Opened 3 years ago

Last modified 3 years ago

#6992 assigned defect

Session restore: cannot peek() on Dropbox file drop

Reported by: chimerax-bug-report@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc: chimerax-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
ChimeraX Version: 1.4rc202205290614 (2022-05-29 06:14:06 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4rc202205290614 (2022-05-29)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "D:/Dropbox (Technion Dropbox)/Ayala_Shiber_lab/Hila/Isgylation -
> computational/AF-Q14258-F1-model_v2_TRIMED.ODA-OPRA_YOMAMA.cxs"

Log from Tue May 31 10:58:21 2022UCSF ChimeraX version: 1.4rc202205290614
(2022-05-29)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "D:\Dropbox (Technion Dropbox)\Ayala_Shiber_lab\Hila\Isgylation -
> computational\AF-Q14258-F1-model_v2_TRIMED.ODA-OPRA.cxs" format session

Log from Tue Feb 15 15:04:19 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/3_proteins_hila.cxs"

Log from Sun Jan 2 18:07:55 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.mobo.free.prot.wt/3-INPUT/YY3_mod_prot_free.pdb"

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.osi.free.prot.wt/1-exp/3-INPUT/YY3_prot_free.pdb"

> mmaker #2 to #1

Reference and/or match model contains no nucleic or amino acid chains.  
Use the command-line 'align' command to superimpose small molecules/ligands.  

> align #2 toAtoms #1

Unequal number of atoms to pair, 71 and 83  

> hide #1 models

> show #1 models

> turn y models #2

[Repeated 2 time(s)]

> turn y models #2 center #2

[Repeated 4 time(s)]

> turn x models #2 center #2

> turn z models #2 center #2

[Repeated 3 time(s)]

> turn x 1 models #2 center #2

[Repeated 155 time(s)]

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.mobo.free.prot.wt/3-INPUT/4zau_A.712-919.ATOM.CA.loops.FH.His.pdb"

Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/EGFR-
HER2/systems/4zau.mobo.free.prot.wt/3-INPUT/4zau_A.712-919.ATOM.CA.loops.FH.His.pdb  
---  
warnings | Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
2188 messages similar to the above omitted  
  
Chain information for 4zau_A.712-919.ATOM.CA.loops.FH.His.pdb #3  
---  
Chain | Description  
A | No description available  
  

> display

> hide

> display :hi

> display :hi*

> label :hi*

> label :hi* height

Missing "height" keyword's argument  

> label :hi* height 2

> display :cy*

> label :cy* 2

Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword  

> label :cy* height 2

> hide

> label :cy* height 2

> display :cy*

> hide

> ~label

> display :cy*

> label :cy* height 2

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.osi.free.prot.wt/1-exp/3-INPUT/4zau_YY3.pdb"

> open 4zau

4zau title:  
AZD9291 complex with wild type EGFR [more info...]  
  
Chain information for 4zau #5  
---  
Chain | Description | UniProt  
A | Epidermal growth factor receptor | EGFR_HUMAN  
  
Non-standard residues in 4zau #5  
---  
YY3 —
N-(2-{[2-(dimethylamino)ethyl](methyl)amino}-4-methoxy-5-{[4-(1-methyl-1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)prop-2-enamide
(Osimertinib, AZD 9291)  
  

> hide

> display liand

> show liand

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> display ligand

> hide #!5 models

> show #!5 models

> display #4

> hide #!5 models

> show #!5 models

> hide #4 models

> show #4 models

> display #5

> style sphere

Changed 6750 atom styles  

> hide #4 models

> hide #!3 models

> hide #2 models

> hide #1 models

> show #4 models

> hide #!5 models

> hide #4 models

> show #1 models

> show #2 models

> view

> display

> stystick

Unknown command: stystick  

> style stick

Changed 6750 atom styles  

> view

> show #!5 models

> hide #2 models

> hide #1 models

> show #4 models

> hide protein

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.mobo.free.prot.wt/3-INPUT/MOBO_prot_free.aligned.4zau.pdb"

MOBO_prot_free.aligned.4zau.pdb title:  
YY3_mod_prot_free [more info...]  
  
Non-standard residues in MOBO_prot_free.aligned.4zau.pdb #6  
---  
YY3 — (YY3)  
  

> hide #!5 models

> hide #4 models

> show #!5 models

> hide #!5 models

> open 4zau

4zau title:  
AZD9291 complex with wild type EGFR [more info...]  
  
Chain information for 4zau #7  
---  
Chain | Description | UniProt  
A | Epidermal growth factor receptor | EGFR_HUMAN  
  
Non-standard residues in 4zau #7  
---  
YY3 —
N-(2-{[2-(dimethylamino)ethyl](methyl)amino}-4-methoxy-5-{[4-(1-methyl-1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)prop-2-enamide
(Osimertinib, AZD 9291)  
  

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.mobo.free.prot.wt/3-INPUT/MOBO_prot_free.aligned.4zau.pdb"

MOBO_prot_free.aligned.4zau.pdb title:  
YY3_mod_prot_free [more info...]  
  
Non-standard residues in MOBO_prot_free.aligned.4zau.pdb #8  
---  
YY3 — (YY3)  
  

> hide #6 models

> show #6 models

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.mobo.free.prot.wt/3-INPUT/4zau_YY3.pdb"

> hide #9 models

> show #9 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> view

> hide #!7 models

> show #!7 models

> hide #9 models

> hide #8 models

> hide #!7 models

> show #9 models

> show #8 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.mobo.free.prot.wt/3-INPUT/MOBO_prot_free.aligned.4zau.pdb"

MOBO_prot_free.aligned.4zau.pdb title:  
MOBO_prot_free [more info...]  
  
Non-standard residues in MOBO_prot_free.aligned.4zau.pdb #10  
---  
YY3 — (YY3)  
  

> hide #8 models

> hide #!7 models

> show #!7 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #6 models

> hide #!7 models

> hide #9 models

> show #9 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> show #9 models

> hide #9 models

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.mobo.free.prot.wt/3-INPUT/4zau.MOB.dry.pdb"

Chain information for 4zau.MOB.dry.pdb #11  
---  
Chain | Description  
? | No description available  
  

> hide #10 models

> show #10 models

> display :MOB

> hide #10 models

> show #10 models

> hide #10 models

> show #6 models

> hide #6 models

> hide #!7 models

> hide #11 models

> show #11 models

> display

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.mobo.free.prot.wt/3-INPUT/4zau.MOB.dry.pdb"

Chain information for 4zau.MOB.dry.pdb #12  
---  
Chain | Description  
? | No description available  
  

> hide #11 models

> show #11 models

> hide #12 models

> show #12 models

> hide #12 models

> show #12 models

> hide #11 models

> show #!7 models

> hide protein

> hide #12 models

> show #12 models

> hide #12 models

> show #12 models

> close

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.mobo.free.prot.wt/3-INPUT/4zau.MOB.dry.pdb"

Chain information for 4zau.MOB.dry.pdb #1  
---  
Chain | Description  
? | No description available  
  

> display ligand

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.mob.free.prot.wt/1-exp/3-INPUT/4zau.MOB.solv.pdb"

