,-0.19201,283.95,0.027992,-0.29862,0.95396,95.752
> view matrix models
> #3,-0.99189,0.079992,-0.0988,598.61,-0.069409,-0.99191,-0.10627,645.33,-0.1065,-0.098552,0.98942,63.998
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.99189,0.079992,-0.0988,603.27,-0.069409,-0.99191,-0.10627,641.92,-0.1065,-0.098552,0.98942,64.23
> fitmap #3 inMap #5
Fit molecule spike_monomer.pdb (#3) to map
Most_full_J406_class_06_00267_volume.mrc (#5) using 16512 atoms
average map value = 0.984, steps = 96
shifted from previous position = 12.7
rotated from previous position = 34 degrees
atoms outside contour = 3129, contour level = 0.49251
Position of spike_monomer.pdb (#3) relative to
Most_full_J406_class_06_00267_volume.mrc (#5) coordinates:
Matrix rotation and translation
0.91460866 -0.36371524 0.17664142 108.75374601
-0.26476325 -0.86889818 -0.41823001 773.53425082
0.30560004 0.33574864 -0.89100024 414.67931558
Axis 0.97754107 -0.16719617 0.12829226
Axis point 0.00000000 353.92044603 280.08237070
Rotation angle (degrees) 157.31586202
Shift along axis 30.17943375
> fitmap #3 inMap #1.1.1.2
Fit molecule spike_monomer.pdb (#3) to map cryosparc_P1022_J624_map_sharp.mrc
(#1.1.1.2) using 16512 atoms
average map value = 0.1389, steps = 88
shifted from previous position = 9.2
rotated from previous position = 6.9 degrees
atoms outside contour = 16506, contour level = 0.052211
Position of spike_monomer.pdb (#3) relative to
cryosparc_P1022_J624_map_sharp.mrc (#1.1.1.2) coordinates:
Matrix rotation and translation
-0.84106608 -0.25289678 -0.47817472 764.74669255
0.43148509 -0.84678135 -0.31109799 517.30347156
-0.32623375 -0.46797923 0.82132026 279.75350994
Axis -0.21838059 -0.21150367 0.95266789
Axis point 364.19763295 364.06818153 0.00000000
Rotation angle (degrees) 158.94940144
Shift along axis -9.90523448
> close #3-4
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session10_ISOLDE.cxs" includeMaps true
Taking snapshot of stepper: all_ISOLDE.pdb
——— End of log from Fri Feb 2 09:56:15 2024 ———
opened ChimeraX session
> hide #2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1.2/A
Alignment identifier is 1.2/A
> select #1.2/A:291
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/A:291-625
5155 atoms, 5225 bonds, 335 residues, 1 model selected
> select #1.2/A:291
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/A:291-675,677-1147
13013 atoms, 13167 bonds, 856 residues, 1 model selected
> select #1.2/A:291
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/A:291-675,677-1147
13013 atoms, 13167 bonds, 856 residues, 1 model selected
> select clear
> select #1.2/A:290
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1.2/A:14-290
4398 atoms, 4464 bonds, 277 residues, 1 model selected
> select #1.2/A:289
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/A:14-289
4386 atoms, 4452 bonds, 276 residues, 1 model selected
> select #1.2/A:292
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/A:14-292
4418 atoms, 4484 bonds, 279 residues, 1 model selected
> show #2 models
> select #1.2/A:14
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.2/A:14-69
910 atoms, 927 bonds, 56 residues, 1 model selected
> isolde stepto #1.2/A:70
> isolde sim start
> #1.2/A:14-318,374-378,383-386,403-408,434-435,501-507,595-608,626-627,810-812,817-818,820-828,841-849,925-926,928-944/B:1,5,8-10,96-118,124-126,138-145,148-152,174-175,264-269
Chain B, residue 253 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 263 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 264 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 265 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 266 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 267 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 268 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
Chain B, residue 269 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.
