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Opened 6 years ago
Closed 5 years ago
#3129 closed enhancement (fixed)
Model panel confirm close
| Reported by: | Tristan Croll | Owned by: | Eric Pettersen |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | General Controls | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 0.93 (2020-04-03)
Description
Should clicking Close on the Models panel with no models selected *really* just close everything in the session? I just accidentally double-clicked it and lost about 15 minutes' work. Perhaps if no models are selected it should pop up an "are you sure?" warning?
Log:
Startup Messages
---
warning | 'clip' is a prefix of an existing command 'clipper'
UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6vxx_1_1_1.pdb
Chain information for 6vxx_1_1_1.pdb #1
---
Chain | Description
A B C | No description available
> open 6vxx
6vxx title:
Structure of the SARS-CoV-2 spike glycoprotein (closed state) [more info...]
Chain information for 6vxx #2
---
Chain | Description
A B C | spike glycoprotein
Non-standard residues in 6vxx #2
---
NAG — N-acetyl-D-glucosamine
> matchmaker #1 to #2
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 6vxx, chain A (#2) with 6vxx_1_1_1.pdb, chain B (#1), sequence
alignment score = 5560.1
RMSD between 912 pruned atom pairs is 0.915 angstroms; (across all 972 pairs:
1.350)
> open 21452 fromDatabase emdb
Opened emd_21452.map, grid size 400,400,400, pixel 1.05, shown at level 0.155,
step 2, values float32
> clipper associate #3 toModel #1
Chain information for 6vxx_1_1_1.pdb
---
Chain | Description
1.2/A 1.2/B 1.2/C | No description available
> set bgColor white
> isolde start
> set selectionWidth 4
Done loading forcefield
> select ~#1&~protein
882 atoms, 945 bonds, 1 model selected
> toolshed show Shell
/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved
warn("IPython History requires SQLite, your history will not be saved")
> select #1&~protein
14295 atoms, 14889 bonds, 12 models selected
> select clear
> clipper spotlight radius 13.00
> clipper spotlight radius 14.00
> clipper spotlight radius 15.00
> clipper spotlight radius 16.00
> clipper spotlight radius 17.00
> clipper spotlight radius 18.00
> clipper spotlight radius 19.00
> clipper spotlight radius 20.00
Undo failed, probably because structures have been modified.
Unknown command: BGsel :ANE
> select :ANE
666 atoms, 666 bonds, 1 model selected
> select :AGA
162 atoms, 162 bonds, 1 model selected
> select :BGA
708 atoms, 708 bonds, 1 model selected
> select clear
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H83, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H83, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
10 atoms were automatically renamed to match the template: H62->H61, N->N2,
HN->HN2, C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83, H61->H62
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: HN->HN2, N->N2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: O->O7, C->C7,
CT->C8, HT1->H83, HT2->H81, HT3->H82, N->N2, HN->HN2
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: HN->HN2, N->N2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: HT2->H81, CT->C8,
HT3->H83, C->C7, N->N2, HN->HN2, O->O7, HT1->H82
8 atoms were automatically renamed to match the template: C->C7, O->O7,
CT->C8, HT1->H83, HT2->H81, HT3->H82, N->N2, HN->HN2
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
10 atoms were automatically renamed to match the template: H62->H61, N->N2,
HN->HN2, C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83, H61->H62
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
10 atoms were automatically renamed to match the template: H62->H61, N->N2,
HN->HN2, C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83, H61->H62
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
10 atoms were automatically renamed to match the template: H62->H61, N->N2,
HN->HN2, C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83, H61->H62
