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Opened 2 years ago
Closed 2 years ago
#10060 closed defect (nonchimerax)
save_pdb() call fails
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Jak sie sprobuje uzyc ikony SavsC20 i nie wybierze sie niczego tylko zamknie sie okno, dostaje error:
TypeError: argument of type 'NoneType' is not iterable
File "C:\x\BioTools\ChimeraX1.5\bin\lib\site-packages\chimerax\pdb\pdb.py", line 180, in save_pdb
file_per_model = "[NAME]" in output or "[ID]" in output
See log for complete Python traceback.
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> toolshed uninstall TRC-read
unloading module chimerax.trc_read
Successfully uninstalled ChimeraX-TRC-read-1.1
Removed ChimeraX-TRC-read (1.1)
> toolshed uninstall SaveC20
unloading module chimerax.save_c20
Successfully uninstalled ChimeraX-SaveC20-1.1
Removed ChimeraX-SaveC20 (1.1)
> toolshed uninstall align_and_seq_viewer_plugin
"align_and_seq_viewer_plugin" does not match any bundles
> toolshed uninstall Align_and_seq_viewer_plugin
"Align_and_seq_viewer_plugin" does not match any bundles
> open C:\x\publikacje\RNAknots\RydC\rydc.seq_08-000789_AA.pdb format pdb
Chain information for rydc.seq_08-000789_AA.pdb #1
---
Chain | Description
A | No description available
> devel install C:\x\usefuldata\shared\install_science\savec20_plugin-main
running build
running build_py
creating build
creating build\lib
creating build\lib\chimerax
creating build\lib\chimerax\save_c20
copying src\alligned_save.py -> build\lib\chimerax\save_c20
copying src\saving_dialog.py -> build\lib\chimerax\save_c20
copying src\tool.py -> build\lib\chimerax\save_c20
copying src\\__init__.py -> build\lib\chimerax\save_c20
creating build\lib\chimerax\save_c20\icons
copying src\icons\Savec20.png -> build\lib\chimerax\save_c20\icons
running bdist_wheel
installing to build\bdist.win-amd64\wheel
running install
running install_lib
creating build\bdist.win-amd64
creating build\bdist.win-amd64\wheel
creating build\bdist.win-amd64\wheel\chimerax
creating build\bdist.win-amd64\wheel\chimerax\save_c20
copying build\lib\chimerax\save_c20\alligned_save.py -> build\bdist.win-
amd64\wheel\\.\chimerax\save_c20
creating build\bdist.win-amd64\wheel\chimerax\save_c20\icons
copying build\lib\chimerax\save_c20\icons\Savec20.png -> build\bdist.win-
amd64\wheel\\.\chimerax\save_c20\icons
copying build\lib\chimerax\save_c20\saving_dialog.py -> build\bdist.win-
amd64\wheel\\.\chimerax\save_c20
copying build\lib\chimerax\save_c20\tool.py -> build\bdist.win-
amd64\wheel\\.\chimerax\save_c20
copying build\lib\chimerax\save_c20\\__init__.py -> build\bdist.win-
amd64\wheel\\.\chimerax\save_c20
running install_egg_info
running egg_info
creating ChimeraX_SaveC20.egg-info
writing ChimeraX_SaveC20.egg-info\PKG-INFO
writing dependency_links to ChimeraX_SaveC20.egg-info\dependency_links.txt
writing requirements to ChimeraX_SaveC20.egg-info\requires.txt
writing top-level names to ChimeraX_SaveC20.egg-info\top_level.txt
writing manifest file 'ChimeraX_SaveC20.egg-info\SOURCES.txt'
reading manifest file 'ChimeraX_SaveC20.egg-info\SOURCES.txt'
writing manifest file 'ChimeraX_SaveC20.egg-info\SOURCES.txt'
Copying ChimeraX_SaveC20.egg-info to build\bdist.win-
amd64\wheel\\.\ChimeraX_SaveC20-1.1-py3.9.egg-info
running install_scripts
creating build\bdist.win-amd64\wheel\ChimeraX_SaveC20-1.1.dist-info\WHEEL
creating 'dist\ChimeraX_SaveC20-1.1-py3-none-any.whl' and adding
'build\bdist.win-amd64\wheel' to it
adding 'chimerax/save_c20/__init__.py'
adding 'chimerax/save_c20/alligned_save.py'
adding 'chimerax/save_c20/saving_dialog.py'
adding 'chimerax/save_c20/tool.py'
adding 'chimerax/save_c20/icons/Savec20.png'
adding 'ChimeraX_SaveC20-1.1.dist-info/METADATA'
adding 'ChimeraX_SaveC20-1.1.dist-info/WHEEL'
adding 'ChimeraX_SaveC20-1.1.dist-info/top_level.txt'
adding 'ChimeraX_SaveC20-1.1.dist-info/RECORD'
removing build\bdist.win-amd64\wheel
Distribution is in C:\x\usefuldata\shared\install_science\savec20_plugin-
main\dist\ChimeraX_SaveC20-1.1-py3-none-any.whl
[toolshed install](help:user/commands/toolshed.html#install)
C:\x\usefuldata\shared\install_science\savec20_plugin-
main\dist\ChimeraX_SaveC20-1.1-py3-none-any.whl
[toolshed install C:\x\usefuldata\shared\install_science\savec20_plugin-
main\dist\ChimeraX_SaveC20-1.1-py3-none-any.whl](cxcmd:toolshed install
C:\\\x\\\usefuldata\\\shared\\\install_science\\\savec20_plugin-
main\\\dist\\\ChimeraX_SaveC20-1.1-py3-none-any.whl)
Errors may have occurred when running pip:
pip standard error:
\---
[notice] A new release of pip available: 22.2.2 -> 23.3.1
[notice] To update, run: C:\x\BioTools\ChimeraX1.5\bin\ChimeraX.exe -m pip
install --upgrade pip
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing c:\x\usefuldata\shared\install_science\savec20_plugin-
main\dist\chimerax_savec20-1.1-py3-none-any.whl
Requirement already satisfied: ChimeraX-UI~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-SaveC20==1.1)
(1.24.3)
Requirement already satisfied: ChimeraX-Core~=1.3 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-SaveC20==1.1)
(1.5)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-
UI~=1.0->ChimeraX-SaveC20==1.1) (1.1.1)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-
UI~=1.0->ChimeraX-SaveC20==1.1) (1.0)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-
UI~=1.0->ChimeraX-SaveC20==1.1) (1.1)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-
Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX-SaveC20==1.1) (1.2)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-
Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX-SaveC20==1.1) (1.0)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-SaveC20==1.1) (1.0.1)
Installing collected packages: ChimeraX-SaveC20
Successfully installed ChimeraX-SaveC20-1.1
\---
Successfully installed ChimeraX-SaveC20-1.1
Installed ChimeraX-SaveC20 (1.1)
> devel clean C:\x\usefuldata\shared\install_science\savec20_plugin-main
> devel install C:\x\usefuldata\shared\install_science\trc_read_plugin-main
running build
running build_py
creating build
creating build\lib
creating build\lib\chimerax
creating build\lib\chimerax\trc_read
copying src\bond_data.py -> build\lib\chimerax\trc_read
copying src\coord_data.py -> build\lib\chimerax\trc_read
copying src\Frames_to_atom_coords.py -> build\lib\chimerax\trc_read
copying src\frame_data.py -> build\lib\chimerax\trc_read
copying src\frame_to_pdb_writer.py -> build\lib\chimerax\trc_read
copying src\main.py -> build\lib\chimerax\trc_read
copying src\pdb_data.py -> build\lib\chimerax\trc_read
copying src\tool.py -> build\lib\chimerax\trc_read
copying src\TRC2PDB.py -> build\lib\chimerax\trc_read
copying src\TRC2TXT.py -> build\lib\chimerax\trc_read
copying src\\__init__.py -> build\lib\chimerax\trc_read
copying src\trc2pdb -> build\lib\chimerax\trc_read
copying src\trc2pdb.exe -> build\lib\chimerax\trc_read
copying src\libgcc_s_seh-1.dll -> build\lib\chimerax\trc_read
copying src\libstdc++-6.dll -> build\lib\chimerax\trc_read
creating build\lib\chimerax\trc_read\data
creating build\lib\chimerax\trc_read\data\protein
