Opened 5 years ago

Closed 5 years ago

#3941 closed defect (fixed)

add_modified() not handling sets

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.dev202011130113 (2020-11-13 01:13:13 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.dev202011130113 (2020-11-13)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> meeting tg

Joining meeting"tg" at chimeraxmeeting.net port 52197  
Log from Fri Nov 13 14:12:51 2020UCSF ChimeraX version: 1.2.dev202011130113
(2020-11-13)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6xrz

Summary of feedback from opening 6xrz fetched from pdb  
---  
note | Fetching compressed mmCIF 6xrz from
http://files.rcsb.org/download/6xrz.cif  
  
6xrz title:  
The 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome [more
info...]  
  
Chain information for 6xrz  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | Frameshift
Stimulation Element from the SARS-CoV-2 RNA Genome  
  

> vr true

started SteamVR rendering  

> close #1.2-10

> nucleotides atoms

> style nucleic stick

Changed 2808 atom styles  

> vr false

> meeting start tg proxy true

Meeting "tg" started at chimeraxmeeting.net port 52197  
Participants can join with command "meeting tg"  
Connection accepted from ::1 port 62430  

——— End of log from Fri Nov 13 14:12:51 2020 ———

> meeting name Meghan

Must specify meeting name, or host or id options  

> meeting name Meghan

Must specify meeting name, or host or id options  

> meeting name Meghan

Must specify meeting name, or host or id options  

> hide #100 models

> show #100 models

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> nucleotides tube/slab shape muffler

> nucleotides ladder

> nucleotides stubs

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> color bynucleotide

> nucleotides tube/slab shape muffler

> nucleotides tube/slab shape ellipsoid

> nucleotides tube/slab shape box

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 2808 atom styles  

> color bynucleotide

> color bynucleotide

Disconnected from 13.56.160.228 port 52197  

> meeting close

> meeting pc

Joining meeting"pc" at chimeraxmeeting.net port 52196  
Log from Fri Nov 13 17:49:46 2020UCSF ChimeraX version: 1.2.dev202011130113
(2020-11-13)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> meeting tg

Joining meeting"tg" at chimeraxmeeting.net port 52197  
Log from Fri Nov 13 14:12:48 2020UCSF ChimeraX version: 1.2.dev202011130113
(2020-11-13)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6xrz

Summary of feedback from opening 6xrz fetched from pdb  
---  
note | Fetching compressed mmCIF 6xrz from
http://files.rcsb.org/download/6xrz.cif  
  
6xrz title:  
The 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome [more
info...]  
  
Chain information for 6xrz  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | Frameshift
Stimulation Element from the SARS-CoV-2 RNA Genome  
  

> vr true

started SteamVR rendering  

> close #1.2-10

> nucleotides atoms

> style nucleic stick

Changed 2808 atom styles  

> vr false

> meeting start tg proxy true

Meeting "tg" started at chimeraxmeeting.net port 52197  
Participants can join with command "meeting tg"  

——— End of log from Fri Nov 13 14:12:48 2020 ———

> meeting name phil

Must specify meeting name, or host or id options  

> hide #100 models

> show #100 models

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> nucleotides tube/slab shape muffler

> nucleotides ladder

> nucleotides stubs

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> color bynucleotide

> nucleotides tube/slab shape muffler

> nucleotides tube/slab shape ellipsoid

> nucleotides tube/slab shape box

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 2808 atom styles  

> color bynucleotide

> color bynucleotide

> meeting close

> meeting start pc proxy true

Meeting "pc" started at chimeraxmeeting.net port 52196  
Participants can join with command "meeting pc"  

——— End of log from Fri Nov 13 17:49:46 2020 ———

> close session

> open 1d8v format mmcif fromDatabase pdb

Summary of feedback from opening 1d8v fetched from pdb  
---  
note | Fetching compressed mmCIF 1d8v from
http://files.rcsb.org/download/1d8v.cif  
  
1d8v title:  
The restrained and minimized average NMR structure of MAP30. [more info...]  
  
