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#9410 closed defect (fixed)
mmCIF writing vs. blank chain IDs
| Reported by: | Tristan Croll | Owned by: | Greg Couch |
|---|---|---|---|
| Priority: | normal | Milestone: | 1.7 |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Managed to break mmCIF writing somehow. I *think* it's probably because I created a molecule with `open {smiles string} from smiles` and then merged it into the working model (using the same code as the `combine` command, but adds the selected model(s) into ISOLDE's current working model rather than creating a new one) without first giving it a chain ID (models created from SMILES have an empty string for the chain ID). I did remedy that after the fact using e.g. `setattr sel res chain_id E`, but mmCIF writing is still broken. I *can* still write to PDB, so no real harm done. Unfortunately I can't share the model in this case without getting a bunch of people to give permission.
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\Tristan Croll\\\Documents\\\Structures\\\anti-
> isrib\\\2023_07_18_emready_map\\\working.cxs"
Opened crysparc_P3_J50_009_sharp.mrc as #1.1.1.1, grid size 400,400,400, pixel
1.14, shown at level 0.612, step 1, values float32
Opened emready_15.mrc as #1.1.1.2, grid size 457,457,457, pixel 1, shown at
level 1.79, step 1, values float32
Restoring stepper: working.cif
Log from Wed Jul 19 18:01:48 2023
> open "C:/Users/Tristan
> Croll/Downloads/cryosparc_P3_J50_009_volume_map_sharp.mrc" "C:/Users/Tristan
> Croll/Downloads/J50_009_volume_map.mrc"
Opened cryosparc_P3_J50_009_volume_map_sharp.mrc as #1.1, grid size
400,400,400, pixel 1.14, shown at level 0.226, step 2, values float32
Opened J50_009_volume_map.mrc as #1.2, grid size 400,400,400, pixel 1.14,
shown at level 0.0316, step 2, values float32
> open "C:/Users/Tristan Croll/Downloads/emready_15.mrc"
Opened emready_15.mrc as #2, grid size 457,457,457, pixel 1, shown at level
0.000433, step 2, values float32
> volume flip #1-2
Opened cryosparc_P3_J50_009_volume_map_sharp.mrc z flip as #3, grid size
400,400,400, pixel 1.14, shown at step 1, values float32
Opened J50_009_volume_map.mrc z flip as #4, grid size 400,400,400, pixel 1.14,
shown at step 1, values float32
Opened emready_15.mrc z flip as #5, grid size 457,457,457, pixel 1, shown at
step 1, values float32
> close #1#1.1-2
> close #2
> volume #5 level 0.6307
> volume #4 level 0.09331
> volume #3 level 0.5017
> volume #3 level 0.4354
> volume #4 level 0.08209
> close #4
> open "C:/Users/Tristan Croll/Documents/Structures/anti-
> isrib/2023_07_18_emready_map/working.cif"
Summary of feedback from opening C:/Users/Tristan
Croll/Documents/Structures/anti-isrib/2023_07_18_emready_map/working.cif
---
warnings | Atom H is not in the residue template for GLY /C:8
Atom H is not in the residue template for GLY /D:8
Atom H is not in the residue template for VAL /E:167
Atom H is not in the residue template for VAL /F:167
Chain information for working.cif #1
---
Chain | Description
A B | No description available
C D | No description available
E | No description available
F | No description available
G H | No description available
I J | No description available
> save crysparc_P3_J50_009_sharp.mrc #3
> save emready_15.mrc #5
> clipper associate #3,5 toModel #1
Opened crysparc_P3_J50_009_sharp.mrc as #1.1.1.1, grid size 400,400,400, pixel
1.14, shown at level 0.72, step 1, values float32
Opened emready_15.mrc as #1.1.1.2, grid size 457,457,457, pixel 1, shown at
level 7.85, step 1, values float32
Chain information for working.cif
---
Chain | Description
1.2/A 1.2/B | No description available
1.2/C 1.2/D | No description available
1.2/E | No description available
1.2/F | No description available
1.2/G 1.2/H | No description available
1.2/I 1.2/J | No description available
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> select clear
> set bgColor white
> st first
> select #1/A
7441 atoms, 7519 bonds, 478 residues, 1 model selected
> isolde sim start /A
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde cisflip /A:41
[Repeated 3 time(s)]
> 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
> isolde sim start /A:41,169
ISOLDE: started sim
> isolde cisflip /A:41
> st
[Repeated 5 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> select #1/A:40-100
971 atoms, 985 bonds, 61 residues, 1 model selected
> isolde sim start /A:40-100
ISOLDE: started sim
> select clear
> st
[Repeated 5 time(s)]
> isolde pepflip /A:54
> st
[Repeated 5 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
> isolde sim start /A:57,457
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 9 time(s)]
> isolde sim start /A:67
ISOLDE: started sim
> st
[Repeated 2 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 15 time(s)]
> isolde sim start /A:86
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start /A:89
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start /A:91
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 11 time(s)]
> isolde sim start /A:103
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start /A:104
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 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> st
[Repeated 4 time(s)]
> isolde sim start /A:109
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 5 time(s)]
> isolde sim start /A:115
ISOLDE: started sim
> 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
> st
[Repeated 6 time(s)]
> isolde sim start /A:122
ISOLDE: started sim
> isolde pepflip #!1.2/A:122
[Repeated 1 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
> st
[Repeated 1 time(s)]
> isolde sim start /A:124
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> isolde sim start /A:131
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 14 time(s)]
> isolde sim start /A:146
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 9 time(s)]
> isolde sim start /A:156
ISOLDE: started sim
> select clear
[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 /A:318
ISOLDE: started sim
> select clear
[Repeated 1 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
> st
[Repeated 19 time(s)]
> isolde sim start /A:176
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start /A:178
ISOLDE: started sim
> select clear
> 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
> st
> isolde sim start /A:180
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start /A:181
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start /A:183
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> isolde sim start /A:188
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 7 time(s)]
> cs 0.25
> open 6o85
6o85 title:
Electron cryo-microscopy of the eukaryotic translation initiation factor 2B
bound to eukaryotic translation initiation factor 2 from Homo sapiens [more
info...]