copying src\data\protein\backbone_local_CB_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\backbone_local_C_O ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\backbone_local_N ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\backbone_pept_bonds_conformers ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_A_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_A_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_C_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_C_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_D_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_D_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_E_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_E_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_F_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_F_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_G_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_G_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_H_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_H_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_I_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_I_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_K_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_K_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_L_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_L_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_M_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_M_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_N_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_N_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_P_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_P_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_Q_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_Q_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_R_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_R_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_S_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_S_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_T_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_T_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_V_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_V_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_W_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_W_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_Y_allAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
copying src\data\protein\conformers_Y_pseAtoms_R13-3.0 ->
build\lib\chimerax\trc_read\data\protein
creating build\lib\chimerax\trc_read\data\rna
copying src\data\rna\A_baseCoords_selfLC ->
build\lib\chimerax\trc_read\data\rna
copying src\data\rna\A_conformers -> build\lib\chimerax\trc_read\data\rna
copying src\data\rna\backbone_conformers ->
build\lib\chimerax\trc_read\data\rna
copying src\data\rna\C_baseCoords_selfLC ->
build\lib\chimerax\trc_read\data\rna
copying src\data\rna\C_conformers -> build\lib\chimerax\trc_read\data\rna
copying src\data\rna\G_baseCoords_selfLC ->
build\lib\chimerax\trc_read\data\rna
copying src\data\rna\G_conformers -> build\lib\chimerax\trc_read\data\rna
copying src\data\rna\U_baseCoords_selfLC ->
build\lib\chimerax\trc_read\data\rna
copying src\data\rna\U_conformers -> build\lib\chimerax\trc_read\data\rna
running bdist_wheel
installing to build\bdist.win-amd64\wheel
running install
running install_lib
creating build\bdist.win-amd64
creating build\bdist.win-amd64\wheel
creating build\bdist.win-amd64\wheel\chimerax
creating build\bdist.win-amd64\wheel\chimerax\trc_read
copying build\lib\chimerax\trc_read\bond_data.py -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read
copying build\lib\chimerax\trc_read\coord_data.py -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read
creating build\bdist.win-amd64\wheel\chimerax\trc_read\data
creating build\bdist.win-amd64\wheel\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\backbone_local_CB_R13-3.0 ->
build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\backbone_local_C_O ->
build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\backbone_local_N ->
build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying
build\lib\chimerax\trc_read\data\protein\backbone_pept_bonds_conformers ->
build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_A_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_A_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_C_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_C_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_D_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_D_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_E_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_E_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_F_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_F_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_G_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_G_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_H_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_H_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_I_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_I_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_K_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_K_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_L_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_L_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_M_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_M_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_N_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_N_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_P_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_P_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_Q_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_Q_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_R_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_R_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_S_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_S_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_T_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_T_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_V_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_V_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_W_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_W_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_Y_allAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
copying build\lib\chimerax\trc_read\data\protein\conformers_Y_pseAtoms_R13-3.0
-> build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\protein
creating build\bdist.win-amd64\wheel\chimerax\trc_read\data\rna
copying build\lib\chimerax\trc_read\data\rna\A_baseCoords_selfLC ->
build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\rna
copying build\lib\chimerax\trc_read\data\rna\A_conformers -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read\data\rna
copying build\lib\chimerax\trc_read\data\rna\backbone_conformers ->
build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\rna
copying build\lib\chimerax\trc_read\data\rna\C_baseCoords_selfLC ->
build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\rna
copying build\lib\chimerax\trc_read\data\rna\C_conformers -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read\data\rna
copying build\lib\chimerax\trc_read\data\rna\G_baseCoords_selfLC ->
build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\rna
copying build\lib\chimerax\trc_read\data\rna\G_conformers -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read\data\rna
copying build\lib\chimerax\trc_read\data\rna\U_baseCoords_selfLC ->
build\bdist.win-amd64\wheel\\.\chimerax\trc_read\data\rna
copying build\lib\chimerax\trc_read\data\rna\U_conformers -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read\data\rna
copying build\lib\chimerax\trc_read\Frames_to_atom_coords.py ->
build\bdist.win-amd64\wheel\\.\chimerax\trc_read
copying build\lib\chimerax\trc_read\frame_data.py -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read
copying build\lib\chimerax\trc_read\frame_to_pdb_writer.py -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read
copying build\lib\chimerax\trc_read\libgcc_s_seh-1.dll -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read
copying build\lib\chimerax\trc_read\libstdc++-6.dll -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read
copying build\lib\chimerax\trc_read\main.py -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read
copying build\lib\chimerax\trc_read\pdb_data.py -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read