Chain information for 1d8v #1  
---  
Chain | Description  
A | ANTI-hiv and ANTI-tumor protein MAP30  
  

> meeting color purple

Must specify meeting name, or host or id options  

> meeting pc color purple

To join another meeting you must exit the meeting you are currently in using
command "meeting close"  

> meeting close

> meeting name Meghan color purple

Must specify meeting name, or host or id options  

> meeting pc name Meghan color purple

Joining meeting"pc" at chimeraxmeeting.net port 52196  
Log from Fri Nov 13 17:51:11 2020UCSF ChimeraX version: 1.2.dev202011130113
(2020-11-13)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> meeting tg

Joining meeting"tg" at chimeraxmeeting.net port 52197  
Log from Fri Nov 13 14:12:48 2020UCSF ChimeraX version: 1.2.dev202011130113
(2020-11-13)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6xrz

Summary of feedback from opening 6xrz fetched from pdb  
---  
note | Fetching compressed mmCIF 6xrz from
http://files.rcsb.org/download/6xrz.cif  
  
6xrz title:  
The 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome [more
info...]  
  
Chain information for 6xrz  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | Frameshift
Stimulation Element from the SARS-CoV-2 RNA Genome  
  

> vr true

started SteamVR rendering  

> close #1.2-10

> nucleotides atoms

> style nucleic stick

Changed 2808 atom styles  

> vr false

> meeting start tg proxy true

Meeting "tg" started at chimeraxmeeting.net port 52197  
Participants can join with command "meeting tg"  

——— End of log from Fri Nov 13 14:12:48 2020 ———

> meeting name phil

Must specify meeting name, or host or id options  

> hide #100 models

> show #100 models

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> nucleotides tube/slab shape muffler

> nucleotides ladder

> nucleotides stubs

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> color bynucleotide

> nucleotides tube/slab shape muffler

> nucleotides tube/slab shape ellipsoid

> nucleotides tube/slab shape box

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 2808 atom styles  

> color bynucleotide

> color bynucleotide

> meeting close

> meeting start pc proxy true

Meeting "pc" started at chimeraxmeeting.net port 52196  
Participants can join with command "meeting pc"  
Connection accepted from ::1 port 52069  
Connection accepted from ::1 port 52071  

> close session

> open 1d8v format mmcif fromDatabase pdb

1d8v title:  
The restrained and minimized average NMR structure of MAP30. [more info...]  
  
Chain information for 1d8v #1  
---  
Chain | Description  
A | ANTI-hiv and ANTI-tumor protein MAP30  
  

> meeting color purple

Must specify meeting name, or host or id options  

> meeting pc color purple

To join another meeting you must exit the meeting you are currently in using
command "meeting close"  
Disconnected from ::1 port 52069  

——— End of log from Fri Nov 13 17:51:11 2020 ———

> select /A:51

14 atoms, 13 bonds, 1 residue, 1 model selected  
Disconnected from 13.56.160.228 port 52196  

> meeting close

> meeting pc

Joining meeting"pc" at chimeraxmeeting.net port 52199  
Log from Fri Nov 13 17:52:49 2020UCSF ChimeraX version: 1.2.dev202011130113
(2020-11-13)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> meeting tg

Joining meeting"tg" at chimeraxmeeting.net port 52197  
Log from Fri Nov 13 14:12:48 2020UCSF ChimeraX version: 1.2.dev202011130113
(2020-11-13)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6xrz

Summary of feedback from opening 6xrz fetched from pdb  
---  
note | Fetching compressed mmCIF 6xrz from
http://files.rcsb.org/download/6xrz.cif  
  
6xrz title:  
The 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome [more
info...]  
  
Chain information for 6xrz  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | Frameshift
Stimulation Element from the SARS-CoV-2 RNA Genome  
  

> vr true

started SteamVR rendering  

> close #1.2-10

> nucleotides atoms

> style nucleic stick

Changed 2808 atom styles  

> vr false

> meeting start tg proxy true

Meeting "tg" started at chimeraxmeeting.net port 52197  
Participants can join with command "meeting tg"  

——— End of log from Fri Nov 13 14:12:48 2020 ———

> meeting name phil

Must specify meeting name, or host or id options  

> hide #100 models

> show #100 models

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> nucleotides tube/slab shape muffler

> nucleotides ladder

> nucleotides stubs

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> color bynucleotide

> nucleotides tube/slab shape muffler

> nucleotides tube/slab shape ellipsoid

> nucleotides tube/slab shape box

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 2808 atom styles  

> color bynucleotide

> color bynucleotide

> meeting close

> meeting start pc proxy true

Meeting "pc" started at chimeraxmeeting.net port 52196  
Participants can join with command "meeting pc"  
Connection accepted from ::1 port 52069  
Connection accepted from ::1 port 52071  

> close session

> open 1d8v format mmcif fromDatabase pdb

1d8v title:  
The restrained and minimized average NMR structure of MAP30. [more info...]  
  
