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Opened 2 years ago
Closed 2 years ago
#10099 closed defect (duplicate)
Unable to restore objects of NewerVersionQuery class
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.7-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202309220027 (2023-09-22 00:27:56 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.7.dev202309220027 (2023-09-22)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/nicollesolange/Downloads/AF-Q4D9B6-F1-model_v4.pdb
AF-Q4D9B6-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for uncharacterized protein (Q4D9B6) [more
info...]
Chain information for AF-Q4D9B6-F1-model_v4.pdb #1
---
Chain | Description | UniProt
A | uncharacterized protein | Q4D9B6_TRYCC 1-202
> set bgColor white
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select #60:79
Nothing selected
> select #60:79
Nothing selected
> select chain A #60:79
Expected an objects specifier or a keyword
> select :A.60-79
Expected an objects specifier or a keyword
> select add #1
1581 atoms, 1619 bonds, 202 residues, 1 model selected
> select :A.60-79
Expected an objects specifier or a keyword
> select #60:79
Nothing selected
> select add #1
1581 atoms, 1619 bonds, 202 residues, 1 model selected
> select #60:79
Nothing selected
> select :A.10-20
Expected an objects specifier or a keyword
> select :A.60:79
Expected an objects specifier or a keyword
> select :A.60-79
Expected an objects specifier or a keyword
> select sequence ALVGILLCCRGRRQDHPSTT
151 atoms, 152 bonds, 20 residues, 1 model selected
> select sequence ALVGILLCCRGRRQDHPSTT
151 atoms, 152 bonds, 20 residues, 1 model selected
> color sel orange
> select sequence CGDRGPSFMPLSPS
99 atoms, 102 bonds, 14 residues, 1 model selected
> select sequence CGDRGPSFMPLSPS
99 atoms, 102 bonds, 14 residues, 1 model selected
> color sel blue
> select sequence CSDTSEKIIMESSAS
107 atoms, 106 bonds, 15 residues, 1 model selected
> select sequence CSDTSEKIIMESSAS
107 atoms, 106 bonds, 15 residues, 1 model selected
> color sel light sea green
> color sel hot pink
> select sequence CNSGNSLAVPGLSDP
Nothing selected
> select sequence CNSGNSLAVPGLSDP
Nothing selected
> select sequence CNSGNSLAVPGLSDP
Nothing selected
> select sequence CYSPRVSAVEGSTEP
Nothing selected
> select sequence CYSPRVSAVEGSTEP
Nothing selected
> select sequence NSGNSLAVPGLSDP
92 atoms, 93 bonds, 14 residues, 1 model selected
> select sequence NSGNSLAVPGLSDP
92 atoms, 93 bonds, 14 residues, 1 model selected
> color sel red
> select sequence YSPRVSAVEGSTEP
103 atoms, 105 bonds, 14 residues, 1 model selected
> select sequence YSPRVSAVEGSTEP
103 atoms, 105 bonds, 14 residues, 1 model selected
> color sel purple
> color sel lime
> lighting simple
> lighting soft
> lighting simple
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> color sel bypolymer
> undo
> select add #1
1581 atoms, 1619 bonds, 202 residues, 1 model selected
> color sel #00f900ff
> color sel #f8f9beff
[Repeated 1 time(s)]
> color sel #a6f99bff
> color sel #a6f99cff
> color sel #a7f99dff
> color sel #a8f9a0ff
> color sel #b0f9acff
> color sel #b5f9b1ff
> color sel #b7f9b4ff
> color sel #b8f9b4ff
> color sel #b9f9b4ff
[Repeated 1 time(s)]
> color sel #baf9b4ff
> color sel #baf9b5ff
[Repeated 1 time(s)]
> color sel #bbf9b5ff
> color sel #bcf9b6ff
> color sel #bdf9b7ff
