Opened 4 years ago

Closed 4 years ago

#5598 closed defect (duplicate)

Alphafold search blast results: 'NoneType' object has no attribute 'split'

Reported by: shabir.najmudin@… Owned by: Zach Pearson
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.5.8-1.el8.elrepo.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.3rc202111090815 (2021-11-09 08:15:14 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3rc202111090815 (2021-11-09)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> select #1/A,B,C,D,E,F

Nothing selected  

> toolshed show

Downloading bundle ChimeraX_Phenix-0.3-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/shabir/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/shabir/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/ChimeraX-
Phenix  
sysconfig: /home/shabir/.local/include/python3.9/ChimeraX-Phenix  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/bin  
sysconfig: /home/shabir/.local/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX  
sysconfig: /home/shabir/.local  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /home/shabir/.local/include/python3.9/UNKNOWN  
WARNING: You are using pip version 21.2.4; however, version 21.3.1 is
available.  
You should consider upgrading via the '/usr/bin/chimerax -m pip install
--upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing ./Downloads/ChimeraX_Phenix-0.3-py3-none-any.whl  
Requirement already satisfied: ChimeraX-Core>=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Phenix==0.3)
(1.3rc202111090815)  
Requirement already satisfied: ChimeraX-Atomic>=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Phenix==0.3) (1.30.2)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.4)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (1.1)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (1.0)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.0.2)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.6.5)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (2.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (1.1)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=4.0 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (4.1.5)  
Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
ConnectStructure~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.0)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.2.2)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.7)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.0.2)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.5)  
Requirement already satisfied: ChimeraX-IO~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-
DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (1.0.1)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.0)  
Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.13.7)  
Requirement already satisfied: ChimeraX-Map~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.1)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (2.0)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (1.6)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.0)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (2.1)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (1.1)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-MapSeries~=2.0->ChimeraX-
Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (2.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (2.0)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic>=1.0->ChimeraX-
Phenix==0.3) (1.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (1.0)  
Installing collected packages: ChimeraX-Phenix  
Successfully installed ChimeraX-Phenix-0.3  
\---  

Successfully installed ChimeraX-Phenix-0.3  
Installed ChimeraX-Phenix (0.3)  
Downloading bundle SEQCROW-1.3-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/shabir/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/shabir/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/Send2Trash  
sysconfig: /home/shabir/.local/include/python3.9/Send2Trash  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/bin  
sysconfig: /home/shabir/.local/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX  
sysconfig: /home/shabir/.local  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/SEQCROW  
sysconfig: /home/shabir/.local/include/python3.9/SEQCROW  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /home/shabir/.local/include/python3.9/UNKNOWN  
WARNING: You are using pip version 21.2.4; however, version 21.3.1 is
available.  
You should consider upgrading via the '/usr/bin/chimerax -m pip install
--upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing ./Downloads/SEQCROW-1.3-py3-none-any.whl  
Requirement already satisfied: psutil in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from SEQCROW==1.3) (5.8.0)  
Requirement already satisfied: scipy in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from SEQCROW==1.3) (1.7.1)  
Collecting Send2Trash  
Using cached Send2Trash-1.8.0-py3-none-any.whl (18 kB)  
Requirement already satisfied: ChimeraX-Core<=1.3,>=1.2 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from SEQCROW==1.3) (1.3rc202111090815)  
Requirement already satisfied: numpy<1.23.0,>=1.16.5 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from scipy->SEQCROW==1.3) (1.21.2)  
Installing collected packages: Send2Trash, SEQCROW  
Successfully installed SEQCROW-1.3 Send2Trash-1.8.0  
\---  

Successfully installed SEQCROW-1.3 Send2Trash-1.8.0  
Installed SEQCROW (1.3)  
Downloading bundle MolecularDynamicsViewer-1.2-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/shabir/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/shabir/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils:
/home/shabir/.local/share/ChimeraX/include/python3.9/MolecularDynamicsViewer  
sysconfig: /home/shabir/.local/include/python3.9/MolecularDynamicsViewer  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/bin  
sysconfig: /home/shabir/.local/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX  
sysconfig: /home/shabir/.local  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /home/shabir/.local/include/python3.9/UNKNOWN  
WARNING: You are using pip version 21.2.4; however, version 21.3.1 is
available.  
You should consider upgrading via the '/usr/bin/chimerax -m pip install
--upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing ./Downloads/MolecularDynamicsViewer-1.2-py3-none-any.whl  
Requirement already satisfied: ChimeraX-Core>=1.2 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from MolecularDynamicsViewer==1.2)
(1.3rc202111090815)  
Installing collected packages: MolecularDynamicsViewer  
Successfully installed MolecularDynamicsViewer-1.2  
\---  