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H83, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: HT3->H81, CT->C8,
C->C7, N->N2, HN->HN2, O->O7, HT1->H83, HT2->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT3->H82, HT2->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H83, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: CT->C8, HT1->H83,
HT2->H81, HT3->H82, C->C7, N->N2, HN->HN2, O->O7
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: HT1->H81, CT->C8,
HT2->H83, HT3->H82, C->C7, N->N2, HN->HN2, O->O7
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H83, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H83, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H83, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H83, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H83, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: O->O7, C->C7,
CT->C8, HT1->H83, HT2->H81, HT3->H82, N->N2, HN->HN2
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
10 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83, H61->H62, H62->H61
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H83, HT2->H81, HT3->H82
8 atoms were automatically renamed to match the template: N->N2, HN->HN2,
C->C7, O->O7, CT->C8, HT1->H81, HT2->H82, HT3->H83
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
2 atoms were automatically renamed to match the template: H62->H63, H63->H62
2 atoms were automatically renamed to match the template: H62->H63, H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
3 atoms were automatically renamed to match the template: H61->H63, H62->H61,
H63->H62
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H62->H61, H61->H62
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H62->H61, H61->H62
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H62->H61, H61->H62
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
2 atoms were automatically renamed to match the template: H61->H62, H62->H61
10 atoms were automatically renamed to match the template: O11->O1A, O12->O1B,
N->N5, HN->HN5, C->C10, O->O10, CT->C11, HT1->H113, HT2->H112, HT3->H111
10 atoms were automatically renamed to match the template: C->C10, O->O10,
CT->C11, HT1->H111, HT2->H112, HT3->H113, N->N5, O11->O1B, O12->O1A, HN->HN5
10 atoms were automatically renamed to match the template: O11->O1A, O12->O1B,
N->N5, HN->HN5, C->C10, O->O10, CT->C11, HT1->H113, HT2->H112, HT3->H111
10 atoms were automatically renamed to match the template: O11->O1A, O12->O1B,
N->N5, HN->HN5, C->C10, O->O10, CT->C11, HT1->H113, HT2->H112, HT3->H111
10 atoms were automatically renamed to match the template: O11->O1A, O12->O1B,
N->N5, HN->HN5, C->C10, O->O10, CT->C11, HT1->H113, HT2->H112, HT3->H111
10 atoms were automatically renamed to match the template: O11->O1A, O12->O1B,
N->N5, HN->HN5, C->C10, O->O10, CT->C11, HT1->H113, HT2->H112, HT3->H111
10 atoms were automatically renamed to match the template: O11->O1A, O12->O1B,
N->N5, HN->HN5, C->C10, O->O10, CT->C11, HT1->H113, HT2->H112, HT3->H111
10 atoms were automatically renamed to match the template: O11->O1A, O12->O1B,
N->N5, HN->HN5, C->C10, O->O10, CT->C11, HT1->H113, HT2->H112, HT3->H111
12 atoms were automatically renamed to match the template: O11->O1B, O12->O1A,
N->N5, HN->HN5, C->C10, O->O10, CT->C11, HT1->H113, HT2->H111, HT3->H112,
H91->H92, H92->H91
10 atoms were automatically renamed to match the template: O11->O1A, O12->O1B,
N->N5, HN->HN5, C->C10, O->O10, CT->C11, HT1->H113, HT2->H112, HT3->H111
12 atoms were automatically renamed to match the template: O11->O1B, O12->O1A,
N->N5, HN->HN5, C->C10, O->O10, CT->C11, HT1->H113, HT2->H111, HT3->H112,
H91->H92, H92->H91
10 atoms were automatically renamed to match the template: O11->O1A, O12->O1B,
N->N5, HN->HN5, C->C10, O->O10, CT->C11, HT1->H113, HT2->H112, HT3->H111
10 atoms were automatically renamed to match the template: O11->O1B, O12->O1A,
N->N5, HN->HN5, C->C10, O->O10, CT->C11, HT1->H113, HT2->H111, HT3->H112
