The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Dear ChimeraX developers,
Once I saved a view by command: view name VIEWNAME, followed by saving such a session, an error message would happen (please see the attached screenshot for the error message). This problem began since yesterday and I could not save a view afterwards. Could you please check what is wrong? Thank you!
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs format session
Opened J1738_deepEMhancer.mrc as #2.1.1.1, grid size 256,256,256, pixel 1.06,
shown at level 0.0266, step 1, values float32
Opened J1738_deepEMhancer.mrc as #5, grid size 256,256,256, pixel 1.06, shown
at level 0.0658, step 1, values float32
Restoring stepper: F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
Log from Wed Sep 13 10:43:45 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Opened J1738_deepEMhancer.mrc as #2.1.1.1, grid size 256,256,256, pixel 1.06,
shown at level 0.0266, step 1, values float32
Opened J1738_deepEMhancer.mrc as #5, grid size 256,256,256, pixel 1.06, shown
at level 0.0658, step 1, values float32
Restoring stepper: F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
Log from Tue Sep 12 21:17:56 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Opened J1738_deepEMhancer.mrc as #2.1.1.1, grid size 256,256,256, pixel 1.06,
shown at level 0.0266, step 1, values float32
Opened J1738_deepEMhancer.mrc as #5, grid size 256,256,256, pixel 1.06, shown
at level 0.0658, step 1, values float32
Restoring stepper: F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
Log from Tue Sep 12 21:15:54 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs format session
Opened J1738_deepEMhancer.mrc as #2.1.1.1, grid size 256,256,256, pixel 1.06,
shown at level 0.0266, step 1, values float32
Opened J1738_deepEMhancer.mrc as #5, grid size 256,256,256, pixel 1.06, shown
at level 0.0658, step 1, values float32
Restoring stepper: F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
Log from Tue Sep 12 17:59:41 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Opened J1738_deepEMhancer.mrc as #2.1.1.1, grid size 256,256,256, pixel 1.06,
shown at level 0.0266, step 1, values float32
Opened J1738_deepEMhancer.mrc as #5, grid size 256,256,256, pixel 1.06, shown
at level 0.0658, step 1, values float32
Restoring stepper: F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
Log from Tue Sep 12 17:52:01 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Opened J1738_deepEMhancer.mrc as #2.1.1.1, grid size 256,256,256, pixel 1.06,
shown at level 0.0266, step 1, values float32
Opened J1738_deepEMhancer.mrc as #5, grid size 256,256,256, pixel 1.06, shown
at level 0.0658, step 1, values float32
Restoring stepper: F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
Log from Tue Sep 12 12:39:21 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Opened J1738_deepEMhancer.mrc as #2.1.1.1, grid size 256,256,256, pixel 1.06,
shown at level 0.0266, step 1, values float32
Opened J1738_deepEMhancer.mrc as #5, grid size 256,256,256, pixel 1.06, shown
at level 0.0658, step 1, values float32
Restoring stepper: F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
Log from Tue Sep 12 12:30:41 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Opened J1738_deepEMhancer.mrc as #2.1.1.1, grid size 256,256,256, pixel 1.06,
shown at level 0.073, step 1, values float32
Log from Mon Sep 11 19:07:01 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> set bgColor white
[Repeated 1 time(s)]
> open /Users/ZhenGong/Documents/Xray/Phenix/F74/J1738_deepEMhancer.mrc
Opened J1738_deepEMhancer.mrc as #1, grid size 256,256,256, pixel 1.06, shown
at level 8.2e-05, step 1, values float32
> open
> /Users/ZhenGong/Documents/Xray/Phenix/F74/RealSpaceRefine_234/F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
Chain information for
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2
---
Chain | Description
A | No description available
B | No description available
> isolde start
> set selectionWidth 4
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 58 residues in model #2 to IUPAC-IUB
standards.
Chain information for
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
---
Chain | Description
2.2/A | No description available
2.2/B | No description available
> clipper associate #1 toModel #2
Opened J1738_deepEMhancer.mrc as #2.1.1.1, grid size 256,256,256, pixel 1.06,
shown at step 1, values float32
> select #2.1/A:392-399
Nothing selected
> volume #2.1.1.1 style surface
> volume #2.1.1.1 color #00ffff66
> select #2.1/A:392-399
Nothing selected
> select #2.2/A:392-399
54 atoms, 54 bonds, 8 residues, 1 model selected
> isolde sim start /A:392-399
Sim termination reason: None
ISOLDE: stopped sim
> addh #2.2
Summary of feedback from adding hydrogens to
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2
---
notes | No usable SEQRES records for
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb (#2.2) chain A;
guessing termini instead
No usable SEQRES records for
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb (#2.2) chain B;
guessing termini instead
Chain-initial residues that are actual N termini: /A HIS 41, /B HIS 41
Chain-initial residues that are not actual N termini: /A ILE 392, /B SER 399,
/B SER 670
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A VAL 692, /A ARG 343, /B
VAL 692, /B ARG 343, /B ALA 660
1029 hydrogen bonds
Adding 'H' to /A ILE 392
Adding 'H' to /B SER 399
Adding 'H' to /B SER 670
/A VAL 692 is not terminus, removing H atom from 'C'
/B VAL 692 is not terminus, removing H atom from 'C'
9703 hydrogens added
Loading residue template for CLR from internal database