Successfully installed MolecularDynamicsViewer-1.2  
Installed MolecularDynamicsViewer (1.2)  
Downloading bundle ChimeraX_TestManager-0.3-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/shabir/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/shabir/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/typing-
extensions  
sysconfig: /home/shabir/.local/include/python3.9/typing-extensions  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/bin  
sysconfig: /home/shabir/.local/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX  
sysconfig: /home/shabir/.local  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/toml  
sysconfig: /home/shabir/.local/include/python3.9/toml  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/pyflakes  
sysconfig: /home/shabir/.local/include/python3.9/pyflakes  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/pycodestyle  
sysconfig: /home/shabir/.local/include/python3.9/pycodestyle  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/mypy-
extensions  
sysconfig: /home/shabir/.local/include/python3.9/mypy-extensions  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/mccabe  
sysconfig: /home/shabir/.local/include/python3.9/mccabe  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/pydocstyle  
sysconfig: /home/shabir/.local/include/python3.9/pydocstyle  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/mypy  
sysconfig: /home/shabir/.local/include/python3.9/mypy  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/flake8  
sysconfig: /home/shabir/.local/include/python3.9/flake8  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/ChimeraX-
TestManager  
sysconfig: /home/shabir/.local/include/python3.9/ChimeraX-TestManager  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /home/shabir/.local/include/python3.9/UNKNOWN  
WARNING: You are using pip version 21.2.4; however, version 21.3.1 is
available.  
You should consider upgrading via the '/usr/bin/chimerax -m pip install
--upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing ./Downloads/ChimeraX_TestManager-0.3-py3-none-any.whl  
Collecting pydocstyle  
Downloading pydocstyle-6.1.1-py3-none-any.whl (37 kB)  
Requirement already satisfied: ChimeraX-Core>=1.1 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-TestManager==0.3)
(1.3rc202111090815)  
Collecting flake8  
Downloading flake8-4.0.1-py2.py3-none-any.whl (64 kB)  
Collecting mypy  
Downloading mypy-0.910-cp39-cp39-manylinux2010_x86_64.whl (23.2 MB)  
Collecting pyflakes  
Downloading pyflakes-2.4.0-py2.py3-none-any.whl (69 kB)  
Collecting mccabe<0.7.0,>=0.6.0  
Downloading mccabe-0.6.1-py2.py3-none-any.whl (8.6 kB)  
Collecting pycodestyle<2.9.0,>=2.8.0  
Downloading pycodestyle-2.8.0-py2.py3-none-any.whl (42 kB)  
Collecting mypy-extensions<0.5.0,>=0.4.3  
Downloading mypy_extensions-0.4.3-py2.py3-none-any.whl (4.5 kB)  
Collecting typing-extensions>=3.7.4  
Downloading typing_extensions-3.10.0.2-py3-none-any.whl (26 kB)  
Collecting toml  
Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB)  
Requirement already satisfied: snowballstemmer in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from pydocstyle->ChimeraX-
TestManager==0.3) (2.1.0)  
Installing collected packages: typing-extensions, toml, pyflakes, pycodestyle,
mypy-extensions, mccabe, pydocstyle, mypy, flake8, ChimeraX-TestManager  
Successfully installed ChimeraX-TestManager-0.3 flake8-4.0.1 mccabe-0.6.1
mypy-0.910 mypy-extensions-0.4.3 pycodestyle-2.8.0 pydocstyle-6.1.1
pyflakes-2.4.0 toml-0.10.2 typing-extensions-3.10.0.2  
\---  