10 atoms were automatically renamed to match the template: O11->O1A, O12->O1B,
N->N5, HN->HN5, C->C10, O->O10, CT->C11, HT1->H113, HT2->H112, HT3->H111
10 atoms were automatically renamed to match the template: HT3->H111, CT->C11,
C->C10, N->N5, O11->O1B, O12->O1A, HN->HN5, O->O10, HT1->H112, HT2->H113
10 atoms were automatically renamed to match the template: O11->O1A, O12->O1B,
N->N5, HN->HN5, C->C10, O->O10, CT->C11, HT1->H113, HT2->H112, HT3->H111
10 atoms were automatically renamed to match the template: O11->O1A, O12->O1B,
N->N5, HN->HN5, C->C10, O->O10, CT->C11, HT1->H113, HT2->H112, HT3->H111
10 atoms were automatically renamed to match the template: O11->O1A, O12->O1B,
N->N5, HN->HN5, C->C10, O->O10, CT->C11, HT1->H113, HT2->H112, HT3->H111
12 atoms were automatically renamed to match the template: O5->O, N->N2,
HN->HN2, C->C7, O->O7, CT->C8, HT1->H8A, HT2->H8B, HT3->H8, H61->H6, H62->H14,
HO6->H15
12 atoms were automatically renamed to match the template: O5->O, N->N2,
HN->HN2, C->C7, O->O7, CT->C8, HT1->H8A, HT2->H8B, HT3->H8, H61->H6, H62->H14,
HO6->H15
12 atoms were automatically renamed to match the template: O5->O, N->N2,
HN->HN2, C->C7, O->O7, CT->C8, HT1->H8A, HT2->H8B, HT3->H8, H61->H6, H62->H14,
HO6->H15
12 atoms were automatically renamed to match the template: O5->O, N->N2,
HN->HN2, C->C7, O->O7, CT->C8, HT1->H8A, HT2->H8B, HT3->H8, H61->H6, H62->H14,
HO6->H15
12 atoms were automatically renamed to match the template: O5->O, N->N2,
HN->HN2, C->C7, O->O7, CT->C8, HT1->H8A, HT2->H8B, HT3->H8, H61->H6, H62->H14,
HO6->H15
12 atoms were automatically renamed to match the template: O5->O, N->N2,
HN->HN2, C->C7, O->O7, H61->H6, H62->H14, HO6->H15, CT->C8, HT1->H8A,
HT2->H8B, HT3->H8
> select #1:ILE
4389 atoms, 4167 bonds, 1 model selected
> select #1:ILE@CD
Nothing selected
> select clear
> select #1
73812 atoms, 75135 bonds, 12 models selected
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.
> select clear
> select clear
> select up
4115 atoms, 4222 bonds, 1 model selected
> select up
6768 atoms, 6879 bonds, 1 model selected
> isolde ignore sel
Changes to the set of ignored residues will notbe applied until you stop the
current simulation.
ISOLDE: currently ignoring 396 residues in model 1.2
> select clear
> clipper spotlight radius 21.00
> clipper spotlight radius 22.00
> volume gaussian #1 bfactor 100
> clipper associate #3 toModel #1
> select clear
> show #!1.1.1.1 models
> hide #1.3 models
> select up
7364 atoms, 7508 bonds, 1 model selected
> isolde ignore sel
ISOLDE: currently ignoring 474 residues in model 1.2
> select up
8235 atoms, 8385 bonds, 1 model selected
> isolde ignore sel
ISOLDE: currently ignoring 474 residues in model 1.2
> select clear
> select #1&~protein
14295 atoms, 14889 bonds, 21 models selected
> select clear
> hide #!2 models
> sequence chain /A
Chains must have same sequence
> sequence chain #1/A
Alignment identifier is 1.2.A
> view sel
> select /A:136
17 atoms, 15 bonds, 2 models selected
> show #1.3 models
> open2 /run/media/tic20/storage/structure_dump/covid-19/charmm-
> gui/redo/6vsb/6vsb_1_1_1_a_rebuilt.pdb
Chain information for 6vsb_1_1_1_a_rebuilt.pdb #3
---
Chain | Description
A B C | No description available
> matchmaker #3 /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 6vxx_1_1_1.pdb, chain A (#1.2) with 6vsb_1_1_1_a_rebuilt.pdb, chain
A (#3), sequence alignment score = 6067.2
RMSD between 785 pruned atom pairs is 1.185 angstroms; (across all 1262 pairs:
11.590)
> isolde restrain distances #1/A:1-250 templateAtoms #3/A alignmentCutoff 6
RMSD between 212 pruned atom pairs is 1.664 angstroms; (across all 239 pairs:
6.124)
RMSD between 5 pruned atom pairs is 3.041 angstroms; (across all 27 pairs:
21.415)
RMSD between 5 pruned atom pairs is 3.781 angstroms; (across all 22 pairs:
24.037)
RMSD between 5 pruned atom pairs is 3.983 angstroms; (across all 17 pairs:
20.060)
No further alignments of 3 or more residues found.