> isolde sim start /A:340,392-401
ISOLDE: started sim
> volume #2.1.1.1 level 0.07301
> view #2.2:396
> 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
> alphafold match #2.2 true
Expected a keyword
> alphafold match #2 true
Expected a keyword
> alphafold match #2.2 trim true
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
1 AlphaFold model found using sequence similarity searches: L8EC40 (chains
A,B)
AlphaFold prediction matching
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | L8EC40 | L8EC40_CAEEL | 3.48 | 652 | 604 | 100
B | L8EC40 | L8EC40_CAEEL | 3.32 | 652 | 588 | 100
Opened 2 AlphaFold models
> hide #1.2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> view #1.1
> 396
Unknown command: 396
> view #1.1:396
> show #1.1 atoms
> hide #1.1 cartoons
> show #!2 models
> hide #!2 models
> color #1.1 byelement
> show #!2 models
> save /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
——— End of log from Mon Sep 11 19:07:01 2023 ———
opened ChimeraX session
> hide #!1 models
> open
> /Users/ZhenGong/Documents/Xray/Phenix/F74/RealSpaceRefine_234/F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
Chain information for
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #3
---
Chain | Description
A | No description available
B | No description available
> hide #!3 models
> view #2.2/B:209
> view #2.2/B:184
> view #2.2/B:230
> view #2.2/B:232
> view #2.2/B:257
[Repeated 1 time(s)]
> select #2.2/B:257
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2.2/B:25
Nothing selected
> select #2.2/B:256
19 atoms, 18 bonds, 1 residue, 1 model selected
> isolde start
> set selectionWidth 4
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> select #2.2/A:392-399
103 atoms, 103 bonds, 8 residues, 1 model selected
> isolde sim start #2.2/A:392-399
ISOLDE: started sim
> ui tool show "Volume Viewer"
> volume #2.1.1.1 level 0.04086
> viewl #2.2/A:392
Unknown command: viewl #2.2/A:392
> view #2.2/A:392
> select #2.2/A:392
19 atoms, 18 bonds, 1 residue, 1 model selected
> view #2.2/A:399
> isolde stepto prev
> view #2.2/A:399
> view #2.2/A:400
> view #2.2/A:399
> isolde pepflip #2.2/B:692
> select #2.2/A:399
11 atoms, 10 bonds, 1 residue, 1 model selected
> isolde pepflip #2.2/A:399
> select #2.2/A:398
17 atoms, 16 bonds, 1 residue, 1 model selected
> view #2.2/A:398
> view #2.2/A:397
> isolde pepflip #2.2/A:398
[Repeated 1 time(s)]
> view #2.2/A:396
> isolde cisflip #2.2/A:398
> view #2.2/A:397
> isolde pepflip #2.2/A:398
> 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
> select #2.2/A:392-399
103 atoms, 103 bonds, 8 residues, 1 model selected
> isolde sim start #2.2/A:392-399
ISOLDE: started sim
> view #2.2/A:399
> select #2.2/A:399
11 atoms, 10 bonds, 1 residue, 1 model selected
> isolde pepflip #2.2/A:399
> view #2.2/A:398
> view #2.2/A:397
> view #2.2/A:396
> select #2.2/A:396
14 atoms, 14 bonds, 1 residue, 1 model selected
> isolde cisflip #2.2/A:396
> select #2.2/A:397
10 atoms, 9 bonds, 1 residue, 1 model selected
> isolde pepflip #2.2/A:397
> select #2.2/A:398
17 atoms, 16 bonds, 1 residue, 1 model selected
> isolde cisflip #2.2/A:398
[Repeated 1 time(s)]
> select #2.2/A:396
14 atoms, 14 bonds, 1 residue, 1 model selected
> isolde cisflip #2.2/A:396
> select #2.2/A:397
10 atoms, 9 bonds, 1 residue, 1 model selected
> isolde pepflip #2.2/A:397
> view #2.2/A:395
> select #2.2/A:395
15 atoms, 14 bonds, 1 residue, 1 model selected
> view #2.2/A:394
> view #2.2/A:393
> volume #2.1.1.1 level 0.02658
> view #2.2/A:392
> select #2.2/A:392
19 atoms, 18 bonds, 1 residue, 1 model selected
> view #2.2/B:184
> view #2.2/B:209
> view #2.2/B:230
> view #2.2/B:232
> select #2.2/B:232
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2.2/B:257
17 atoms, 16 bonds, 1 residue, 1 model selected
> view #2.2/B:257
> select #2.2/B:232
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2.2/A:392-399
103 atoms, 103 bonds, 8 residues, 1 model selected
> 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 #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show Contacts
> contacts sel restrict cross overlapCutoff -0.3 interModel false intraMol
> false select true showDist true reveal true log true
Allowed overlap: -0.3
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
29 contacts
atom1 atom2 overlap distance
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A GLU 395 OE2 F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B LYS 233 HZ2 0.322 1.928
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A PRO 396 HD3 F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B ARG 209 CD 0.241 2.729
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A ILE 392 O F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B GLN 230 HE21 0.230 2.020
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A PRO 396 HD3 F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B ARG 209 HD3 0.153 2.247
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A ILE 392 C F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B GLN 230 HE21 0.054 2.916
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A GLY 393 HA3 F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B LEU 232 HD11 -0.079 2.479
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A ILE 392 HA F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B GLN 230 NE2 -0.105 2.805
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A ALA 394 O F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B ARG 209 HD2 -0.109 2.759
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A PRO 396 HD3 F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B ARG 209 HD2 -0.111 2.511