Successfully installed ChimeraX-TestManager-0.3 flake8-4.0.1 mccabe-0.6.1
mypy-0.910 mypy-extensions-0.4.3 pycodestyle-2.8.0 pydocstyle-6.1.1
pyflakes-2.4.0 toml-0.10.2 typing-extensions-3.10.0.2  
Installed ChimeraX-TestManager (0.3)  
Downloading bundle ChimeraX_Maestro-1.8.1-py3-none-any.whl  
Bundle installation canceled  
Downloading bundle ChimeraX_PDBImages-1.1-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
WARNING: Value for scheme.platlib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/shabir/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.purelib does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/shabir/.local/lib/python3.9/site-packages  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/ChimeraX-
PDBImages  
sysconfig: /home/shabir/.local/include/python3.9/ChimeraX-PDBImages  
WARNING: Value for scheme.scripts does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/bin  
sysconfig: /home/shabir/.local/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX  
sysconfig: /home/shabir/.local  
WARNING: Additional context:  
user = True  
home = None  
root = None  
prefix = None  
WARNING: Value for scheme.headers does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/shabir/.local/share/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /home/shabir/.local/include/python3.9/UNKNOWN  
WARNING: You are using pip version 21.2.4; however, version 21.3.1 is
available.  
You should consider upgrading via the '/usr/bin/chimerax -m pip install
--upgrade pip' command.  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing ./Downloads/ChimeraX_PDBImages-1.1-py3-none-any.whl  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-PDBImages==1.1) (1.6)  
Requirement already satisfied: ChimeraX-Core~=1.0rc1 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-PDBImages==1.1)
(1.3rc202111090815)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.1) (2.4)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.1) (2.0)  
Requirement already satisfied: ChimeraX-Atomic~=1.17 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.1) (1.30.2)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.1) (1.1)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.1) (1.1)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.1) (2.0)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.17->ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.1) (2.0.2)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=4.0 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
Atomic~=1.17->ChimeraX-StdCommands~=1.0->ChimeraX-PDBImages==1.1) (4.1.5)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.17->ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.1) (2.6.5)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Atomic~=1.17->ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.1) (1.0)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
Atomic~=1.17->ChimeraX-StdCommands~=1.0->ChimeraX-PDBImages==1.1) (2.0)  
Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
ConnectStructure~=2.0->ChimeraX-Atomic~=1.17->ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.1) (1.0)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-MapFit~=2.0->ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.1) (2.0)  
Requirement already satisfied: ChimeraX-Map~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-MapFit~=2.0->ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.1) (1.1)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
MapFit~=2.0->ChimeraX-StdCommands~=1.0->ChimeraX-PDBImages==1.1) (1.7)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
MapFit~=2.0->ChimeraX-StdCommands~=1.0->ChimeraX-PDBImages==1.1) (1.5)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
MapFit~=2.0->ChimeraX-StdCommands~=1.0->ChimeraX-PDBImages==1.1) (2.1)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
MapFit~=2.0->ChimeraX-StdCommands~=1.0->ChimeraX-PDBImages==1.1) (1.1)  
Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
MapFit~=2.0->ChimeraX-StdCommands~=1.0->ChimeraX-PDBImages==1.1) (1.13.7)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Map~=1.0->ChimeraX-
MapFit~=2.0->ChimeraX-StdCommands~=1.0->ChimeraX-PDBImages==1.1) (2.0)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-MapData~=2.0->ChimeraX-
MapFit~=2.0->ChimeraX-StdCommands~=1.0->ChimeraX-PDBImages==1.1) (1.2.2)  
Requirement already satisfied: ChimeraX-IO~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-
DataFormats~=1.0->ChimeraX-MapData~=2.0->ChimeraX-MapFit~=2.0->ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.1) (1.0.1)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-mmCIF~=2.0->ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.1) (1.0.2)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.17->ChimeraX-StdCommands~=1.0->ChimeraX-
PDBImages==1.1) (1.0)  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
UI~=1.0->ChimeraX-Map~=1.0->ChimeraX-MapFit~=2.0->ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.1) (1.0)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-Map~=1.0->ChimeraX-
MapFit~=2.0->ChimeraX-StdCommands~=1.0->ChimeraX-PDBImages==1.1) (1.0)  
Installing collected packages: ChimeraX-PDBImages  
Successfully installed ChimeraX-PDBImages-1.1  
\---  

Successfully installed ChimeraX-PDBImages-1.1  
Installed ChimeraX-PDBImages (1.1)  

> ui tool show AlphaFold

> alphafold search
> MVSRFLIAEYRHLIENPSENFKISVNENNITEWDVILRGPPDTLYEGGLFKAKVAFPPEYPYAPPKLTFTSEMWHPNIYPDGRLCISILHGDNAEEQGMTWSPAQKIDTILLSVISLLNEPNPDSPANVDAAKSYRKYVYKEDLESYPMEVKKTVKKSLDECSPEDIEYFKNAASNVPPIPSDAYEDECEEMEDDTYILTYDDDEEEEDEEMDDE