> hide #3 models
> select #1/A:1-250
3987 atoms, 4044 bonds, 1 model selected
> select #1/A:-20-250
4271 atoms, 4331 bonds, 1 model selected
> delete :-20-0
> select up
4163 atoms, 4227 bonds, 1 model selected
> select up
4260 atoms, 4328 bonds, 1 model selected
> select up
4457 atoms, 4533 bonds, 1 model selected
> select up
4542 atoms, 4621 bonds, 1 model selected
> select up
4734 atoms, 4821 bonds, 1 model selected
> select up
4845 atoms, 4936 bonds, 1 model selected
> select up
4867 atoms, 4959 bonds, 1 model selected
> select up
4914 atoms, 5008 bonds, 1 model selected
> select up
5076 atoms, 5179 bonds, 1 model selected
> select up
5177 atoms, 5282 bonds, 1 model selected
> select up
5251 atoms, 5359 bonds, 1 model selected
> select up
5265 atoms, 5371 bonds, 1 model selected
> select up
5294 atoms, 5403 bonds, 1 model selected
> select up
5400 atoms, 5515 bonds, 1 model selected
> select up
5560 atoms, 5682 bonds, 1 model selected
> select up
5669 atoms, 5795 bonds, 1 model selected
> select up
5759 atoms, 5887 bonds, 1 model selected
> select up
5806 atoms, 5936 bonds, 1 model selected
> select sel|/A:1-290
12611 atoms, 12866 bonds, 4 pseudobonds, 5 models selected
> select clear
> select clear
> isolde adjust distances #1 displayThreshold 0.5
> view /A:280
> view #1/A:280
> isolde release distances sel
> select clear
> show #3 models
> select #3/A:74
13 atoms, 12 bonds, 1 model selected
> hide #3 models
> isolde release distances sel
> select clear
> isolde release distances #1
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 112, in __init__
pointers = numpy.array([i._c_pointer.value for i in items], cptr)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 112, in <listcomp>
pointers = numpy.array([i._c_pointer.value for i in items], cptr)
AttributeError: 'NoneType' object has no attribute '_c_pointer'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2234, in _flip_peptide_bond
self.flip_peptide_bond(res)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 3187, in flip_peptide_bond
pf = Peptide_Bond_Flipper(self, res)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/manipulations/peptide_flip.py", line 58, in __init__
phipsi = self.phipsi = ProperDihedralRestraints([phi, psi])
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/molarray.py", line 720, in __init__
super().__init__(c_pointers, ProperDihedralRestraint,
ProperDihedralRestraints)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/molarray.py", line 632, in __init__
super().__init__(c_pointers, singular_py_class, array_py_class)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 117, in __init__
raise ValueError('Collection items of unrecognized type "%s"' % t)
ValueError: Collection items of unrecognized type "<class 'list'>"
ValueError: Collection items of unrecognized type ""
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 117, in __init__
raise ValueError('Collection items of unrecognized type "%s"' % t)
See log for complete Python traceback.
