id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14506 Crash in garbage collection pett@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.2.1-arm64-arm-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in __iter__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/hbond.py"", line 774 in _find_acceptors File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/hbond.py"", line 498 in find_hbonds File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/cmd.py"", line 94 in cmd_hbonds File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File 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All rights reserved. How to cite UCSF ChimeraX > runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc > alias picmovie view orient ; save ""/Users/neyrinck/Google Drive/My > Drive/$1/$2/$2_$3.jpg"" supersample 2 ; movie record ; turn y 2 180 ; wait > 180 ; movie encode ""/Users/neyrinck/Google Drive/My > Drive/$1/$2/$2_$3_rot.mp4"" > alias makepicture close ; set bgColor white ; windowsize 480 480 ;open > ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb"" ; alphafold pae > #1 file ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json"" ; > view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ; > color /A indianred ; color /B royalblue ; alphafold contacts /A to /B > palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius > 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ; > picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key > true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key > true ; picmovie $1 $2 hydrophobic > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults W173 > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W173/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 4 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W173/W173_contacts_hbonds.jpg"" > supersample 2 Cannot save '/Users/neyrinck/Google Drive/My Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W173/W173_contacts_hbonds.jpg': [Errno 70] Stale NFS file handle: '/Users/neyrinck/Google Drive/My Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W173/W173_contacts_hbonds.jpg' > runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc > alias picmovie view orient ; save ""/Users/neyrinck/Google Drive/My > Drive/$1/$2/$2_$3.jpg"" supersample 2 ; movie record ; turn y 2 180 ; wait > 180 ; movie encode ""/Users/neyrinck/Google Drive/My > Drive/$1/$2/$2_$3_rot.mp4"" > alias makepicture close ; set bgColor white ; windowsize 480 480 ;open > ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb"" ; alphafold pae > #1 file ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json"" ; > view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ; > color /A indianred ; color /B royalblue ; alphafold contacts /A to /B > palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius > 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ; > picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key > true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key > true ; picmovie $1 $2 hydrophobic > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults W181 > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 4 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg"" > supersample 2 Cannot save '/Users/neyrinck/Google Drive/My Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg': [Errno 70] Stale NFS file handle: '/Users/neyrinck/Google Drive/My Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg' > runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc > alias picmovie view orient ; save ""/Users/neyrinck/Google Drive/My > Drive/$1/$2/$2_$3.jpg"" supersample 2 ; movie record ; turn y 2 180 ; wait > 180 ; movie encode ""/Users/neyrinck/Google Drive/My > Drive/$1/$2/$2_$3_rot.mp4"" > alias makepicture close ; set bgColor white ; windowsize 480 480 ;open > ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb"" ; alphafold pae > #1 file ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json"" ; > view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ; > color /A indianred ; color /B royalblue ; alphafold contacts /A to /B > palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius > 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ; > picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key > true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key > true ; picmovie $1 $2 hydrophobic > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults W181 > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 4 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg"" > supersample 2 Cannot save '/Users/neyrinck/Google Drive/My Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg': [Errno 70] Stale NFS file handle: '/Users/neyrinck/Google Drive/My Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg' > runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc > alias picmovie view orient ; save ""/Users/neyrinck/Google Drive/My > Drive/$1/$2/$2_$3.jpg"" supersample 2 ; movie record ; turn y 2 180 ; wait > 180 ; movie encode ""/Users/neyrinck/Google Drive/My > Drive/$1/$2/$2_$3_rot.mp4"" > alias makepicture close ; set bgColor white ; windowsize 480 480 ;open > ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb"" ; alphafold pae > #1 file ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json"" ; > view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ; > color /A indianred ; color /B royalblue ; alphafold contacts /A to /B > palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius > 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ; > picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key > true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key > true ; picmovie $1 $2 hydrophobic > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults W181 > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 4 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg"" > supersample 2 Cannot save '/Users/neyrinck/Google Drive/My Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg': [Errno 70] Stale NFS file handle: '/Users/neyrinck/Google Drive/My Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg' > runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc > alias picmovie view orient ; save ""/Users/neyrinck/Google Drive/My > Drive/$1/$2/$2_$3.jpg"" supersample 2 ; movie record ; turn y 2 180 ; wait > 180 ; movie encode ""/Users/neyrinck/Google Drive/My > Drive/$1/$2/$2_$3_rot.mp4"" > alias makepicture close ; set bgColor white ; windowsize 480 480 ;open > ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb"" ; alphafold pae > #1 file ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json"" ; > view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ; > color /A indianred ; color /B royalblue ; alphafold contacts /A to /B > palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius > 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ; > picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key > true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key > true ; picmovie $1 $2 hydrophobic > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults W181 > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 4 