Chain information for 6o85 #2
---
Chain | Description | UniProt
A B | Translation initiation factor eIF-2B subunit epsilon | EI2BE_HUMAN 1-721
C D | Translation initiation factor eIF-2B subunit beta | EI2BB_HUMAN 2-351
E F | Translation initiation factor eIF-2B subunit delta | EI2BD_HUMAN 1-523
G H | Translation initiation factor eIF-2B subunit alpha | EI2BA_HUMAN 1-305
I J | Translation initiation factor eIF-2B subunit gamma | EI2BG_HUMAN 1-452
L | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 1-314
S | Eukaryotic translation initiation factor 2 subunit 3 | IF2G_HUMAN 1-472
d | Eukaryotic translation initiation factor 2 subunit beta |
Non-standard residues in 6o85 #2
---
C7B —
2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide
(ISRIB)
> matchmaker #2/A to #1/A
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 working.cif, chain A (#1.2) with 6o85, chain A (#2), sequence
alignment score = 2178.7
RMSD between 400 pruned atom pairs is 0.599 angstroms; (across all 426 pairs:
4.115)
> alphafold match #2/A
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
1 AlphaFold model found using UniProt identifier: Q13144 (chain A)
AlphaFold prediction matching 6o85
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | Q13144 | EI2BE_HUMAN | 4.37 | 721 | 426 | 100
Opened 1 AlphaFold model
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #3
> hide #!3 models
> delete #1/A:500-516
> isolde sim start #1.2/A:196,304
ISOLDE: started sim
> select clear
> 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
> ui mousemode right "mark point"
> marker #4 position 171.1,234.4,235.8 color yellow radius 1
> label sel text "Odd density - modified Cys? Metal? "
> show #!3 models
> select #3:CYS
78 atoms, 66 bonds, 13 residues, 1 model selected
> hide #!3 models
> st
[Repeated 6 time(s)]
> isolde sim start #1.2/A:203
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 10 time(s)]
> isolde sim start #1.2/A:214,216
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> isolde sim start #1.2/A:219
ISOLDE: started sim
> select clear
> isolde pepflip #1.2/A:220
[Repeated 2 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
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/A:223
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> isolde sim start #1.2/A:230
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> select up
93 atoms, 93 bonds, 6 residues, 2 models selected
> isolde sim start #1.2/A:228-237
ISOLDE: started sim
> select clear
> isolde pepflip #1.2/A:233
[Repeated 1 time(s)]
> isolde pepflip #1.2/A:232
> isolde pepflip #1.2/A:233
> isolde pepflip #1.2/A:234
> isolde pepflip #1.2/A:235
> isolde pepflip #1.2/A:234
> isolde pepflip #1.2/A:235
[Repeated 1 time(s)]
> isolde pepflip #1.2/A:233
> isolde pepflip #1.2/A:236
> isolde pepflip #1.2/A:235
[Repeated 1 time(s)]
> isolde pepflip #1.2/A:236
> isolde pepflip #1.2/A:237
> isolde pepflip #1.2/A:236
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ht ND
Set protonation of HIS #1.2/I:196 to ND
> isolde sim start #1.2/A:236
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> isolde sim start #1.2/A:239
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/A:241
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 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 8 time(s)]
> isolde sim start #1.2/A:250
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/A:253
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> isolde sim start #1.2/A:258
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 15 time(s)]
> isolde sim start #1.2/A:274
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/A:276
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/A:278,281,284
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 10 time(s)]
> isolde sim start #1.2/A:289
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> ht ND
Set protonation of HIS #1.2/A:290 to ND
> isolde sim start #1.2/A:290
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ht ND
No histidine residues specified!
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/A:294/D:292
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 10 time(s)]
> isolde sim start #1.2/A:305
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 8 time(s)]
> isolde sim start #1.2/A:314
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start #1.2/A:315
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/A:318
ISOLDE: started sim
> select clear
[Repeated 1 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
> st
[Repeated 5 time(s)]
> isolde sim start #1.2/A:324
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 6 time(s)]
> isolde sim start #1.2/A:331
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> isolde sim start #1.2/A:336
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/A:339
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/A:342
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> isolde sim start #1.2/A:349
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> isolde sim start #1.2/A:354
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 22 time(s)]
> isolde sim start #1.2/A:377
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 16 time(s)]
> isolde sim start #1.2/A:394
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/A:398
ISOLDE: started sim
> 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
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/A:401
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> isolde sim start #1.2/A:408
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> ht ND
Set protonation of HIS #1.2/A:409 to ND
> isolde sim start #1.2/A:409
ISOLDE: started sim
> 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
> ht NE
Set protonation of HIS #1.2/A:409 to NE
> isolde sim start #1.2/A:409
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 12 time(s)]
> isolde sim start #1.2/A:422,440
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/A:426
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/A:429
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/A:433
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start #1.2/A:434
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start #1.2/A:435
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start #1.2/A:436
ISOLDE: started sim
> select clear
> 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
> st
> isolde sim start #1.2/A:437
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start #1.2/A:438,441
ISOLDE: started sim
> isolde cisflip #1.2/A:439
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/A:440
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 12 time(s)]
> delete /A:457-480
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/A:455
ISOLDE: started sim
> isolde pepflip #1.2/A:455
> isolde pepflip #1.2/A:456
[Repeated 2 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/A:481
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> isolde sim start #!1.2/A:488
ISOLDE: started sim
> 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
> st
[Repeated 7 time(s)]
> isolde sim start #1.2/A:496
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/B:40
ISOLDE: started sim
> select clear
> isolde cisflip #1.2/B:40
> 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
> save working.cxs
Taking snapshot of stepper: working.cif
> isolde restrain torsions #1/B templateResidues #1/A angleRange 180
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> select #1/B
7441 atoms, 7519 bonds, 478 residues, 1 model selected
> isolde sim start #1.2/B
ISOLDE: started sim
> select clear
> st
[Repeated 15 time(s)]
> 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
> delete #1/B:501-516
> isolde sim start #1.2/B:500
ISOLDE: started sim
> select clear
> rt
> isolde pepflip #1.2/B:500
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> delete #1/B:457-480
> rt