Chain information for 1d8v #1  
---  
Chain | Description  
A | ANTI-hiv and ANTI-tumor protein MAP30  
  

> meeting color purple

Must specify meeting name, or host or id options  

> meeting pc color purple

To join another meeting you must exit the meeting you are currently in using
command "meeting close"  
Disconnected from ::1 port 52069  
Connection accepted from ::1 port 52077  

> select /A:51

14 atoms, 13 bonds, 1 residue, 1 model selected  
Connection accepted from ::1 port 52081  

> meeting close

> meeting start pc color yellow name phil

Meeting "pc" started at chimeraxmeeting.net port 52199  
Participants can join with command "meeting pc"  

——— End of log from Fri Nov 13 17:52:49 2020 ———

> select /A:197

19 atoms, 18 bonds, 1 residue, 1 model selected  

> vr true

started SteamVR rendering  

> meeting faceImage "C:/Users/ACE MALI VR 1/Desktop/MeghanMcCarthy.jpg"

Must specify meeting name, or host or id options  

> meeting pc faceImage "C:/Users/ACE MALI VR 1/Desktop/MeghanMcCarthy.jpg"

To join another meeting you must exit the meeting you are currently in using
command "meeting close"  

> meeting close

> meeting pc name Meghan color red faceImage "C:/Users/ACE MALI VR
> 1/Desktop/MeghanMcCarthy.jpg"

Joining meeting"pc" at chimeraxmeeting.net port 52199  
Log from Fri Nov 13 17:59:25 2020UCSF ChimeraX version: 1.2.dev202011130113
(2020-11-13)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> meeting tg

Joining meeting"tg" at chimeraxmeeting.net port 52197  
Log from Fri Nov 13 14:12:48 2020UCSF ChimeraX version: 1.2.dev202011130113
(2020-11-13)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6xrz

Summary of feedback from opening 6xrz fetched from pdb  
---  
note | Fetching compressed mmCIF 6xrz from
http://files.rcsb.org/download/6xrz.cif  
  
6xrz title:  
The 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome [more
info...]  
  
Chain information for 6xrz  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | Frameshift
Stimulation Element from the SARS-CoV-2 RNA Genome  
  

> vr true

started SteamVR rendering  

> close #1.2-10

> nucleotides atoms

> style nucleic stick

Changed 2808 atom styles  

> vr false

> meeting start tg proxy true

Meeting "tg" started at chimeraxmeeting.net port 52197  
Participants can join with command "meeting tg"  

——— End of log from Fri Nov 13 14:12:48 2020 ———

> meeting name phil

Must specify meeting name, or host or id options  

> hide #100 models

> show #100 models

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> nucleotides tube/slab shape muffler

> nucleotides ladder

> nucleotides stubs

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> color bynucleotide

> nucleotides tube/slab shape muffler

> nucleotides tube/slab shape ellipsoid

> nucleotides tube/slab shape box

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 2808 atom styles  

> color bynucleotide

> color bynucleotide

> meeting close

> meeting start pc proxy true

Meeting "pc" started at chimeraxmeeting.net port 52196  
Participants can join with command "meeting pc"  
Connection accepted from ::1 port 52069  
Connection accepted from ::1 port 52071  

> close session

> open 1d8v format mmcif fromDatabase pdb

1d8v title:  
The restrained and minimized average NMR structure of MAP30. [more info...]  
  