copying build\lib\chimerax\trc_read\tool.py -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read
copying build\lib\chimerax\trc_read\trc2pdb -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read
copying build\lib\chimerax\trc_read\trc2pdb.exe -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read
copying build\lib\chimerax\trc_read\TRC2PDB.py -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read
copying build\lib\chimerax\trc_read\TRC2TXT.py -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read
copying build\lib\chimerax\trc_read\\__init__.py -> build\bdist.win-
amd64\wheel\\.\chimerax\trc_read
running install_egg_info
running egg_info
creating ChimeraX_TRC_read.egg-info
writing ChimeraX_TRC_read.egg-info\PKG-INFO
writing dependency_links to ChimeraX_TRC_read.egg-info\dependency_links.txt
writing requirements to ChimeraX_TRC_read.egg-info\requires.txt
writing top-level names to ChimeraX_TRC_read.egg-info\top_level.txt
writing manifest file 'ChimeraX_TRC_read.egg-info\SOURCES.txt'
reading manifest file 'ChimeraX_TRC_read.egg-info\SOURCES.txt'
writing manifest file 'ChimeraX_TRC_read.egg-info\SOURCES.txt'
Copying ChimeraX_TRC_read.egg-info to build\bdist.win-
amd64\wheel\\.\ChimeraX_TRC_read-1.1-py3.9.egg-info
running install_scripts
creating build\bdist.win-amd64\wheel\ChimeraX_TRC_read-1.1.dist-info\WHEEL
creating 'dist\ChimeraX_TRC_read-1.1-py3-none-any.whl' and adding
'build\bdist.win-amd64\wheel' to it
adding 'chimerax/trc_read/Frames_to_atom_coords.py'
adding 'chimerax/trc_read/TRC2PDB.py'
adding 'chimerax/trc_read/TRC2TXT.py'
adding 'chimerax/trc_read/__init__.py'
adding 'chimerax/trc_read/bond_data.py'
adding 'chimerax/trc_read/coord_data.py'
adding 'chimerax/trc_read/frame_data.py'
adding 'chimerax/trc_read/frame_to_pdb_writer.py'
adding 'chimerax/trc_read/libgcc_s_seh-1.dll'
adding 'chimerax/trc_read/libstdc++-6.dll'
adding 'chimerax/trc_read/main.py'
adding 'chimerax/trc_read/pdb_data.py'
adding 'chimerax/trc_read/tool.py'
adding 'chimerax/trc_read/trc2pdb'
adding 'chimerax/trc_read/trc2pdb.exe'
adding 'chimerax/trc_read/data/protein/backbone_local_CB_R13-3.0'
adding 'chimerax/trc_read/data/protein/backbone_local_C_O'
adding 'chimerax/trc_read/data/protein/backbone_local_N'
adding 'chimerax/trc_read/data/protein/backbone_pept_bonds_conformers'
adding 'chimerax/trc_read/data/protein/conformers_A_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_A_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_C_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_C_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_D_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_D_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_E_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_E_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_F_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_F_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_G_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_G_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_H_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_H_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_I_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_I_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_K_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_K_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_L_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_L_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_M_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_M_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_N_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_N_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_P_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_P_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_Q_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_Q_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_R_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_R_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_S_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_S_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_T_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_T_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_V_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_V_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_W_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_W_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_Y_allAtoms_R13-3.0'
adding 'chimerax/trc_read/data/protein/conformers_Y_pseAtoms_R13-3.0'
adding 'chimerax/trc_read/data/rna/A_baseCoords_selfLC'
adding 'chimerax/trc_read/data/rna/A_conformers'
adding 'chimerax/trc_read/data/rna/C_baseCoords_selfLC'
adding 'chimerax/trc_read/data/rna/C_conformers'
adding 'chimerax/trc_read/data/rna/G_baseCoords_selfLC'
adding 'chimerax/trc_read/data/rna/G_conformers'
adding 'chimerax/trc_read/data/rna/U_baseCoords_selfLC'
adding 'chimerax/trc_read/data/rna/U_conformers'
adding 'chimerax/trc_read/data/rna/backbone_conformers'
adding 'ChimeraX_TRC_read-1.1.dist-info/METADATA'
adding 'ChimeraX_TRC_read-1.1.dist-info/WHEEL'
adding 'ChimeraX_TRC_read-1.1.dist-info/top_level.txt'
adding 'ChimeraX_TRC_read-1.1.dist-info/RECORD'
removing build\bdist.win-amd64\wheel
Distribution is in C:\x\usefuldata\shared\install_science\trc_read_plugin-
main\dist\ChimeraX_TRC_read-1.1-py3-none-any.whl
[toolshed install](help:user/commands/toolshed.html#install)
C:\x\usefuldata\shared\install_science\trc_read_plugin-
main\dist\ChimeraX_TRC_read-1.1-py3-none-any.whl
[toolshed install C:\x\usefuldata\shared\install_science\trc_read_plugin-
main\dist\ChimeraX_TRC_read-1.1-py3-none-any.whl](cxcmd:toolshed install
C:\\\x\\\usefuldata\\\shared\\\install_science\\\trc_read_plugin-
main\\\dist\\\ChimeraX_TRC_read-1.1-py3-none-any.whl)
Errors may have occurred when running pip:
pip standard error:
\---
[notice] A new release of pip available: 22.2.2 -> 23.3.1
[notice] To update, run: C:\x\BioTools\ChimeraX1.5\bin\ChimeraX.exe -m pip
install --upgrade pip
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing c:\x\usefuldata\shared\install_science\trc_read_plugin-
main\dist\chimerax_trc_read-1.1-py3-none-any.whl
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-TRC-read==1.1)
(1.2.2)
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-TRC-read==1.1)
(1.9.1)
Requirement already satisfied: ChimeraX-Core~=1.1 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-TRC-read==1.1)
(1.5)
Requirement already satisfied: ChimeraX-UI~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-TRC-read==1.1)
(1.24.3)
Requirement already satisfied: ChimeraX-SaveCommand~=1.4 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-
DataFormats~=1.0->ChimeraX-TRC-read==1.1) (1.5.1)
Requirement already satisfied: ChimeraX-IO~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-
DataFormats~=1.0->ChimeraX-TRC-read==1.1) (1.0.1)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-
UI~=1.0->ChimeraX-TRC-read==1.1) (1.1)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-
UI~=1.0->ChimeraX-TRC-read==1.1) (1.1.1)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-
UI~=1.0->ChimeraX-TRC-read==1.1) (1.0)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-
Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX-TRC-read==1.1) (1.0)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-
Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX-TRC-read==1.1) (1.2)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
c:\x\biotools\chimerax1.5\bin\lib\site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-TRC-read==1.1) (1.0.1)
Installing collected packages: ChimeraX-TRC-read
Successfully installed ChimeraX-TRC-read-1.1
\---
Successfully installed ChimeraX-TRC-read-1.1
Installed ChimeraX-TRC-read (1.1)
Replacing data format 'TRC' as defined by ChimeraX-TRC-read with definition
from ChimeraX-TRC-read
WORKS!
JOB DONE.