> isolde sim start #1.2/B:57
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> rt
> isolde sim start #1.2/B:61
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 24 time(s)]
> isolde sim start #1.2/B:86
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 59 time(s)]
> isolde sim start #1.2/B:146
ISOLDE: started sim
> rt
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> rt
> st
[Repeated 13 time(s)]
> isolde sim start #1.2/B:161
ISOLDE: started sim
> rt
[Repeated 2 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> view /A:184
> isolde sim start #1.2/B:184
ISOLDE: started sim
> select clear
> 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:184
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 128 time(s)]
> isolde sim start #1.2/B:289
ISOLDE: started sim
> rt
> 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
> st
[Repeated 47 time(s)]
> isolde sim start #1.2/B:338,343
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 134 time(s)]
> isolde sim start #1.2/B:497
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> save working.cxs
Taking snapshot of stepper: working.cif
> st
[Repeated 3 time(s)]
> select /C
7826 atoms, 7923 bonds, 1 pseudobond, 663 residues, 3 models selected
> isolde sim start #1.2/C #2/C
ISOLDE: started sim
> select clear
> st
[Repeated 8 time(s)]
> isolde pepflip #1.2/C:27
> st
[Repeated 4 time(s)]
> 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
> isolde sim start #1.2/C:21,26
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde pepflip #1.2/C:27
[Repeated 1 time(s)]
> isolde pepflip #1.2/C:26
> isolde pepflip #1.2/C:27
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> delete :CL
> isolde sim start #1.2/C:31
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/C:33
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/C:37
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/C:39
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 9 time(s)]
> isolde sim start #1.2/C:49
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 8 time(s)]
> isolde sim start #1.2/C:58
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/C:60
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/C:64
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/C:68
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/C:72,75
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/C:76,238
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 13 time(s)]
> isolde sim start #1.2/C:90
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start #1.2/C:91
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/C:95
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 3 time(s)]
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
50 atoms, 49 bonds, 4 residues, 2 models selected
> isolde sim start #1.2/C:99,101-104,106
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde pepflip #1.2/C:105
> isolde pepflip #1.2/C:107
> isolde pepflip #1.2/C:105
> isolde pepflip #1.2/C:100
[Repeated 2 time(s)]
> isolde pepflip #1.2/C:101
[Repeated 1 time(s)]
> isolde pepflip #1.2/C:100
[Repeated 1 time(s)]
> select clear
> isolde pepflip #1.2/C:99
> isolde pepflip #1.2/C:98
> 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 up
53 atoms, 50 bonds, 3 residues, 2 models selected
> select up
169 atoms, 169 bonds, 12 residues, 2 models selected
> isolde sim start #1.2/C:97-108
ISOLDE: started sim
> select clear
> isolde pepflip #1.2/C:106
[Repeated 1 time(s)]
> isolde pepflip #1.2/C:103
> 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
> st
[Repeated 6 time(s)]
> isolde sim start #1.2/C:106
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 5 time(s)]
> isolde sim start #1.2/G:27
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start #1.2/C:114
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
215 atoms, 218 bonds, 15 residues, 2 models selected
> isolde sim start #1.2/C:114-128
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde pepflip #1.2/C:116
[Repeated 1 time(s)]
> select clear
[Repeated 1 time(s)]
> isolde pepflip #1.2/C:118
[Repeated 1 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 15 time(s)]
> isolde sim start #1.2/C:130
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/C:133
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/C:137
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 7 time(s)]
> isolde sim start #1.2/C:145
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/C:147
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 10 time(s)]
> select clear
> st
[Repeated 14 time(s)]
> isolde sim start #1.2/C:173
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 11 time(s)]
> isolde sim start #1.2/C:185
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 8 time(s)]
> isolde sim start #1.2/C:194
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 31 time(s)]
> isolde sim start #1.2/C:226
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> st
> isolde sim start #1.2/C:227
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> aw
> isolde sim start #1.2/C:234,1000
ISOLDE: started sim
> 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
> delete sel
> st prev
[Repeated 6 time(s)]
> ht ND
Set protonation of HIS #1.2/C:261 to ND
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/C:1000-1001
ISOLDE: started sim
> select clear
> isolde sim pause
> hbonds sel interModel false
6 hydrogen bonds found
> open "C:/Users/Tristan Croll/Downloads/J50_009_volume_map.mrc"
Opened J50_009_volume_map.mrc as #5, grid size 400,400,400, pixel 1.14, shown
at level 0.0316, step 2, values float32
> volume flip #5
Opened J50_009_volume_map.mrc z flip as #6, grid size 400,400,400, pixel 1.14,
shown at step 1, values float32
> close #5
> volume #6 level 0.141
> volume #6 level 0.06806
> close #6
> select clear
> delete sel
Sim termination reason: coord length mismatch
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st next
> st
[Repeated 7 time(s)]
> isolde sim start #1.2/C:236
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/C:238
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 10 time(s)]
> isolde sim start #1.2/C:249
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 10 time(s)]
> select clear
> st
[Repeated 14 time(s)]
> isolde sim start #1.2/C:275
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 5 time(s)]
> isolde sim start #1.2/C:281
ISOLDE: started sim
> isolde pepflip #1.2/C:282
> isolde pepflip #1.2/C:283
[Repeated 1 time(s)]
> isolde pepflip #1.2/C:282
> isolde pepflip #1.2/C:281
> isolde pepflip #1.2/C:282
> isolde pepflip #1.2/C:281
> isolde pepflip #1.2/C:282
> isolde pepflip #1.2/C:281
> 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
> st
[Repeated 10 time(s)]
> isolde sim start #1.2/C:292
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 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 11 time(s)]
> isolde sim start #1.2/C:304
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 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
> isolde sim start #1.2/C:305
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> isolde sim start #1.2/C:309
ISOLDE: started sim
> select clear
> 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/C:307/F:384
ISOLDE: started sim
> 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
> st
[Repeated 10 time(s)]
> isolde sim start #1.2/C:321
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 12 time(s)]
> isolde sim start #1.2/C:334
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> isolde sim start #1.2/C:341
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 8 time(s)]
> isolde sim start #1.2/C:350
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde restrain torsions #1/D templateResidues #1/C angleRange 180
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #1/D templateAtoms #1/D useCoordinateAlignment
> false
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.