[Repeated 1 time(s)]
> color sel #bef9b7ff
[Repeated 1 time(s)]
> color sel #bef9b8ff
[Repeated 1 time(s)]
> color sel #bff9b9ff
[Repeated 1 time(s)]
> color sel #c0f9baff
[Repeated 2 time(s)]
> color sel #bff9baff
> color sel #bff9bbff
[Repeated 1 time(s)]
> color sel #bef9baff
[Repeated 1 time(s)]
> color sel #bbf9b9ff
[Repeated 1 time(s)]
> color sel #b9f9b8ff
> color sel #b8f9b8ff
> color sel #b7f9b9ff
> color sel #b6f9b9ff
> color sel #b5f9b9ff
> color sel #b3f9b7ff
> color sel #b2f9b6ff
> color sel #b0f9b4ff
> color sel #aff9b3ff
> color sel #aef9b2ff
> color sel #adf9b1ff
> color sel #abf9afff
[Repeated 1 time(s)]
> color sel #aaf9adff
> color sel #a8f9abff
> color sel #a4f9a7ff
> color sel #a2f9a4ff
> color sel #9df99fff
> color sel #9cf99dff
> color sel #9df99eff
[Repeated 1 time(s)]
> color sel #9df99efe
> color sel #9df99ef9
> color sel #9df99ef3
> color sel #9df99eeb
> color sel #9df99ee7
> color sel #9df99ee3
> color sel #9df99ee2
> color sel #9df99ee1
> color sel #9df99ede
> color sel #9df99ed9
> color sel #9df99ed0
> color sel #9df99ecc
> color sel #9df99eca
[Repeated 1 time(s)]
> color sel #9df99ec9
[Repeated 1 time(s)]
> color sel #9df99ec7
> color sel #9df99ec4
> color sel #9df99ec0
> color sel #9df99ebd
> color sel #9df99ebc
> color sel #9df99eb8
> color sel #9df99eb3
> color sel #9df99eae
[Repeated 1 time(s)]
> color sel #9df99ead
> select subtract #1
Nothing selected
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting full
> lighting simple
> lighting flat
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> save /Users/nicollesolange/Desktop/image5.png supersample 3
> lighting soft
> lighting full
> lighting simple
> lighting full
> lighting flat
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> select sequence ALVGILLCCRGRRQDHPSTT
151 atoms, 152 bonds, 20 residues, 1 model selected
> select sequence ALVGILLCCRGRRQDHPSTT
151 atoms, 152 bonds, 20 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #a0f9a2ad
[Repeated 1 time(s)]
> color sel #a3f9a2ad
> color sel #aff9aaad
> color sel #d6f9c0ad
> color sel #f1f9c8ad
> color sel #f9f4c7ad
> color sel #f9f0c6ad
> color sel #f9eec6ad
[Repeated 1 time(s)]
> color sel #f9edc6ad
> color sel #f9ecc7ad
> color sel #f9ebc7ad
> color sel #f9eac8ad
> color sel #f9e9c8ad
> color sel #f9e6c8ad
> color sel #f9e4c8ad
> color sel #f9e2c9ad
> color sel #f9e0c9ad
> color sel #f9dfcaad
> color sel #f9ddcaad
> color sel #f9dccaad
> color sel #f9dacbad
[Repeated 1 time(s)]
> color sel #f9d9cbad
> color sel #f9d8cbad
[Repeated 1 time(s)]
> color sel #f9d8caad
> color sel #f9d7caad
[Repeated 2 time(s)]
> color sel #f9d6c9ad
> color sel #f9d5c9ad
> color sel #f9d5c8ad
> color sel #f9d4c8ad
> color sel #f9d3c7ad
> color sel #f9cec6ad
> color sel #f9c8c4ad
> color sel #f9c5c4ad
> color sel #f9c4c4ad
> color sel #f9c3c4ad
> color sel #f9c3c5ad
> color sel #f9c2c7ad
> color sel #f9bfccad
> color sel #f9bccead
> color sel #f9bbd0ad
> color sel #f9bad2ad
> color sel #f9b9d3ad
[Repeated 1 time(s)]
> color sel #f9bbd5ad
> color sel #f9c8e5ad
> color sel #f9d0f1ad
> color sel #f7d5f9ad
> color sel #ecd7f9ad
> color sel #ded2f9ad
> color sel #dbd1f9ad
> color sel #d4cff9ad
> color sel #d1cef9ad
> color sel #d0cef9ad
> color sel #ccccf9ad
> color sel #c7cff9ad
> color sel #c4d0f9ad
> color sel #c0d0f9ad
> color sel #c0d1f9ad