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A ALA 394 C F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B LEU 232 CD2 -0.118 3.658
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A GLU 395 HG2 F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B LEU 232 HD21 -0.147 2.547
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A GLY 393 C F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B LEU 232 CD1 -0.154 3.694
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A GLU 395 HG2 F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B LEU 232 CD2 -0.156 3.126
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A ALA 394 C F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B LEU 232 HD22 -0.170 3.140
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A GLU 395 CD F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B LYS 233 HZ2 -0.182 3.152
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A ILE 392 HA F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B GLN 230 HE21 -0.204 2.604
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A ILE 392 HG22 F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B GLN 230 HE21 -0.210 2.610
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A ALA 394 C F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B LEU 232 HD23 -0.214 3.184
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A GLY 393 C F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B LEU 232 HD11 -0.215 3.185
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A PRO 396 CD F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B ARG 209 HD3 -0.217 3.187
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A ILE 392 CA F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B GLN 230 HE21 -0.231 3.201
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A GLU 395 CG F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B LEU 232 HD22 -0.248 3.218
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A PRO 396 CD F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B ARG 209 CD -0.249 3.789
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A GLU 395 HA F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B LEU 232 CD2 -0.251 3.221
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A GLY 393 C F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B LEU 232 HD13 -0.261 3.231
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A ILE 392 HA F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B GLN 230 HE22 -0.269 2.669
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A GLU 395 N F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B LEU 232 HD22 -0.280 2.980
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A GLU 395 OE2 F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B LYS 233 NZ -0.292 2.842
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/A GLY 393 CA F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb #2.2/B LEU 232 HD11 -0.295 3.265
29 contacts
> label height 0.6
> label (#!2.2 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"
> label height 0.6
> select #2.2/A:392-399
103 atoms, 103 bonds, 8 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #000000 showDist true restrict cross interModel false
> intraRes false select true reveal true
8 hydrogen bonds found
> hide #!2.2.13 models
> show #!2.2.13 models
> color #2.2.13 #00fdffff models
> select #2.2/A:392-399
103 atoms, 103 bonds, 8 residues, 1 model selected
> isolde sim start #2.2/A:392-399
ISOLDE: started sim
> view #2.2/B233
No objects specified.
> view #2.2/B:233
> view #2.2/B:207
> ui tool show "Side View"
> view #2.2/B:207
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #2.2/A:392-399
103 atoms, 103 bonds, 8 residues, 1 model selected
> isolde sim start #2.2/A:392-399
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save
> /Users/ZhenGong/Documents/Xray/Phenix/F74/RealSpaceRefine_234/F74_real_space_refined_234_ISOLDE.pdb
> models #2
> hide #!2 models
> open
> /Users/ZhenGong/Documents/Xray/Phenix/F74/RealSpaceRefine_234/F74_real_space_refined_234_ISOLDE.pdb
Chain information for F74_real_space_refined_234_ISOLDE.pdb #4
---
Chain | Description
A | No description available
B | No description available
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> open /Users/ZhenGong/Documents/Xray/Phenix/F74/J1738_deepEMhancer.mrc
Opened J1738_deepEMhancer.mrc as #5, grid size 256,256,256, pixel 1.06, shown
at level 8.2e-05, step 1, values float32
> volume #5 level 0.06575
> volume #5 color #b2b2b25a
> open
> /Users/ZhenGong/Documents/Xray/Phenix/F74/RealSpaceRefine_236/F74_real_space_refined_234_ISOLDE-
> noH_real_space_refined_236.pdb
Chain information for F74_real_space_refined_234_ISOLDE-
noH_real_space_refined_236.pdb #6
---
Chain | Description
A | No description available
B | No description available
> hide #!5 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> color #6 #00fdffff
> color #6 #00f900ff
> color #6 #6de8f5ff
> combine #6
> select #7
9543 atoms, 9775 bonds, 3 pseudobonds, 1199 residues, 2 models selected
> hide #!6 models
> cartoon style protein modeHelix tube radius 2 sides 24
> hide #!7 models
> show #!6 models
> close #7
> show #!4 models
> hide #!4 models
> cartoon style #6 xsection oval modeHelix default
> select #6
9543 atoms, 9775 bonds, 3 pseudobonds, 1199 residues, 2 models selected
> hide sel atoms
> color #6/A green
> color #6/B rgb(60%,60%,100%)
> select #6:80,92,155,801-803
132 atoms, 132 bonds, 12 residues, 1 model selected
> display sel atoms
> color #6:80,92,155,801-803@O** byelement
> color #4:80,92,155,801-803@N** byelement
> select #4/C:1