> st
[Repeated 1 time(s)]
> select /D
7805 atoms, 7902 bonds, 1 pseudobond, 662 residues, 3 models selected
> isolde sim start #1.2/D #2/D
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim pause
> save working_2.cif #1
> open working_2.cif
Summary of feedback from opening working_2.cif
---
warnings | Atom H is not in the residue template for GLY /C:8
Atom H is not in the residue template for GLY /D:8
Atom H is not in the residue template for VAL /E:167
Atom H is not in the residue template for VAL /F:167
Chain information for working_2.cif #5
---
Chain | Description
A B | No description available
C D | No description available
E | No description available
F | No description available
G H | No description available
I J | No description available
> matchmaker #5/C to #1/D
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 working.cif, chain D (#1.2) with working_2.cif, chain C (#5),
sequence alignment score = 1730.6
RMSD between 332 pruned atom pairs is 0.274 angstroms; (across all 344 pairs:
0.911)
> select #5
58552 atoms, 59080 bonds, 2 pseudobonds, 3728 residues, 2 models selected
> style sel stick
Changed 58552 atom styles
> hide HC
> color #5 byhetero
> isolde release distances #1/D
> isolde restrain distances #1/D templateAtoms #1/C useCoordinateAlignment
> false
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> hide #!5 models
> isolde sim resume
> isolde adjust torsions #1/D springConstant 50
> isolde sim pause
> st
[Repeated 50 time(s)]
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> ra
> isolde sim resume
> select clear
> isolde sim pause
> st
[Repeated 69 time(s)]
> isolde sim resume
> st
[Repeated 2 time(s)]
> ra
> isolde sim pause
> st
[Repeated 2 time(s)]
> ra
> isolde sim resume
> isolde sim pause
> st
[Repeated 14 time(s)]
> select up
15 atoms, 14 bonds, 1 residue, 1 model selected
> ra
> isolde sim resume
> isolde sim pause
> select clear
> st
[Repeated 10 time(s)]
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> ra
> isolde sim resume
> isolde sim pause
> st
[Repeated 87 time(s)]
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> ra
> isolde sim resume
> select clear
> st
> isolde sim pause
> st
[Repeated 25 time(s)]
> select up
14 atoms, 13 bonds, 1 residue, 1 model selected
> ra
> isolde sim resume
> select clear
> isolde sim pause
> st
[Repeated 1 time(s)]
> select up
20 atoms, 20 bonds, 1 residue, 1 model selected
> ra
> isolde sim resume
> isolde sim pause
> st
[Repeated 52 time(s)]
> ra
> isolde sim resume
> isolde sim pause
> st
[Repeated 19 time(s)]
> 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
> select /D
13185 atoms, 13333 bonds, 1 pseudobond, 1006 residues, 4 models selected
> isolde sim start #1.2/D #2/D #5/D
ISOLDE: started sim
> select /D
13185 atoms, 13333 bonds, 1 pseudobond, 1006 residues, 4 models selected
> ra
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> open 6o85
6o85 title:
Electron cryo-microscopy of the eukaryotic translation initiation factor 2B
bound to eukaryotic translation initiation factor 2 from Homo sapiens [more
info...]
Chain information for 6o85 #6
---
Chain | Description | UniProt
A B | Translation initiation factor eIF-2B subunit epsilon | EI2BE_HUMAN 1-721
C D | Translation initiation factor eIF-2B subunit beta | EI2BB_HUMAN 2-351
E F | Translation initiation factor eIF-2B subunit delta | EI2BD_HUMAN 1-523
G H | Translation initiation factor eIF-2B subunit alpha | EI2BA_HUMAN 1-305
I J | Translation initiation factor eIF-2B subunit gamma | EI2BG_HUMAN 1-452
L | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 1-314
S | Eukaryotic translation initiation factor 2 subunit 3 | IF2G_HUMAN 1-472
d | Eukaryotic translation initiation factor 2 subunit beta |
Non-standard residues in 6o85 #6
---
C7B —
2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide
(ISRIB)
> hide #!6 models
> sequence chain #6/E
Alignment identifier is 6/E
> st
[Repeated 2 time(s)]
> save working.cxs
Taking snapshot of stepper: working.cif
> st
> isolde sim start #1.2/E:171
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #!1.2/E:175
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 5 time(s)]
> isolde sim start #1.2/E:181
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/E:185
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/E:189
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start #1.2/E:190
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:2001
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/E:193
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start #1.2/E:190,194,2001
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/E:202
ISOLDE: started sim
> isolde pepflip #1.2/E:202
[Repeated 1 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/E:2002-2003
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/E:197
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:2004
ISOLDE: started sim
> 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
> delete sel
> st
[Repeated 16 time(s)]
> isolde sim start #1.2/E:215
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> st
[Repeated 4 time(s)]
> al CL
> isolde sim start #1.2/E:220,2000,2004
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> view /E:ZN
> st
> isolde sim start #1.2/E:225
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 9 time(s)]
> isolde sim start #1.2/E:235
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 5 time(s)]
> isolde sim start #1.2/E:241
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select up
121 atoms, 123 bonds, 8 residues, 2 models selected
> isolde sim start #1.2/E:240-247
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/E:242
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 9 time(s)]
> isolde sim start #1.2/E:253
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 7 time(s)]
> isolde sim start #1.2/E:261
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 8 time(s)]
> isolde sim start #1.2/E:270
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 9 time(s)]
> isolde sim start #1.2/E:280
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> isolde sim start #1.2/E:285
ISOLDE: started sim
> select clear
[Repeated 1 time(s)]
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> isolde sim start #1.2/E:292
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/E:294
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 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/E:298
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> st
[Repeated 7 time(s)]
> isolde sim start #1.2/E:305
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 4 time(s)]
> isolde sim start #1.2/E:310
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 2 time(s)]
> isolde sim start #!1.2/E:314
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/E:317
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 34 time(s)]
> isolde sim start #1.2/E:352
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/E:355
ISOLDE: started sim
> select clear
[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 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> aw
> isolde sim start #1.2/E:357,2005
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/E:361
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> zoom
Pixel size at center of rotation is 0.0149
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/E:363
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start #1.2/E:364
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/E:368
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/E:372
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/E:374
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 11 time(s)]
> select clear
[Repeated 1 time(s)]
> isolde sim start #1.2/E:386
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> isolde sim start #1.2/E:386,394
ISOLDE: started sim
> 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
> st
[Repeated 5 time(s)]
> ht NE
Set protonation of HIS #1.2/D:252 to NE
> isolde sim start #1.2/D:252/E:392
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/E:394
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> isolde sim start #1.2/E:399
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start #1.2/E:400
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 5 time(s)]
> isolde sim start #1.2/E:222,406
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:2006
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/E:408
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/E:412,510
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 9 time(s)]
> isolde sim start #1.2/E:422
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/D:1000
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start #1.2/E:423
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 4 time(s)]
> isolde sim start #1.2/E:428
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/E:425-431
ISOLDE: started sim
> select clear
> 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
> aw
> isolde sim start #1.2/E:2007
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:2007-2008
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 15 time(s)]
> isolde sim start #1.2/E:444
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/E:447
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/E:449
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:446-452,2009
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> isolde sim start #1.2/E:456
ISOLDE: started sim
> select clear
> 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
> st
> aw
> isolde sim start #1.2/E:457,2010
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 7 time(s)]
> aw
> isolde sim start #1.2/E:465,2011
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #!1.2/E:467
ISOLDE: started sim
> select clear
> 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/E:467
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/E:470
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> isolde sim start #1.2/E:477
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:474-480,2012
ISOLDE: started sim
> isolde pepflip #1.2/E:478
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/E:479
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> st
[Repeated 5 time(s)]
> aw
> isolde sim start #1.2/E:485,2013
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> aw
> isolde sim start #1.2/E:486,2014
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/D:1001/E:487,2015
ISOLDE: started sim
> select clear
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim resume
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/E:225
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 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:267,2016
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> awsf
> isolde sim start #1.2/E:225,264-270,2016-2017
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> aw
> isolde sim start #1.2/E:490,2018
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 8 time(s)]
> isolde sim start #1.2/E:499
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/E:502
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> aw
> isolde sim start #1.2/E:503,2019
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 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/E:506
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 10 time(s)]
> isolde sim start #1.2/E:517
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 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
> isolde sim start #1.2/E:518
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/E:520
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> save working.cxs
Taking snapshot of stepper: working.cif
> save working_through_chain_E.cif #1
> st /E
Multiple residues selected! Going to the first...