Chain information for 4zau.MOB.solv.pdb #2  
---  
Chain | Description  
? | No description available  
  

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.mob.free.prot.wt/1-exp/3-INPUT/4zau.solv.pdb"

Chain information for 4zau.solv.pdb #3  
---  
Chain | Description  
? | No description available  
  

> display

> view

> hide #2 models

> hide #1 models

> style stick 0.05

Expected a keyword  

> size stickRadius 0.05

Changed 62785 bond radii  

> display ligabd

> show ligabd

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> style ligand sphere

Changed 166 atom styles  

> display ligand

> style sphere

Changed 87406 atom styles  

> hide solvent

> hide protein

> display :mob

> hide #3 models

> show #2 models

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/IBIag/models/TR.models/CHS-3A/TR048738_results/model1.pdb"

Chain information for model1.pdb #4  
---  
Chain | Description  
A | No description available  
  

> close

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/IBIag/models/TR.models/CHS-3A/TR048738_results/model1.pdb"

Chain information for model1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> display :20-28

> display :20-29

> style sphere

Changed 1746 atom styles  

> delete Hh

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete H

> display

> color :20-28 & C orange

> close

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/systems/NatA/6hd5/md.ff19SB.COM.300ns.50ns/CAT.25C.1-300ns.50ns/3-INPUT/NatACatSc.dry.pdb"

Chain information for NatACatSc.dry.pdb #1  
---  
Chain | Description  
? | No description available  
  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/systems/NatB/models.Sc/md.ff19SB.COM.300ns.50ns/CAT.25C.1-300ns.50ns/3-INPUT/NatBCatAFSc.dry.pdb"

Chain information for NatBCatAFSc.dry.pdb #2  
---  
Chain | Description  
? | No description available  
  

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker NatACatSc.dry.pdb, chain (blank) (#1) with NatBCatAFSc.dry.pdb,
chain (blank) (#2), sequence alignment score = 229.6  
RMSD between 67 pruned atom pairs is 1.378 angstroms; (across all 179 pairs:
15.801)  
  

> view

> color #2 :105-110 red

> open /Users/admin/Downloads/AF-Q06504-F1-model_v2.cif

Chain information for AF-Q06504-F1-model_v2.cif #3  
---  
Chain | Description | UniProt  
A | N-terminal acetyltransferase B complex catalytic subunit NAT3 | NAT3_YEAST  
  

> hide #1 models

> hide #2 models

> view

> mmaker #3 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 NatBCatAFSc.dry.pdb, chain (blank) (#2) with
AF-Q06504-F1-model_v2.cif, chain A (#3), sequence alignment score = 931.7  
RMSD between 113 pruned atom pairs is 1.270 angstroms; (across all 195 pairs:
3.282)  
  

> view

> show #2 models

> show #1 models

> hide #2 models

> hide #1 models

> color bfactor #3

1612 atoms, 195 residues, atom bfactor range 66.9 to 98.1  

> color bfactor #3 pal blue:white:red

1612 atoms, 195 residues, atom bfactor range 66.9 to 98.1  

> color bfactor #3 pal red:white:blue

1612 atoms, 195 residues, atom bfactor range 66.9 to 98.1  

> show #2 models

> show #1 models

> hide #3 models

> open 5k18

5k18 title:  
The NatB Acetyltransferase Complex Bound To bisubstrate inhibitor [more
info...]  
  
Chain information for 5k18 #4  
---  
Chain | Description | UniProt  
A C | Uncharacterized protein | C4YFL7_CANAW  
B D | N-terminal acetyltransferase B complex subunit NAT3 | C4YDZ9_CANAW  
E F | Bisubstrate inhibitor |  
  
Non-standard residues in 5k18 #4  
---  
ACY — acetic acid  
COA — coenzyme A  
  
5k18 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> delete #4 & ~/b

> hide

> ribbon

> mmaker #4 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 NatBCatAFSc.dry.pdb, chain (blank) (#2) with 5k18, chain B (#4),
sequence alignment score = 532.5  
RMSD between 99 pruned atom pairs is 1.224 angstroms; (across all 177 pairs:
3.240)  
  

> color #4 gold

> show #3 models

> hide #!4 models

> hide #3 models

> show #!4 models

> hide #!4 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> color #2:1-15 orange

> delete #1:50-90

> ~ribbon

> ribbon :1-60

> select :1-60

2794 atoms, 2854 bonds, 228 residues, 4 models selected  

> mmaker #2 & sel to #1 & sel

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 NatACatSc.dry.pdb, chain (blank) (#1) with NatBCatAFSc.dry.pdb,
chain (blank) (#2), sequence alignment score = 93.9  
RMSD between 26 pruned atom pairs is 1.077 angstroms; (across all 49 pairs:
3.180)  
  

> select clear

> color #1 green

> hide #2 models

> show #2 models

> color #2:22-28 gold

> show #!4 models

> hide #!4 models

> show #3 models

> hide #2 models

> hide #!1 models

> show #!1 models

> show #2 models

> hide #2 models

> show #!4 models

> show #2 models

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/systems/NatB/models.Sc/md.ff19SB.CAT.1000ns/3-INPUT/AF_7096.FH.His.pdb"

Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/ayalaS/systems/NatB/models.Sc/md.ff19SB.CAT.1000ns/3-INPUT/AF_7096.FH.His.pdb  
---  
warnings | Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
9768 messages similar to the above omitted  
  
Chain information for AF_7096.FH.His.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> view

> hide #!4 models

> hide #3 models

> hide #!1 models

> show #3 models

> hide #2 models

> mmaker #5 to #3

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 AF-Q06504-F1-model_v2.cif, chain A (#3) with AF_7096.FH.His.pdb,
chain B (#5), sequence alignment score = 1031.9  
RMSD between 195 pruned atom pairs is 0.010 angstroms; (across all 195 pairs:
0.010)  
  

> hide #5 models

> show #5 models

> hide #3 models

> show #3 models

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> ribbon

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> open /Users/admin/Downloads/ma-bak-cepc-0753.cif

ma-bak-cepc-0753.cif title:  
Predicted interaction between CSL4 and RRP40 [more info...]  
  
Chain information for ma-bak-cepc-0753.cif #6  
---  
Chain | Description  
A | CSL4  
B | RRP40  
  

> close

> open /Users/admin/Downloads/ma-bak-cepc-0753.cif

ma-bak-cepc-0753.cif title:  
Predicted interaction between CSL4 and RRP40 [more info...]  
  