Command "copy_trc2pdb" is missing a synopsis
> copy_trc2pdb C:\x\usefuldata\shared\install_science\trc_read_plugin-main
> devel clean C:\x\usefuldata\shared\install_science\trc_read_plugin-main
> close session
> ui tool show "TRC read"
Chosen pdb file:
C:/x/publikacje/1000RNAs/manA/Tetramer_SimRNACry1/Variant_4_based/trc_file/manA_V4_D4_SS_run_01_01-000001.pdb
Chosen trc file:
C:/x/publikacje/1000RNAs/manA/Tetramer_SimRNACry1/Variant_4_based/trc_file/manA_V4_D4_SS_run_01_ALL.trc
Chosen hdr file:
C:/x/publikacje/1000RNAs/manA/Tetramer_SimRNACry1/Variant_4_based/trc_file/manA_V4_D4_SS_run_01_01.hdr
> open
> C:/x/publikacje/1000RNAs/manA/Tetramer_SimRNACry1/Variant_4_based/trc_file/manA_V4_D4_SS_run_01_ALL.trc
> pdbName
> C:/x/publikacje/1000RNAs/manA/Tetramer_SimRNACry1/Variant_4_based/trc_file/manA_V4_D4_SS_run_01_01-000001.pdb
> speed 5 hdrName
> C:/x/publikacje/1000RNAs/manA/Tetramer_SimRNACry1/Variant_4_based/trc_file/manA_V4_D4_SS_run_01_01.hdr
Summary of feedback from opening
C:/x/publikacje/1000RNAs/manA/Tetramer_SimRNACry1/Variant_4_based/trc_file/manA_V4_D4_SS_run_01_ALL.trc
---
notes | 0
RES atom set: [Counter({1: 5, 2: 5, 3: 5, 4: 5, 5: 5, 6: 5, 7: 5, 8: 5, 9: 5,
10: 5, 11: 5, 12: 5, 13: 5, 14: 5, 15: 5, 16: 5, 17: 5, 18: 5, 19: 5, 20: 5,
21: 5, 22: 5, 23: 5, 24: 5, 25: 5, 26: 5, 27: 5, 28: 5, 29: 5, 30: 5, 31: 5,
32: 5, 33: 5, 34: 5, 35: 5, 36: 5, 37: 5, 38: 5, 39: 5, 40: 5, 41: 5, 42: 5,
43: 5, 44: 5, 45: 5, 46: 5, 47: 5, 48: 5, 49: 5, 50: 5, 51: 5, 52: 5, 53: 5,
54: 5, 55: 5, 56: 5, 57: 5, 58: 5, 59: 5, 60: 5, 61: 5, 62: 5, 63: 5, 64: 5,
65: 5, 66: 5, 67: 5, 68: 5, 69: 5, 70: 5, 71: 5, 72: 5, 73: 5, 74: 5, 75: 5,
76: 5, 77: 5, 78: 5, 79: 5, 80: 5, 81: 5, 82: 5, 83: 5, 84: 5, 85: 5, 86: 5,
87: 5, 88: 5, 89: 5, 90: 5, 91: 5, 92: 5, 93: 5, 94: 5, 95: 5, 96: 5, 97: 5,
98: 5, 99: 5, 100: 5, 101: 5, 102: 5, 103: 5, 104: 5, 105: 5, 106: 5, 107: 5,
108: 5, 109: 5, 110: 5, 111: 5, 112: 5, 113: 5, 114: 5, 115: 5, 116: 5, 117:
5, 118: 5, 119: 5, 120: 5, 121: 5, 122: 5, 123: 5, 124: 5, 125: 5, 126: 5,
127: 5, 128: 5, 129: 5, 130: 5, 131: 5, 132: 5, 133: 5, 134: 5, 135: 5, 136:
5, 137: 5, 138: 5, 139: 5, 140: 5, 141: 5, 142: 5, 143: 5, 144: 5, 145: 5,
146: 5, 147: 5, 148: 5, 149: 5, 150: 5, 151: 5, 152: 5, 153: 5, 154: 5, 155:
5, 156: 5, 157: 5, 158: 5, 159: 5, 160: 5, 161: 5, 162: 5, 163: 5, 164: 5,
165: 5, 166: 5, 167: 5}), Counter({1: 5, 2: 5, 3: 5, 4: 5, 5: 5, 6: 5, 7: 5,
8: 5, 9: 5, 10: 5, 11: 5, 12: 5, 13: 5, 14: 5, 15: 5, 16: 5, 17: 5, 18: 5, 19:
5, 20: 5, 21: 5, 22: 5, 23: 5, 24: 5, 25: 5, 26: 5, 27: 5, 28: 5, 29: 5, 30:
5, 31: 5, 32: 5, 33: 5, 34: 5, 35: 5, 36: 5, 37: 5, 38: 5, 39: 5, 40: 5, 41:
5, 42: 5, 43: 5, 44: 5, 45: 5, 46: 5, 47: 5, 48: 5, 49: 5, 50: 5, 51: 5, 52:
5, 53: 5, 54: 5, 55: 5, 56: 5, 57: 5, 58: 5, 59: 5, 60: 5, 61: 5, 62: 5, 63:
5, 64: 5, 65: 5, 66: 5, 67: 5, 68: 5, 69: 5, 70: 5, 71: 5, 72: 5, 73: 5, 74:
5, 75: 5, 76: 5, 77: 5, 78: 5, 79: 5, 80: 5, 81: 5, 82: 5, 83: 5, 84: 5, 85:
5, 86: 5, 87: 5, 88: 5, 89: 5, 90: 5, 91: 5, 92: 5, 93: 5, 94: 5, 95: 5, 96:
5, 97: 5, 98: 5, 99: 5, 100: 5, 101: 5, 102: 5, 103: 5, 104: 5, 105: 5, 106:
5, 107: 5, 108: 5, 109: 5, 110: 5, 111: 5, 112: 5, 113: 5, 114: 5, 115: 5,
116: 5, 117: 5, 118: 5, 119: 5, 120: 5, 121: 5, 122: 5, 123: 5, 124: 5, 125:
5, 126: 5, 127: 5, 128: 5, 129: 5, 130: 5, 131: 5, 132: 5, 133: 5, 134: 5,
135: 5, 136: 5, 137: 5, 138: 5, 139: 5, 140: 5, 141: 5, 142: 5, 143: 5, 144:
5, 145: 5, 146: 5, 147: 5, 148: 5, 149: 5, 150: 5, 151: 5, 152: 5, 153: 5,
154: 5, 155: 5, 156: 5, 157: 5, 158: 5, 159: 5, 160: 5, 161: 5, 162: 5, 163:
5, 164: 5, 165: 5, 166: 5, 167: 5}), Counter({1: 5, 2: 5, 3: 5, 4: 5, 5: 5, 6:
5, 7: 5, 8: 5, 9: 5, 10: 5, 11: 5, 12: 5, 13: 5, 14: 5, 15: 5, 16: 5, 17: 5,
18: 5, 19: 5, 20: 5, 21: 5, 22: 5, 23: 5, 24: 5, 25: 5, 26: 5, 27: 5, 28: 5,
29: 5, 30: 5, 31: 5, 32: 5, 33: 5, 34: 5, 35: 5, 36: 5, 37: 5, 38: 5, 39: 5,
40: 5, 41: 5, 42: 5, 43: 5, 44: 5, 45: 5, 46: 5, 47: 5, 48: 5, 49: 5, 50: 5,
51: 5, 52: 5, 53: 5, 54: 5, 55: 5, 56: 5, 57: 5, 58: 5, 59: 5, 60: 5, 61: 5,
62: 5, 63: 5, 64: 5, 65: 5, 66: 5, 67: 5, 68: 5, 69: 5, 70: 5, 71: 5, 72: 5,
73: 5, 74: 5, 75: 5, 76: 5, 77: 5, 78: 5, 79: 5, 80: 5, 81: 5, 82: 5, 83: 5,
84: 5, 85: 5, 86: 5, 87: 5, 88: 5, 89: 5, 90: 5, 91: 5, 92: 5, 93: 5, 94: 5,
95: 5, 96: 5, 97: 5, 98: 5, 99: 5, 100: 5, 101: 5, 102: 5, 103: 5, 104: 5,
105: 5, 106: 5, 107: 5, 108: 5, 109: 5, 110: 5, 111: 5, 112: 5, 113: 5, 114:
5, 115: 5, 116: 5, 117: 5, 118: 5, 119: 5, 120: 5, 121: 5, 122: 5, 123: 5,
124: 5, 125: 5, 126: 5, 127: 5, 128: 5, 129: 5, 130: 5, 131: 5, 132: 5, 133:
5, 134: 5, 135: 5, 136: 5, 137: 5, 138: 5, 139: 5, 140: 5, 141: 5, 142: 5,
143: 5, 144: 5, 145: 5, 146: 5, 147: 5, 148: 5, 149: 5, 150: 5, 151: 5, 152:
5, 153: 5, 154: 5, 155: 5, 156: 5, 157: 5, 158: 5, 159: 5, 160: 5, 161: 5,
162: 5, 163: 5, 164: 5, 165: 5, 166: 5, 167: 5}), Counter({1: 5, 2: 5, 3: 5,
4: 5, 5: 5, 6: 5, 7: 5, 8: 5, 9: 5, 10: 5, 11: 5, 12: 5, 13: 5, 14: 5, 15: 5,
16: 5, 17: 5, 18: 5, 19: 5, 20: 5, 21: 5, 22: 5, 23: 5, 24: 5, 25: 5, 26: 5,
27: 5, 28: 5, 29: 5, 30: 5, 31: 5, 32: 5, 33: 5, 34: 5, 35: 5, 36: 5, 37: 5,
38: 5, 39: 5, 40: 5, 41: 5, 42: 5, 43: 5, 44: 5, 45: 5, 46: 5, 47: 5, 48: 5,
49: 5, 50: 5, 51: 5, 52: 5, 53: 5, 54: 5, 55: 5, 56: 5, 57: 5, 58: 5, 59: 5,
60: 5, 61: 5, 62: 5, 63: 5, 64: 5, 65: 5, 66: 5, 67: 5, 68: 5, 69: 5, 70: 5,
71: 5, 72: 5, 73: 5, 74: 5, 75: 5, 76: 5, 77: 5, 78: 5, 79: 5, 80: 5, 81: 5,
82: 5, 83: 5, 84: 5, 85: 5, 86: 5, 87: 5, 88: 5, 89: 5, 90: 5, 91: 5, 92: 5,
93: 5, 94: 5, 95: 5, 96: 5, 97: 5, 98: 5, 99: 5, 100: 5, 101: 5, 102: 5, 103:
5, 104: 5, 105: 5, 106: 5, 107: 5, 108: 5, 109: 5, 110: 5, 111: 5, 112: 5,
113: 5, 114: 5, 115: 5, 116: 5, 117: 5, 118: 5, 119: 5, 120: 5, 121: 5, 122:
5, 123: 5, 124: 5, 125: 5, 126: 5, 127: 5, 128: 5, 129: 5, 130: 5, 131: 5,
132: 5, 133: 5, 134: 5, 135: 5, 136: 5, 137: 5, 138: 5, 139: 5, 140: 5, 141:
5, 142: 5, 143: 5, 144: 5, 145: 5, 146: 5, 147: 5, 148: 5, 149: 5, 150: 5,
151: 5, 152: 5, 153: 5, 154: 5, 155: 5, 156: 5, 157: 5, 158: 5, 159: 5, 160:
5, 161: 5, 162: 5, 163: 5, 164: 5, 165: 5, 166: 5, 167: 5})]
['RNA_A', 'RNA_B', 'RNA_D', 'RNA_C']
_o: RNA_A
_o: RNA_B
_o: RNA_D
_o: RNA_C
len frame coordinates: {'RNA_A': 840, 'RNA_B': 840, 'RNA_D': 840, 'RNA_C':
840}
Frame composition: ['RNA_A', 'RNA_B', 'RNA_D', 'RNA_C']
Frame Chain: ['RNA_A', 'RNA_B', 'RNA_D', 'RNA_C']
['RNA_A', 'RNA_B', 'RNA_D', 'RNA_C']
_o: RNA_A
_o: RNA_B
_o: RNA_D
_o: RNA_C
len frame coordinates: {'RNA_A': 840, 'RNA_B': 840, 'RNA_D': 840, 'RNA_C':
840}
Frame composition: ['RNA_A', 'RNA_B', 'RNA_D', 'RNA_C']
Frame Chain: ['RNA_A', 'RNA_B', 'RNA_D', 'RNA_C']
THERE IS A MISSMATCH BETWEEN ATOMS FROM PDB AND ATOMS FROM COORDINATES IN
FRAME!
PDB: 3340 vs COORDINATES: 3360
DUMMY ATOMS DETECTED !
Molecule type lookup dict: {'RNA_A': 'RNA', 'RNA_B': 'RNA', 'RNA_D': 'RNA',
'RNA_C': 'RNA'}
Chain id: RNA_A
Data from frame: {'RNA_A': 840, 'RNA_B': 840, 'RNA_D': 840, 'RNA_C': 840}
1: 835
I tak sobie adjustuje
Chain id: RNA_B
Data from frame: {'RNA_A': 840, 'RNA_B': 840, 'RNA_D': 840, 'RNA_C': 840}
1: 835
I tak sobie adjustuje
Chain id: RNA_D
Data from frame: {'RNA_A': 840, 'RNA_B': 840, 'RNA_D': 840, 'RNA_C': 840}
1: 835
I tak sobie adjustuje
Chain id: RNA_C
Data from frame: {'RNA_A': 840, 'RNA_B': 840, 'RNA_D': 840, 'RNA_C': 840}
1: 835
I tak sobie adjustuje
MOLECULES UPDATED WITH DUMMY ATOM DATA
DEBUG PRINTS
_______________________________
res_atom_set: [Counter({1: 5, 2: 5, 3: 5, 4: 5, 5: 5, 6: 5, 7: 5, 8: 5, 9: 5,
10: 5, 11: 5, 12: 5, 13: 5, 14: 5, 15: 5, 16: 5, 17: 5, 18: 5, 19: 5, 20: 5,
21: 5, 22: 5, 23: 5, 24: 5, 25: 5, 26: 5, 27: 5, 28: 5, 29: 5, 30: 5, 31: 5,
32: 5, 33: 5, 34: 5, 35: 5, 36: 5, 37: 5, 38: 5, 39: 5, 40: 5, 41: 5, 42: 5,
43: 5, 44: 5, 45: 5, 46: 5, 47: 5, 48: 5, 49: 5, 50: 5, 51: 5, 52: 5, 53: 5,
54: 5, 55: 5, 56: 5, 57: 5, 58: 5, 59: 5, 60: 5, 61: 5, 62: 5, 63: 5, 64: 5,
65: 5, 66: 5, 67: 5, 68: 5, 69: 5, 70: 5, 71: 5, 72: 5, 73: 5, 74: 5, 75: 5,
76: 5, 77: 5, 78: 5, 79: 5, 80: 5, 81: 5, 82: 5, 83: 5, 84: 5, 85: 5, 86: 5,
87: 5, 88: 5, 89: 5, 90: 5, 91: 5, 92: 5, 93: 5, 94: 5, 95: 5, 96: 5, 97: 5,
98: 5, 99: 5, 100: 5, 101: 5, 102: 5, 103: 5, 104: 5, 105: 5, 106: 5, 107: 5,
108: 5, 109: 5, 110: 5, 111: 5, 112: 5, 113: 5, 114: 5, 115: 5, 116: 5, 117:
5, 118: 5, 119: 5, 120: 5, 121: 5, 122: 5, 123: 5, 124: 5, 125: 5, 126: 5,
127: 5, 128: 5, 129: 5, 130: 5, 131: 5, 132: 5, 133: 5, 134: 5, 135: 5, 136:
5, 137: 5, 138: 5, 139: 5, 140: 5, 141: 5, 142: 5, 143: 5, 144: 5, 145: 5,
146: 5, 147: 5, 148: 5, 149: 5, 150: 5, 151: 5, 152: 5, 153: 5, 154: 5, 155:
5, 156: 5, 157: 5, 158: 5, 159: 5, 160: 5, 161: 5, 162: 5, 163: 5, 164: 5,
165: 5, 166: 5, 167: 5, 168: 5}), Counter({1: 5, 2: 5, 3: 5, 4: 5, 5: 5, 6: 5,
7: 5, 8: 5, 9: 5, 10: 5, 11: 5, 12: 5, 13: 5, 14: 5, 15: 5, 16: 5, 17: 5, 18:
5, 19: 5, 20: 5, 21: 5, 22: 5, 23: 5, 24: 5, 25: 5, 26: 5, 27: 5, 28: 5, 29:
5, 30: 5, 31: 5, 32: 5, 33: 5, 34: 5, 35: 5, 36: 5, 37: 5, 38: 5, 39: 5, 40:
5, 41: 5, 42: 5, 43: 5, 44: 5, 45: 5, 46: 5, 47: 5, 48: 5, 49: 5, 50: 5, 51:
5, 52: 5, 53: 5, 54: 5, 55: 5, 56: 5, 57: 5, 58: 5, 59: 5, 60: 5, 61: 5, 62:
5, 63: 5, 64: 5, 65: 5, 66: 5, 67: 5, 68: 5, 69: 5, 70: 5, 71: 5, 72: 5, 73:
5, 74: 5, 75: 5, 76: 5, 77: 5, 78: 5, 79: 5, 80: 5, 81: 5, 82: 5, 83: 5, 84:
5, 85: 5, 86: 5, 87: 5, 88: 5, 89: 5, 90: 5, 91: 5, 92: 5, 93: 5, 94: 5, 95:
5, 96: 5, 97: 5, 98: 5, 99: 5, 100: 5, 101: 5, 102: 5, 103: 5, 104: 5, 105: 5,
106: 5, 107: 5, 108: 5, 109: 5, 110: 5, 111: 5, 112: 5, 113: 5, 114: 5, 115:
5, 116: 5, 117: 5, 118: 5, 119: 5, 120: 5, 121: 5, 122: 5, 123: 5, 124: 5,
125: 5, 126: 5, 127: 5, 128: 5, 129: 5, 130: 5, 131: 5, 132: 5, 133: 5, 134:
5, 135: 5, 136: 5, 137: 5, 138: 5, 139: 5, 140: 5, 141: 5, 142: 5, 143: 5,
144: 5, 145: 5, 146: 5, 147: 5, 148: 5, 149: 5, 150: 5, 151: 5, 152: 5, 153:
5, 154: 5, 155: 5, 156: 5, 157: 5, 158: 5, 159: 5, 160: 5, 161: 5, 162: 5,
163: 5, 164: 5, 165: 5, 166: 5, 167: 5, 168: 5}), Counter({1: 5, 2: 5, 3: 5,
4: 5, 5: 5, 6: 5, 7: 5, 8: 5, 9: 5, 10: 5, 11: 5, 12: 5, 13: 5, 14: 5, 15: 5,
16: 5, 17: 5, 18: 5, 19: 5, 20: 5, 21: 5, 22: 5, 23: 5, 24: 5, 25: 5, 26: 5,
27: 5, 28: 5, 29: 5, 30: 5, 31: 5, 32: 5, 33: 5, 34: 5, 35: 5, 36: 5, 37: 5,
38: 5, 39: 5, 40: 5, 41: 5, 42: 5, 43: 5, 44: 5, 45: 5, 46: 5, 47: 5, 48: 5,
49: 5, 50: 5, 51: 5, 52: 5, 53: 5, 54: 5, 55: 5, 56: 5, 57: 5, 58: 5, 59: 5,
60: 5, 61: 5, 62: 5, 63: 5, 64: 5, 65: 5, 66: 5, 67: 5, 68: 5, 69: 5, 70: 5,
71: 5, 72: 5, 73: 5, 74: 5, 75: 5, 76: 5, 77: 5, 78: 5, 79: 5, 80: 5, 81: 5,
82: 5, 83: 5, 84: 5, 85: 5, 86: 5, 87: 5, 88: 5, 89: 5, 90: 5, 91: 5, 92: 5,
93: 5, 94: 5, 95: 5, 96: 5, 97: 5, 98: 5, 99: 5, 100: 5, 101: 5, 102: 5, 103:
5, 104: 5, 105: 5, 106: 5, 107: 5, 108: 5, 109: 5, 110: 5, 111: 5, 112: 5,
113: 5, 114: 5, 115: 5, 116: 5, 117: 5, 118: 5, 119: 5, 120: 5, 121: 5, 122:
5, 123: 5, 124: 5, 125: 5, 126: 5, 127: 5, 128: 5, 129: 5, 130: 5, 131: 5,
132: 5, 133: 5, 134: 5, 135: 5, 136: 5, 137: 5, 138: 5, 139: 5, 140: 5, 141:
5, 142: 5, 143: 5, 144: 5, 145: 5, 146: 5, 147: 5, 148: 5, 149: 5, 150: 5,
151: 5, 152: 5, 153: 5, 154: 5, 155: 5, 156: 5, 157: 5, 158: 5, 159: 5, 160:
5, 161: 5, 162: 5, 163: 5, 164: 5, 165: 5, 166: 5, 167: 5, 168: 5}),
Counter({1: 5, 2: 5, 3: 5, 4: 5, 5: 5, 6: 5, 7: 5, 8: 5, 9: 5, 10: 5, 11: 5,
12: 5, 13: 5, 14: 5, 15: 5, 16: 5, 17: 5, 18: 5, 19: 5, 20: 5, 21: 5, 22: 5,
23: 5, 24: 5, 25: 5, 26: 5, 27: 5, 28: 5, 29: 5, 30: 5, 31: 5, 32: 5, 33: 5,
34: 5, 35: 5, 36: 5, 37: 5, 38: 5, 39: 5, 40: 5, 41: 5, 42: 5, 43: 5, 44: 5,
45: 5, 46: 5, 47: 5, 48: 5, 49: 5, 50: 5, 51: 5, 52: 5, 53: 5, 54: 5, 55: 5,
56: 5, 57: 5, 58: 5, 59: 5, 60: 5, 61: 5, 62: 5, 63: 5, 64: 5, 65: 5, 66: 5,
67: 5, 68: 5, 69: 5, 70: 5, 71: 5, 72: 5, 73: 5, 74: 5, 75: 5, 76: 5, 77: 5,
78: 5, 79: 5, 80: 5, 81: 5, 82: 5, 83: 5, 84: 5, 85: 5, 86: 5, 87: 5, 88: 5,
89: 5, 90: 5, 91: 5, 92: 5, 93: 5, 94: 5, 95: 5, 96: 5, 97: 5, 98: 5, 99: 5,
100: 5, 101: 5, 102: 5, 103: 5, 104: 5, 105: 5, 106: 5, 107: 5, 108: 5, 109:
5, 110: 5, 111: 5, 112: 5, 113: 5, 114: 5, 115: 5, 116: 5, 117: 5, 118: 5,
119: 5, 120: 5, 121: 5, 122: 5, 123: 5, 124: 5, 125: 5, 126: 5, 127: 5, 128:
5, 129: 5, 130: 5, 131: 5, 132: 5, 133: 5, 134: 5, 135: 5, 136: 5, 137: 5,
138: 5, 139: 5, 140: 5, 141: 5, 142: 5, 143: 5, 144: 5, 145: 5, 146: 5, 147:
5, 148: 5, 149: 5, 150: 5, 151: 5, 152: 5, 153: 5, 154: 5, 155: 5, 156: 5,
157: 5, 158: 5, 159: 5, 160: 5, 161: 5, 162: 5, 163: 5, 164: 5, 165: 5, 166:
5, 167: 5, 168: 5})]
molecule_type_lookup_dict: {'RNA_A': 'RNA', 'RNA_B': 'RNA', 'RNA_D': 'RNA',
'RNA_C': 'RNA'}
Data from frame frame chains: ['RNA_A', 'RNA_B', 'RNA_D', 'RNA_C']
vPDB_files [<_io.StringIO object at 0x000002A20B4374C0>, <_io.StringIO object
at 0x000002A20B437430>, <_io.StringIO object at 0x000002A20B3C4CA0>,
<_io.StringIO object at 0x000002A20B3C4A60>]
_______________________________
res_gen <generator object create_structure.<locals>.My_gen at
0x000002A20BCA0270>
[]
inside loop: dict_keys([1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54,
55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73,
74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109,
110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124,
125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139,
140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154,
155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168])
0
168
=== Calculating RNA bonds ===
['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A']
inside loop: dict_keys([1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54,
55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73,
74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109,
110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124,
125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139,
140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154,