> st
[Repeated 2 time(s)]
> aw
> isolde sim start #1.2/E:170,2020
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save working.cxs
Taking snapshot of stepper: working.cif
——— End of log from Wed Jul 19 18:01:48 2023 ———
opened ChimeraX session
Deferring bundle installation
> select clear
> st
[Repeated 5 time(s)]
> awsf
> set selectionWidth 4
> 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
> awsf
> isolde sim start
> #1.2/A-D,G-J/E:167-522,2001-2003,2005-2006,2007-2014,2015-2022/F:167-521
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222)
ISOLDE: started sim
> select clear
> 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/E:2021-2022
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st interp 5
> cs 0.25
> aw
> isolde sim start #1.2/C:1000/E:177
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/C:1000-1001/D:1002/E:174-180
ISOLDE: started sim
> 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
> awsf
> isolde sim start #1.2/C:1000-1001/D:1002-1003/E:171-183
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "2D Builder"
Please register the custom scheme 'editor' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.
> open C1=C(Cl)C=C2C(=C1)C=C(C(N)=O)C=C2 fromDatabase smiles
Translated SMILES to 3D structure via NCI web service (SMILES:
C1=C(Cl)C=C2C(=C1)C=C(C(N)=O)C=C2)
> select #7
22 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected atoms"
> usage open
open names [format format] [fromDatabase fromDatabase] [name a text string]
[format/database-specific arguments]
— read and display data
names: file names to open; a name of 'browse' will bring up a file browser
format: one of aln, amber, amira, apbs, bild, brix, ccd, ccp4, cellpack,
clustal, cmap, cmd, cod, collada, com, compiled python, coords, corecif, cube,
dat, dcd, defattr, delphi, dicom, dock, dsn6, dv, dynamo, emanhdf, fasta,
fchk, fsc, generic_particles, geomodel, gltf, gopenmol, gro, hdf, hssp, html,
ihm, images, imagic, imod, imodmap, ims, log, macmolplt, markers, mmcif, mmtf,
model2point, mol2, mole, motivelist, motl, mrc, msf, mtz, nbo31, nbo47,
netcdfmap, nifti, nrrd, obj, out, pcod, pdb, pdbqt, peet, pfam, photo, pif,
pir, positions, priism, profec, pseudobonds, psf, python, qout, relion, rmf,
rsf, schrodinger maestro, sdf, segger, session, sff, situs, smallcif, smiles,
spider, sqmout, star, stl, stockholm, storm, swc, swissdock, tbl, tom_em, trr,
uhbd, uniprot, viperdb, vtk, web fetch, xplor, xtc, xyz, or zdock
fromDatabase: one of alphafold, ccd, cellpack, cod, eds, edsdiff, emdb,
emdb_china, emdb_europe, emdb_japan, emdb_us, esmfold, ftp, help, http, https,
pcod, pdb, pdbdev, pdbe, pdbe_bio, pdbj, pubchem, rcsb_bio, smiles, tcia, or
uniprot
format/database-specific arguments: format- or database-specific arguments; to
see their syntax use 'usage open format format' or 'usage open database
database' commands respectively, where format and database are as per the
above
> usage open format smiles
'smiles' is a database format type; use the command 'usage open database' with
the corresponding database type instead
> usage open database smiles
open names [ignoreCache true or false] [resName a text string]
— read and display data
names: file names to open; a name of 'browse' will bring up a file browser
> show #!2 models
> cartoon #2
> hide #2
> show #2&~protein
> hide #!2 models
ISOLDE: merge models
Merging models #7 into #1.2.
> hide #7 models
> select up
22 atoms, 23 bonds, 1 residue, 1 model selected
> setattr sel res chain_id E
Assigning chain_id attribute to 1 item
> isolde parameterise sel
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TRISTA~1\AppData\Local\Temp\tmpp6_pj6vr\ante.in.mol2 -fi mol2 -o
C:\Users\TRISTA~1\AppData\Local\Temp\tmpp6_pj6vr\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n
(UNL) ``
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`
(UNL) ``
(UNL) `Info: Finished reading file
(C:\Users\TRISTA~1\AppData\Local\Temp\tmpp6_pj6vr\ante.in.mol2); atoms read
(22), bonds read (23).`
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) ``
(UNL) ``
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) `Info: Total number of electrons: 106; net charge: 0`
(UNL) ``
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) ``
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) ``
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(UNL) `bash.exe: warning: could not find /tmp, please create!`
(UNL) ``
Charges for residue UNL determined
OpenMM ffXML file UNL written to the current working directory.
New template added to forcefield as USER_UNL. This ligand should now work in
all remaining simulations for this session. To use in future sessions, load
the ffXML file with ISOLDE's Load Residue MD Definition(s) button.
> show #7 models
> select #7
22 atoms, 23 bonds, 1 residue, 1 model selected
> show #!2 models
ISOLDE: merge models
Merging models #7 into #1.2.