[Repeated 1 time(s)]
> color sel #bfd1f9ad
[Repeated 2 time(s)]
> color sel #bed1f9ad
[Repeated 1 time(s)]
> color sel #bdd1f9ad
[Repeated 1 time(s)]
> color sel #bed1f9ad
[Repeated 2 time(s)]
> color sel #becff9ad
> color sel #bfcff9ad
[Repeated 2 time(s)]
> color sel #bfcef9ad
[Repeated 2 time(s)]
> color sel #bfcdf9ad
> select add #1
1581 atoms, 1619 bonds, 202 residues, 1 model selected
> select subtract #1
Nothing selected
> select sequence ALVGILLCCRGRRQDHPSTT
151 atoms, 152 bonds, 20 residues, 1 model selected
> select sequence ALVGILLCCRGRRQDHPSTT
151 atoms, 152 bonds, 20 residues, 1 model selected
> ui tool show "Color Actions"
> color sel khaki
> select add #1
1581 atoms, 1619 bonds, 202 residues, 1 model selected
> select subtract #1
Nothing selected
> select main
1581 atoms, 1619 bonds, 202 residues, 1 model selected
> color sel #f2993eff
> color sel #d3e8e4ff
> select subtract #1
Nothing selected
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting flat
> lighting simple
> select sequence ALVGILLCCRGRRQDHPSTT
151 atoms, 152 bonds, 20 residues, 1 model selected
> select sequence ALVGILLCCRGRRQDHPSTT
151 atoms, 152 bonds, 20 residues, 1 model selected
> color sel #f6f4d6ff
> select add #1
1581 atoms, 1619 bonds, 202 residues, 1 model selected
> select subtract #1
Nothing selected
> select sequence ALVGILLCCRGRRQDHPSTT
151 atoms, 152 bonds, 20 residues, 1 model selected
> select sequence ALVGILLCCRGRRQDHPSTT
151 atoms, 152 bonds, 20 residues, 1 model selected
> color sel #f6f3d8ff
> color sel #f5f3d8ff
> color sel #eeecd2ff
> color sel #e7e5cbff
> color sel #e3e1c8ff
> color sel #e1dfc6ff
> color sel #e0ddc5ff
> color sel #dedcc3ff
> color sel #dddbc3ff
> color sel #dbd9c1ff
> color sel #dad8c0ff
[Repeated 1 time(s)]
> color sel #d9d7bfff
> color sel #d6d4bdff
> color sel #d5d3bbff
> color sel #d4d2bbff
[Repeated 2 time(s)]
> color sel #d4d1baff
> color sel #d3d1baff
[Repeated 1 time(s)]
> color sel #d4d2bbff
> color sel #d5d3bcff
> color sel #d9d7bfff
> color sel #e0dec5ff
> color sel #e4e1c8ff
> color sel #e5e3caff
> color sel #e8e5ccff
> color sel #ebe9cfff
> color sel #f0eed3ff
> color sel #f3f0d6ff
> color sel #f6f4d9ff
> color sel #f8f5daff
> color sel #f8f6dbff
> color sel #faf7dcff
> color sel #fbf8ddff
> color sel #fbf9ddff
> color sel #fcf9deff
[Repeated 1 time(s)]
> color sel #fcfadeff
[Repeated 1 time(s)]
> color sel #fdfadeff
[Repeated 1 time(s)]
> color sel #fdfadefd
> color sel #fdfadef2
> color sel #fdfadedd
> color sel #fdfaded2
> color sel #fdfadec9
> color sel #fdfadebe
> color sel #fdfadeb6
> color sel #fdfadeb2
> color sel #fdfadeae
> color sel #fdfadeab
> color sel #fdfadeaa
[Repeated 1 time(s)]
> color sel #fdfadeab
> color sel #fdfadeba
> color sel #fdfadee6
> color sel #fdfadefd
> color sel #fdfadeff
> color sel #fcfadeff
> color sel #faf8dcff
> color sel #f6f3d8ff
> color sel #f4f1d7ff
> color sel #f3f1d6ff
[Repeated 1 time(s)]
> color sel #f3f0d6ff
> color sel #f2efd5ff
> color sel #f1efd4ff
> color sel #eef1cfff
[Repeated 1 time(s)]
> color sel #eef1ceff
[Repeated 1 time(s)]
> color sel #edf1cdff
> color sel #edf1ccff
> color sel #ecf1cbff
> color sel #ecf1caff
> color sel #ebf1c9ff
[Repeated 1 time(s)]
> color sel #ebf1c8ff
> color sel #eaf1c8ff
[Repeated 1 time(s)]
> color sel #eaf1c7ff
[Repeated 1 time(s)]
> color sel #eaf1c6ff