74 atoms, 77 bonds, 1 residue, 1 model selected
> display sel atoms
> color #6/C:1 rgb(100%,60%,70%)
> color #6/C:1@O** byelement
> select #6/C
28 atoms, 31 bonds, 1 residue, 1 model selected
> display sel atoms
> color #6/C@C** rgb(100%,60%,70%)
> ~select
Nothing selected
> size #6/C stickRadius +0.2
Changed 31 bond radii
> size #6:801-803 stickRadius +0.1
Changed 84 bond radii
> select #6/A:392-399
54 atoms, 54 bonds, 8 residues, 1 model selected
> save /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Taking snapshot of stepper:
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
> ui tool show Contacts
> contacts sel restrict cross overlapCutoff -0.3 interModel false intraMol
> false select true showDist true reveal true log true
Allowed overlap: -0.3
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
8 contacts
atom1 atom2 overlap distance
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6/A PRO 396 CD F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6/B ARG 209 CD 0.086 3.674
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6/A ILE 392 CG2 F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6/B GLN 230 NE2 0.040 3.480
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6/A ILE 392 CA F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6/B GLN 230 NE2 -0.008 3.528
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6/A GLU 395 CG F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6/B LEU 232 CD2 -0.070 3.830
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6/A GLU 395 CA F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6/B LEU 232 CD2 -0.082 3.842
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6/A GLU 395 N F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6/B LEU 232 CD2 -0.212 3.732
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6/A ALA 394 C F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6/B LEU 232 CD2 -0.225 3.715
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6/A GLY 393 C F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6/B LEU 232 CD1 -0.235 3.725
8 contacts
> select up
61 atoms, 58 bonds, 8 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> color sel byelement
> select #6/A:392-399
54 atoms, 54 bonds, 8 residues, 1 model selected
> ui tool show H-Bonds
> windowsize 600 600
> ui tool show H-Bonds
> hbonds sel color #00fdff showDist true restrict cross interModel false
> intraRes false select true reveal true
6 hydrogen bonds found
> select #6/A:1-391
2379 atoms, 2420 bonds, 303 residues, 1 model selected
> select #6/A:380-391
Nothing selected
> select #6/A:330-391
122 atoms, 122 bonds, 14 residues, 1 model selected
> hide sel atoms
> select #6/A:400-410
93 atoms, 94 bonds, 11 residues, 1 model selected
> hide sel atoms
> ui mousemode right select
> delete sel
> hide sel
> select clear
> hide sel
> show #!2 models
> hide #!6 models
> hide #!2 models
> show #!6 models
> select #6/B:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byelement
> select #6/A:395@OE2
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #6/A:395@OE2
1 atom, 1 residue, 1 model selected
> select clear
> select #6/B:233@NZ
1 atom, 1 residue, 1 model selected
> select #6/A:395@OE2
1 atom, 1 residue, 1 model selected
> select clear
> select #6/A:395@OE2
1 atom, 1 residue, 1 model selected
> select #6/B:233@NZ
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #6/A:395@OE2
1 atom, 1 residue, 1 model selected
> select #6/A:395@OE2
1 atom, 1 residue, 1 model selected
> select #6/A:395@OE2 /B
4701 atoms, 4812 bonds, 2 pseudobonds, 592 residues, 2 models selected
> select #6/A:395@OE2 /B:232
9 atoms, 7 bonds, 2 residues, 1 model selected
> select #6/A:395@OE2 /B:232
9 atoms, 7 bonds, 2 residues, 1 model selected
> select #6/A:395@OE2/B:232
9 atoms, 7 bonds, 2 residues, 1 model selected
> select #6/A:395@OE2/B:233
10 atoms, 8 bonds, 2 residues, 1 model selected
> select #6/A:395@OE2/B:233@NZ
2 atoms, 2 residues, 1 model selected
> distance sel
Distance between F74_real_space_refined_234_ISOLDE-
noH_real_space_refined_236.pdb #6/A GLU 395 OE2 and /B LYS 233 NZ: 3.6
> show #!5 models
> select #6/A
4815 atoms, 4932 bonds, 6 pseudobonds, 607 residues, 3 models selected
> save
> /Users/ZhenGong/Documents/Xray/Phenix/F74/RealSpaceRefine_234/F74_refined_234_chainA.pdb
> models #6 selectedOnly true
> select #6/B
4700 atoms, 4812 bonds, 2 pseudobonds, 591 residues, 2 models selected
> save
> /Users/ZhenGong/Documents/Xray/Phenix/F74/RealSpaceRefine_234/F74_refined_234_chainB.pdb
> models #6 selectedOnly true
> hide #!5 models
> ~select
Nothing selected
> ui tool show "Side View"
> save /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Taking snapshot of stepper:
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
——— End of log from Tue Sep 12 12:30:41 2023 ———
opened ChimeraX session
> open
> /Users/ZhenGong/Documents/Xray/Phenix/F74/RealSpaceRefine_222/F74_refined_222out.pdb
Chain information for F74_refined_222out.pdb
---
Chain | Description
8.1/A | No description available
8.1/B | No description available
> measure rotation #8.1 toModel #6
Position of F74_refined_222out.pdb #8.1 relative to
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6
coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
Rotation angle is near zero (0 degrees)
> hide #!8.1 models
> show #!8.1 models
> hide #!6 models
> show #!6 models
> measure rotation #8.1 toModel #6
Position of F74_refined_222out.pdb #8.1 relative to
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #6
coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
Rotation angle is near zero (0 degrees)
> combine #8.1