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg"" > supersample 2 Cannot save '/Users/neyrinck/Google Drive/My Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg': [Errno 70] Stale NFS file handle: '/Users/neyrinck/Google Drive/My Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg' > runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc > alias picmovie view orient ; save ""/Users/neyrinck/Google Drive/My > Drive/$1/$2/$2_$3.jpg"" supersample 2 ; movie record ; turn y 2 180 ; wait > 180 ; movie encode ""/Users/neyrinck/Google Drive/My > Drive/$1/$2/$2_$3_rot.mp4"" > alias makepicture close ; set bgColor white ; windowsize 480 480 ;open > ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb"" ; alphafold pae > #1 file ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json"" ; > view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ; > color /A indianred ; color /B royalblue ; alphafold contacts /A to /B > palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius > 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ; > picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key > true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key > true ; picmovie $1 $2 hydrophobic > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > AF122 > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF122/best_model.pdb"" Cannot open files: [Errno 60] Operation timed out > runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc > alias picmovie view orient ; save ""/Users/neyrinck/Google Drive/My > Drive/$1/$2/$2_$3.jpg"" supersample 2 ; movie record ; turn y 2 180 ; wait > 180 ; movie encode ""/Users/neyrinck/Google Drive/My > Drive/$1/$2/$2_$3_rot.mp4"" > alias makepicture close ; set bgColor white ; windowsize 480 480 ;open > ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb"" ; alphafold pae > #1 file ""/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json"" ; > view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ; > color /A indianred ; color /B royalblue ; alphafold contacts /A to /B > palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius > 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ; > picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key > true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key > true ; picmovie $1 $2 hydrophobic > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > AF122 > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF122/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 5 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF122/AF122_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AF122/AF122_contacts_hbonds_rot.mp4 Changed 8618 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF122/AF122_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AF122/AF122_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -24.67, mean -4.45, maximum 15.72 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -14.64, mean -0.38, maximum 11.56 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF122/AF122_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AF122/AF122_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -27.89, mean -5.06, maximum 23.83 Map values for surface ""best_model.pdb_B SES surface"": minimum -28.22, mean -4.673, maximum 23.95 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF122/AF122_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AF122/AF122_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > AF182 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF182/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 10 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF182/AF182_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AF182/AF182_contacts_hbonds_rot.mp4 Changed 7870 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF182/AF182_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AF182/AF182_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -25.41, mean -4.28, maximum 18.51 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -21.53, mean -2.50, maximum 8.95 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF182/AF182_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AF182/AF182_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -30.69, mean -5.172, maximum 25.37 Map values for surface ""best_model.pdb_B SES surface"": minimum -28.23, mean -5.938, maximum 21.78 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF182/AF182_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AF182/AF182_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > AG123 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG123/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 1 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG123/AG123_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AG123/AG123_contacts_hbonds_rot.mp4 Changed 8313 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG123/AG123_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AG123/AG123_sphere_rot.mp4 Changed 0 atom styles Exception ignored in tp_clear of: Traceback (most recent call last): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molarray.py"", line 161, in self._object_list = [c.c_ptr_to_py_inst(p) for p in self._pointers] ^^^^^^^^^^^^^^^^^^^^^ TypeError: NoneType takes no arguments Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -18.51, mean -0.84, maximum 14.74 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -17.17, mean -0.75, maximum 13.58 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG123/AG123_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AG123/AG123_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -30.62, mean -6.387, maximum 26.65 Map values for surface ""best_model.pdb_B SES surface"": minimum -27.46, mean -1.412, maximum 24.61 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG123/AG123_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AG123/AG123_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > AG172 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG172/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 1 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG172/AG172_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AG172/AG172_contacts_hbonds_rot.mp4 Changed 7440 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG172/AG172_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AG172/AG172_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -17.63, mean -0.66, maximum 13.56 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -11.30, mean -0.42, maximum 13.19 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG172/AG172_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AG172/AG172_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -30.18, mean -6.405, maximum 25.47 Map values for surface ""best_model.pdb_B SES surface"": minimum -27.92, mean -1.069, maximum 22.69 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG172/AG172_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AG172/AG172_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > AG185 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG185/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 21 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG185/AG185_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AG185/AG185_contacts_hbonds_rot.mp4 