> color sel #e9f1c6ff
[Repeated 1 time(s)]
> color sel #e9f1c5ff
[Repeated 1 time(s)]
> color sel #e9f1c4ff
> color sel #e8f1c3ff
> color sel #e8f1c4ff
> color sel #e9f1c4ff
> color sel #eaf1c4ff
> color sel #ecf1c5ff
> color sel #edf1c5ff
> color sel #eff1c5ff
> color sel #f0f1c4ff
> color sel #f1f1c4ff
[Repeated 1 time(s)]
> color sel #f1f0c4ff
[Repeated 1 time(s)]
> color sel #f1efc4ff
[Repeated 1 time(s)]
> color sel #f1efc3ff
> color sel #f1eec3ff
[Repeated 1 time(s)]
> color sel #f1edc3ff
[Repeated 3 time(s)]
> color sel #ede8bfff
> color sel #eae6bdff
> color sel #e9e4bcff
> color sel #e8e4bcff
[Repeated 2 time(s)]
> color sel #e9e4bcff
> color sel #e9e5bcff
> color sel #e9e5bdff
> color sel #eae6bdff
[Repeated 1 time(s)]
> color sel #ebe7beff
> color sel #ece8bfff
> color sel #efebc1ff
> color sel #f0ecc2ff
[Repeated 1 time(s)]
> select add #1
1581 atoms, 1619 bonds, 202 residues, 1 model selected
> select subtract #1
Nothing selected
> select sequence ALVGILLCCRGRRQDHPSTT
151 atoms, 152 bonds, 20 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale green
> select add #1
1581 atoms, 1619 bonds, 202 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #1
1581 atoms, 1619 bonds, 202 residues, 1 model selected
> show sel surfaces
> transparency (#!1 & sel) 40
> transparency (#!1 & sel) 10
> transparency (#!1 & sel) 80
> select subtract #1
1 model selected
> hide surfaces
> select sequence CGDRGPSFMPLSPS
99 atoms, 102 bonds, 14 residues, 1 model selected
> select sequence CGDRGPSFMPLSPS
99 atoms, 102 bonds, 14 residues, 1 model selected
> ui tool show "Color Actions"
> color sel plum
> select add #1
1581 atoms, 1619 bonds, 202 residues, 2 models selected
> select subtract #1
1 model selected
> lighting flat
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting flat
> lighting soft
> lighting flat
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting simple
> lighting shadows true
> lighting shadows false
> select add #1
1581 atoms, 1619 bonds, 202 residues, 1 model selected
> color (#!1 & sel) #d3e8e4ff
> select subtract #1
1 model selected
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting simple
> lighting soft
> color #a6d5ccff
> select sequence ALVGILLCCRGRRQDHPSTT
151 atoms, 152 bonds, 20 residues, 1 model selected
> select sequence ALVGILLCCRGRRQDHPSTT
151 atoms, 152 bonds, 20 residues, 1 model selected
> ui tool show "Color Actions"
> color sel khaki
> select add #1
1581 atoms, 1619 bonds, 202 residues, 2 models selected
> select subtract #1
1 model selected
> select sequence CGDRGPSFMPLSPS
99 atoms, 102 bonds, 14 residues, 1 model selected
> select sequence CGDRGPSFMPLSPS
99 atoms, 102 bonds, 14 residues, 1 model selected
> ui tool show "Color Actions"
> color sel khaki
> select add #1
1581 atoms, 1619 bonds, 202 residues, 2 models selected
> select subtract #1
1 model selected
> select sequence CSDTSEKIIMESSAS
107 atoms, 106 bonds, 15 residues, 1 model selected
> select sequence CSDTSEKIIMESSAS
107 atoms, 106 bonds, 15 residues, 1 model selected
> ui tool show "Color Actions"
> color sel khaki
> select add #1
1581 atoms, 1619 bonds, 202 residues, 2 models selected
> select subtract #1
1 model selected
> select sequence NSGNSLAVPGLSDP
92 atoms, 93 bonds, 14 residues, 1 model selected
> select sequence NSGNSLAVPGLSDP
92 atoms, 93 bonds, 14 residues, 1 model selected