> select :136
83 atoms, 74 bonds, 3 models selected
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> select clear
> select clear
> select clear
> select clear
> select clear
> select clear
> select clear
> show #3 models
> hide #3 models
> show #3 models
> show #3
> hide HC
> hide #3 models
> select up
21 atoms, 21 bonds, 1 model selected
> pwd
Current working directory is:
/run/media/tic20/storage/structure_dump/covid-19/charmm-gui/redo/6vxx
> save working.cxs
> delete sel
> preset custom "make bond"
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select clear
> open2 /run/media/tic20/storage/structure_dump/covid-19/charmm-
> gui/redo/6vyb_1_1_1.pdb
Summary of feedback from opening <_io.textiowrapper
name="/run/media/tic20/storage/structure_dump/covid-19/charmm-
gui/redo/6vyb_1_1_1.pdb" mode="rt" encoding="utf-8">
---
warnings | Duplicate atom serial number found: 69982
Duplicate atom serial number found: 69983
Duplicate atom serial number found: 69984
Duplicate atom serial number found: 69985
Duplicate atom serial number found: 69981
925 messages similar to the above omitted
Chain information for 6vyb_1_1_1.pdb #4
---
Chain | Description
A B C | No description available
> select #4/A:1-250
9062 atoms, 9301 bonds, 1 model selected
> select #4/A:1-250@CA
250 atoms, 1 model selected
> select #1/A:1-250@CA
250 atoms, 1 model selected
> matchmaker #4/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 6vxx_1_1_1.pdb, chain A (#1.2) with 6vyb_1_1_1.pdb, chain A (#4),
sequence alignment score = 6265.4
RMSD between 1063 pruned atom pairs is 0.991 angstroms; (across all 1273
pairs: 5.299)
> select #4/A:300-600
4666 atoms, 4730 bonds, 1 model selected
> select #1/A:300-600
4666 atoms, 4730 bonds, 1 model selected
> hide #4 models
> open 21457 fromDatabase emdb
Opened emd_21457.map, grid size 400,400,400, pixel 1.05, shown at level 0.127,
step 2, values float32
> volume #1.1.1.2 level 0.4188
> volume #5 level 0.5015
> volume #5 level 0.6645
> volume #5 step 1
> volume #5 level 1.047
> volume #5 level 0.7801
> close #5
> select clear
> select down
1 atom, 1 model selected
> select up
24 atoms, 23 bonds, 1 model selected
> select up
235 atoms, 238 bonds, 1 model selected
> select up
133 atoms, 137 bonds, 1 model selected
> select up
282 atoms, 292 bonds, 1 model selected
> select up
295 atoms, 305 bonds, 1 model selected
> select up
517 atoms, 531 bonds, 1 model selected
> select up
524 atoms, 537 bonds, 1 model selected
> select up
549 atoms, 563 bonds, 1 model selected
> open2 /home/tic20/my-
> gits/coronavirus_structural_task_force/pdb/surface_glycoprotein/SARS-
> CoV-2/6vyb/ccpem/6vyb_extended_refined.pdb
Summary of feedback from opening <_io.textiowrapper name="/home/tic20/my-
gits/coronavirus_structural_task_force/pdb/surface_glycoprotein/SARS-
CoV-2/6vyb/ccpem/6vyb_extended_refined.pdb" mode="rt" encoding="utf-8">
---
warnings | Ignored bad PDB record found on line 104
LINKR C1 NAG A1301 ND2 ASN A 61 NAG-ASN
Ignored bad PDB record found on line 105
LINKR C1 NAG A1302 ND2 ASN A 122 NAG-ASN
Ignored bad PDB record found on line 106
LINKR C1 NAG A1303 ND2 ASN A 234 NAG-ASN
Ignored bad PDB record found on line 107
LINKR C1 NAG A1305 ND2 ASN A 282 NAG-ASN
Ignored bad PDB record found on line 108
LINKR C1 NAG A1306 ND2 ASN A 331 NAG-ASN
84 messages similar to the above omitted
6vyb_extended_refined.pdb title:
Sars-cov-2 spike ectodomain structure (open state) [more info...]