Chain information for 1d8v #1  
---  
Chain | Description  
A | ANTI-hiv and ANTI-tumor protein MAP30  
  

> meeting color purple

Must specify meeting name, or host or id options  

> meeting pc color purple

To join another meeting you must exit the meeting you are currently in using
command "meeting close"  
Disconnected from ::1 port 52069  
Connection accepted from ::1 port 52077  

> select /A:51

14 atoms, 13 bonds, 1 residue, 1 model selected  
Connection accepted from ::1 port 52081  

> meeting close

> meeting start pc color yellow name phil

Meeting "pc" started at chimeraxmeeting.net port 52199  
Participants can join with command "meeting pc"  
Connection accepted from ::1 port 52088  
Connection accepted from ::1 port 52089  
Connection accepted from ::1 port 52090  

> select /A:197

19 atoms, 18 bonds, 1 residue, 1 model selected  

> vr true

started SteamVR rendering  
Disconnected from ::1 port 52088  

——— End of log from Fri Nov 13 17:59:25 2020 ———

> meeting close

> meeting pc2

Joining meeting"pc2" at 52.0.163.3 port 52202  
Log from Fri Nov 13 18:13:07 2020UCSF ChimeraX version: 1.2.dev202011130113
(2020-11-13)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> meeting tg

Joining meeting"tg" at chimeraxmeeting.net port 52197  
Log from Fri Nov 13 14:12:48 2020UCSF ChimeraX version: 1.2.dev202011130113
(2020-11-13)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6xrz

Summary of feedback from opening 6xrz fetched from pdb  
---  
note | Fetching compressed mmCIF 6xrz from
http://files.rcsb.org/download/6xrz.cif  
  
6xrz title:  
The 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome [more
info...]  
  
Chain information for 6xrz  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | Frameshift
Stimulation Element from the SARS-CoV-2 RNA Genome  
  

> vr true

started SteamVR rendering  

> close #1.2-10

> nucleotides atoms

> style nucleic stick

Changed 2808 atom styles  

> vr false

> meeting start tg proxy true

Meeting "tg" started at chimeraxmeeting.net port 52197  
Participants can join with command "meeting tg"  

——— End of log from Fri Nov 13 14:12:48 2020 ———

> meeting name phil

Must specify meeting name, or host or id options  

> hide #100 models

> show #100 models

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> nucleotides tube/slab shape muffler

> nucleotides ladder

> nucleotides stubs

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> color bynucleotide

> nucleotides tube/slab shape muffler

> nucleotides tube/slab shape ellipsoid

> nucleotides tube/slab shape box

> nucleotides slab

> style nucleic stick

Changed 2808 atom styles  

> nucleotides fill

> style nucleic stick

Changed 2808 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 2808 atom styles  

> color bynucleotide

> color bynucleotide

> meeting close

> meeting start pc proxy true

Meeting "pc" started at chimeraxmeeting.net port 52196  
Participants can join with command "meeting pc"  
Connection accepted from ::1 port 52069  
Connection accepted from ::1 port 52071  

> close session

> open 1d8v format mmcif fromDatabase pdb

1d8v title:  
The restrained and minimized average NMR structure of MAP30. [more info...]  
  
Chain information for 1d8v #1  
---  
Chain | Description  
A | ANTI-hiv and ANTI-tumor protein MAP30  
  

> meeting color purple

Must specify meeting name, or host or id options  

> meeting pc color purple

To join another meeting you must exit the meeting you are currently in using
command "meeting close"  
Disconnected from ::1 port 52069  
Connection accepted from ::1 port 52077  

> select /A:51

14 atoms, 13 bonds, 1 residue, 1 model selected  
Connection accepted from ::1 port 52081  

> meeting close

> meeting start pc color yellow name phil

Meeting "pc" started at chimeraxmeeting.net port 52199  
Participants can join with command "meeting pc"  
Connection accepted from ::1 port 52088  
Connection accepted from ::1 port 52089  
Connection accepted from ::1 port 52090  

> select /A:197

19 atoms, 18 bonds, 1 residue, 1 model selected  

> vr true

started SteamVR rendering  
Disconnected from ::1 port 52088  
Connection accepted from ::1 port 52231  
Disconnected from ::1 port 52231  

> meeting close

> meeting close

> meeting close

> meeting close

> meeting close

> meeting start pc2 proxyServer chimerax@52.0.163.3 proxyKey
> C:\Users/BioViz7\Desktop\chimerax-user.pem

Meeting "pc2" started at 52.0.163.3 port 52202  
Participants can join with command "meeting pc2"  

> close session

> close session

Connection accepted from ::1 port 52268  
Connection accepted from ::1 port 52269  

——— End of log from Fri Nov 13 18:13:07 2020 ———

> vr false

> close session

> open 1d8v format mmcif fromDatabase pdb

1d8v title:  
The restrained and minimized average NMR structure of MAP30. [more info...]  
  