> ui tool show "Color Actions"
> color sel khaki
> select add #1
1581 atoms, 1619 bonds, 202 residues, 2 models selected
> select subtract #1
1 model selected
> select sequence YSPRVSAVEGSTEP
103 atoms, 105 bonds, 14 residues, 1 model selected
> select sequence YSPRVSAVEGSTEP
103 atoms, 105 bonds, 14 residues, 1 model selected
> ui tool show "Color Actions"
> color sel khaki
> select add #1
1581 atoms, 1619 bonds, 202 residues, 2 models selected
> select subtract #1
1 model selected
> select sequence YSPRVSAVEGSTEP
103 atoms, 105 bonds, 14 residues, 1 model selected
> select sequence YSPRVSAVEGSTEP
103 atoms, 105 bonds, 14 residues, 1 model selected
> show sel surfaces
> transparency (#!1 & sel) 80
> select add #1
1581 atoms, 1619 bonds, 202 residues, 2 models selected
> select subtract #1
1 model selected
> select sequence YSPRVSAVEGSTEP
103 atoms, 105 bonds, 14 residues, 1 model selected
> hide sel surfaces
> show sel atoms
> select add #1
1581 atoms, 1619 bonds, 202 residues, 2 models selected
> select subtract #1
1 model selected
> select sequence YSPRVSAVEGSTEP
103 atoms, 105 bonds, 14 residues, 1 model selected
> hide sel atoms
> color (#!1 & sel) #a0d5c7ff
> color (#!1 & sel) #a1d5c6ff
> color (#!1 & sel) #a5d5b9ff
> color (#!1 & sel) #a5d5a9ff
> color (#!1 & sel) #a8d5a7ff
> color (#!1 & sel) #b3d5abff
> color (#!1 & sel) #b7d5acff
> color (#!1 & sel) #c4d5b0ff
> color (#!1 & sel) #cbd5b1ff
> color (#!1 & sel) #ccd5b0ff
> color (#!1 & sel) #aed560ff
[Repeated 1 time(s)]
> color (#!1 & sel) #abd55fff
> color (#!1 & sel) #acd561ff
> color (#!1 & sel) #b3d575ff
> color (#!1 & sel) #b3d574ff
> color (#!1 & sel) #b2d573ff
> color (#!1 & sel) #b2d572ff
> color (#!1 & sel) #aad571ff
> color (#!1 & sel) #a6d570ff
> color (#!1 & sel) #a6d56fff
> color (#!1 & sel) #a7d56eff
> color (#!1 & sel) #a0d545ff
> color (#!1 & sel) #a1d542ff
> color (#!1 & sel) #a9d542ff
> color (#!1 & sel) #abd543ff
> color (#!1 & sel) #b3d56aff
> color (#!1 & sel) #b8d591ff
> color (#!1 & sel) #b8d593ff
> color (#!1 & sel) #b8d592ff
> color (#!1 & sel) #b5d590ff
> color (#!1 & sel) #aed587ff
> color (#!1 & sel) #a8d57dff
> color (#!1 & sel) #a7d57aff
> color (#!1 & sel) #abd579ff
> color (#!1 & sel) #add576ff
> color (#!1 & sel) #add575ff
> color (#!1 & sel) #acd575ff
> color (#!1 & sel) #acd574ff
> color (#!1 & sel) #a4d563ff
> color (#!1 & sel) #a2d55eff
> color (#!1 & sel) #a3d55eff
[Repeated 2 time(s)]
> color (#!1 & sel) #a5d561ff
> color (#!1 & sel) #acd563ff
> color (#!1 & sel) #b7d560ff
> color (#!1 & sel) #b8d557ff
> color (#!1 & sel) #b6d537ff
> color (#!1 & sel) #b8d533ff
> color (#!1 & sel) #bad532ff
> color (#!1 & sel) #bed533ff
> color (#!1 & sel) #d1d531ff
> color (#!1 & sel) #d4d531ff
> color (#!1 & sel) #d5cd2dff
> color (#!1 & sel) #d5cc2bff
> color (#!1 & sel) #d5cb2cff
> color (#!1 & sel) #d5cc2bff
> color (#!1 & sel) #d5ce28ff
> color (#!1 & sel) #d5d127ff
> color (#!1 & sel) #d5d524ff
> color (#!1 & sel) #d3d522ff
> color (#!1 & sel) #ced51aff
[Repeated 1 time(s)]
> color (#!1 & sel) #ccd518ff
> color (#!1 & sel) #c9d516ff
> color (#!1 & sel) #c9d51aff
> color (#!1 & sel) #c4d522ff
> color (#!1 & sel) #c2d525ff
> color (#!1 & sel) #c2d527ff
[Repeated 1 time(s)]
> color (#!1 & sel) #c2d528ff
> color (#!1 & sel) #ced554ff
> color (#!1 & sel) #cfd559ff
> color (#!1 & sel) #ced559ff