ISOLDE: started sim
> select clear
[Repeated 2 time(s)]
> isolde stepto #1.2/A:71
> isolde stepto next
[Repeated 7 time(s)]
> isolde pepflip #1.2/A:79
[Repeated 2 time(s)]
> select clear
> isolde stepto next
[Repeated 41 time(s)]
> isolde stepto #1.2/A:121
> select clear
> volume #1.1.1.2 level 0.1518
> isolde stepto #1.2/A:121
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> isolde sim start #1.2/A:124
ISOLDE: started sim
> isolde stepto next
[Repeated 9 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
[Repeated 1 time(s)]
> isolde sim start #1.2/A:131
ISOLDE: started sim
> select clear
> isolde stepto next
> isolde stepto prev
> isolde stepto next
[Repeated 2 time(s)]
> isolde stepto prev
[Repeated 1 time(s)]
> isolde stepto next
[Repeated 1 time(s)]
> isolde pepflip #1.2/A:134
> isolde cisflip #1.2/A:134
[Repeated 1 time(s)]
> isolde stepto #1.2/A:134
> isolde stepto next
> ui mousemode right "translate selected atoms"
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui mousemode right "translate selected atoms"
> isolde sim start #1.2/A:135
ISOLDE: started sim
> isolde stepto #1.2/A:135
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui mousemode right "translate selected atoms"
> isolde sim start #1.2/A:136
ISOLDE: started sim
> isolde stepto next
[Repeated 4 time(s)]
> isolde stepto prev
> isolde pepflip #1.2/A:139
> isolde stepto #1.2/A:140
> isolde stepto next
[Repeated 1 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #1.2/A:142
ISOLDE: started sim
> select clear
[Repeated 2 time(s)]
> isolde stepto #1.2/A:142
> isolde stepto #1.2/A:153
> isolde stepto next
[Repeated 3 time(s)]
> select clear
> isolde pepflip #1.2/A:155
[Repeated 1 time(s)]
> isolde stepto #1.2/A:155
> isolde stepto next
[Repeated 2 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #1.2/A:158
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start
> #1.2/A:14-42,46-324,536-539,550-551,588-675,677-706,1073-1074
ISOLDE: started sim
> select clear
> select #1.2/A:70
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.2/A:70-120
791 atoms, 799 bonds, 51 residues, 1 model selected
> select #1.2/A:121
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/A:121
14 atoms, 13 bonds, 1 residue, 1 model selected
> isolde stepto #1.2/A:121
> isolde stepto next
[Repeated 5 time(s)]
> isolde stepto prev
[Repeated 1 time(s)]
> isolde stepto next
> isolde stepto prev
> isolde stepto next
[Repeated 4 time(s)]
> isolde pepflip #1.2/A:130
> isolde stepto next
[Repeated 3 time(s)]
> select clear
> isolde stepto #1.2/A:137
> isolde stepto prev
[Repeated 3 time(s)]
> isolde stepto #1.2/A:133
[Repeated 1 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 9 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui mousemode right "translate selected atoms"
> isolde sim start #1.2/A:14-43,49-277,285-294,297,630-631,633-635
ISOLDE: started sim
> select clear
> isolde stepto #1.2/A:137
> select #1.2/A:121
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1.2/A:121
14 atoms, 13 bonds, 1 residue, 1 model selected
> isolde stepto #1.2/A:121
> isolde stepto next
[Repeated 12 time(s)]
> isolde stepto #1.2/A:139
> isolde stepto next
> isolde stepto #1.2/A:139
[Repeated 1 time(s)]
> isolde stepto next
[Repeated 4 time(s)]
> isolde pepflip #1.2/A:144
[Repeated 1 time(s)]
> isolde cisflip #1.2/A:144
> isolde cisflip #1.2/A:143
[Repeated 1 time(s)]
> select clear
> isolde cisflip #1.2/A:144
> isolde stepto next
> isolde cisflip #1.2/A:145
[Repeated 1 time(s)]
> isolde stepto next
[Repeated 4 time(s)]
> volume #1.1.1.2 level 0.05157
> volume #1.1.1.2 level 0.1326
> isolde stepto next
[Repeated 7 time(s)]
> select clear
> isolde stepto #1.2/A:160
> isolde stepto next
> isolde stepto #1.2/A:160
> select clear
> volume #1.1.1.2 level 0.01362
> isolde stepto #1.2/A:160
> volume #1.1.1.2 level 0.02518
> isolde stepto next
[Repeated 3 time(s)]
> isolde pepflip #1.2/A:163
> isolde pepflip #1.2/A:164
[Repeated 1 time(s)]
> isolde stepto next
[Repeated 6 time(s)]
> volume #1.1.1.2 level 0.191
> isolde stepto next
[Repeated 1 time(s)]
> volume #1.1.1.2 level 0.08689
> select #1.2/A:173
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #1.2/A:173
17 atoms, 16 bonds, 1 residue, 1 model selected
> isolde stepto #1.2/A:173
> isolde stepto prev
[Repeated 1 time(s)]
> isolde stepto next
> select #1.2/A:160
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #1.2/A:160
21 atoms, 21 bonds, 1 residue, 1 model selected
> isolde stepto #1.2/A:160
> isolde stepto next
[Repeated 3 time(s)]
> select #1.2/A:131,160
31 atoms, 30 bonds, 2 residues, 1 model selected
> select #1.2/A:166
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/A:166
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #1.2/A:131,166
20 atoms, 18 bonds, 2 residues, 1 model selected
Created disulphide bond between A131 and A166.