> hide #!2 models
> hide #7 models
> select up
22 atoms, 23 bonds, 1 residue, 1 model selected
> setattr sel res chain_id F
Assigning chain_id attribute to 1 item
> isolde sim start #1.2/E-F:1
ISOLDE: started sim
> select clear
> isolde sim pause
> select up
22 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected atoms"
> ui mousemode right "isolde tug atom"
> isolde sim resume
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> isolde sim start #1.2/E:483
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:480-486,2023
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/D:1004/E:477-489,2023
ISOLDE: started sim
> 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 up
3 atoms, 2 bonds, 1 residue, 1 model selected
> delete sel
> st
[Repeated 3 time(s)]
> isolde sim start #1.2/E:182
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> awsf
[Repeated 6 time(s)]
> isolde sim start #1.2/E:183,2024-2030
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:180-186,2024-2031
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:177-189,2024-2032
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:174-192,2024-2033
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/E:2032
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> al CL
> awsf
> isolde sim start #1.2/E:2032,2034-2035
ISOLDE: started sim
> 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
> delete sel
> isolde pepflip #1.2/E:221
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:218-224,2036
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/E:220
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> al BNZ
Fetching CCD BNZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/BNZ/BNZ.cif
Loading residue template for BNZ from internal database
> ui mousemode right "translate selected atoms"
> isolde sim start #1.2/E:2037
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> delete sel
> al IMD
Fetching CCD IMD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/IMD/IMD.cif
Loading residue template for IMD from internal database
> isolde sim start #1.2/E:2037
ISOLDE: started sim
> select clear
> 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
> delete sel
> isolde parameterise sel override true
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TRISTA~1\AppData\Local\Temp\tmp8kpt9rv2\ante.in.mol2 -fi mol2 -o
C:\Users\TRISTA~1\AppData\Local\Temp\tmp8kpt9rv2\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n
(IMD) ``
(IMD) `Welcome to antechamber 20.0: molecular input file processor.`
(IMD) ``
(IMD) `Info: Finished reading file
(C:\Users\TRISTA~1\AppData\Local\Temp\tmp8kpt9rv2\ante.in.mol2); atoms read
(9), bonds read (9).`
(IMD) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(IMD) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(IMD) `bash.exe: warning: could not find /tmp, please create!`
(IMD) ``
(IMD) ``
(IMD) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(IMD) `bash.exe: warning: could not find /tmp, please create!`
(IMD) `Info: Total number of electrons: 36; net charge: 0`
(IMD) ``
(IMD) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`
(IMD) `bash.exe: warning: could not find /tmp, please create!`
(IMD) ``
(IMD) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`
(IMD) `bash.exe: warning: could not find /tmp, please create!`
(IMD) ``
(IMD) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(IMD) `bash.exe: warning: could not find /tmp, please create!`
(IMD) ``
Charges for residue IMD determined
OpenMM ffXML file IMD written to the current working directory.
New template added to forcefield as USER_IMD. This ligand should now work in
all remaining simulations for this session. To use in future sessions, load
the ffXML file with ISOLDE's Load Residue MD Definition(s) button.
> isolde sim start #1.2/E:2037
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select up
9 atoms, 9 bonds, 1 residue, 1 model selected
> color sel brown
> color byhetero
> isolde sim start #1.2/E:2037
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #7 models
> select #7
22 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected atoms"
> hide #7 models
> label sel residues
> select clear
> cofr showPivot false
> label sel residues text "??? ?
Invalid "text" argument: Expected 'default' or a text string
> label sel residues text "??? "
> select clear
> movie record
> rock y 40 120 cycle 120
> movie stop
> movie reset
> movie record
> movie stop
> movie encode mystery_ligand.mp4
Movie saved to mystery_ligand.mp4
> isolde sim start #1.2/E:374
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> select /E:226,271,455
108 atoms, 96 bonds, 12 residues, 4 models selected
> style sel & #!1.2 sphere
Changed 35 atom styles
> show #!2 models
> matchmaker #2/E to #1/E
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 working.cif, chain E (#1.2) with 6o85, chain E (#2), sequence
alignment score = 1689.9
RMSD between 354 pruned atom pairs is 0.596 angstroms; (across all 356 pairs:
0.664)
> close #2
> open 6o9z
6o9z title:
Electron cryo-microscopy of the eukaryotic translation initiation factor 2B
bound to eukaryotic translation initiation factor 2 from Homo sapiens [more
info...]
Chain information for 6o9z #2
---
Chain | Description | UniProt
A B | Translation initiation factor eIF-2B subunit epsilon | EI2BE_HUMAN 1-721
C D | Translation initiation factor eIF-2B subunit beta | EI2BB_HUMAN 2-351
E F | Translation initiation factor eIF-2B subunit delta | EI2BD_HUMAN 1-523
G H | Translation initiation factor eIF-2B subunit alpha | EI2BA_HUMAN 1-305
I J | Translation initiation factor eIF-2B subunit gamma | EI2BG_HUMAN 1-452
L M | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 1-314
> matchmaker #2/E to #1/E
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 working.cif, chain E (#1.2) with 6o9z, chain E (#2), sequence
alignment score = 1710.3
RMSD between 347 pruned atom pairs is 0.590 angstroms; (across all 352 pairs:
0.651)
> cartoon #2
> hide #2
> show #2/E
> select #2
25788 atoms, 26213 bonds, 10 pseudobonds, 3605 residues, 2 models selected
> style sel stick
Changed 25788 atom styles
> select clear
> close #2
> open "C:/Users/Tristan Croll/Documents/Structures/anti-
> isrib/6o9z_peIF2/7l70_to_6o9z.cif"
Summary of feedback from opening C:/Users/Tristan
Croll/Documents/Structures/anti-isrib/6o9z_peIF2/7l70_to_6o9z.cif
---
warnings | Atom H is not in the residue template for GLY /C:8
Atom H is not in the residue template for GLY /D:8
Atom H is not in the residue template for VAL /E:167
Atom H is not in the residue template for VAL /F:167
Chain information for 7l70_to_6o9z.cif #2
---
Chain | Description
A B | No description available
C D | No description available
E | No description available
F | No description available
G H | No description available
I J | No description available
L M | Eukaryotic translation initiation factor 2 subunit 1
> matchmaker #2/E to #1/E
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 working.cif, chain E (#1.2) with 7l70_to_6o9z.cif, chain E (#2),
sequence alignment score = 1795.5
RMSD between 344 pruned atom pairs is 0.585 angstroms; (across all 356 pairs:
0.845)
> select #2
64139 atoms, 64702 bonds, 4 pseudobonds, 4066 residues, 2 models selected
> style sel stick
Changed 64139 atom styles
> select clear
> hide HC
> hide #!2 models
>
Incomplete command: toolshed
> st
> select #1
58726 atoms, 59215 bonds, 2 pseudobonds, 3772 residues, 29 models selected
> style sel stick
Changed 58726 atom styles
> select clear
> st
> isolde sim start #1.2/E:2028-2029
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> aw
> isolde sim start #1.2/E:187,2038
ISOLDE: started sim
> 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
> delete sel
> st
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/E:188,2038-2039
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> isolde sim start #1.2/E:191
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> awsf
[Repeated 2 time(s)]
> isolde sim start #1.2/E:193,2040-2041/I:1000
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> aw
> isolde sim start #1.2/E:196,2042
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> aw
> isolde sim start #1.2/E:197,2043
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> aw
> isolde sim start #1.2/E:199,2044
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/E:2044/I:99
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 9 time(s)]
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/E:209,2045/I:1001
ISOLDE: started sim
> 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
> awsf
> isolde sim start #1.2/E:2045-2046/I:1001
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> delete sel
> st
[Repeated 1 time(s)]
> awsf
[Repeated 3 time(s)]
> isolde sim start #1.2/E:211,2046/I:1002-1004
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 7 time(s)]
> aw
> isolde sim start #1.2/E:219,2047
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> al CL
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/E:220,2048-2050
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> awsf
[Repeated 1 time(s)]No existing atoms found within the given distance cutoff
of the target position. You may repeat with a larger cutoff or explicitly
specify the B-factor and chain ID, but keep in mind that placing waters
outside of H-bonding distance to the model is generally inadvisable.