Chain information for ma-bak-cepc-0753.cif #1  
---  
Chain | Description  
A | CSL4  
B | RRP40  
  

> rainbow chains

> rainbow /a

> color /b grey

> surface

> close

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/systems/NatB/models.Sc/md.ff19SB.CAT.1000ns/3-INPUT/AF_7096.dry.pdb"

Chain information for AF_7096.dry.pdb #1  
---  
Chain | Description  
? | No description available  
  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/systems/NatB/models.Sc/md.ff19SB.CAT.1000ns/3-INPUT/AF_7096.CAT.dry.pdb"

Chain information for AF_7096.CAT.dry.pdb #2  
---  
Chain | Description  
? | No description available  
  

> close

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/systems/NatB/models.Sc/md.ff19SB.CAT.1000ns/3-INPUT/AF_7096.CAT.dry.pdb"

Chain information for AF_7096.CAT.dry.pdb #1  
---  
Chain | Description  
? | No description available  
  

> color :1-165 red

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/systems/NatA/6hd5/md.ff19SB.CAT.1000ns/3-INPUT/6hd5.CAT.dry.pdb"

Chain information for 6hd5.CAT.dry.pdb #2  
---  
Chain | Description  
? | No description available  
  

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF_7096.CAT.dry.pdb, chain (blank) (#1) with 6hd5.CAT.dry.pdb,
chain (blank) (#2), sequence alignment score = 223  
RMSD between 93 pruned atom pairs is 1.111 angstroms; (across all 176 pairs:
12.851)  
  

> rainbow structures

> color #1 lightgreen

> color #2 green

> select down

Nothing selected  

> color :1-165 gold

> color #2 green

> color #1 lightgreen

> color #1:48-58 gold

> color #2:45-90 gold

> color #2:45-90 orange

> color #2:100-110 orange

> color #2:100-110 red

> display #1:22

> color #1:22 blue

> delete H

> color ~C byatom

> color #1:22 cyan

> color ~C byatom

[Repeated 1 time(s)]

> hide #2 models

> display

> show #2 models

> hide

> display #1:20-22

> display :1-40

> hide #2 models

> show #2 models

> move x models #2

[Repeated 40 time(s)]

> view

> hide :50-11111 ribbons

> select :1-40

686 atoms, 708 bonds, 80 residues, 2 models selected  

> mmaker #2 & sel to #1 & sel

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 AF_7096.CAT.dry.pdb, chain (blank) (#1) with 6hd5.CAT.dry.pdb,
chain (blank) (#2), sequence alignment score = 81  
RMSD between 27 pruned atom pairs is 1.221 angstroms; (across all 40 pairs:
2.530)  
  

> view

> select clear

[Repeated 1 time(s)]

> style sphere

Changed 3524 atom styles  

> color C & #1 lightgreen

> color C & #2 green

> move x models #1

[Repeated 31 time(s)]

> view

> ribbon

> style stick

Changed 3524 atom styles  

> hide ribbons

> hide

> display :1-50

> ribbon :1-50

> mmaker #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 6hd5.CAT.dry.pdb, chain (blank) (#2) with AF_7096.CAT.dry.pdb,
chain (blank) (#1), sequence alignment score = 223.8  
RMSD between 92 pruned atom pairs is 1.111 angstroms; (across all 176 pairs:
12.867)  
  

> move x models #1

[Repeated 29 time(s)]

> hide

> ribbon

> view

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> move x models #1

[Repeated 13 time(s)]

> view

> color #1:120-140 red

> color #1 lightgreen

> color :120-135 red

> color :80-90 orange

> color #2:120-130 orange

> color #2:120-140 orange

> color #2:165-175 red

> color #2:160-175 red

> color #2:160-180 red

> color #2:155-180 red

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/systems/NatB/5k18/md.ff19SB.CAT.500ns.30C/3-INPUT/5K18.AB.modloop.FH.clean.pdb"

Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/ayalaS/systems/NatB/5k18/md.ff19SB.CAT.500ns.30C/3-INPUT/5K18.AB.modloop.FH.clean.pdb  
---  
warnings | Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
7608 messages similar to the above omitted  
  
Chain information for 5K18.AB.modloop.FH.clean.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> close

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/systems/NatB/5k18/md.ff19SB.CAT.500ns.30C/3-INPUT/5K18.AB.modloop.FH.clean.pdb"

Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/ayalaS/systems/NatB/5k18/md.ff19SB.CAT.500ns.30C/3-INPUT/5K18.AB.modloop.FH.clean.pdb  
---  
warnings | Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
7608 messages similar to the above omitted  
  
Chain information for 5K18.AB.modloop.FH.clean.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open 5k18

5k18 title:  
The NatB Acetyltransferase Complex Bound To bisubstrate inhibitor [more
info...]  
  
Chain information for 5k18 #2  
---  
Chain | Description | UniProt  
A C | Uncharacterized protein | C4YFL7_CANAW  
B D | N-terminal acetyltransferase B complex subunit NAT3 | C4YDZ9_CANAW  
E F | Bisubstrate inhibitor |  
  
Non-standard residues in 5k18 #2  
---  
ACY — acetic acid  
COA — coenzyme A  
  
5k18 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> delete #2 & ~/b

> hide

> ribbon

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5K18.AB.modloop.FH.clean.pdb, chain B (#1) with 5k18, chain B (#2),
sequence alignment score = 944.4  
RMSD between 178 pruned atom pairs is 0.042 angstroms; (across all 179 pairs:
0.172)  
  

> close

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/systems/NatB/5k18/md.ff19SB.CAT.500ns.30C/3-INPUT/5K18.AB.modloop.FH.clean.pdb"

Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/ayalaS/systems/NatB/5k18/md.ff19SB.CAT.500ns.30C/3-INPUT/5K18.AB.modloop.FH.clean.pdb  
---  
warnings | Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
7608 messages similar to the above omitted  
  
Chain information for 5K18.AB.modloop.FH.clean.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> display :cys

> style sphere

Changed 15159 atom styles  

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.osi.free.prot.T790M_L858R/1-exp/3-INPUT/4zau_A.712-919.ATOM.CA.loops.T790M_L858R.FH.His.YY3.pdb"

Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/EGFR-
HER2/systems/4zau.osi.free.prot.T790M_L858R/1-exp/3-INPUT/4zau_A.712-919.ATOM.CA.loops.T790M_L858R.FH.His.YY3.pdb  
---  
warnings | Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
2263 messages similar to the above omitted  
  
Chain information for 4zau_A.712-919.ATOM.CA.loops.T790M_L858R.FH.His.YY3.pdb
#2  
---  
Chain | Description  
A | No description available  
  

> clsoe

Unknown command: clsoe  

> close

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.osi.free.prot.T790M_L858R/1-exp/3-INPUT/4zau_A.712-919.ATOM.CA.loops.T790M_L858R.FH.His.YY3.pdb"

Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/EGFR-
HER2/systems/4zau.osi.free.prot.T790M_L858R/1-exp/3-INPUT/4zau_A.712-919.ATOM.CA.loops.T790M_L858R.FH.His.YY3.pdb  
---  
warnings | Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
2263 messages similar to the above omitted  
  
Chain information for 4zau_A.712-919.ATOM.CA.loops.T790M_L858R.FH.His.YY3.pdb
#1  
---  
Chain | Description  
A | No description available  
  

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.mob.free.prot.wt/1000ns_4rep/3-INPUT/4zau_A.712-919.ATOM.CA.loops.FH.His.MOB.pdb"

Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/EGFR-
HER2/systems/4zau.mob.free.prot.wt/1000ns_4rep/3-INPUT/4zau_A.712-919.ATOM.CA.loops.FH.His.MOB.pdb  
---  
warnings | Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
2271 messages similar to the above omitted  
  