> color (#!1 & sel) #cfd55aff
> color (#!1 & sel) #d0d567ff
> color (#!1 & sel) #d5d0b6ff
> color (#!1 & sel) #d5d1bbff
[Repeated 1 time(s)]
> color (#!1 & sel) #d5d4b8ff
> color (#!1 & sel) #ccd5a8ff
> color (#!1 & sel) #ccd5a7ff
> color (#!1 & sel) #cad5a4ff
> color (#!1 & sel) #cad59eff
> color (#!1 & sel) #cad59dff
[Repeated 1 time(s)]
> color (#!1 & sel) #c8d58aff
[Repeated 1 time(s)]
> color (#!1 & sel) #c8d587ff
> color (#!1 & sel) #cad57cff
> color (#!1 & sel) #cdd57aff
> color (#!1 & sel) #d5d577ff
> color (#!1 & sel) #d5d377ff
> color (#!1 & sel) #d5d378ff
> color (#!1 & sel) #d5d078ff
> color (#!1 & sel) #d5c975ff
> color (#!1 & sel) #d5c673ff
> color (#!1 & sel) #d5c271ff
> color (#!1 & sel) #d5bd6dff
> color (#!1 & sel) #d5b869ff
> color (#!1 & sel) #d5b768ff
> color (#!1 & sel) #d5bb67ff
> color (#!1 & sel) #d5c264ff
> color (#!1 & sel) #d5d154ff
> color (#!1 & sel) #d5d253ff
> color (#!1 & sel) #cad545ff
> color (#!1 & sel) #c2d53dff
> color (#!1 & sel) #bfd53aff
> color (#!1 & sel) #bed53aff
> color (#!1 & sel) #b7d533ff
> color (#!1 & sel) #b6d533ff
> color (#!1 & sel) #b4d52fff
> color (#!1 & sel) #aed527ff
[Repeated 1 time(s)]
> color (#!1 & sel) #a8d520ff
> color (#!1 & sel) #a6d51eff
> color (#!1 & sel) #a6d51fff
> color (#!1 & sel) #a2d51eff
[Repeated 1 time(s)]
> color (#!1 & sel) #a1d51eff
> color (#!1 & sel) #a1d51fff
[Repeated 2 time(s)]
> color (#!1 & sel) #a3d522ff
> color (#!1 & sel) #aad529ff
> color (#!1 & sel) #b3d524ff
> color (#!1 & sel) #b7d522ff
> color (#!1 & sel) #b9d521ff
> color (#!1 & sel) #bfd51fff
> color (#!1 & sel) #c2d51dff
[Repeated 1 time(s)]
> color (#!1 & sel) #c6d51bff
> color (#!1 & sel) #c9d51aff
> color (#!1 & sel) #cad51aff
> color (#!1 & sel) #d5d11aff
> color (#!1 & sel) #d5ce1aff
> color (#!1 & sel) #d5ca1aff
> color (#!1 & sel) #d5c618ff
> color (#!1 & sel) #d5c518ff
> color (#!1 & sel) #d5c517ff
> color (#!1 & sel) #d5bd12ff
> color (#!1 & sel) #d5b70dff
> color (#!1 & sel) #d5b60dff
> color (#!1 & sel) #d5b60cff
> color (#!1 & sel) #d5b60bff
[Repeated 1 time(s)]
> color (#!1 & sel) #d5b709ff
> color (#!1 & sel) #d5ba07ff
> color (#!1 & sel) #d5c102ff
> color (#!1 & sel) #d5c301ff
> color (#!1 & sel) #d5c300ff
> color (#!1 & sel) #d5c500ff
> color (#!1 & sel) #d5cf00ff
> color (#!1 & sel) #d5d100ff
> color (#!1 & sel) #d5d200ff
> color (#!1 & sel) #d5d300ff
> color (#!1 & sel) #ced500ff
> color (#!1 & sel) #d0d500ff
> color (#!1 & sel) #d3d500ff
> color (#!1 & sel) #d5d500ff
> select add #1
1581 atoms, 1619 bonds, 202 residues, 2 models selected
> select subtract #1
1 model selected
> save
> /Users/nicollesolange/Documents/UPC_LAB/Kathy_Project/TcCLB.510323.60.cxs
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x10676a750>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x10676a750>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save
> /Users/nicollesolange/Documents/UPC_LAB/Kathy_Project/TcCLB.510323.60.cxs
> includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x10676a750>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 299, in process
return copy_state(data, convert=convert)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 219, in copy_state
return _copy(data)
^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in _copy
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 204, in <listcomp>