> mmaker #9 to #6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb,
chain A (#6) with copy of F74_refined_222out.pdb, chain A (#9), sequence
alignment score = 3045.4
RMSD between 598 pruned atom pairs is 0.548 angstroms; (across all 604 pairs:
0.603)
> measure rotation #8.1 toModel #9
Position of F74_refined_222out.pdb #8.1 relative to copy of
F74_refined_222out.pdb #9 coordinates:
Matrix rotation and translation
0.96685059 -0.04865621 0.25066414 -154.36099650
-0.05052947 0.92580563 0.37460739 -166.70049073
-0.25029325 -0.37485531 0.89265715 -19.37558431
Axis -0.83137432 0.55570893 -0.00207799
Axis point 0.00000000 -183.68202669 461.63162975
Rotation angle (degrees) 26.79099300
Shift along axis 35.73507916
> hide #!9 models
> define axis #10
Axis 'rotation axis #10/axis' centered at [ -23.71912775 -167.82763856
461.57234473] with direction [-0.83137432 0.55570893 -0.00207799], radius
1.96901, and length 157.521
> turn #10.1 -26.79099300 coordinateSystem #6 models #8
> move #10.1 -35.73507916 coordinateSystem #6 models #8
> hide #8.2 models
> show #8.2 models
> close #9
> close #10
> save /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Taking snapshot of stepper:
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
> hide #!8 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> ui tool show "Side View"
> view #6
> center #6
Unknown command: center #6
> view orient
> view initial
> view
> view orient
[Repeated 1 time(s)]
> view
> define centroid #6
Centroid 'centroid' placed at [135.11711558 132.21986891 146.51525403]
> cofr 135.11711558,132.21986891,146.51525403
> save /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Taking snapshot of stepper:
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
——— End of log from Tue Sep 12 12:39:21 2023 ———
opened ChimeraX session
> select #A:396
Expected an objects specifier or a keyword
> select #6/A:396
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> ~select
Nothing selected
> /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Unknown command: /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
> save /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Taking snapshot of stepper:
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
> show #!8 models
> mmaker #6 to #8.1
No matrix compatible with both reference structure and all match structures
> hide #6.1 models
> show #6.1 models
> hide #6.5 models
> show #6.5 models
> hide #!6.4 models
> show #!6.4 models
> hide #6.3 models
> show #6.3 models
> hide #!6.2 models
> show #!6.2 models
> select #6
9544 atoms, 9775 bonds, 18 pseudobonds, 1200 residues, 9 models selected
> hide #!6 models
> open
> /Users/ZhenGong/Documents/Xray/Phenix/F74/RealSpaceRefine_236/F74_real_space_refined_234_ISOLDE-
> noH_real_space_refined_236.pdb
Chain information for F74_real_space_refined_234_ISOLDE-
noH_real_space_refined_236.pdb #9
---
Chain | Description
A | No description available
B | No description available
> select #9
9543 atoms, 9775 bonds, 3 pseudobonds, 1199 residues, 2 models selected
> hide sel atoms
> color #9/A green
> color #9/B rgb(60%,60%,100%)
> select #9:80,92,155,801-803
132 atoms, 132 bonds, 12 residues, 1 model selected
> display sel atoms
> color #9:80,92,155,801-803@O** byelement
> color #4:80,92,155,801-803@N** byelement
> select #4/C:1
74 atoms, 77 bonds, 1 residue, 1 model selected
> display sel atoms
> color #9/C:1 rgb(100%,60%,70%)
> color #9/C:1@O** byelement
> select #9/C
28 atoms, 31 bonds, 1 residue, 1 model selected
> display sel atoms
> color #9/C@C** rgb(100%,60%,70%)
> ~select
Nothing selected
> size #9/C stickRadius +0.2
Changed 31 bond radii
> size #9:801-803 stickRadius +0.1
Changed 84 bond radii
> mmaker #9 to #8.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker F74_refined_222out.pdb, chain A (#8.1) with
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb, chain A
(#9), sequence alignment score = 3045.4
RMSD between 598 pruned atom pairs is 0.548 angstroms; (across all 604 pairs:
0.603)
> ui tool show "Side View"
> view #9
> hide #!8 models
> ui mousemode right zoom
[Repeated 1 time(s)]
> save /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Taking snapshot of stepper:
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
> show #!6 models
> hide #!9 models
> hide #6.2.1 models
> show #6.2.1 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6.2 models
> show #!6.2 models
> select #6/A:392-399
54 atoms, 54 bonds, 8 residues, 1 model selected
> show sel atoms
> undo
[Repeated 1 time(s)]
> select #6/A:392-395
26 atoms, 25 bonds, 4 residues, 1 model selected
> hide #!6 models
> show #!9 models
> view #9
> show #!6 models
> hide #!9 models
> open 4a9y
Summary of feedback from opening 4a9y fetched from pdb
---
notes | Fetching compressed mmCIF 4a9y from
http://files.rcsb.org/download/4a9y.cif
Fetching CCD AQZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/AQZ/AQZ.cif
4a9y title:
P38Α map kinase bound to CMPD 8 [more info...]
Chain information for 4a9y #10
---
Chain | Description | UniProt
A | MITOGEN-ACTIVATED PROTEIN KINASE 14 | MK14_HUMAN 2-360
Non-standard residues in 4a9y #10
---
AQZ —
N-(3-{[7-methoxy-6-(2-pyrrolidin-1-ylethoxy)quinazolin-4-yl]amino}-4-methylphenyl)-2-morpholin-4-ylisonicotinamide
> close #10
> open 4ay9
Summary of feedback from opening 4ay9 fetched from pdb
---
notes | Fetching compressed mmCIF 4ay9 from
http://files.rcsb.org/download/4ay9.cif
Fetching CCD TYS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/TYS/TYS.cif
4ay9 title:
Structure of follicle-stimulating hormone in complex with the entire
ectodomain of its receptor [more info...]