Changed 8884 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG185/AG185_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AG185/AG185_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -21.18, mean -1.04, maximum 24.85 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -13.87, mean 0.51, maximum 20.70 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG185/AG185_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AG185/AG185_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -31.84, mean -6.422, maximum 27.62 Map values for surface ""best_model.pdb_B SES surface"": minimum -28.14, mean -5.46, maximum 22.87 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG185/AG185_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../AG185/AG185_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > T123 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T123/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 2 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T123/T123_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T123/T123_contacts_hbonds_rot.mp4 Changed 3522 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T123/T123_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T123/T123_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -20.06, mean -2.88, maximum 11.81 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -14.95, mean -0.67, maximum 14.16 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T123/T123_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T123/T123_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -25.56, mean -5.424, maximum 22.49 Map values for surface ""best_model.pdb_B SES surface"": minimum -30.2, mean -1.372, maximum 24.34 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T123/T123_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T123/T123_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > T128 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T128/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B Exception ignored in tp_clear of: Traceback (most recent call last): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molarray.py"", line 161, in self._object_list = [c.c_ptr_to_py_inst(p) for p in self._pointers] ^^^^^^^^^^^^^^^^^^^^^ TypeError: NoneType takes no arguments 0 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T128/T128_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T128/T128_contacts_hbonds_rot.mp4 Changed 4102 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T128/T128_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T128/T128_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -18.14, mean -3.19, maximum 12.44 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -13.21, mean 1.95, maximum 21.27 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T128/T128_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T128/T128_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -25.49, mean -5.152, maximum 22.32 Map values for surface ""best_model.pdb_B SES surface"": minimum -26.95, mean -1.046, maximum 24.12 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T128/T128_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../T128/T128_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > U110 > key lipophilicity :-20 :0 :20 white: white: white: white: white: white: > white: white: white: white: > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U110/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 0 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U110/U110_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U110/U110_contacts_hbonds_rot.mp4 Changed 671 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U110/U110_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U110/U110_sphere_rot.mp4 Changed 0 atom styles Exception ignored in tp_clear of: Traceback (most recent call last): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/grako/ast.py"", line 59, in update def upairs(d): TypeError: NoneType takes no arguments Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -16.21, mean -5.66, maximum 8.34 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -11.94, mean -1.25, maximum 8.75 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U110/U110_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U110/U110_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -24.43, mean -4.109, maximum 24.15 Map values for surface ""best_model.pdb_B SES surface"": minimum -22.87, mean -3.776, maximum 25.35 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U110/U110_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U110/U110_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > U126 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U126/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 3 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U126/U126_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U126/U126_contacts_hbonds_rot.mp4 Changed 3648 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U126/U126_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U126/U126_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -17.88, mean -5.58, maximum 10.28 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -16.59, mean 0.10, maximum 12.63 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U126/U126_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U126/U126_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -25.53, mean -4.704, maximum 23.87 Map values for surface ""best_model.pdb_B SES surface"": minimum -29.31, mean -4.227, maximum 23.19 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U126/U126_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U126/U126_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > U127 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U127/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 11 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U127/U127_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U127/U127_contacts_hbonds_rot.mp4 Changed 3769 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U127/U127_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U127/U127_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -25.55, mean -7.54, maximum 9.34 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -15.49, mean -1.52, maximum 18.02 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U127/U127_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U127/U127_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -29.54, mean -4.686, maximum 21.33 Map values for surface ""best_model.pdb_B SES surface"": minimum -29.63, mean -5.687, maximum 23.3 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U127/U127_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U127/U127_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > U168 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U168/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B Exception ignored in tp_clear of: Traceback (most recent call last): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/geometry/matrix.py"", line 33, in apply_matrix r = matrix_multiply(points, transpose(tf[:, :3])) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: NoneType takes no arguments 8 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U168/U168_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U168/U168_contacts_hbonds_rot.mp4 Changed 7517 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U168/U168_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U168/U168_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -26.29, mean -6.88, maximum 11.42 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -27.34, mean -3.20, maximum 11.62 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U168/U168_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U168/U168_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -29.78, mean -4.178, maximum 24.02 Map values for surface ""best_model.pdb_B SES surface"": minimum -28.65, mean -5.09, maximum 23.77 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U168/U168_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U168/U168_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > U181 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U181/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 5 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U181/U181_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U181/U181_contacts_hbonds_rot.mp4 Changed 8811 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U181/U181_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U181/U181_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -17.51, mean -5.36, maximum 10.83 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -22.93, mean -0.07, maximum 18.91 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U181/U181_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U181/U181_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -24.06, mean -3.834, maximum 20.12 Map values for surface ""best_model.pdb_B SES surface"": minimum -28.14, mean -3.16, maximum 24.29 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U181/U181_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../U181/U181_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > V139 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V139/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 13 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V139/V139_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V139/V139_contacts_hbonds_rot.mp4 Changed 6417 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V139/V139_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V139/V139_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -15.63, mean -1.93, maximum 18.79 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -19.55, mean -2.60, maximum 11.98 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V139/V139_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V139/V139_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -30.7, mean -5.511, maximum 22.83 Map values for surface ""best_model.pdb_B SES surface"": minimum -30.93, mean -5.365, maximum 24.34 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V139/V139_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V139/V139_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > V142 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V142/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 6 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V142/V142_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V142/V142_contacts_hbonds_rot.mp4 Changed 7491 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V142/V142_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V142/V142_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -17.17, mean -1.14, maximum 17.41 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -17.17, mean 1.17, maximum 20.04 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V142/V142_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V142/V142_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -27.59, mean -5.329, maximum 21.93 Map values for surface ""best_model.pdb_B SES surface"": minimum -30.22, mean -3.754, maximum 24.74 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V142/V142_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V142/V142_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > V143 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V143/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 11 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V143/V143_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V143/V143_contacts_hbonds_rot.mp4 Changed 7562 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V143/V143_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V143/V143_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -17.31, mean -1.24, maximum 18.49 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -20.42, mean 0.45, maximum 19.37 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V143/V143_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V143/V143_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -28.81, mean -5.284, maximum 21.46 Map values for surface ""best_model.pdb_B SES surface"": minimum -30.01, mean -3.498, maximum 25.47 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V143/V143_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V143/V143_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > V173 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V173/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 5 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V173/V173_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V173/V173_contacts_hbonds_rot.mp4 Changed 6995 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V173/V173_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V173/V173_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -20.55, mean -2.48, maximum 17.12 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -16.14, mean -0.35, maximum 17.74 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V173/V173_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V173/V173_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -24.15, mean -4.967, maximum 27.85 Map values for surface ""best_model.pdb_B SES surface"": minimum -32.62, mean -4.467, maximum 25.2 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V173/V173_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V173/V173_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > V181 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V181/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 1 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V181/V181_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V181/V181_contacts_hbonds_rot.mp4 Changed 9108 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V181/V181_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V181/V181_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -19.93, mean -1.17, maximum 16.60 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -20.19, mean -0.13, maximum 16.80 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V181/V181_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V181/V181_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -26.24, mean -5.43, maximum 22.03 Map values for surface ""best_model.pdb_B