Broke disulphide bond between A131 and A166.
> select clear
[Repeated 7 time(s)]
> isolde stepto #1.2/A:169
> isolde stepto next
[Repeated 2 time(s)]
> isolde stepto #1.2/A:172
> select clear
> isolde stepto #1.2/A:172
[Repeated 1 time(s)]
> isolde stepto #1.2/A:186
> isolde stepto next
[Repeated 5 time(s)]
> volume #1.1.1.2 level 0.299
> volume #1.1.1.2 level 0.3877
> isolde stepto next
[Repeated 18 time(s)]
> volume #1.1.1.2 level 0.11
> isolde stepto next
[Repeated 35 time(s)]
> isolde stepto #1.2/A:246
> isolde stepto #1.2/A:251
> volume #1.1.1.2 level 0.191
> isolde stepto next
[Repeated 25 time(s)]
> ui mousemode right "isolde tug atom"
> isolde stepto next
[Repeated 3 time(s)]
> isolde stepto #1.2/A:281
> isolde stepto next
[Repeated 30 time(s)]
> volume #1.1.1.2 level 0.06375
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 12 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session11_ISOLDE_head_good.cxs" includeMaps true
Taking snapshot of stepper: all_ISOLDE.pdb
——— End of log from Mon Feb 5 15:00:23 2024 ———
opened ChimeraX session
> close session
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/all_ISOLDE_head_830reg.pdb"
all_ISOLDE_head_830reg.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for all_ISOLDE_head_830reg.pdb #1
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 14-1211
B | spike glycoprotein | SPIKE_SARS2 14-1211
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/6vxx.pdb"
6vxx.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for 6vxx.pdb #2
---
Chain | Description | UniProt
A B C | spike glycoprotein | SPIKE_SARS2 14-1211
Non-standard residues in 6vxx.pdb #2
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> show sel atoms
Alignment identifier is 1/A
> select #1/A:331
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:331
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:165
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:165
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:234
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:234
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:122
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:122
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:17
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:17
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:149
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:149
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:228
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:228
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:603
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:603
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:616
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:616
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:657
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:657
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:801
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:801
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:717
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:717
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:1074
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:1074
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:709
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:709
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:1098
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:1098
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:1134
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:1134
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #2 models
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> select add #1
26032 atoms, 26919 bonds, 1403 residues, 1 model selected
> select subtract #1
Nothing selected
> select clear
[Repeated 3 time(s)]
> delete atoms #1,3-19
> delete bonds #1,3-19
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/all_ISOLDE_head_830reg.pdb"
all_ISOLDE_head_830reg.pdb title:
Structure of the sars-cov-2 spike glycoprotein (closed state) [more info...]
