ISOLDE downloaded but not installed

[satyshur@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.45.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)I tried to install isolde and clipper and it does not install. When I install phenix, it indicates that it is installed. But Isolde and clipper are the "isolde is provided by the uninstalled bundle ISOLDE version 1.3" Also I get errors when installing MolecularDynamics. "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/satyshur/.local/share/ChimeraX/1.3/site-packages
sysconfig: /home/satyshur/.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/satyshur/.local/share/ChimeraX/1.3/site-packages
sysconfig: /home/satyshur/.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/satyshur/.local/share/ChimeraX/include/python3.9/MolecularDynamicsViewer
sysconfig: /home/satyshur/.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/satyshur/.local/share/ChimeraX/bin
sysconfig: /home/satyshur/.local/bin
WARNING: Value for scheme.data does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
distutils: /home/satyshur/.local/share/ChimeraX
sysconfig: /home/satyshur/.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/satyshur/.local/share/ChimeraX/include/python3.9/UNKNOWN
sysconfig: /home/satyshur/.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 /home/satyshur/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) (1.3)
Installing collected packages: MolecularDynamicsViewer
Successfully installed MolecularDynamicsViewer-1.2
---
Successfully installed MolecularDynamicsViewer-1.2
Installed MolecularDynamicsViewer (1.2)
toolshed showDownloading 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/satyshur/.local/share/ChimeraX/1.3/site-packages
sysconfig: /home/satyshur/.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/satyshur/.local/share/ChimeraX/1.3/site-packages
sysconfig: /home/satyshur/.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/satyshur/.local/share/ChimeraX/include/python3.9/ChimeraX-Phenix
sysconfig: /home/satyshur/.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/satyshur/.local/share/ChimeraX/bin
sysconfig: /home/satyshur/.local/bin
WARNING: Value for scheme.data does not match. Please report this to <https://github.com/pypa/pip/issues/10151>
distutils: /home/satyshur/.local/share/ChimeraX
sysconfig: /home/satyshur/.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/satyshur/.local/share/ChimeraX/include/python3.9/UNKNOWN
sysconfig: /home/satyshur/.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 /home/satyshur/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) (1.3)
Requirement already satisfied: ChimeraX-Atomic>=1.0 in /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-Phenix==0.3) (1.31)
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-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-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-AtomicLibrary~=4.2 in /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-Atomic>=1.0->ChimeraX-Phenix==0.3) (4.2)
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-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-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-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-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-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-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-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-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-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-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) (1.6.1)
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-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-MapFilter~=2.0 in /usr/libexec/UCSF-C

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> help help:quickstart

[Repeated 1 time(s)]

> open /home/satyshur/projects/keck/PriA-PriB/PriA-PriB-Cryoem/Refine_22/pria-
> prib-DNA-mrc_real_space_refined_022-coot-0.pdb

Chain information for pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
H | No description available  
J | No description available  
Z | No description available  
  

> hide atoms

> show atoms

> style stick

Changed 7181 atom styles  

> show cartoons

> hide cartoons

> show cartoons

> hide atoms

> open /home/satyshur/projects/keck/PriA-PriB/PriA-PriB-
> Cryoem/monomer_sharpened_scale_recentre.mrc

Opened monomer_sharpened_scale_recentre.mrc as #2, grid size 192,192,192,
pixel 1.08, shown at level 0.105, step 1, values float32  

> volume #2 level 0.1622

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset "initial styles" "original look"

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

> preset cartoons/nucleotides ribbons/slabs

Changed 7043 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> ui tool show "Fit in Map"

Opened pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3 as #3, grid
size 93,107,130, pixel 1, shown at level 0.109, step 1, values float32  
Fit map pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3 in map
monomer_sharpened_scale_recentre.mrc using 76530 points  
correlation = 0.7629, correlation about mean = 0.489, overlap = 7439  
steps = 40, shift = 0.0103, angle = 0.0143 degrees  
  
Position of pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3 (#3)
relative to monomer_sharpened_scale_recentre.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999997 -0.00020305 -0.00012422 0.02909626  
0.00020304 0.99999998 -0.00007445 -0.01376822  
0.00012423 0.00007442 0.99999999 -0.01100925  
Axis 0.29846410 -0.49810179 0.81413377  
Axis point 51.68606129 133.61973360 0.00000000  
Rotation angle (degrees) 0.01428942  
Shift along axis 0.00657916  
  
Average map value = 0.2123 for 7181 atoms, 2946 outside contour  
Opened pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 2.5 as #3, grid
size 108,124,153, pixel 0.833, shown at level 0.134, step 1, values float32  
Fit map pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 2.5 in map
monomer_sharpened_scale_recentre.mrc using 98851 points  
correlation = 0.7263, correlation about mean = 0.3428, overlap = 1.376e+04  
steps = 40, shift = 0.0173, angle = 0.0119 degrees  
  