> awsf
> isolde sim start #1.2/E:217-223,2049-2052
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:2053
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/E:2053-2055
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 14 time(s)]
> isolde sim start #1.2/E:301
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 19 time(s)]
> aw
> isolde sim start #1.2/E:255,2056
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> aw
> isolde sim start #1.2/E:257,2057
ISOLDE: started sim
> 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
> delete sel
> st
[Repeated 1 time(s)]
> aw
> isolde sim start #1.2/E:259,2057
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 8 time(s)]
> aw
> isolde sim start #1.2/E:268,2058
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:265-271,2058-2059
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> awsf
[Repeated 2 time(s)]
> isolde sim start #1.2/E:262-274,2058-2062
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/E:259-277,2058-2064
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 20 time(s)]
> aw
> isolde sim start #1.2/E:289,2065
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:286-292,2065-2066
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:283-295,2065-2067
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 15 time(s)]
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/E:305,2068-2069
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select clear
> st
[Repeated 1 time(s)]
> aw
> isolde sim start #1.2/E:307,2070
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:304-310,2070-2071
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 12 time(s)]
> aw
> isolde sim start #1.2/E:320,2072
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/E:317-323,2072-2074
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 6 time(s)]
> aw
> isolde sim start #1.2/E:327,2075
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 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> delete sel
> st
> isolde sim start #1.2/E:328
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/E:325-331
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 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> awsf
[Repeated 2 time(s)]
> isolde sim start #1.2/E:335,2075-2077
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> awsf
[Repeated 2 time(s)]
> isolde sim start #1.2/E:332-338,2075-2080
ISOLDE: started sim
> select clear
> 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/E:2078-2080
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:2081
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:2081-2082
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/E:336,2083-2084
ISOLDE: started sim
> 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
> delete sel
> st
[Repeated 1 time(s)]
> aw
> isolde sim start #1.2/E:338,2083
ISOLDE: started sim
> 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
> delete sel
> st
> aw
> isolde sim start #1.2/E:339,2083
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/E:336-342,2083
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:2084
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 23 time(s)]
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/E:363,2085-2086
ISOLDE: started sim
> 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
> delete sel
> st
> al CL
> isolde sim start #1.2/E:364,2085
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:361-367,2086
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/D:1004/E:358-370,2086
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> delete sel
> awsf
> isolde sim start #1.2/D:1004-1005/E:2086
ISOLDE: started sim
> 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
> delete sel
> al CL
> isolde sim start #1.2/D:1004-1005/E:2086
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> aw
> isolde sim start #1.2/E:367,2087
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 9 time(s)]
> aw
> isolde sim start #1.2/E:377,2088
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:374-380,2088-2089
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:371-383,2088-2090
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 8 time(s)]
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/E:386,2091-2092
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/D:1006/E:383-389,2091-2092
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> awsf
> isolde sim start #1.2/D:1006-1007/E:380-392,2091-2092
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/D:1008/E:389,2093
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> awsf
[Repeated 2 time(s)]
> isolde sim start #1.2/E:393,2094-2096
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/D:1009-1010/E:390-396,2094-2096
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 5 time(s)]
> isolde sim start #1.2/E:399
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 8 time(s)]
> isolde sim start #1.2/E:408
ISOLDE: started sim
> 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
> st
[Repeated 1 time(s)]
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/C:1002-1003/E:410
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/C:1002-1004/E:407-413
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
> aw
> isolde sim start #1.2/C:1005/E:411
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/E:413
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:410-416,2097
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 7 time(s)]
> awsf
[Repeated 2 time(s)]
> isolde sim start #1.2/D:1011/E:421,2098-2099
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/D:1011/E:418-424,2098-2099,2100
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/D:1011,1012/E:415-427,2098-2099,2100
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/D:1011,1012/E:412-430,2098-2099,2100,2101
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/D:1011,1012/E:409-433,2098-2099,2100,2101
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save working_waters.cxs
Taking snapshot of stepper: working.cif
> st
[Repeated 17 time(s)]
> aw
> isolde sim start #1.2/E:439,2102
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> aw
> isolde sim start #1.2/E:446,2103
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:443-449,2103-2104
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/E:448,2105-2106
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 6 time(s)]
> awsf
> isolde sim start #1.2/E:415,455,2107
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 3 time(s)]
> aw
> isolde sim start #1.2/E:459,2108
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> aw
> isolde sim start #1.2/E:462,2109
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 2 time(s)]
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/D:1013/E:465,2110
ISOLDE: started sim
> select clear
> 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/D:202,1013
ISOLDE: started sim
> select clear
> 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
> st
[Repeated 9 time(s)]
> aw
> isolde sim start #1.2/E:475,2111
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> isolde sim start #1.2/E:477
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/E:479,2112-2113
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> delete sel
> st
[Repeated 18 time(s)]
> aw
> isolde sim start #1.2/E:498,2114
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 9 time(s)]
> awsf
[Repeated 2 time(s)]
> isolde sim start #1.2/E:2115-2117
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:2115-2118
ISOLDE: started sim
> select clear
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 1 time(s)]
> aswf
Unknown command: aswf
> awsf
[Repeated 1 time(s)]
> isolde sim start #1.2/E:510,2119-2120
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:507-513,2119-2121
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> aw
> isolde sim start #1.2/E:504-516,2119-2121/G:1000
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> st
[Repeated 10 time(s)]
> save chain_e_waters_done.cif #1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 112, in save
mmcif_write.write_mmcif(session, path, **kw)
File "src\mmcif_write.pyx", line 149, in
chimerax.mmcif.mmcif_write.write_mmcif
File "src\mmcif_write.pyx", line 156, in
chimerax.mmcif.mmcif_write.write_mmcif
File "src\mmcif_write.pyx", line 485, in
chimerax.mmcif.mmcif_write.save_structure.lambda4
File "src\mmcif_write.pyx", line 485, in
chimerax.mmcif.mmcif_write.save_structure.lambda4
File "src\mmcif_write.pyx", line 252, in
chimerax.mmcif.mmcif_write._chain_id_ordinal
ValueError: not a legal chain id
ValueError: not a legal chain id
File "src\mmcif_write.pyx", line 252, in
chimerax.mmcif.mmcif_write._chain_id_ordinal
See log for complete Python traceback.