Chain information for 4ay9 #10
---
Chain | Description | UniProt
A D G | GLYCOPROTEIN HORMONES, ALPHA POLYPEPTIDE | Q96QJ4_HUMAN 1-92
B E H | FOLLITROPIN SUBUNIT BETA | FSHB_HUMAN 1-111
X Y Z | FOLLICLE-STIMULATING HORMONE RECEPTOR | FSHR_HUMAN 17-366
Non-standard residues in 4ay9 #10
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose
4ay9 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
3| software_defined_assembly
> hide sel atoms
> show sel cartoons
> select #10
12344 atoms, 12432 bonds, 3 pseudobonds, 1745 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> select #10/C-F
1608 atoms, 1617 bonds, 239 residues, 1 model selected
> select #10/A,B
1596 atoms, 1611 bonds, 233 residues, 1 model selected
> select #10/C,D
728 atoms, 732 bonds, 109 residues, 1 model selected
> select #10/C,E
880 atoms, 885 bonds, 130 residues, 1 model selected
> delete #10/C,E
> delete #10/C
> delete #10/D
> delete #10/Y
> delete #10/Z
> delete #10/H-G
> delete #10/H
> delete #10/G
> mmaker #10/X to #9/B
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb,
chain B (#9) with 4ay9, chain X (#10), sequence alignment score = 482.1
RMSD between 176 pruned atom pairs is 1.197 angstroms; (across all 288 pairs:
7.008)
> show #!9 models
> hide #!10 models
> save /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Taking snapshot of stepper:
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
> combine #9/A:392-395
> select #11
9543 atoms, 9775 bonds, 3 pseudobonds, 1199 residues, 2 models selected
> hide #!11 models
> show #!11 models
> hide #!11 models
> close #11
> copy #9/A:392-395
Unknown command: copy #9/A:392-395
> hide #!6 models
> hide #!9 models
> open
> /Users/ZhenGong/Documents/Xray/Phenix/86_1/ReadySet_36/86_1_refine_29_ReadySet36_noH.pdb.pdb
Chain information for 86_1_refine_29_ReadySet36_noH.pdb.pdb #11
---
Chain | Description
A | No description available
> select #11:247,346
15 atoms, 14 bonds, 2 residues, 1 model selected
> close #11
> view #9
> show #!9 models
> combine #9
> select #10
4100 atoms, 4142 bonds, 1 pseudobond, 569 residues, 2 models selected
> hide #!9,11 cartoons
> undo
> hide #!9 models
> hide #!11 models
> show #!11 models
> select #11
9543 atoms, 9775 bonds, 3 pseudobonds, 1199 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show #!9 models
> hide #!9 models
> select #11/A:392-395
26 atoms, 25 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel@O** byelement
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #11/A:392-395@O**N** byelment
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #11/A:392-395@O** byelment
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select #11/A:392-395@O**
6 atoms, 4 residues, 1 model selected
> color sel byelement
> select #11/A:392-395@N**
4 atoms, 4 residues, 1 model selected
> color sel byelement
> ~select
Nothing selected
> cofr
Center of rotation: 3.2725 -2.8234 60.277 center of view
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!11 models
> show #!9 models
> select #9:392-399
60 atoms, 59 bonds, 9 residues, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross overlapCutoff -0.3 interModel false intraMol
> false select true showDist true reveal true log true
Allowed overlap: -0.3
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
8 contacts
atom1 atom2 overlap distance
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #9/A PRO 396 CD F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #9/B ARG 209 CD 0.086 3.674
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #9/A ILE 392 CG2 F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #9/B GLN 230 NE2 0.040 3.480
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #9/A ILE 392 CA F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #9/B GLN 230 NE2 -0.008 3.528
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #9/A GLU 395 CG F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #9/B LEU 232 CD2 -0.070 3.830
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #9/A GLU 395 CA F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #9/B LEU 232 CD2 -0.082 3.842
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #9/A GLU 395 N F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #9/B LEU 232 CD2 -0.212 3.732
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #9/A ALA 394 C F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #9/B LEU 232 CD2 -0.225 3.715
F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #9/A GLY 393 C F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #9/B LEU 232 CD1 -0.235 3.725
8 contacts
> select up
61 atoms, 58 bonds, 8 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 1
> show #!11 models
> hide #!9 models
> show #!9 models
> select #9/A:392-399
54 atoms, 54 bonds, 8 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #9/A:392-399
54 atoms, 54 bonds, 8 residues, 1 model selected
> show sel cartoons
> hide #9.1 models
> hide #!9.2 models
> hide #9.3 models
> show #9.3 models
> show #!9.2 models
> show #9.1 models
> hide #!9.2 models
> select #11
9543 atoms, 9775 bonds, 3 pseudobonds, 1199 residues, 2 models selected
> show sel atoms
> hide #!9 models
> select #11/A:392-399
54 atoms, 54 bonds, 8 residues, 1 model selected
> select #9/A:392-399
54 atoms, 54 bonds, 8 residues, 1 model selected
> select #11/A:392-399
54 atoms, 54 bonds, 8 residues, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross overlapCutoff -0.3 interModel false intraModel
> false select true showDist true reveal true log true
Allowed overlap: -0.3
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
0 contacts
atom1 atom2 overlap distance
No contacts
> select #11/A:392-399
54 atoms, 54 bonds, 8 residues, 1 model selected
> contacts sel restrict cross overlapCutoff -0.3 interModel false intraMol
> false select true showDist true reveal true log true
Allowed overlap: -0.3
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
8 contacts
atom1 atom2 overlap distance
copy of F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #11/A PRO 396 CD copy of F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #11/B ARG 209 CD 0.086 3.674
copy of F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #11/A ILE 392 CG2 copy of F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #11/B GLN 230 NE2 0.040 3.480
copy of F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #11/A ILE 392 CA copy of F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #11/B GLN 230 NE2 -0.008 3.528
copy of F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #11/A GLU 395 CG copy of F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #11/B LEU 232 CD2 -0.070 3.830