Chain information for 4zau_A.712-919.ATOM.CA.loops.FH.His.MOB.pdb #2  
---  
Chain | Description  
A | No description available  
  

> delete H

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> display :712,719

> hide

> display :712,919

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> display :712,919

> hide

> display :712,919

> close

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.mob.free.prot.wt/1000ns_4rep/3-INPUT/4zau_A.712-919.ATOM.CA.loops.FH.His.MOB.pdb"

Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/EGFR-
HER2/systems/4zau.mob.free.prot.wt/1000ns_4rep/3-INPUT/4zau_A.712-919.ATOM.CA.loops.FH.His.MOB.pdb  
---  
warnings | Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
2271 messages similar to the above omitted  
  
Chain information for 4zau_A.712-919.ATOM.CA.loops.FH.His.MOB.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.osi.free.prot.T790M_L858R/1-exp/3-INPUT/4zau_A.712-919.ATOM.CA.loops.T790M_L858R.FH.His.YY3.pdb"

Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/EGFR-
HER2/systems/4zau.osi.free.prot.T790M_L858R/1-exp/3-INPUT/4zau_A.712-919.ATOM.CA.loops.T790M_L858R.FH.His.YY3.pdb  
---  
warnings | Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
2263 messages similar to the above omitted  
  
Chain information for 4zau_A.712-919.ATOM.CA.loops.T790M_L858R.FH.His.YY3.pdb
#2  
---  
Chain | Description  
A | No description available  
  

> HIDE

Unknown command: HIDE  

> hide

> display

> 790,858

Unknown command: 790,858  

> hide

> display :790,858

> display ligand

> delete H

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/systems/NatB/5k18/md.ff19SB.CAT.500ns.30C/3-INPUT/5K18.AB.modloop.FH.clean.pdb"

Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/ayalaS/systems/NatB/5k18/md.ff19SB.CAT.500ns.30C/3-INPUT/5K18.AB.modloop.FH.clean.pdb  
---  
warnings | Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
7608 messages similar to the above omitted  
  
Chain information for 5K18.AB.modloop.FH.clean.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> close

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/systems/NatB/5k18/md.ff19SB.CAT.500ns.30C/3-INPUT/5K18.AB.modloop.FH.clean.pdb"

Summary of feedback from opening /Users/admin/Dropbox (Technion
Dropbox)/PROJECTS/ayalaS/systems/NatB/5k18/md.ff19SB.CAT.500ns.30C/3-INPUT/5K18.AB.modloop.FH.clean.pdb  
---  
warnings | Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
Duplicate atom serial number found: 0  
7608 messages similar to the above omitted  
  
Chain information for 5K18.AB.modloop.FH.clean.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> close

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/systems/NatB/models.Sc/md.ff19SB.CAT.500ns.30C/3-INPUT/AF_7096.CAT.dry.pdb"

Chain information for AF_7096.CAT.dry.pdb #1  
---  
Chain | Description  
? | No description available  
  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/systems/NatB/5k18/md.ff19SB.CAT.500ns.30C/3-INPUT/5k18.CAT.dry.pdb"

Chain information for 5k18.CAT.dry.pdb #2  
---  
Chain | Description  
? | No description available  
  

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF_7096.CAT.dry.pdb, chain (blank) (#1) with 5k18.CAT.dry.pdb,
chain (blank) (#2), sequence alignment score = 565.4  
RMSD between 151 pruned atom pairs is 0.907 angstroms; (across all 184 pairs:
2.155)  
  

> display :65-75

> delete H

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/systems/NatA/6hd5/md.ff19SB.CAT.500ns.30C/3-INPUT/6hd5.CAT.dry.pdb"

Chain information for 6hd5.CAT.dry.pdb #3  
---  
Chain | Description  
? | No description available  
  

> mmaker #3 top #1

> matchmaker #3 top #1

Expected a keyword  

> mmaker #3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF_7096.CAT.dry.pdb, chain (blank) (#1) with 6hd5.CAT.dry.pdb,
chain (blank) (#3), sequence alignment score = 223  
RMSD between 93 pruned atom pairs is 1.111 angstroms; (across all 176 pairs:
12.851)  
  

> display #3:110-120

> hide

> hide #1 models

> show #1 models

> hide #2 models

> display :lseu

> display :leu,ile,val,phe,val,met

> delete H

> mmaker #3:1-50 to #1:1-50

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 AF_7096.CAT.dry.pdb, chain (blank) (#1) with 6hd5.CAT.dry.pdb,
chain (blank) (#3), sequence alignment score = 92  
RMSD between 34 pruned atom pairs is 1.189 angstroms; (across all 50 pairs:
2.473)  
  

> style sphere

Changed 5062 atom styles  

> hide

> display :leu,ile,val,phe,val,met & :1-50

> move x 10 models #1

[Repeated 4 time(s)]

> view

> color grey

> display

> delete #3:45-90

> delete #3:200-1111111

> hide

> delete #1:48-58

> display :leu,ile,val,phe,val,met & :1-50

> display

> color :leu,ile,val,phe,val,met & :1-50 tan

> color :met grey

> mlp #!1,3

Map values for surface "6hd5.CAT.dry.pdb_ SES surface": minimum -30.89, mean
1.445, maximum 136.1  
Map values for surface "AF_7096.CAT.dry.pdb_ SES surface": minimum -27.68,
mean -3.674, maximum 22.7  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.mob.free.prot.T790M_L858R/1000ns_4rep/3-INPUT/4zau.MOB.T790M_L858R.dry.pdb"

Chain information for 4zau.MOB.T790M_L858R.dry.pdb #4  
---  
Chain | Description  
? | No description available  
  

> close

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.mob.free.prot.T790M_L858R/1000ns_4rep/3-INPUT/4zau.MOB.T790M_L858R.dry.pdb"

Chain information for 4zau.MOB.T790M_L858R.dry.pdb #1  
---  
Chain | Description  
? | No description available  
  

> open 4zau

4zau title:  
AZD9291 complex with wild type EGFR [more info...]  
  