Position of pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 2.5 (#3)
relative to monomer_sharpened_scale_recentre.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999999 -0.00013307 0.00000758 0.01501597  
0.00013307 0.99999999 0.00006928 -0.02351284  
-0.00000759 -0.00006928 1.00000000 0.00132225  
Axis -0.46121735 0.05052105 0.88584772  
Axis point 174.07206067 88.77170472 0.00000000  
Rotation angle (degrees) 0.00860661  
Shift along axis -0.00694220  
  
Average map value = 0.2123 for 7181 atoms, 2949 outside contour  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/map_fit/fitgui.py", line 395, in _fit  
smap = self._simulated_map()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/map_fit/fitgui.py", line 342, in _simulated_map  
res = self._simulate_resolution.value  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
ValueError: could not convert string to float: '3,5'  
  
ValueError: could not convert string to float: '3,5'  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 185, in _get_value  
return self.string_to_value(self._line_edit.text())  
  
See log for complete Python traceback.  
  
Opened pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3.5 as #3, grid
size 83,94,114, pixel 1.17, shown at level 0.0988, step 1, values float32  
Opened pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 5 as #3, grid
size 63,71,86, pixel 1.67, shown at level 0.0951, step 1, values float32  
Fit map pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 5 in map
monomer_sharpened_scale_recentre.mrc using 27999 points  
correlation = 0.6864, correlation about mean = 0.7259, overlap = 1110  
steps = 28, shift = 0.0222, angle = 0.00893 degrees  
  
Position of pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 5 (#3)
relative to monomer_sharpened_scale_recentre.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999997 -0.00025504 0.00001500 0.01181247  
0.00025504 0.99999997 -0.00002757 -0.03069470  
-0.00001499 0.00002758 1.00000000 0.00823601  
Axis 0.10731535 0.05836722 0.99251029  
Axis point 122.10999983 43.08185306 0.00000000  
Rotation angle (degrees) 0.01472284  
Shift along axis 0.00765042  
  
Average map value = 0.2123 for 7181 atoms, 2944 outside contour  
Opened pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 2.8 as #3, grid
size 99,113,138, pixel 0.933, shown at level 0.117, step 1, values float32  
Fit map pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 2.8 in map
monomer_sharpened_scale_recentre.mrc using 84772 points  
correlation = 0.7503, correlation about mean = 0.4325, overlap = 9418  
steps = 36, shift = 0.0135, angle = 0.00999 degrees  
  
Position of pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 2.8 (#3)
relative to monomer_sharpened_scale_recentre.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999994 -0.00031548 -0.00012086 0.03944060  
0.00031549 0.99999995 0.00006338 -0.04734375  
0.00012084 -0.00006342 0.99999999 -0.00785517  
Axis -0.18444238 -0.35157987 0.91780859  
Axis point 147.67666536 126.25355315 0.00000000  
Rotation angle (degrees) 0.01969477  
Shift along axis 0.00216105  
  
Average map value = 0.2123 for 7181 atoms, 2941 outside contour  
Opened pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3 as #3, grid
size 93,107,130, pixel 1, shown at level 0.109, step 1, values float32  
Fit map pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3 in map
monomer_sharpened_scale_recentre.mrc using 76530 points  
correlation = 0.7629, correlation about mean = 0.4889, overlap = 7438  
steps = 44, shift = 0.00619, angle = 0.00695 degrees  
  
Position of pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3 (#3)
relative to monomer_sharpened_scale_recentre.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999993 -0.00033388 -0.00019395 0.04281279  
0.00033387 0.99999994 -0.00003162 -0.04023553  
0.00019396 0.00003155 0.99999998 -0.02466680  
Axis 0.08153138 -0.50064881 0.86180241  
Axis point 116.97026690 127.62301105 0.00000000  
Rotation angle (degrees) 0.02219712  
Shift along axis 0.00237655  
  
Average map value = 0.2123 for 7181 atoms, 2937 outside contour  
Opened pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3.2 as #3, grid
size 89,101,123, pixel 1.07, shown at level 0.104, step 1, values float32  
Fit map pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3.2 in map
monomer_sharpened_scale_recentre.mrc using 68896 points  
correlation = 0.7668, correlation about mean = 0.5396, overlap = 6137  
steps = 44, shift = 0.0257, angle = 0.0252 degrees  
  
Position of pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3.2 (#3)
relative to monomer_sharpened_scale_recentre.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000000 0.00003272 -0.00005647 0.01646588  
-0.00003271 0.99999999 0.00016837 -0.01836833  
0.00005648 -0.00016837 0.99999998 0.01318036  
Axis -0.93240034 -0.31274829 -0.18115770  
Axis point 0.00000000 65.36472329 131.38544755  
Rotation angle (degrees) 0.01034606  
Shift along axis -0.01199585  
  