Chain information for all_ISOLDE_head_830reg.pdb #1
---
Chain | Description | UniProt
A | spike glycoprotein | SPIKE_SARS2 14-1211
B | spike glycoprotein | SPIKE_SARS2 14-1211
> close #2
Alignment identifier is 1/A
Alignment identifier is 1/B
> select /A:17
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:17
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:122
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:122
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:17,122
28 atoms, 26 bonds, 2 residues, 1 model selected
> select /A:17,122,149
42 atoms, 39 bonds, 3 residues, 1 model selected
> select /A:17,122,149,165
56 atoms, 52 bonds, 4 residues, 1 model selected
> select /A:17,122,149,165,234
70 atoms, 65 bonds, 5 residues, 1 model selected
> select /A:17,122,149,165,228,234
82 atoms, 76 bonds, 6 residues, 1 model selected
> select /A:17,122,149,165,228,234,331
96 atoms, 89 bonds, 7 residues, 1 model selected
> select /A:17,122,149,165,228,234,331,343
110 atoms, 102 bonds, 8 residues, 1 model selected
> select /A:17,122,149,165,228,234,331,343,603
124 atoms, 115 bonds, 9 residues, 1 model selected
> select /A:17,122,149,165,228,234,331,343,603,616
138 atoms, 128 bonds, 10 residues, 1 model selected
> select /A:17,122,149,165,228,234,331,343,603,616,657
152 atoms, 141 bonds, 11 residues, 1 model selected
> select /A:17,122,149,165,228,234,331,343,603,616,657,709
166 atoms, 154 bonds, 12 residues, 1 model selected
> select /A:17,122,149,165,228,234,331,343,603,616,657,709,717
180 atoms, 167 bonds, 13 residues, 1 model selected
> select /A:17,122,149,165,228,234,331,343,603,616,657,709,717,801
194 atoms, 180 bonds, 14 residues, 1 model selected
> select /A:17,122,149,165,228,234,331,343,603,616,657,709,717,801,1074
208 atoms, 193 bonds, 15 residues, 1 model selected
> select /A:17,122,149,165,228,234,331,343,603,616,657,709,717,801,1074,1098
222 atoms, 206 bonds, 16 residues, 1 model selected
> select
> /A:17,122,149,165,228,234,331,343,603,616,657,709,717,801,1074,1098,1134
236 atoms, 219 bonds, 17 residues, 1 model selected
> show sel atoms
> select clear
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> select add #2
29 atoms, 30 bonds, 3 residues, 1 model selected
> view matrix models #2,1,0,0,-78.159,0,1,0,4.3822,0,0,1,12.91
> view matrix models #2,1,0,0,-51.986,0,1,0,9.1819,0,0,1,10.571
> view matrix models #2,1,0,0,-43.588,0,1,0,-15.402,0,0,1,1.8835
> view matrix models #2,1,0,0,-19.219,0,1,0,-5.3501,0,0,1,-3.7133
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.94874,-0.31586,-0.011439,90.656,0.31396,0.94596,-0.081213,-50.371,0.036472,0.073458,0.99663,-34.121
> view matrix models
> #2,0.87553,-0.48113,0.044292,140.82,0.47913,0.87638,0.048882,-118.75,-0.062336,-0.021575,0.99782,20.621
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.87553,-0.48113,0.044292,139.52,0.47913,0.87638,0.048882,-117.97,-0.062336,-0.021575,0.99782,23.381
> view matrix models
> #2,0.87553,-0.48113,0.044292,139.43,0.47913,0.87638,0.048882,-117.94,-0.062336,-0.021575,0.99782,23.351
> view matrix models
> #2,0.87553,-0.48113,0.044292,139.45,0.47913,0.87638,0.048882,-117.82,-0.062336,-0.021575,0.99782,23.118
> view matrix models
> #2,0.87553,-0.48113,0.044292,139.22,0.47913,0.87638,0.048882,-117.17,-0.062336,-0.021575,0.99782,22.733
> view matrix models
> #2,0.87553,-0.48113,0.044292,138.75,0.47913,0.87638,0.048882,-116.76,-0.062336,-0.021575,0.99782,22.848
> view matrix models
> #2,0.87553,-0.48113,0.044292,138.85,0.47913,0.87638,0.048882,-117.06,-0.062336,-0.021575,0.99782,22.724
> view matrix models
> #2,0.87553,-0.48113,0.044292,139.68,0.47913,0.87638,0.048882,-117.14,-0.062336,-0.021575,0.99782,23.1
> view matrix models
> #2,0.87553,-0.48113,0.044292,139.26,0.47913,0.87638,0.048882,-116.57,-0.062336,-0.021575,0.99782,23.494
> view matrix models
> #2,0.87553,-0.48113,0.044292,139.24,0.47913,0.87638,0.048882,-116.56,-0.062336,-0.021575,0.99782,23.488
> open "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new spike/NAC.pdb"
Summary of feedback from opening /home/carl/Documents/Phenix/2F PXT-apt and
Spike/new spike/NAC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 294
LEU A 303 1 10