SES surface"": minimum -29.84, mean -3.222, maximum 27.55 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V181/V181_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../V181/V181_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > W123 > key lipophilicity :-20 :0 :20 white: > key darkcyan:-20 white:0 darkgoldenrod:20 white: white: > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W123/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 0 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W123/W123_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W123/W123_contacts_hbonds_rot.mp4 Changed 3494 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W123/W123_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W123/W123_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -20.12, mean -3.52, maximum 8.53 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -24.87, mean -0.67, maximum 11.88 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W123/W123_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W123/W123_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -27.02, mean -6.604, maximum 22.22 Map values for surface ""best_model.pdb_B SES surface"": minimum -27.4, mean -1.407, maximum 24.07 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W123/W123_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W123/W123_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > W135 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W135/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 1 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W135/W135_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W135/W135_contacts_hbonds_rot.mp4 Changed 4940 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W135/W135_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W135/W135_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -22.35, mean -4.28, maximum 8.59 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -23.99, mean 0.69, maximum 17.52 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W135/W135_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W135/W135_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -33.07, mean -6.808, maximum 22.97 Map values for surface ""best_model.pdb_B SES surface"": minimum -29.32, mean -2.714, maximum 24.53 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W135/W135_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W135/W135_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > W139 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W139/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 10 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W139/W139_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W139/W139_contacts_hbonds_rot.mp4 Changed 6397 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W139/W139_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W139/W139_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -19.85, mean -5.49, maximum 7.56 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -34.76, mean -2.90, maximum 13.36 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W139/W139_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W139/W139_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -26.99, mean -6.956, maximum 22.21 Map values for surface ""best_model.pdb_B SES surface"": minimum -34.58, mean -5.318, maximum 23.88 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W139/W139_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W139/W139_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > W142 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W142/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 3 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W142/W142_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W142/W142_contacts_hbonds_rot.mp4 Changed 7471 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W142/W142_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W142/W142_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -21.38, mean -4.72, maximum 10.92 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -16.31, mean 1.27, maximum 19.35 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W142/W142_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W142/W142_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -28.4, mean -6.661, maximum 21.77 Map values for surface ""best_model.pdb_B SES surface"": minimum -32.41, mean -3.752, maximum 24.66 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W142/W142_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W142/W142_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > W143 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W143/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B 6 hydrogen bonds found > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W143/W143_contacts_hbonds.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W143/W143_contacts_hbonds_rot.mp4 Changed 7542 atom styles > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W143/W143_sphere.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W143/W143_sphere_rot.mp4 Changed 0 atom styles Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -19.48, mean -4.31, maximum 10.66 Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -20.19, mean 0.44, maximum 20.10 > key red-white-blue :-10 :0 :10 showTool true > ui mousemode right ""color key"" > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W143/W143_coulombic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W143/W143_coulombic_rot.mp4 Changed 0 atom styles Map values for surface ""best_model.pdb_A SES surface"": minimum -34.86, mean -6.835, maximum 21.92 Map values for surface ""best_model.pdb_B SES surface"": minimum -29.08, mean -3.558, maximum 24.54 > key lipophilicity :-20 :0 :20 showTool true > save ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W143/W143_hydrophobic.jpg"" > supersample 2 Movie saved to /Users/neyrinck/.../W143/W143_hydrophobic_rot.mp4 > makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy > W168 > ui mousemode right translate > open ""/Users/neyrinck/Google Drive/My > Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W168/best_model.pdb"" Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available Alignment identifier is 1/A Alignment identifier is 1/B Exception ignored in tp_clear of: Traceback (most recent call last): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molarray.py"", line 161, in self._object_list = [c.c_ptr_to_py_inst(p) for p in self._pointers] ^^^^^^^^^^^^^^^^^^^^^ TypeError: NoneType takes no arguments ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,2 Model Number: Z14W00106LL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 10151.61.4 OS Loader Version: 10151.61.4 Software: System Software Overview: System Version: macOS 14.2.1 (23C71) Kernel Version: Darwin 23.2.0 Time since boot: 16 hours, 31 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 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: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 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: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core fixed Tom Goddard Greg Couch yakonfire@yahoo.com all ChimeraX