copy of F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #11/A GLU 395 CA copy of F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #11/B LEU 232 CD2 -0.082 3.842
copy of F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #11/A GLU 395 N copy of F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #11/B LEU 232 CD2 -0.212 3.732
copy of F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #11/A ALA 394 C copy of F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #11/B LEU 232 CD2 -0.225 3.715
copy of F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #11/A GLY 393 C copy of F74_real_space_refined_234_ISOLDE-noH_real_space_refined_236.pdb #11/B LEU 232 CD1 -0.235 3.725
8 contacts
> select up
61 atoms, 58 bonds, 8 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> color #11/B:209,230,232@O** byelement
> color #11/B:209,230,232@N** byelement
> ui tool show "Side View"
> label height 1
> color #11/A:392-396@N** byelement
> select #11/A:392-399
54 atoms, 54 bonds, 8 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #00fdff showDist true restrict cross interModel false
> intraModel false intraRes false select true reveal true
0 hydrogen bonds found
> select #11/A:392-399
54 atoms, 54 bonds, 8 residues, 1 model selected
> hbonds sel color #00fdff showDist true restrict cross interModel false
> intraMol false intraRes false select true reveal true
1 hydrogen bonds found
> show #!5 models
> hide #9.1 models
> hide #!5 models
> hide #9.3 models
> hide #!11 models
> show #!6 models
> hide #!6 models
> show #!2 models
> view #2
> view #2/B:230
> hide #!2 models
> show #!11 models
> view #11
> label height 1
> color #11/B:233@O** byelement
> color #11/B:233@N** byelement
> select #11/B:233
9 atoms, 8 bonds, 1 residue, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 1
> ~select
Nothing selected
> combine #11
> hide #!12 models
> select #11/A:1-391
2379 atoms, 2420 bonds, 303 residues, 1 model selected
> hide sel atoms
> select #11/A:399-720
2346 atoms, 2415 bonds, 294 residues, 1 model selected
> select #11/A:399-803
2388 atoms, 2457 bonds, 297 residues, 1 model selected
> hide sel atoms
> color #11/A:396-399@O** byelement
> color #11/A:396-399@N** byelement
> select #11/A:397-399
21 atoms, 20 bonds, 3 residues, 1 model selected
> hide sel atoms
> select #11/B:400-803
2315 atoms, 2381 bonds, 1 pseudobond, 287 residues, 2 models selected
> hide sel atoms
> select #11/B:300-803
2694 atoms, 2771 bonds, 2 pseudobonds, 332 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #11/B:1-180
1074 atoms, 1092 bonds, 140 residues, 1 model selected
> hide sel atoms
> select #11/c
28 atoms, 31 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #11/B:233@NZ
1 atom, 1 residue, 1 model selected
Drag select of 1 atoms
> distance sel
Distance between copy of F74_real_space_refined_234_ISOLDE-
noH_real_space_refined_236.pdb #11/B LYS 233 NZ and /A GLU 395 OE2: 3.6
> distance sel
Distance already exists; modify distance properties with 'distance style'
> ui tool show Distances
> ~distance #!6/A:395@OE2 #!6/B:233@NZ
> ~distance #11/B:233@NZ #11/A:395@OE2
> distance #11/B:233@NZ #11/A:395@OE2
Distance between copy of F74_real_space_refined_234_ISOLDE-
noH_real_space_refined_236.pdb #11/B LYS 233 NZ and /A GLU 395 OE2: 3.6
> label height 1
> select up
18 atoms, 16 bonds, 2 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label height 1
> save /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Taking snapshot of stepper:
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
> select #11/B:1-208
1299 atoms, 1320 bonds, 168 residues, 1 model selected
> hide sel atoms
> select #11/B:234-803
3199 atoms, 3283 bonds, 2 pseudobonds, 398 residues, 2 models selected
> hide sel atoms
Drag select of 1 atoms, 1 bonds
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
161 atoms, 163 bonds, 20 residues, 1 model selected
Drag select of 11 atoms, 12 bonds
> select #11/B:210-230
163 atoms, 164 bonds, 21 residues, 1 model selected
> select #11/B:210-229
154 atoms, 155 bonds, 20 residues, 1 model selected
> hide sel atoms
> select #11/B:231
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> select #11/B:209
11 atoms, 10 bonds, 1 residue, 1 model selected
> show (sel-residues & sidechain) target ab
> select #11@CA
1192 atoms, 1192 residues, 1 model selected
Drag select of 1 atoms, 1 bonds
Drag select of 2 atoms, 1 bonds
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
> select #11@CA
1192 atoms, 1192 residues, 1 model selected
> style sel ball
Changed 1192 atom styles
Drag select of 2 atoms, 1 bonds
> hide sel atoms
> select clear
Drag select of 1 atoms
> hide sel atoms
> save /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Taking snapshot of stepper:
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
> hide #11.3 models
> show #11.3 models
> hide #11.4.1 models
> show #11.4.1 models
> hide #11.4.1 models
> hide #11.2.1 models
> show #11.2.1 models
> hide #11.2.1 models
> crossfade
> ~cofr
[Repeated 3 time(s)]
> show #11.2.1 models
> hide #11.2.1 models
> show #!9 models
> ui tool show "Side View"
> cofr -2.5,1,20
> show #!8 models
> hide #!8.1 models
> save /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Taking snapshot of stepper:
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
——— End of log from Tue Sep 12 17:52:01 2023 ———
opened ChimeraX session
> marker position #13 3.743,11.190,81.560 col blue radius 1
Missing or invalid "markerSet" argument: Expected a marker set or a model id
> marker #13 position 3.743,11.190,81.560 color blue radius 1
> close #13
> marker #13 position 3.743,11.190,81.560 color orange radius 1
> marker #14 position -2.5,1,80 color orange radius 1
> close #14
> marker #14 position -2.5,1,80 color blue radius 1
> marker #15 position -2.5,1,-20 color blue radius 1
> select #13-15
3 atoms, 3 residues, 3 models selected
> define plane sel radius 0.2
Plane 'plane' placed at [-0.41899999 4.39666653 47.18666585] with normal [
8.52693833e-01 -5.22410976e-01 1.11022302e-16] and radius 0.2
> close #16
> define plane sel thickness 0.2
Plane 'plane' placed at [-0.41899999 4.39666653 47.18666585] with normal [
8.52693833e-01 -5.22410976e-01 1.11022302e-16] and radius 67.3
> color #16 #0000ff66
> save /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Taking snapshot of stepper:
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
——— End of log from Tue Sep 12 17:59:41 2023 ———
opened ChimeraX session
> ~select
Nothing selected
> hide #!11 models
> show #!11 models
> hide #16 models
> hide #15 models
> hide #14 models
> hide #13 models
> hide #!9 models
> show #!8.1 models
> hide #!8 models
> show #!9 models
> ui tool show "Side View"
> cofr showPivot false
> ui mousemode right zoom
> view list
No named views.