Chain information for 4zau #2  
---  
Chain | Description | UniProt  
A | Epidermal growth factor receptor | EGFR_HUMAN  
  
Non-standard residues in 4zau #2  
---  
YY3 —
N-(2-{[2-(dimethylamino)ethyl](methyl)amino}-4-methoxy-5-{[4-(1-methyl-1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)prop-2-enamide
(Osimertinib, AZD 9291)  
  

> hide

> display ligand

> display :790,858

> display :790,858 :< 1

> hide H

> open "/Users/admin/Dropbox (Technion Dropbox)/PROJECTS/EGFR-
> HER2/systems/4zau.mob.free.prot.T790M_L858R/1000ns_4rep/3-INPUT/4zau.MOB.dry.pdb"

Chain information for 4zau.MOB.dry.pdb #3  
---  
Chain | Description  
? | No description available  
  

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #!2 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q9UII4-F1-model_v2.opra.pdb"

Chain information for AF-Q9UII4-F1-model_v2.opra.pdb #4  
---  
Chain | Description  
A | No description available  
  

> close

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q9UII4-F1-model_v2.opra.pdb"

Chain information for AF-Q9UII4-F1-model_v2.opra.pdb #1  
---  
Chain | Description  
A | No description available  
  

> rainbow

> color bfactor

8218 atoms, 1024 residues, atom bfactor range -3.46 to 0.7  

> color grey

> color @@bfactor < -1

> color @@bfactor < -1 red

> display

> color @@bfactor

> color bfactor

8218 atoms, 1024 residues, atom bfactor range -3.46 to 0.7  

> select down

Nothing selected  

> color bfactor range -1,1

8218 atoms, 1024 residues, atom bfactor range -3.46 to 0.7  

> color bfactor range -1,1 pal red:white:blue

8218 atoms, 1024 residues, atom bfactor range -3.46 to 0.7  

> display

> style sphere

Changed 8218 atom styles  

> color bfactor range -2,1 pal red:white:blue

8218 atoms, 1024 residues, atom bfactor range -3.46 to 0.7  

> color bfactor range -2,2 pal red:white:blue

8218 atoms, 1024 residues, atom bfactor range -3.46 to 0.7  

> open /Users/admin/Downloads/AF-Q14258-F1-model_v2.cif

Chain information for AF-Q14258-F1-model_v2.cif #2  
---  
Chain | Description | UniProt  
A | E3 ubiquitin/ISG15 ligase TRIM25 | TRI25_HUMAN  
  

> close

> open /Users/admin/Downloads/AF-Q14258-F1-model_v2-1.cif

Chain information for AF-Q14258-F1-model_v2-1.cif #1  
---  
Chain | Description | UniProt  
A | E3 ubiquitin/ISG15 ligase TRIM25 | TRI25_HUMAN  
  

> color bfactor

4978 atoms, 630 residues, atom bfactor range 27.5 to 98.8  

> display :arg

> style sphere

Changed 4978 atom styles  

> display :arg,lys

> his

Unknown command: his  

> display :his

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AF-Q14258-F1-model_v2-1.cif_A SES surface #1.1: minimum,
-15.78, mean -0.05, maximum 12.14  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide

[Repeated 1 time(s)]

> hide surfaces

> close

> open /Users/admin/Downloads/AF-Q14258-F1-model_v2-2.cif

Chain information for AF-Q14258-F1-model_v2-2.cif #1  
---  
Chain | Description | UniProt  
A | E3 ubiquitin/ISG15 ligase TRIM25 | TRI25_HUMAN  
  

> color bfactor

4978 atoms, 630 residues, atom bfactor range 27.5 to 98.8  

> display @@bcolor < 50

bad color: 50: Color must be 3 or 4 comma-separated numbers 0-100  

> display @@bfactor < 50

> hide

> display @@bfactor < 40

> hide

> display @@bfactor < 50

> hide

> display @@bfactor < 30

> delete @@bfactor < 50

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AF-Q14258-F1-model_v2-2.cif_A SES surface #1.2: minimum,
-15.82, mean -0.26, maximum 12.20  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close

> open 5TTE

Summary of feedback from opening 5TTE fetched from pdb  
---  
note | Fetching compressed mmCIF 5tte from
http://files.rcsb.org/download/5tte.cif  
  
5tte title:  
Crystal Structure of an RBR E3 ubiquitin ligase in complex with an E2-Ub
thioester intermediate mimic [more info...]  
  
Chain information for 5tte #1  
---  
Chain | Description | UniProt  
B | E3 ubiquitin-protein ligase ARIH1 | ARI1_HUMAN  
E | Ubiquitin-conjugating enzyme E2 L3 | UB2L3_HUMAN  
F | ubiquitin | A0A1D6DHW0_WHEAT  
  
Non-standard residues in 5tte #1  
---  
ZN — zinc ion  
  

> open /Users/admin/Downloads/AF-Q9Y4X5-F1-model_v2.cif

Chain information for AF-Q9Y4X5-F1-model_v2.cif #2  
---  
Chain | Description | UniProt  
A | E3 ubiquitin-protein ligase ARIH1 | ARI1_HUMAN  
  

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5tte, chain B (#1) with AF-Q9Y4X5-F1-model_v2.cif, chain A (#2),
sequence alignment score = 2738.9  
RMSD between 372 pruned atom pairs is 0.938 angstroms; (across all 442 pairs:
1.665)  
  

> hide #2 models

> rainbow chains

> show #2 models

> rainbow structures

> rainbow chains

> delete /e

> delete /f

> color tan

> color #2 grey

> display :arg

> display :lys

> display :his

> color ~C byatom

> style speh

Expected a keyword  

> style sphere

Changed 8155 atom styles  

> close

> open 5TTE

5tte title:  
Crystal Structure of an RBR E3 ubiquitin ligase in complex with an E2-Ub
thioester intermediate mimic [more info...]  
  
Chain information for 5tte #1  
---  
Chain | Description | UniProt  
B | E3 ubiquitin-protein ligase ARIH1 | ARI1_HUMAN  
E | Ubiquitin-conjugating enzyme E2 L3 | UB2L3_HUMAN  
F | ubiquitin | A0A1D6DHW0_WHEAT  
  
Non-standard residues in 5tte #1  
---  
ZN — zinc ion  
  

> rainbow chains

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/5TTE_B.opra.pdb"

Chain information for 5TTE_B.opra.pdb #2  
---  
Chain | Description  
B | No description available  
  

> display #2

> style she

Expected a keyword  

> style sphere

Changed 9216 atom styles  

> color bfactor #2

3668 atoms, 442 residues, atom bfactor range -1.62 to 0.8  

> color bfactor #2 range -1,1 pal red:white:blue

3668 atoms, 442 residues, atom bfactor range -1.62 to 0.8  

> hide #!1 models

> show #!1 models

> hide #1

> hide #2 ribbons

> coulombic

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
5tte #1/F GLY 76 OXT  

Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 1 time(s)]Coulombic values for 5tte_B SES surface #1.3: minimum,
-16.69, mean -0.68, maximum 15.56  
Coulombic values for 5tte_E SES surface #1.4: minimum, -14.06, mean 0.06,
maximum 11.32  
Coulombic values for 5tte_F SES surface #1.5: minimum, -14.29, mean -0.57,
maximum 9.37  
Coulombic values for 5TTE_B.opra.pdb_B SES surface #2.2: minimum, -16.91, mean
-0.07, maximum 15.91  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide

> hide surfaces

> display

> hide

> display #2

> surface #2

> hide

> open /Users/admin/Downloads/AF-Q14258-F1-model_v2-3.cif

Chain information for AF-Q14258-F1-model_v2-3.cif #3  
---  
Chain | Description | UniProt  
A | E3 ubiquitin/ISG15 ligase TRIM25 | TRI25_HUMAN  
  

> close

> open /Users/admin/Downloads/AF-Q14258-F1-model_v2-4.cif

Chain information for AF-Q14258-F1-model_v2-4.cif #1  
---  
Chain | Description | UniProt  
A | E3 ubiquitin/ISG15 ligase TRIM25 | TRI25_HUMAN  
  