ChimeraX REST job id: job_wsu32yiv  
BlastProtein finished.  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 676, in customEvent  
func(*args, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/blastprotein/job.py", line 72, in on_finish  
BlastProteinResults.from_job(  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 83, in from_job  
return cls(  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 79, in __init__  
self._build_ui()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 197, in _build_ui  
param_str = self._format_param_str()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 174, in _format_param_str  
model_no = int(values[0].split('/')[0][1:])  
AttributeError: 'NoneType' object has no attribute 'split'  
  
AttributeError: 'NoneType' object has no attribute 'split'  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 174, in _format_param_str  
model_no = int(values[0].split('/')[0][1:])  
  
See log for complete Python traceback.  
  

> alphafold match
> MVSRFLIAEYRHLIENPSENFKISVNENNITEWDVILRGPPDTLYEGGLFKAKVAFPPEYPYAPPKLTFTSEMWHPNIYPDGRLCISILHGDNAEEQGMTWSPAQKIDTILLSVISLLNEPNPDSPANVDAAKSYRKYVYKEDLESYPMEVKKTVKKSLDECSPEDIEYFKNAASNVPPIPSDAYEDECEEMEDDTYILTYDDDEEEEDEEMDDE

Fetching compressed AlphaFold C6T1V1 from
https://alphafold.ebi.ac.uk/files/AF-C6T1V1-F1-model_v1.cif  
1 AlphaFold model found using sequence similarity searches: C6T1V1 (1
sequences)  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
C6T1V1_SOYBN | MVSRF...EMDDE | 41.6 | 57.2  
Opened 1 AlphaFold model  

> alphafold predict
> MVSRFLIAEYRHLIENPSENFKISVNENNITEWDVILRGPPDTLYEGGLFKAKVAFPPEYPYAPPKLTFTSEMWHPNIYPDGRLCISILHGDNAEEQGMTWSPAQKIDTILLSVISLLNEPNPDSPANVDAAKSYRKYVYKEDLESYPMEVKKTVKKSLDECSPEDIEYFKNAASNVPPIPSDAYEDECEEMEDDTYILTYDDDEEEEDEEMDDE

Running AlphaFold prediction  
[Repeated 5 time(s)]

> alphafold predict
> MVSRFLIAEYRHLIENPSENFKISVNENNITEWDVILRGPPDTLYEGGLFKAKVAFPPEYPYAPPKLTFTSEMWHPNIYPDGRLCISILHGDNAEEQGMTWSPAQKIDTILLSVISLLNEPNPDSPANVDAAKSYRKYVYKEDLESYPMEVKKTVKKSLDECSPEDIEYFKNAASNVPPIPSDAYEDECEEMEDDTYILTYDDDEEEEDEEMDDE

Running AlphaFold prediction  

> alphafold predict
> MVSRFLIAEYRHLIENPSENFKISVNENNITEWDVILRGPPDTLYEGGLFKAKVAFPPEYPYAPPKLTFTSEMWHPNIYPDGRLCISILHGDNAEEQGMTWSPAQKIDTILLSVISLLNEPNPDSPANVDAAKSYRKYVYKEDLESYPMEVKKTVKKSLDECSPEDIEYFKNAASNVPPIPSDAYEDECEEMEDDTYILTYDDDEEEEDEEMDDE

Running AlphaFold prediction  
| Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
  
AlphaFold prediction finished  
Results in /home/shabir/Downloads/ChimeraX/AlphaFold/prediction_1  

> save /home/shabir/ASFV_E2.cxs

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 283, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 142, in take_snapshot  
, 'table_session': self.table.session_info()  
AttributeError: 'BlastProteinResults' object has no attribute 'table'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 286, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff229826d30> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7ff1eca5a880>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save  
mgr.discovery(self._state_containers)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff229826d30> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x7ff1eca5a880>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff229826d30> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7ff1eca5a880>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 283, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 142, in take_snapshot  
, 'table_session': self.table.session_info()  
AttributeError: 'BlastProteinResults' object has no attribute 'table'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 286, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff229826d30> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7ff1eca5a880>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save  
mgr.discovery(self._state_containers)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff229826d30> -> <chimerax.blastprotein.ui.results.BlastProteinResults
object at 0x7ff1eca5a880>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff229826d30> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at
0x7ff1eca5a880>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> ui tool show AlphaFold

