id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15248 SEQCROW: Buried Volume: Could not find atom dobromirak@… Tony Schaefer "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 1.8rc202405171936 (2024-05-17 19:36:10 UTC) Description Hello, I encountered a bug while trying to create a steric map for buried volume. The log file is attached. Basically, I select the ligand as in this video https://www.youtube.com/watch?v=kPr4uNgMIWo and then I select the atom I want to create the steric map for and the error (""LookupError: Could not find atom: []"") in the attached log appears. Since I am interested in finding the steric map for a single atom of an entire molecule in an enzyme pocket the steric map for the entire molecule is not what I want, although if I try for the entire molecule I don't get the error. I tried deleting the rest of the atoms in the molecule and finding the steric map from the buried volume again, but the same error appears. Best Regards, Dobromir Log: Startup Messages --- notes | available bundle cache has not been initialized yet Database-fetch provider 'redo' in bundle Map specified unknown data format 'MTZ' UCSF ChimeraX version: 1.8rc202405171936 (2024-05-17) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:\Users\Samaray\Desktop\t.pdb format pdb Summary of feedback from opening C:\Users\Samaray\Desktop\t.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 HIS A 2 ALA A 10 1 9 Start residue of secondary structure not found: HELIX 2 2 ASP A 21 LEU A 29 1 9 End residue of secondary structure not found: HELIX 3 3 MET A 34 GLN A 40 1 7 Start residue of secondary structure not found: HELIX 4 4 GLU A 56 ILE A 60 1 5 Start residue of secondary structure not found: HELIX 5 5 GLU A 63 LEU A 67 1 5 Start residue of secondary structure not found: HELIX 6 6 SER A 97 LEU A 99 1 3 Start residue of secondary structure not found: HELIX 7 7 SER A 100 LEU A 109 1 10 Start residue of secondary structure not found: HELIX 8 8 GLY A 115 THR A 120 1 6 4 messages similar to the above omitted End residue of secondary structure not found: SHEET 5 5 1 LEU A 124 ASP A 134 0 Start residue of secondary structure not found: SHEET 6 6 1 LEU A 137 LEU A 146 0 Start residue of secondary structure not found: SHEET 7 7 1 LYS A 149 PHE A 157 0 t.pdb title: Chorismate lyase with inhibitor vanillate [more info...] Chain information for t.pdb #1 --- Chain | Description | UniProt A | chorismate lyase | UBIC_ECOLI 1-164 Non-standard residues in t.pdb #1 --- VNL — 4-hydroxy-3-methoxybenzoate (vanillate) 5 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > set bgColor white > lighting full > graphics silhouettes true > color byelement > size /a atomRadius 1.3 Changed 138 atom radii > size stickRadius 0.13 Changed 127 bond radii > hide cartoons > show cartoons > hide cartoons > hide atoms > show atoms > style ball Changed 138 atom styles > ui mousemode right ""structure eraser"" > ui mousemode right select Drag select of 138 atoms, 127 bonds > select subtract /A:181@O1 137 atoms, 127 bonds, 17 residues, 1 model selected > ui tool show ""Buried Volume"" > select clear > select /A:181@O1 1 atom, 1 residue, 1 model selected Traceback (most recent call last): File ""C:\Users\Samaray\AppData\Local\UCSF\ChimeraX\1.8\Python311\site- packages\SEQCROW\tools\percent_Vbur.py"", line 655, in calc_vbur info = percent_vbur_cmd( ^^^^^^^^^^^^^^^^^ File ""C:\Users\Samaray\AppData\Local\UCSF\ChimeraX\1.8\Python311\site- packages\SEQCROW\commands\percent_Vbur.py"", line 386, in percent_vbur results = [d.result() for d in data] ^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Users\Samaray\AppData\Local\UCSF\ChimeraX\1.8\Python311\site- packages\SEQCROW\commands\percent_Vbur.py"", line 386, in results = [d.result() for d in data] ^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.8rc202405171936\bin\Lib\concurrent\futures\\_base.py"", line 456, in result return self.