155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168])
1
168
=== Calculating RNA bonds ===
['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B']
inside loop: dict_keys([1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54,
55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73,
74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109,
110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124,
125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139,
140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154,
155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168])
2
168
=== Calculating RNA bonds ===
['A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A',
'A', 'A', 'A', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
'B', 'B', 'B', 'B', 'B', 'B', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D',
'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D',
'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D',
'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D',
'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D',
'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D',
'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D',
'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D',
'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D',
'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D',
'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D',
'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D', 'D']
inside loop: dict_keys([1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54,
55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73,
74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109,
110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124,
125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139,
140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154,
155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168])
3
168
=== Calculating RNA bonds ===
['G', 'G', 'G', 'A', 'G', 'U', 'G', 'A', 'C', 'U', 'G', 'A', 'A', 'U', 'A',
'A', 'A', 'C', 'U', 'U', 'A', 'C', 'U', 'G', 'G', 'C', 'A', 'U', 'A', 'U',
'A', 'G', 'C', 'U', 'G', 'G', 'U', 'U', 'A', 'A', 'G', 'G', 'U', 'G', 'A',
'U', 'G', 'A', 'G', 'A', 'C', 'A', 'C', 'A', 'G', 'G', 'U', 'G', 'G', 'U',
'G', 'C', 'U', 'G', 'C', 'U', 'G', 'C', 'G', 'A', 'A', 'A', 'G', 'C', 'A',
'G', 'A', 'A', 'U', 'C', 'G', 'A', 'C', 'U', 'U', 'A', 'C', 'C', 'A', 'G',
'U', 'C', 'G', 'G', 'G', 'U', 'C', 'U', 'C', 'A', 'G', 'G', 'C', 'A', 'G',
'A', 'G', 'G', 'A', 'G', 'U', 'U', 'U', 'U', 'U', 'C', 'U', 'A', 'A', 'A',
'C', 'U', 'G', 'U', 'A', 'G', 'A', 'A', 'A', 'U', 'G', 'C', 'C', 'C', 'U',
'C', 'C', 'U', 'C', 'U', 'U', 'G', 'U', 'C', 'G', 'G', 'U', 'A', 'C', 'A',
'C', 'A', 'G', 'G', 'A', 'A', 'U', 'C', 'C', 'G', 'A', 'C', 'C', 'U', 'C',
'C', 'C', 'G', 'G', 'G', 'G', 'A', 'G', 'U', 'G', 'A', 'C', 'U', 'G', 'A',
'A', 'U', 'A', 'A', 'A', 'C', 'U', 'U', 'A', 'C', 'U', 'G', 'G', 'C', 'A',
'U', 'A', 'U', 'A', 'G', 'C', 'U', 'G', 'G', 'U', 'U', 'A', 'A', 'G', 'G',
'U', 'G', 'A', 'U', 'G', 'A', 'G', 'A', 'C', 'A', 'C', 'A', 'G', 'G', 'U',
'G', 'G', 'U', 'G', 'C', 'U', 'G', 'C', 'U', 'G', 'C', 'G', 'A', 'A', 'A',
'G', 'C', 'A', 'G', 'A', 'A', 'U', 'C', 'G', 'A', 'C', 'U', 'U', 'A', 'C',
'C', 'A', 'G', 'U', 'C', 'G', 'G', 'G', 'U', 'C', 'U', 'C', 'A', 'G', 'G',
'C', 'A', 'G', 'A', 'G', 'G', 'A', 'G', 'U', 'U', 'U', 'U', 'U', 'C', 'U',
'A', 'A', 'A', 'C', 'U', 'G', 'U', 'A', 'G', 'A', 'A', 'A', 'U', 'G', 'C',
'C', 'C', 'U', 'C', 'C', 'U', 'C', 'U', 'U', 'G', 'U', 'C', 'G', 'G', 'U',
'A', 'C', 'A', 'C', 'A', 'G', 'G', 'A', 'A', 'U', 'C', 'C', 'G', 'A', 'C',
'C', 'U', 'C', 'C', 'C', 'G', 'G', 'G', 'G', 'A', 'G', 'U', 'G', 'A', 'C',
'U', 'G', 'A', 'A', 'U', 'A', 'A', 'A', 'C', 'U', 'U', 'A', 'C', 'U', 'G',
'G', 'C', 'A', 'U', 'A', 'U', 'A', 'G', 'C', 'U', 'G', 'G', 'U', 'U', 'A',
'A', 'G', 'G', 'U', 'G', 'A', 'U', 'G', 'A', 'G', 'A', 'C', 'A', 'C', 'A',
'G', 'G', 'U', 'G', 'G', 'U', 'G', 'C', 'U', 'G', 'C', 'U', 'G', 'C', 'G',
'A', 'A', 'A', 'G', 'C', 'A', 'G', 'A', 'A', 'U', 'C', 'G', 'A', 'C', 'U',
'U', 'A', 'C', 'C', 'A', 'G', 'U', 'C', 'G', 'G', 'G', 'U', 'C', 'U', 'C',
'A', 'G', 'G', 'C', 'A', 'G', 'A', 'G', 'G', 'A', 'G', 'U', 'U', 'U', 'U',
'U', 'C', 'U', 'A', 'A', 'A', 'C', 'U', 'G', 'U', 'A', 'G', 'A', 'A', 'A',
'U', 'G', 'C', 'C', 'C', 'U', 'C', 'C', 'U', 'C', 'U', 'U', 'G', 'U', 'C',
'G', 'G', 'U', 'A', 'C', 'A', 'C', 'A', 'G', 'G', 'A', 'A', 'U', 'C', 'C',
'G', 'A', 'C', 'C', 'U', 'C', 'C', 'C', 'G', 'G', 'G', 'G', 'A', 'G', 'U',
'G', 'A', 'C', 'U', 'G', 'A', 'A', 'U', 'A', 'A', 'A', 'C', 'U', 'U', 'A',