> ui tool show Shell
> select #1&~:UNL
58984 atoms, 59369 bonds, 2 pseudobonds, 3872 residues, 29 models selected
> save chain_e_waters_done.cif #1 selectedOnly true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 112, in save
mmcif_write.write_mmcif(session, path, **kw)
File "src\mmcif_write.pyx", line 149, in
chimerax.mmcif.mmcif_write.write_mmcif
File "src\mmcif_write.pyx", line 156, in
chimerax.mmcif.mmcif_write.write_mmcif
File "src\mmcif_write.pyx", line 485, in
chimerax.mmcif.mmcif_write.save_structure.lambda4
File "src\mmcif_write.pyx", line 485, in
chimerax.mmcif.mmcif_write.save_structure.lambda4
File "src\mmcif_write.pyx", line 252, in
chimerax.mmcif.mmcif_write._chain_id_ordinal
ValueError: not a legal chain id
ValueError: not a legal chain id
File "src\mmcif_write.pyx", line 252, in
chimerax.mmcif.mmcif_write._chain_id_ordinal
See log for complete Python traceback.
> select clear
> select :UNL
66 atoms, 69 bonds, 3 residues, 2 models selected
> select #1&:UNL
44 atoms, 46 bonds, 2 residues, 1 model selected
> select #1/E:UNL
22 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/E:1000
Nothing selected
> select #1/E:UNL
22 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/F:UNL
22 atoms, 23 bonds, 1 residue, 1 model selected
> save chain_e_waters_done.cif #1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 112, in save
mmcif_write.write_mmcif(session, path, **kw)
File "src\mmcif_write.pyx", line 149, in
chimerax.mmcif.mmcif_write.write_mmcif
File "src\mmcif_write.pyx", line 156, in
chimerax.mmcif.mmcif_write.write_mmcif
File "src\mmcif_write.pyx", line 485, in
chimerax.mmcif.mmcif_write.save_structure.lambda4
File "src\mmcif_write.pyx", line 485, in
chimerax.mmcif.mmcif_write.save_structure.lambda4
File "src\mmcif_write.pyx", line 252, in
chimerax.mmcif.mmcif_write._chain_id_ordinal
ValueError: not a legal chain id
ValueError: not a legal chain id
File "src\mmcif_write.pyx", line 252, in
chimerax.mmcif.mmcif_write._chain_id_ordinal
See log for complete Python traceback.
> save chain_e_waters_done.pdb #1
> open chain-e_waters_done.pdb
No such file/path: chain-e_waters_done.pdb
> open chain_e_waters_done.pdb
Chain information for chain_e_waters_done.pdb #8
---
Chain | Description
A B | No description available
C D | No description available
E | No description available
F | No description available
G H | No description available
I J | No description available
> cartoon #8
> hide #8&protein
> usage merge
"merge" is not a command name
> usage combine
combine [structures] [close true or false] [modelId modelId] [name a text
string]
— Copy/combine structure models
structures: an atomic structures specifier or nothing
modelId: a model id
OpenGL version: 3.3.0 NVIDIA 518.01
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows
Manufacturer: HP
Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 34,007,068,672
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-GB
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
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: 2023.5.7
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-QScore: 1.0
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
comtypes: 1.1.14
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: 2022.9.26
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
nvidia-cuda-nvrtc-cu11: 11.8.89
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
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
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
pywin32: 305
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
rdkit: 2022.9.5
requests: 2.28.2
scipy: 1.9.3
Send2Trash: 1.8.2
SEQCROW: 1.7.2
setuptools: 67.4.0
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
WMI: 1.5.1
zipp: 3.15.0
Change History (6)
comment:1 by , 2 years ago
| Platform: | → all |
|---|---|
| Project: | → ChimeraX |
comment:2 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Input/Output |
| Owner: | set to |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → mmCIF writing vs. blank chain IDs |
comment:3 by , 2 years ago
Many small-molecule formats have no (and therefore blank) chain IDs and many program-generated PDB files have blank chain IDs, so I think mmCIF writing has to do something reasonable with blank IDs, like issue a warning and use 'A' (or the first available ID) in the file. There really is no reason for a (standalone) small molecule to have a chain ID.
You can reproduce the problem that Tristan is having by "open smiles:c1ccccc1" and then try to save an mmCIF. The problem then continues to happen even after assigning a chain ID with "setattr #1 r chain_id E".
comment:4 by , 2 years ago
| Milestone: | → 1.7 |
|---|
comment:5 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
The label_asym value in a mmCIF file is an ASCII-ish identifier. In particular, it has no whitespace in it. Generated asym ids are alphanumeric. Strict compliance is not enforced, except for not having blanks in it.
comment:6 by , 2 years ago
Revised fix to write out inapplicable chain ids as a period. And when reading in a mmCIF file convert all question mark (?) and period (.) chain id values to blank -- because chain ids must not be empty.
Note:
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I'm thinking a partial remedy for this is to simply make it illegal for a residue to have an empty
chain_id? Allowing that feels like a recipe for trouble.