Chain information for 6vyb_extended_refined.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
Non-standard residues in 6vyb_extended_refined.pdb #5
---
NAG — (NAG)
> matchmaker #5/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 6vxx_1_1_1.pdb, chain A (#1.2) with 6vyb_extended_refined.pdb,
chain A (#5), sequence alignment score = 4661.5
RMSD between 932 pruned atom pairs is 0.928 angstroms; (across all 1009 pairs:
1.962)
> close #5
> open 5x4s
5x4s title:
Structure of the N-terminal domain (NTD)of SARS-CoV spike protein [more
info...]
Chain information for 5x4s #5
---
Chain | Description
A | Spike glycoprotein
Non-standard residues in 5x4s #5
---
NAG — N-acetyl-D-glucosamine
> matchmaker #5 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 6vxx_1_1_1.pdb, chain A (#1.2) with 5x4s, chain A (#5), sequence
alignment score = 792.4
RMSD between 216 pruned atom pairs is 1.020 angstroms; (across all 268 pairs:
3.184)
> show #5
> select #1/A:1-250
3985 atoms, 4043 bonds, 1 model selected
> select clear
> select up
17 atoms, 16 bonds, 1 model selected
> select up
581 atoms, 592 bonds, 1 model selected
> select up
686 atoms, 703 bonds, 1 model selected
> select up
773 atoms, 792 bonds, 1 model selected
> select clear
> select up
19 atoms, 18 bonds, 1 model selected
> select up
135 atoms, 136 bonds, 1 model selected
> save working.cxs
> hide #!5 models
> select up
17 atoms, 16 bonds, 1 model selected
> select up
381 atoms, 382 bonds, 1 model selected
> select clear
> select clear
> show #!5 models
> select up
15 atoms, 14 bonds, 1 model selected
> select up
581 atoms, 592 bonds, 1 model selected
> select clear
> hide #!5 models
> select clear
> select up
22 atoms, 21 bonds, 1 model selected
> select up
42 atoms, 41 bonds, 1 model selected
> select up
45 atoms, 44 bonds, 1 model selected
> select up
716 atoms, 728 bonds, 1 model selected
> select clear
> select up
24 atoms, 23 bonds, 1 model selected
> select clear
> show #!5 models
> hide #!5 models
> show #!5 models
> select up
14 atoms, 13 bonds, 1 model selected
> select up
256 atoms, 258 bonds, 1 model selected
> select up
14 atoms, 13 bonds, 1 model selected
> select up
256 atoms, 258 bonds, 1 model selected
> select clear
> select up
19 atoms, 18 bonds, 1 model selected
> select up
235 atoms, 237 bonds, 1 model selected
> select up
16 atoms, 15 bonds, 1 model selected
> select up
95 atoms, 95 bonds, 1 model selected
> select up
11 atoms, 10 bonds, 1 model selected
> select up
135 atoms, 136 bonds, 1 model selected
> select up
7 atoms, 6 bonds, 1 model selected
> select up
84 atoms, 85 bonds, 1 model selected
> select clear
> select up
10 atoms, 9 bonds, 1 model selected
> select up
84 atoms, 85 bonds, 1 model selected
> save working.cxs
> hide #!5 models
> show #3 models
> hide #2&~protein
> hide #3&~protein
> hide #3
> view #1/A:300
> show #3&~protein
> hide #3&~protein
> show #3&protein&~H
> select :HSD
1734 atoms, 1734 bonds, 2 models selected
> select clear
> save working.pdb #1
> matchmaker #3/A:300-900 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 6vxx_1_1_1.pdb, chain A (#1.2) with 6vsb_1_1_1_a_rebuilt.pdb, chain
A (#3), sequence alignment score = 2815.2
RMSD between 269 pruned atom pairs is 0.847 angstroms; (across all 601 pairs:
15.734)
> hide #3 models
> select up
192 atoms, 199 bonds, 1 model selected
> select up
40 atoms, 39 bonds, 1 model selected
> show sel
> select up
85 atoms, 87 bonds, 1 model selected
> select up
40 atoms, 39 bonds, 1 model selected
> select up
61 atoms, 61 bonds, 1 model selected
> select up
98 atoms, 99 bonds, 1 model selected