'C', 'U', 'G', 'G', 'C', 'A', 'U', 'A', 'U', 'A', 'G', 'C', 'U', 'G', 'G',
'U', 'U', 'A', 'A', 'G', 'G', 'U', 'G', 'A', 'U', 'G', 'A', 'G', 'A', 'C',
'A', 'C', 'A', 'G', 'G', 'U', 'G', 'G', 'U', 'G', 'C', 'U', 'G', 'C', 'U',
'G', 'C', 'G', 'A', 'A', 'A', 'G', 'C', 'A', 'G', 'A', 'A', 'U', 'C', 'G',
'A', 'C', 'U', 'U', 'A', 'C', 'C', 'A', 'G', 'U', 'C', 'G', 'G', 'G', 'U',
'C', 'U', 'C', 'A', 'G', 'G', 'C', 'A', 'G', 'A', 'G', 'G', 'A', 'G', 'U',
'U', 'U', 'U', 'U', 'C', 'U', 'A', 'A', 'A', 'C', 'U', 'G', 'U', 'A', 'G',
'A', 'A', 'A', 'U', 'G', 'C', 'C', 'C', 'U', 'C', 'C', 'U', 'C', 'U', 'U',
'G', 'U', 'C', 'G', 'G', 'U', 'A', 'C', 'A', 'C', 'A', 'G', 'G', 'A', 'A',
'U', 'C', 'C', 'G', 'A', 'C', 'C', 'U', 'C', 'C', 'C', 'G']
Chain information for manA_V4_D4_SS_run_01_ALL.trc #1
---
Chain | Description
A B C D | No description available
> style stick
Changed 3360 atom styles
CreatePDBfile()
All atom = True
dir name:
C:/x/publikacje/1000RNAs/manA/Tetramer_SimRNACry1/Variant_4_based/trc_file/manA_V4_D4_SS_run_01_ALL_pdb_frames
file_path:
C:/x/publikacje/1000RNAs/manA/Tetramer_SimRNACry1/Variant_4_based/trc_file/manA_V4_D4_SS_run_01_ALL_pdb_frames/allatom.pdb
===== Initiating TRC2PDB: =====
this_file_path: C:\Users\iamb\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\trc_read
DIR NAME: C:\Users\iamb\AppData\Local\UCSF\ChimeraX\1.5\site-packages\chimerax
FILES IN DIR =
['bond_data.py', 'coord_data.py', 'data', 'Frames_to_atom_coords.py',
'frame_data.py', 'frame_to_pdb_writer.py', 'libgcc_s_seh-1.dll',
'libstdc++-6.dll', 'main.py', 'pdb_data.py', 'tool.py', 'trc2pdb',
'trc2pdb.exe', 'TRC2PDB.py', 'TRC2TXT.py', '__init__.py', '__pycache__']
trc2pdb located
Moving forward.
Command =
C:\Users\iamb\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\trc_read\trc2pdb.exe
C:/x/publikacje/1000RNAs/manA/Tetramer_SimRNACry1/Variant_4_based/trc_file/manA_V4_D4_SS_run_01_01-000001.pdb
C:/x/publikacje/1000RNAs/manA/Tetramer_SimRNACry1/Variant_4_based/trc_file/manA_V4_D4_SS_run_01_ALL.trc
C:/x/publikacje/1000RNAs/manA/Tetramer_SimRNACry1/Variant_4_based/trc_file/manA_V4_D4_SS_run_01_01.hdr
/x/publikacje/1000RNAs/manA/Tetramer_SimRNACry1/Variant_4_based/trc_file/allatom.pdb
1072 AA
this_file_path.strip()[:-11]
C:\Users\iamb\AppData\Local\UCSF\ChimeraX\1.5\site-packages\chimerax\trc_read
TRC2PDB process DONE.
> open
> C:/x/publikacje/1000RNAs/manA/Tetramer_SimRNACry1/Variant_4_based/trc_file/manA_V4_D4_SS_run_01_ALL-001072_AA.pdb
Chain information for manA_V4_D4_SS_run_01_ALL-001072_AA.pdb #2
---
Chain | Description
A B C D | No description available
Filename None
Traceback (most recent call last):
File "C:\x\BioTools\ChimeraX1.5\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\x\BioTools\ChimeraX1.5\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\x\BioTools\ChimeraX1.5\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1289, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Users\iamb\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\save_c20\\__init__.py", line 32, in run_provider
alligned_save.save_align(session)
File "C:\Users\iamb\AppData\Local\UCSF\ChimeraX\1.5\site-
packages\chimerax\save_c20\alligned_save.py", line 20, in save_align
save_pdb(session, filename, selected_only=selected_only, **kw)
File "C:\x\BioTools\ChimeraX1.5\bin\lib\site-packages\chimerax\pdb\pdb.py",
line 180, in save_pdb
file_per_model = "[NAME]" in output or "[ID]" in output
TypeError: argument of type 'NoneType' is not iterable
TypeError: argument of type 'NoneType' is not iterable
File "C:\x\BioTools\ChimeraX1.5\bin\lib\site-packages\chimerax\pdb\pdb.py",
line 180, in save_pdb
file_per_model = "[NAME]" in output or "[ID]" in output
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 31.0.101.2121
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: LENOVO
Model: 20KH006MPB
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 17,022,533,632
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.5
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
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-SaveC20: 1.1
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: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-TRC-read: 1.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
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
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.11.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → save_pdb() call fails |
comment:2 by , 2 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | accepted → closed |
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Hi Dominik,
--Eric