items = [(_copy(k), _copy(v)) for k, v in data.items()]
^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/state.py", line 217, in _copy
return convert(data)
^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 298, in convert
return add_obj(obj, parents)
^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 270, in _add_obj
uid = _UniqueName.from_obj(self.session, obj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 143, in from_obj
raise RuntimeError(
RuntimeError: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 901, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 625, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tasks' -> <chimerax.core.tasks.Tasks object at
0x10676a750>: Unable to restore objects of NewerVersionQuery class in
ChimeraX-Core bundle because the class name is not listed in the name to class
table for session restore
ValueError: error processing: 'tasks' -> : Unable to restore objects of
NewerVersionQuery class in ChimeraX-Core bundle because the class name is not
listed in the name to class table for session restore
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-18.8.6
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir7,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 1.8 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 3 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 481.0.0.0.0
OS Loader Version: 540.120.3~37
SMC Version (system): 2.27f2
Software:
System Software Overview:
System Version: macOS 12.7 (21G816)
Kernel Version: Darwin 21.6.0
Time since boot: 3 days 45 minutes
Graphics/Displays:
Intel HD Graphics 6000:
Chipset Model: Intel HD Graphics 6000
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1626
Revision ID: 0x0009
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: LCD
Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
UI Looks like: 1440 x 900
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.0
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.2
charset-normalizer: 3.2.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.11
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.48
ChimeraX-AtomicLibrary: 10.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.3
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.4
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202309220027
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.12
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.10
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.32.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3
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: 1.1.2
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.4
contourpy: 1.1.1
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.42.1
funcparserlib: 1.0.1
glfw: 2.6.2
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.7.10
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.6
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.10.0
prompt-toolkit: 3.0.39
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.0
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.2
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.8.0
tzdata: 2023.3
urllib3: 2.0.5
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Unable to restore objects of NewerVersionQuery class |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #9924