Start residue of secondary structure not found: HELIX 2 2 PRO A 337 GLY A 339
1 3
Start residue of secondary structure not found: HELIX 3 3 TYR A 365 SER A 371
1 7
Start residue of secondary structure not found: HELIX 4 4 LYS A 386 ASN A 388
1 3
Start residue of secondary structure not found: HELIX 5 5 GLY A 404 GLN A 409
1 6
79 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (291 )
Cannot find LINK/SSBOND residue CYS (336 )
Cannot find LINK/SSBOND residue CYS (379 )
Cannot find LINK/SSBOND residue CYS (391 )
Cannot find LINK/SSBOND residue CYS (480 )
8 messages similar to the above omitted
> save "/home/carl/Documents/Phenix/2F PXT-apt and Spike/new
> spike/session12_ISOLDE_NAC.cxs" includeMaps true
Taking snapshot of stepper: all_ISOLDE.pdb
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/models.py", line 361, in take_snapshot
'positions': self.positions.array(),
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'isolde residue stepper 1 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7f0919f3dd10> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7f08d2b88f10>
'all_ISOLDE.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'isolde residue stepper 1 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7f0919f3dd10> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7f08d2b88f10>
'all_ISOLDE.pdb': Error while saving session data for 'isolde residue stepper
1 1' -> <chimerax.isolde.navigate.ResidueStepper object at 0x7f0919f3dd10> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7f08d2b88f10>
'all_ISOLDE.pdb'
ValueError: error processing: 'isolde residue stepper 1 1' -> ->
'all_ISOLDE.pdb': Error while saving session data for 'isolde residue stepper
1 1' -> -> 'all_ISOLDE.pdb'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 296, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1417, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 218, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/models.py", line 361, in take_snapshot
'positions': self.positions.array(),
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 273, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'isolde residue stepper 1 1'
-> <chimerax.isolde.navigate.ResidueStepper object at 0x7f0919f3dd10> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7f08d2b88f10>
'all_ISOLDE.pdb'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 636, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'isolde residue stepper 1 1' ->
<chimerax.isolde.navigate.ResidueStepper object at 0x7f0919f3dd10> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7f08d2b88f10>
'all_ISOLDE.pdb': Error while saving session data for 'isolde residue stepper
1 1' -> <chimerax.isolde.navigate.ResidueStepper object at 0x7f0919f3dd10> ->
<chimerax.atomic.structure.AtomicStructure object at 0x7f08d2b88f10>
'all_ISOLDE.pdb'
ValueError: error processing: 'isolde residue stepper 1 1' -> ->
'all_ISOLDE.pdb': Error while saving session data for 'isolde residue stepper
1 1' -> -> 'all_ISOLDE.pdb'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 277, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 535.154.05
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:0
Manufacturer: ASUS
Model: System Product Name
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD Ryzen 9 3950X 16-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 125Gi 7.2Gi 107Gi 37Mi 11Gi 117Gi
Swap: 0B 0B 0B
Graphics:
09:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102 [GeForce RTX 3090] [10de:2204] (rev a1)
Subsystem: ASUSTeK Computer Inc. GA102 [GeForce RTX 3090] [1043:87af]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.3
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (3)
comment:1 by , 21 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Third Party |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ISOLDE: ResidueStepper: self.positions is None |
comment:2 by , 21 months ago
Note:
See TracTickets
for help on using tickets.
The following error indicates the session save was trying to save a closed model, one with model.positions = None. I'll leave it to Tristan to figure out how a reference to a closed model was arose.