> delete @@bfactor < 50

> color bfactor

4305 atoms, 538 residues, atom bfactor range 50.1 to 98.8  

> color bfactor

4305 atoms, 538 residues, atom bfactor range 50.1 to 98.8  

> color bfactor range 50,100

4305 atoms, 538 residues, atom bfactor range 50.1 to 98.8  

> color bfactor range 50,100 pal red:white:blue

4305 atoms, 538 residues, atom bfactor range 50.1 to 98.8  

> color bfactor range 70,100 pal red:white:blue

4305 atoms, 538 residues, atom bfactor range 50.1 to 98.8  

> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q14258-F1-model_v2_TRIMED.pdb"
> relModel #1

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q14258-F1-model_v2_TRIMED.pdb"

Chain information for AF-Q14258-F1-model_v2_TRIMED.pdb #2  
---  
Chain | Description  
A | No description available  
  

> hide #!1 models

> show #!1 models

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q14258-F1-model_v2_TRIMED.opra.pdb"

Chain information for AF-Q14258-F1-model_v2_TRIMED.opra.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #!2 models

> hide #!1 models

> color @@bfactor

> color factor

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color bfactor

12914 atoms, 1614 residues, atom bfactor range -1.2 to 98.8  

> color @@bfactor < -1 red

> surface

> color @@bfactor < -1 red

> close

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/5TTE.pdb"

5TTE.pdb title:  
Crystal structure of an RBR E3 ubiquitin ligase In complex with an E2- ub
thioester intermediate mimic [more info...]  
  
Chain information for 5TTE.pdb #1  
---  
Chain | Description | UniProt  
B | E3 ubiquitin-protein ligase ARIH1 | ARI1_HUMAN  
E | ubiquitin-conjugating enzyme E2 L3 | UB2L3_HUMAN  
F | ubiquitin |  
  
Non-standard residues in 5TTE.pdb #1  
---  
ZN — zinc ion  
  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/5TTE_B.opra.pdb"

Chain information for 5TTE_B.opra.pdb #2  
---  
Chain | Description  
B | No description available  
  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/5TTE_B.pdb"

Chain information for 5TTE_B.pdb #3  
---  
Chain | Description  
B | No description available  
  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/5TTE_E.pdb"

Chain information for 5TTE_E.pdb #4  
---  
Chain | Description  
E | No description available  
  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/5TTE_F.pdb"

Chain information for 5TTE_F.pdb #5  
---  
Chain | Description  
F | No description available  
  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q14258-F1-model_v2_TRIMED.opra.pdb"

Chain information for AF-Q14258-F1-model_v2_TRIMED.opra.pdb #6  
---  
Chain | Description  
A | No description available  
  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q14258-F1-model_v2_TRIMED.pdb"

Chain information for AF-Q14258-F1-model_v2_TRIMED.pdb #7  
---  
Chain | Description  
A | No description available  
  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q9UII4-F1-model_v2.opra.pdb"

Chain information for AF-Q9UII4-F1-model_v2.opra.pdb #8  
---  
Chain | Description  
A | No description available  
  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q14258-F1-model_v2.pdb"

AF-Q14258-F1-model_v2.pdb title:  
Alphafold monomer V2.0 prediction for E3 ubiquitin/ISG15 ligase TRIM25
(Q14258) [more info...]  
  
Chain information for AF-Q14258-F1-model_v2.pdb #9  
---  
Chain | Description | UniProt  
A | E3 ubiquitin/ISG15 ligase TRIM25 | TRI25_HUMAN  
  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q9UII4-F1-model_v2.pdb"

AF-Q9UII4-F1-model_v2.pdb title:  
Alphafold monomer V2.0 prediction for E3 ISG15--protein ligase HERC5 (Q9UII4)
[more info...]  
  
Chain information for AF-Q9UII4-F1-model_v2.pdb #10  
---  
Chain | Description | UniProt  
A | E3 ISG15--protein ligase HERC5 | HERC5_HUMAN  
  

> close

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/5TTE_B.opra.pdb"

Chain information for 5TTE_B.opra.pdb #1  
---  
Chain | Description  
B | No description available  
  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q14258-F1-model_v2_TRIMED.opra.pdb"

Chain information for AF-Q14258-F1-model_v2_TRIMED.opra.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q9UII4-F1-model_v2.opra.pdb"

Chain information for AF-Q9UII4-F1-model_v2.opra.pdb #3  
---  
Chain | Description  
A | No description available  
  

> view

> color @@bfactor < -1 red

> mmaker #2,3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5TTE_B.opra.pdb, chain B (#1) with
AF-Q14258-F1-model_v2_TRIMED.opra.pdb, chain A (#2), sequence alignment score
= 215.3  
RMSD between 8 pruned atom pairs is 1.620 angstroms; (across all 307 pairs:
44.649)  
  
Matchmaker 5TTE_B.opra.pdb, chain B (#1) with AF-Q9UII4-F1-model_v2.opra.pdb,
chain A (#3), sequence alignment score = 109.1  
RMSD between 7 pruned atom pairs is 1.432 angstroms; (across all 350 pairs:
35.536)  
  

> view

> move x 10 models #2,3

[Repeated 10 time(s)]

> move x 10 models #3

[Repeated 11 time(s)]

> view

> surface

> color grey

> color @@bfactor < -1 red

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
[Repeated 2 time(s)]Coulombic values for 5TTE_B.opra.pdb_B SES surface #1.2:
minimum, -16.91, mean -0.07, maximum 15.91  
Coulombic values for AF-Q14258-F1-model_v2_TRIMED.opra.pdb_A SES surface #2.2:
minimum, -15.74, mean -0.03, maximum 15.08  
Coulombic values for AF-Q9UII4-F1-model_v2.opra.pdb_A SES surface #3.1:
minimum, -16.52, mean -0.92, maximum 20.34  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color grey

> color @@bfactor < -1 red

> hide #!3 models

> hide #!2 models

> color @@bfactor < -2 violet

> show #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #!1 models

> coulombic #!3

Coulombic values for AF-Q9UII4-F1-model_v2.opra.pdb_A SES surface #3.1:
minimum, -16.52, mean -0.92, maximum 20.34  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color grey

> color @@bfactor < -1 red

> color @@bfactor < -2 violet

> hide

> hide surfaces

> display :arg

> color ~C byatom

> hide

> display \:700-1000

> show \:700-1000

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> display :700-1000

> display :700-1000 green

> show :700-1000 green

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> color :700-1000 green

> display

> stp sphe

Unknown command: stp sphe  

> style sphere

Changed 16190 atom styles  

> color grey

> color :700-1000 green

> hide

> color :100-350 fols

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color :100-350 gold

> display

> ~ribbon

> color @@bfactor < -1 red

> hide

> ribbon

> display

> label :arg,lys,his

> label :arg,lys,his height 2

> ~label

> label :arg height 2

> hide

> label :lys height 2

> display

> ~label

> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/3_proteins_hila.cxs"