> select clear
> preset custom "make bond"
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> show #3 models
> show #3
> hide #3 models
> select up
27 atoms, 27 bonds, 1 model selected
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> select up
122 atoms, 125 bonds, 1 model selected
> show #!2 models
> hide #!2 models
> show #3 models
> matchmaker #3/A:350-400 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 6vxx_1_1_1.pdb, chain A (#1.2) with 6vsb_1_1_1_a_rebuilt.pdb, chain
A (#3), sequence alignment score = 255.8
RMSD between 49 pruned atom pairs is 0.840 angstroms; (across all 51 pairs:
1.067)
> hide #3 models
> select up
10 atoms, 9 bonds, 1 model selected
> select up
339 atoms, 342 bonds, 1 model selected
> open 6vxx
6vxx title:
Structure of the SARS-CoV-2 spike glycoprotein (closed state) [more info...]
Chain information for 6vxx #6
---
Chain | Description
A B C | spike glycoprotein
Non-standard residues in 6vxx #6
---
NAG — N-acetyl-D-glucosamine
> close #6
> close
Deleting atomic symmetry model...
> open /run/media/tic20/storage/structure_dump/covid-19/charmm-
> gui/redo/6vxx/working.cxs format session
Unable to restore session, resetting.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/session.py", line 661, in restore
obj = sm.restore_snapshot(self, data)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/molobject.py", line 2977, in restore_snapshot
drm.set_state_from_snapshot(session, data)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/molobject.py", line 2985, in set_state_from_snapshot
drs = self._get_restraints(*atoms, True)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/molobject.py", line 2685, in _get_restraints
num = f(self._c_pointer, atoms1._c_pointers, atoms2._c_pointers, create, n,
pointer(ret))
ValueError: Can't create a distance restraint between bonded atoms!
Summary of feedback from opening
/run/media/tic20/storage/structure_dump/covid-19/charmm-
gui/redo/6vxx/working.cxs
---
warning | restore_snapshot for "RotamerRestraintMgr" returned None
opened ChimeraX session
> open /run/media/tic20/storage/structure_dump/covid-19/charmm-
> gui/redo/6vxx/working.pdb format PDB
Chain information for working.pdb #1
---
Chain | Description
A B C | No description available
Chain information for working.pdb
---
Chain | Description
1.2/A 1.2/B 1.2/C | No description available
> open 21452 fromDatabase emdb
Opened emd_21452.map, grid size 400,400,400, pixel 1.05, shown at level 0.155,
step 2, values float32
> volume gaussian #1 bfactor 150
> volume gaussian #2 bfactor 150
> clipper associate #2,3 toModel #1
> hide #1.3 models
> select up
6371 atoms, 6484 bonds, 1 model selected
> select up
7018 atoms, 7133 bonds, 1 model selected
> isolde ignore sel
ISOLDE: currently ignoring 413 residues in model 1.2
> select clear
> open 6vxx
6vxx title:
Structure of the SARS-CoV-2 spike glycoprotein (closed state) [more info...]
Chain information for 6vxx #2
---
Chain | Description
A B C | spike glycoprotein
Non-standard residues in 6vxx #2
---
NAG — N-acetyl-D-glucosamine
OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Graphics:
03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:11df]
Kernel driver in use: nvidia
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → General Controls |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Model panel confirm close |
| Type: | defect → enhancement |
comment:2 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
If 'Close' would close multiple top-level models without them being explicitly selected, it now asks for confirmation.