Chain information for 1d8v #1  
---  
Chain | Description  
A | ANTI-hiv and ANTI-tumor protein MAP30  
  

> vr true

started SteamVR rendering  

> graphics restart

> style ball

Changed 4208 atom styles  

> style sphere

Changed 4208 atom styles  

> style stick

Changed 4208 atom styles  

> style sphere

Changed 4208 atom styles  

> color byhetero

> rainbow

> coulombic

Coulombic values for 1d8v_A SES surface #1.1: minimum, -20.32, mean 1.32,
maximum 17.98  

> mlp

Map values for surface "1d8v_A SES surface": minimum -24.05, mean -2.864,
maximum 28.49  

> color bfactor

4208 atoms, 263 residues, 1 surfaces, atom bfactor range 0.19 to 17.3  

> color byhetero

> hide surfaces

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides fill

> style nucleic stick

Changed 0 atom styles  

> rainbow

> mlp

Map values for surface "1d8v_A SES surface": minimum -24.05, mean -2.864,
maximum 28.49  

> lighting soft

> lighting full

> lighting shadows false

> graphics silhouettes true

> sequence chain #1/A

Alignment identifier is 1/A  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.dev202011130113\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 319, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX 1.2.dev202011130113\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 84, in _intercept  
return interceptor(request_info, *args)  
File "C:\Program Files\ChimeraX 1.2.dev202011130113\bin\lib\site-
packages\chimerax\log\tool.py", line 202, in link_intercept  
chimerax_intercept(request_info, *args, session=self.session, view=self, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202011130113\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 447, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(qurl.None_), from_dir)  
File "C:\Program Files\ChimeraX 1.2.dev202011130113\bin\lib\site-
packages\chimerax\ui\gui.py", line 347, in thread_safe  
func(*args, **kw)  
File "C:\Program Files\ChimeraX 1.2.dev202011130113\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 440, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX 1.2.dev202011130113\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 456, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.dev202011130113\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.dev202011130113\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.dev202011130113\bin\lib\site-
packages\chimerax\seqalign\cmd.py", line 140, in seqalign_chain  
alignment = session.alignments.new_alignment([chain], ident, seq_viewer="sv",  
File "C:\Program Files\ChimeraX 1.2.dev202011130113\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 232, in new_alignment  
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,  
File "C:\Program Files\ChimeraX 1.2.dev202011130113\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 128, in __init__  
self._set_residue_attributes()  
File "C:\Program Files\ChimeraX 1.2.dev202011130113\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 721, in _set_residue_attributes  
self.session.change_tracker.add_modified(assigned, attr_name + " changed")  
File "C:\Program Files\ChimeraX 1.2.dev202011130113\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1914, in add_modified  
f(self._c_pointer, self._inst_to_int(item), modded._c_pointer,  
AttributeError: 'set' object has no attribute '_c_pointer'  
  
AttributeError: 'set' object has no attribute '_c_pointer'  
  
File "C:\Program Files\ChimeraX 1.2.dev202011130113\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1914, in add_modified  
f(self._c_pointer, self._inst_to_int(item), modded._c_pointer,  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 456.55
OpenGL renderer: GeForce RTX 2070 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Alienware
Model: Alienware m15
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 34,143,154,176
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.11.8
    cftime: 1.2.1
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.9.3
    ChimeraX-AtomicLibrary: 1.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202011130113
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.1
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.3.1
    ChimeraX-PDB: 2.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.2.2
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.3.1
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.6.3
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.5.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    netifaces: 0.10.9
    networkx: 2.5
    numexpr: 2.7.1
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 20.2.3
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.8
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.1
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.1
    python-dateutil: 2.8.1
    pytz: 2020.4
    pywin32: 228
    pyzmq: 20.0.0
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.0
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.35.1
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → add_modified() not handling sets

comment:2 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: accepted → closed
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