> coulombic #!3

Coulombic values for AF-Q9UII4-F1-model_v2.opra.pdb_A SES surface #3.1:
minimum, -16.52, mean -0.92, maximum 20.34  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q9UII4-F1-model_v2.oda.pdb"

Chain information for AF-Q9UII4-F1-model_v2.oda.pdb #4  
---  
Chain | Description  
A | No description available  
  

> hide #!3 models

> show #!3 models

> mmaker #4 to #3

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 AF-Q9UII4-F1-model_v2.opra.pdb, chain A (#3) with
AF-Q9UII4-F1-model_v2.oda.pdb, chain A (#4), sequence alignment score = 5360.8  
RMSD between 1024 pruned atom pairs is 0.000 angstroms; (across all 1024
pairs: 0.000)  
  

> move x 10 models #4

[Repeated 9 time(s)]

> color grey

> surface

> color grey

> color #3 @@bfactor < -1 red

> color #4 @@bfactor < -10 violet

> show #!1 models

> color #1 @@bfactor < -1 red

> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/3_proteins_hila.cxs"

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/5TTE_B.oda.pdb"

Chain information for 5TTE_B.oda.pdb #5  
---  
Chain | Description  
B | No description available  
  

> mmaker #5 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5TTE_B.opra.pdb, chain B (#1) with 5TTE_B.oda.pdb, chain B (#5),
sequence alignment score = 2423.3  
RMSD between 442 pruned atom pairs is 0.000 angstroms; (across all 442 pairs:
0.000)  
  

> move x 10 models #5

[Repeated 8 time(s)]

> surface #5

> color #5 grey

> color #5 @@bfactor < -10 violet

> hide

> hide surfaces

> rainbow #5

> color #5 grey

> color #5 @@bfactor < -10 violet

> display

> style sphere

Changed 28076 atom styles  

> coulombic #!1,3-5

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue CYX (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/2r/4900tztj6ql4xvyskskryrch0000gq/T/tmpcyn0llt8/ante.in.mol2 -fi
mol2 -o
/var/folders/2r/4900tztj6ql4xvyskskryrch0000gq/T/tmpcyn0llt8/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(CYX) ``  
(CYX) `Welcome to antechamber 20.0: molecular input file processor.`  
(CYX) ``  
(CYX) `Info: Finished reading file
(/var/folders/2r/4900tztj6ql4xvyskskryrch0000gq/T/tmpcyn0llt8/ante.in.mol2);
atoms read (26), bonds read (25).`  
(CYX) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(CYX) `Running:
/Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(CYX) ``  
(CYX) ``  
(CYX) `Running:
/Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(CYX) `Info: Total number of electrons: 102; net charge: 0`  
(CYX) ``  
(CYX) `Running: /Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(CYX) ``  
(CYX) `Running: /Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.3.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(CYX) ``  
(CYX) `Running:
/Applications/ChimeraX-1.3.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(CYX) ``  
Charges for residue CYX determined  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 5TTE_B.opra.pdb_B SES surface #1.2: minimum, -16.91, mean
-0.07, maximum 15.91  
Coulombic values for AF-Q9UII4-F1-model_v2.opra.pdb_A SES surface #3.1:
minimum, -16.52, mean -0.92, maximum 20.34  
Coulombic values for AF-Q9UII4-F1-model_v2.oda.pdb_A SES surface #4.1:
minimum, -16.52, mean -0.92, maximum 20.34  
Coulombic values for 5TTE_B.oda.pdb_B SES surface #5.2: minimum, -16.90, mean
-0.07, maximum 15.91  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide

> hide surfaces

> display

> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/3_proteins_hila.cxs"

——— End of log from Sun Jan 2 18:07:55 2022 ———

opened ChimeraX session  

> close

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q14258-F1-model_v2.pdb"

AF-Q14258-F1-model_v2.pdb title:  
Alphafold monomer V2.0 prediction for E3 ubiquitin/ISG15 ligase TRIM25
(Q14258) [more info...]  
  
Chain information for AF-Q14258-F1-model_v2.pdb #1  
---  
Chain | Description | UniProt  
A | E3 ubiquitin/ISG15 ligase TRIM25 | TRI25_HUMAN  
  

> color bfactor

4978 atoms, 630 residues, atom bfactor range 27.5 to 98.8  

> color bfactor pal red:white:blue

4978 atoms, 630 residues, atom bfactor range 27.5 to 98.8  

> delete @@bfactor < 50

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q14258-F1-model_v2.pdb"

AF-Q14258-F1-model_v2.pdb title:  
Alphafold monomer V2.0 prediction for E3 ubiquitin/ISG15 ligase TRIM25
(Q14258) [more info...]  
  
Chain information for AF-Q14258-F1-model_v2.pdb #2  
---  
Chain | Description | UniProt  
A | E3 ubiquitin/ISG15 ligase TRIM25 | TRI25_HUMAN  
  

> hide #2 models

> color :100-350 red

> color :440-600 green

> surface

> color :440-600 green

> color :100-350 red

> delete @@bfactor < 50

> color bfactor pal red:white:blue

8610 atoms, 1076 residues, 2 surfaces, atom bfactor range 50.1 to 98.8  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q14258-F1-model_v2_TRIMED.opra.pdb"

Chain information for AF-Q14258-F1-model_v2_TRIMED.opra.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #!1 models

> color bfacotr

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color bfactor

12914 atoms, 1614 residues, 2 surfaces, atom bfactor range -1.2 to 98.8  

> color bfactor range -2,2

12914 atoms, 1614 residues, 2 surfaces, atom bfactor range -1.2 to 98.8  

> color bfactor range -1,1

12914 atoms, 1614 residues, 2 surfaces, atom bfactor range -1.2 to 98.8  

> color bfactor range -1,1 pal red:white:blue

12914 atoms, 1614 residues, 2 surfaces, atom bfactor range -1.2 to 98.8  

> display

> style sphere

Changed 12914 atom styles  

> hdie

Unknown command: hdie  

> hide

> display :lys,arg

> display

> color bfactor range -.5,.5 pal red:white:blue

12914 atoms, 1614 residues, 2 surfaces, atom bfactor range -1.2 to 98.8  

> hide

> color bfactor range -1,1 pal red:white:blue

12914 atoms, 1614 residues, 2 surfaces, atom bfactor range -1.2 to 98.8  

> display

> surface

> color bfactor range -1,1 pal red:white:blue

12914 atoms, 1614 residues, 3 surfaces, atom bfactor range -1.2 to 98.8  

> hide

> coulombic #!3

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AF-Q14258-F1-model_v2_TRIMED.opra.pdb_A SES surface #3.2:
minimum, -15.74, mean -0.03, maximum 15.08  
To also show corresponding color key, enter the above coulombic command and
add key true  

> open "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q14258-F1-model_v2_TRIMED.oda.pdb"

Chain information for AF-Q14258-F1-model_v2_TRIMED.oda.pdb #4  
---  
Chain | Description  
A | No description available  
  

> move x models #4

[Repeated 78 time(s)]