> alphafold match
> MVSRFLIAEYRHLIENPSENFKISVNENNITEWDVILRGPPDTLYEGGLFKAKVAFPPEYPYAPPKLTFTSEMWHPNIYPDGRLCISILHGDNAEEQGMTWSPAQKIDTILLSVISLLNEPNPDSPANVSIIHNYRKYVYKEDLESYPMEVKKTVKKSLDECSPEDIEYFKNAASNVPPIPSDAYEDECEEMEDDTYILTYDDDEEEEDEEMDDE

1 AlphaFold model found using sequence similarity searches: C6T1V1 (1
sequences)  
Sequence Similarity  
---  
AlphaFold Model| Query Sequence| Identity %| Coverage %  
C6T1V1_SOYBN | MVSRF...EMDDE | 39.8 | 55.8  
Opened 1 AlphaFold model  

> alphafold search
> MVSRFLIAEYRHLIENPSENFKISVNENNITEWDVILRGPPDTLYEGGLFKAKVAFPPEYPYAPPKLTFTSEMWHPNIYPDGRLCISILHGDNAEEQGMTWSPAQKIDTILLSVISLLNEPNPDSPANVSIIHNYRKYVYKEDLESYPMEVKKTVKKSLDECSPEDIEYFKNAASNVPPIPSDAYEDECEEMEDDTYILTYDDDEEEEDEEMDDE

ChimeraX REST job id: job_vc8ewq54  
BlastProtein finished.  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 676, in customEvent  
func(*args, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/blastprotein/job.py", line 72, in on_finish  
BlastProteinResults.from_job(  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 83, in from_job  
return cls(  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 79, in __init__  
self._build_ui()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 197, in _build_ui  
param_str = self._format_param_str()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 174, in _format_param_str  
model_no = int(values[0].split('/')[0][1:])  
AttributeError: 'NoneType' object has no attribute 'split'  
  
AttributeError: 'NoneType' object has no attribute 'split'  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 174, in _format_param_str  
model_no = int(values[0].split('/')[0][1:])  
  
See log for complete Python traceback.  
  

> alphafold predict
> MVSRFLIAEYRHLIENPSENFKISVNENNITEWDVILRGPPDTLYEGGLFKAKVAFPPEYPYAPPKLTFTSEMWHPNIYPDGRLCISILHGDNAEEQGMTWSPAQKIDTILLSVISLLNEPNPDSPANVSIIHNYRKYVYKEDLESYPMEVKKTVKKSLDECSPEDIEYFKNAASNVPPIPSDAYEDECEEMEDDTYILTYDDDEEEEDEEMDDE

Running AlphaFold prediction  




OpenGL version: 3.3.0 NVIDIA 440.64
OpenGL renderer: GeForce RTX 2080 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: CentOS Linux 8 
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 AMD Ryzen 9 3950X 16-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           78Gi       8.6Gi       810Mi       191Mi        69Gi        68Gi
	Swap:         7.9Gi        24Mi       7.8Gi

Graphics:
	09:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104 [GeForce RTX 2080 SUPER] [10de:1e81] (rev a1)	
	Subsystem: eVga.com. Corp. Device [3842:3081]	
	Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.7
    ChimeraX-AddCharge: 1.1.5
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.2
    ChimeraX-AtomicLibrary: 4.1.5
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3rc202111090815
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 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: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-TestManager: 0.3
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    flake8: 4.0.1
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.5.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    mccabe: 0.6.1
    MolecularDynamicsViewer: 1.2
    msgpack: 1.0.2
    mypy: 0.910
    mypy-extensions: 0.4.3
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.2
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.22
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycodestyle: 2.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    pydocstyle: 6.1.1
    pyflakes: 2.4.0
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    Send2Trash: 1.8.0
    SEQCROW: 1.3
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    toml: 0.10.2
    tornado: 6.1
    traitlets: 5.1.1
    typing-extensions: 3.10.0.2
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 4 years ago

Cc: Tom Goddard added
Component: Unassigned → Structure Prediction
Owner: set to Zach Pearson
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Alphafold search blast results: 'NoneType' object has no attribute 'split'

comment:2 by pett, 4 years ago

Resolution: → duplicate
Status: assigned → closed
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