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> select #9/A,B
9515 atoms, 9744 bonds, 11 pseudobonds, 1198 residues, 3 models selected
> hide sel atoms
> ~select
Nothing selected
> ui tool show Axes/Planes/Centroids
> define axis #14,15
Axis 'root #/axis' centered at [-2.5 1. 30. ] with direction [ 0. 0. -1.],
radius 0.5, and length 100
> view #17 zalign #17
> turn z 180
> turn z -180
> turn x 180
> view #16 zalign #16
No displayed objects specified.
> view #17 zalign #17
> turn x 180
> turn x -180
> turn x 90
> hide #16 models
> show #16 models
> cofr -2.5,1,20
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> turn x -90
> show #16 models
> turn z 30
> turn z -1
> turn x 180
> ui tool show "Side View"
> save /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Taking snapshot of stepper:
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
——— End of log from Tue Sep 12 21:15:54 2023 ———
opened ChimeraX session
> ui tool show "Side View"
> view
> ui mousemode right zoom
> cofr frontCenter
> cofr
Center of rotation: 6.0736 -7.1834 -31.815 front center
> cofr -2.5,1,20
> cofr showPivot false
> save /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Taking snapshot of stepper:
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
——— End of log from Tue Sep 12 21:17:56 2023 ———
opened ChimeraX session
> view list
No named views.
> ui tool show "Side View"
> ui mousemode right zoom
> cofr -2.5,1,20 showPivot false
> select #11/A:392@N
1 atom, 1 residue, 1 model selected
> hide sel
> hide #11/A:396/C
> hide #11/A:396@O
> hide #11/A:396@C
> hide #9/A:392-395
> select #9/A:392-395
26 atoms, 25 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select #9/B:209,230,232,233
37 atoms, 34 bonds, 4 residues, 1 model selected
> select #11/B:209,230,232,233
37 atoms, 34 bonds, 4 residues, 1 model selected
> hide sel atoms
> show (sel-residues & sidechain) target ab
> select #11/B:231
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #!11.2 models
> hide #!7 models
> color #11.4 black models
> hide #11.3 models
> show #11.3 models
> hide #11.3 models
> show #11.3 models
> ui mousemode right select
> size sel pseudobondRadius +0.04
Changed 1 pseudobond radii
> ~select
Nothing selected
> save /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Taking snapshot of stepper:
F74_refine_222_ISOLDE_1-coot-1_real_space_refined_234.pdb
——— End of log from Wed Sep 13 10:43:45 2023 ———
opened ChimeraX session
> view name 11
> save /Users/ZhenGong/Desktop/F74_draft/Figure4/Fig4e.cxs
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/psession.py", line 46, in take_snapshot
data = {'shift_and_scale': sas} if sas else {'array': places.array()}
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x7fd99254dee0> ->
<chimerax.std_commands.view.NamedView object at 0x7fd9b13bc040> ->
<chimerax.geometry.place.Places object at 0x7fd9c208c340>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x7fd99254dee0> ->
<chimerax.std_commands.view.NamedView object at 0x7fd9b13bc040> ->
<chimerax.geometry.place.Places object at 0x7fd9c208c340>: Error while saving
session data for 'named views' -> <chimerax.std_commands.view.NamedViews
object at 0x7fd99254dee0> -> <chimerax.std_commands.view.NamedView object at
0x7fd9b13bc040> -> <chimerax.geometry.place.Places object at 0x7fd9c208c340>
ValueError: error processing: 'named views' -> -> -> : Error while saving
session data for 'named views' -> -> ->
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, 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
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/psession.py", line 46, in take_snapshot
data = {'shift_and_scale': sas} if sas else {'array': places.array()}
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x7fd99254dee0> ->
<chimerax.std_commands.view.NamedView object at 0x7fd9b13bc040> ->
<chimerax.geometry.place.Places object at 0x7fd9c208c340>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'named views' ->
<chimerax.std_commands.view.NamedViews object at 0x7fd99254dee0> ->
<chimerax.std_commands.view.NamedView object at 0x7fd9b13bc040> ->
<chimerax.geometry.place.Places object at 0x7fd9c208c340>: Error while saving
session data for 'named views' -> <chimerax.std_commands.view.NamedViews
object at 0x7fd99254dee0> -> <chimerax.std_commands.view.NamedView object at
0x7fd9b13bc040> -> <chimerax.geometry.place.Places object at 0x7fd9c208c340>
ValueError: error processing: 'named views' -> -> -> : Error while saving
session data for 'named views' -> -> ->
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-20.6.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 1968.140.7.0.0 (iBridge: 20.16.6072.0.0,0)
OS Loader Version: 577.140.2~15
Software:
System Software Overview:
System Version: macOS 13.5.2 (22G91)
Kernel Version: Darwin 22.6.0
Time since boot: 1 day, 20 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2410:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: C592M15RF7DL
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: Analog VGA or Analog Over DVI-I
DELL U2410:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: C592M15RFMVL
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
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: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
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: 1.1.1
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: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
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: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
File attachment: Screenshot 2023-09-13 at 10.59.14.png
Screenshot 2023-09-13 at 10.59.14.png
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Added by email2trac