> select down

Nothing selected  

> color bfactor range -1,1 pal red:white:blue

17218 atoms, 2152 residues, 3 surfaces, atom bfactor range -33.7 to 98.8  

> color bfactor #4 range -1,1 pal red:white:blue

4304 atoms, 538 residues, atom bfactor range -33.7 to 12.3  

> color bfactor #4 range -10,10 pal red:white:blue

4304 atoms, 538 residues, atom bfactor range -33.7 to 12.3  

> color bfactor #4 range -10,10 pal red:white:violet

4304 atoms, 538 residues, atom bfactor range -33.7 to 12.3  

> color bfactor #4 range -10,10 pal violet:white:Lblue

> color byattribute bfactor #4 range -10,10 palette violet:white:Lblue

Invalid "palette" argument: Invalid color name or specifier  

> color bfactor #4 range -10,10 pal violet:white:Lbluedisp

> color byattribute bfactor #4 range -10,10 palette violet:white:Lbluedisp

Invalid "palette" argument: Invalid color name or specifier  

> color bfactor #4 range -10,10 pal violet:white:blue

4304 atoms, 538 residues, atom bfactor range -33.7 to 12.3  

> display

> style sphere

Changed 17218 atom styles  

> hide surfaces

> hide ribbons

> hide

> ribbon

> rainbow

> color bfactor #4 range -10,10 pal violet:white:blue

4304 atoms, 538 residues, atom bfactor range -33.7 to 12.3  

> color bfactor #4 range -1,1 pal red:white:blue

4304 atoms, 538 residues, atom bfactor range -33.7 to 12.3  

> color bfactor #3 range -1,1 pal red:white:blue

4304 atoms, 538 residues, 1 surfaces, atom bfactor range -1.2 to 0.8  

> color bfactor #4 range -1,1 pal red:white:blue

4304 atoms, 538 residues, atom bfactor range -33.7 to 12.3  

> color bfactor #4 range -10,10 pal violet:white:blue

4304 atoms, 538 residues, atom bfactor range -33.7 to 12.3  

> display

> color grey

> color #4 & @@bfactor < -10, violet

> color #4 & @@bfactor < -10 violet

> color #3 & @@bfactor < -1 red

> color #3 & @@bfactor < -.5 red

> color #3 grey

> color #3 & @@bfactor < -.8 red

> color #3 & @@bfactor < -.7 red

> save "/Users/admin/Dropbox (Technion
> Dropbox)/PROJECTS/ayalaS/students/hila/AF-Q14258-F1-model_v2_TRIMED.ODA-
> OPRA.cxs"

——— End of log from Tue Feb 15 15:04:19 2022 ———

opened ChimeraX session  

> show #!3-4 surfaces

> lighting full

> lighting soft

[Repeated 1 time(s)]

> lighting full

[Repeated 3 time(s)]

> lighting flat

> lighting simple

> lighting soft

> lighting simple

[Repeated 1 time(s)]

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> graphics silhouettes false

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> color bfactor #!3-4

8608 atoms, 1076 residues, 2 surfaces, atom bfactor range -33.7 to 12.3  

> color #1 by bfactor range 1, 9

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color bfactor 4978 atoms, 630 residues, atom bfactor range 27.5 to 98.8

> color byattribute bfactor 4978 atoms, 630 residues, atom bfactor range 27.5
> to 98.8

Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword  

> color bfactor #4 range -10,10 pal violet:white:blue

4304 atoms, 538 residues, 1 surfaces, atom bfactor range -33.7 to 12.3  

> color #4 & @@bfactor < -10, violet

> color #4 & @@bfactor < -10 violet

> color grey

> color #4 & @@bfactor < -10 violet

> color #3 & @@bfactor < -.7 red

> mmaker #3 #4

> matchmaker #3 #4

Missing required "to" argument  

> mmaker #3 to #4

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 AF-Q14258-F1-model_v2_TRIMED.oda.pdb, chain A (#4) with
AF-Q14258-F1-model_v2_TRIMED.opra.pdb, chain A (#3), sequence alignment score
= 2849.4  
RMSD between 538 pruned atom pairs is 0.000 angstroms; (across all 538 pairs:
0.000)  
  

> move x models #4

[Repeated 75 time(s)]

> save "D:/Dropbox (Technion Dropbox)/Ayala_Shiber_lab/Hila/Isgylation -
> computational/AF-Q14258-F1-model_v2_TRIMED.ODA-OPRA_YOMAMA.cxs"

——— End of log from Tue May 31 10:58:21 2022 ———

opened ChimeraX session  

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> hide #!3-4 atoms

> show #!3-4 cartoons

> transparency #3-4 60

> open "D:/Dropbox (Technion Dropbox)/Ayala_Shiber_lab/Hila/Isgylation -
> computational/3_proteins_hila.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\ui\graphics.py", line 51, in event  
if self.handle_drag_and_drop(event):  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\ui\graphics.py", line 116, in handle_drag_and_drop  
mw.dropEvent(event)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\ui\gui.py", line 594, in dropEvent  
_open_dropped_file(self.session, p)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\ui\gui.py", line 1945, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 458, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\session.py", line 1001, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\session.py", line 641, in restore  
use_pickle = stream.peek(1)[0] != ord(b'#')  
IndexError: index out of range  
  
IndexError: index out of range  
  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\session.py", line 641, in restore  
use_pickle = stream.peek(1)[0] != ord(b'#')  
  
See log for complete Python traceback.  
  

> open "D:/Dropbox (Technion Dropbox)/Ayala_Shiber_lab/Hila/Isgylation -
> computational/3_proteins_hila.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 458, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\session.py", line 1001, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\session.py", line 641, in restore  
use_pickle = stream.peek(1)[0] != ord(b'#')  
IndexError: index out of range  
  
IndexError: index out of range  
  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\session.py", line 641, in restore  
use_pickle = stream.peek(1)[0] != ord(b'#')  
  
See log for complete Python traceback.  
  

> open "D:/Dropbox (Technion Dropbox)/Ayala_Shiber_lab/Hila/Isgylation -
> computational/3_proteins_hila.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 458, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\session.py", line 1001, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\session.py", line 641, in restore  
use_pickle = stream.peek(1)[0] != ord(b'#')  
IndexError: index out of range  
  
IndexError: index out of range  
  
File "C:\Program Files\ChimeraX 1.4rc202205290614\bin\lib\site-
packages\chimerax\core\session.py", line 641, in restore  
use_pickle = stream.peek(1)[0] != ord(b'#')  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 30.0.100.9864
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7070
OS: Microsoft Windows 10 Enterprise (Build 19042)
Memory: 16,951,218,176
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4rc202205290614
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.2
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 23.0.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (3)

comment:1 by Eric Pettersen, 3 years ago

Cc: chimerax-programmers added
Component: Unassigned → Sessions
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Session restore: cannot peek() on Dropbox file drop

1.4rc

comment:2 by Greg Couch, 3 years ago

Unclear what went wrong since there appear to be successful opening of sessions from DropBox in the log. Perhaps there was a network error? Will need to setup DropBox on a PC to try to duplicate this.

comment:3 by Eric Pettersen, 3 years ago

Could you catch the IndexError and assume (guess really) in that case that the file is not pickled?

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