Average map value = 0.2123 for 7181 atoms, 2952 outside contour  
Opened pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3.5 as #3, grid
size 83,94,114, pixel 1.17, shown at level 0.0988, step 1, values float32  
Fit map pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3.5 in map
monomer_sharpened_scale_recentre.mrc using 59058 points  
correlation = 0.7759, correlation about mean = 0.6004, overlap = 4326  
steps = 40, shift = 0.0101, angle = 0.0199 degrees  
  
Position of pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3.5 (#3)
relative to monomer_sharpened_scale_recentre.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999998 -0.00020264 0.00006035 0.01810733  
0.00020264 0.99999998 -0.00005945 -0.02049787  
-0.00006034 0.00005946 1.00000000 0.00209458  
Axis 0.27071916 0.27474818 0.92261833  
Axis point 102.79502022 87.74098552 0.00000000  
Rotation angle (degrees) 0.01258403  
Shift along axis 0.00120275  
  
Average map value = 0.2123 for 7181 atoms, 2948 outside contour  
Opened pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3.9 as #3, grid
size 76,86,105, pixel 1.3, shown at level 0.0954, step 1, values float32  
Fit map pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3.9 in map
monomer_sharpened_scale_recentre.mrc using 48080 points  
correlation = 0.7673, correlation about mean = 0.6607, overlap = 2904  
steps = 44, shift = 0.0098, angle = 0.00557 degrees  
  
Position of pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3.9 (#3)
relative to monomer_sharpened_scale_recentre.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999996 -0.00027562 0.00008719 0.01709753  
0.00027563 0.99999996 -0.00011768 -0.01583312  
-0.00008715 0.00011770 0.99999999 0.00424536  
Axis 0.37706745 0.27928388 0.88307455  
Axis point 63.30350137 54.12494057 0.00000000  
Rotation angle (degrees) 0.01788291  
Shift along axis 0.00577396  
  
Average map value = 0.2123 for 7181 atoms, 2949 outside contour  
Opened pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3.5 as #3, grid
size 83,94,114, pixel 1.17, shown at level 0.0988, step 1, values float32  
Fit map pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3.5 in map
monomer_sharpened_scale_recentre.mrc using 59058 points  
correlation = 0.7758, correlation about mean = 0.6004, overlap = 4326  
steps = 36, shift = 0.00685, angle = 0.00607 degrees  
  
Position of pria-prib-DNA-mrc_real_space_refined_022-coot-0.pdb map 3.5 (#3)
relative to monomer_sharpened_scale_recentre.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999997 -0.00025838 -0.00001707 0.02365314  
0.00025837 0.99999996 -0.00011081 -0.02089134  
0.00001710 0.00011080 0.99999999 -0.00413172  
Axis 0.39341498 -0.06067145 0.91735687  
Axis point 79.27663368 81.20741205 0.00000000  
Rotation angle (degrees) 0.01613745  
Shift along axis 0.00678275  
  
Average map value = 0.2123 for 7181 atoms, 2945 outside contour  

> save /home/satyshur/projects/keck/PriA-PriB/PriA-PriB-
> Cryoem/refn22-original.cxs

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.3-cp39-cp39-manylinux_2_17_x86_64.whl  
[Repeated 1 time(s)]

> open 6mhz

Summary of feedback from opening 6mhz fetched from pdb  
---  
notes | Fetching compressed mmCIF 6mhz from
http://files.rcsb.org/download/6mhz.cif  
Fetching CCD AOV from http://ligand-expo.rcsb.org/reports/A/AOV/AOV.cif  
  
6mhz title:  
Vanadate trapped Cryo-EM Structure of E.coli LptB2FG Transporter [more
info...]  
  
Chain information for 6mhz #4  
---  
Chain | Description | UniProt  
A B | Lipopolysaccharide export system ATP-binding protein LptB | LPTB_ECOLI  
F | Lipopolysaccharide export system permease protein LptF | LPTF_ECOLI  
G | Lipopolysaccharide export system permease protein LptG | LPTG_ECOLI  
  
Non-standard residues in 6mhz #4  
---  
AOV — adp orthovanadate  
  

> open 9118 fromDatabase emdb

Summary of feedback from opening 9118 fetched from emdb  
---  
note | Fetching compressed map 9118 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-9118/map/emd_9118.map.gz  
  
Opened emdb 9118 as #5, grid size 192,192,192, pixel 1.23, shown at level
0.0393, step 1, values float32  

> close #1

> close #2

> close #3

> lighting simple

> set bgColor white

> set silhouettes true

> hide

> cartoon

> color bychain

> color byhetero

> volume #2 level 0.1

No volumes specified  

> volume #5 level 0.1

> select #4/A,G

3620 atoms, 3681 bonds, 8 pseudobonds, 464 residues, 3 models selected  

> view initial #4

> view matrix models
> #1,0.198,-0.674,0.699,86.9,0.821,0.511,0.260,-63.7,-0.534,0.522,0.655,53.6

Invalid "models" argument: No models specified by "#1"  

> view initial #4

> view matrix models
> #4,0.198,-0.674,0.699,86.9,0.821,0.511,0.260,-63.7,-0.534,0.522,0.655,53.6

> fitmap #4/A,G inMap #5

Fit molecule 6mhz (#4) to map emdb 9118 (#5) using 3620 atoms  
average map value = 0.04229, steps = 92  
shifted from previous position = 5.59  
rotated from previous position = 10.6 degrees  
atoms outside contour = 3070, contour level = 0.1  
  
Position of 6mhz (#4) relative to emdb 9118 (#5) coordinates:  
Matrix rotation and translation  
0.20397820 -0.53842290 0.80678158 60.51587984  
0.76323569 0.61057869 0.21678452 -63.39391917  
-0.61177216 0.57024157 0.53603540 70.90289792  
Axis 0.18057178 0.72470126 0.66498264  
Axis point 89.96139317 0.00000000 16.44820834  
Rotation angle (degrees) 79.84552389  
Shift along axis 12.13500315  
  

> isolde start

isolde is provided by the uninstalled bundle ISOLDE version 1.3  

> clipper assoc #5 to #4

clipper is provided by the uninstalled bundle Clipper versions 0.15.0 – 0.17.0  

> set silhouettes false

Falling back to using screens root_visual.  

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.3-cp39-cp39-manylinux_2_17_x86_64.whl  
Downloading bundle ChimeraX_Clipper-0.17.0-cp39-cp39-manylinux_2_17_x86_64.whl  
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/satyshur/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/satyshur/.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/satyshur/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/satyshur/.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/satyshur/.local/share/ChimeraX/include/python3.9/MolecularDynamicsViewer  
sysconfig: /home/satyshur/.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/satyshur/.local/share/ChimeraX/bin  
sysconfig: /home/satyshur/.local/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/satyshur/.local/share/ChimeraX  
sysconfig: /home/satyshur/.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/satyshur/.local/share/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /home/satyshur/.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 /home/satyshur/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) (1.3)  
Installing collected packages: MolecularDynamicsViewer  
Successfully installed MolecularDynamicsViewer-1.2  
\---  

Successfully installed MolecularDynamicsViewer-1.2  
Installed MolecularDynamicsViewer (1.2)  

> 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/satyshur/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/satyshur/.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/satyshur/.local/share/ChimeraX/1.3/site-packages  
sysconfig: /home/satyshur/.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/satyshur/.local/share/ChimeraX/include/python3.9/ChimeraX-
Phenix  
sysconfig: /home/satyshur/.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/satyshur/.local/share/ChimeraX/bin  
sysconfig: /home/satyshur/.local/bin  
WARNING: Value for scheme.data does not match. Please report this to
<https://github.com/pypa/pip/issues/10151>  
distutils: /home/satyshur/.local/share/ChimeraX  
sysconfig: /home/satyshur/.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/satyshur/.local/share/ChimeraX/include/python3.9/UNKNOWN  
sysconfig: /home/satyshur/.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 /home/satyshur/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) (1.3)  
Requirement already satisfied: ChimeraX-Atomic>=1.0 in /usr/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages (from ChimeraX-Phenix==0.3) (1.31)  
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-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-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-AtomicLibrary~=4.2 in
/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages (from ChimeraX-
Atomic>=1.0->ChimeraX-Phenix==0.3) (4.2)  
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-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-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-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-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-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-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-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-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-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-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) (1.6.1)  
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-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-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-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 ChimeraX_Clipper-0.17.0-cp39-cp39-manylinux_2_17_x86_64.whl  




OpenGL version: 3.3.0 NVIDIA 470.74
OpenGL renderer: Quadro K4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision WorkStation T5500
OS: Red Hat Enterprise Linux Workstation 7.9 Maipo
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 Intel(R) Xeon(R) CPU           X5570  @ 2.93GHz
Cache Size: 8192 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            23G        5.1G        1.6G        120M         16G         17G
	Swap:           11G        7.8M         11G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK106GL [Quadro K4000] [10de:11fa] (rev a1)	
	Subsystem: Hewlett-Packard Company Device [103c:079c]	
	Kernel driver in use: nvidia
Locale: ('en_US', '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: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    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: 1.31
    ChimeraX-AtomicLibrary: 4.2
    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: 2.6.1
    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: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    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-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: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    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: 1.6.1
    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-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
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    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
    MolecularDynamicsViewer: 1.2
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    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: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    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
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[pett]

Reported by Ken Satyshur