__get_result() ^^^^^^^^^^^^^^^^^^^ File ""C:\Program Files\ChimeraX 1.8rc202405171936\bin\Lib\concurrent\futures\\_base.py"", line 401, in __get_result raise self._exception File ""C:\Program Files\ChimeraX 1.8rc202405171936\bin\Lib\concurrent\futures\thread.py"", line 58, in run result = self.fn(*self.args, **self.kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""C:\Users\Samaray\AppData\Local\UCSF\ChimeraX\1.8\Python311\site- packages\SEQCROW\commands\percent_Vbur.py"", line 184, in _vbur steric_info = rescol.steric_map( ^^^^^^^^^^^^^^^^^^ File ""C:\Users\Samaray\AppData\Local\UCSF\ChimeraX\1.8\Python311\site- packages\AaronTools\geometry.py"", line 3058, in steric_map key_atoms = self.find(key_atoms) ^^^^^^^^^^^^^^^^^^^^ File ""C:\Users\Samaray\AppData\Local\UCSF\ChimeraX\1.8\Python311\site- packages\AaronTools\geometry.py"", line 1374, in find raise LookupError( LookupError: Could not find atom: [] on t.pdb 138 N 24.13000 -6.89000 35.03400 C 23.97400 -6.67300 33.59200 C 22.80900 -7.47800 33.00800 O 22.98600 -8.20700 32.04400 C 25.24100 -7.06500 32.85200 C 26.45000 -6.39800 33.43100 C 27.74400 -6.76700 32.71200 O 27.96600 -6.32100 31.56100 O 28.54200 -7.50300 33.33300 N 21.62000 -7.32500 33.57200 C 20.44600 -8.07800 33.08100 C 19.29300 -7.46700 33.85800 O 19.52200 -6.73000 34.81300 C 20.53300 -9.54600 33.52800 C 19.70400 -10.49400 32.66600 O 18.95000 -10.04600 31.81000 O 19.82000 -11.72000 32.82700 N 18.07400 -7.85000 33.47100 C 16.80400 -7.47800 34.13800 C 16.84600 -8.32400 35.44800 O 17.72900 -9.14600 35.58900 C 15.63200 -7.97500 33.28000 O 15.55500 -9.41200 33.36500 N 15.85900 -8.19200 36.35300 C 15.82300 -8.94900 37.59700 C 15.16700 -10.32500 37.51000 O 15.18400 -11.13600 38.44500 C 15.09100 -8.08800 38.65200 C 15.84100 -6.85000 39.04800 S 17.43400 -7.39700 39.80700 C 18.44700 -6.20800 38.85400 N 14.63200 -10.64900 36.34900 C 13.89600 -11.91700 36.23500 C 14.52000 -13.19400 36.78700 O 13.99100 -13.81300 37.72700 C 13.47900 -12.09600 34.79600 O 12.63300 -10.97600 34.44500 C 12.70700 -13.48700 34.61800 N 6.23200 0.91900 28.18900 C 5.83600 -0.32200 28.85000 C 6.07000 -0.16100 30.37200 O 7.19500 0.09400 30.81000 C 6.62700 -1.51200 28.27600 C 6.51400 -2.86100 29.07700 C 7.65700 -3.78200 28.74900 N 7.66800 -5.01100 29.49300 C 6.89200 -6.08100 29.31700 N 5.95000 -6.13000 28.36900 N 7.12800 -7.16300 30.09300 N 6.20100 -6.29300 38.85800 C 6.70700 -7.65200 38.84100 C 6.47400 -8.28200 40.19600 O 6.94100 -7.76700 41.18100 C 8.18100 -7.66600 38.56900 C 8.79600 -9.05600 38.26000 C 8.48000 -9.51500 36.85100 C 10.25900 -8.94000 38.22500 N 8.66300 -1.40000 36.89300 C 9.61600 -1.04000 35.86600 C 8.98100 -0.25000 34.72100 O 7.84300 -0.49300 34.39600 C 10.33400 -2.25100 35.31700 N 8.13100 -11.53800 31.19800 C 9.09400 -10.56100 31.72900 C 10.37200 -10.53500 30.91500 O 10.87700 -11.59100 30.45700 C 9.31600 -11.03600 33.14700 C 9.19400 -12.53500 33.05700 C 8.19400 -12.82300 31.93900 N 10.88300 -9.32300 30.74800 C 12.08500 -9.00300 29.98700 C 13.33800 -9.66000 30.59300 O 13.43200 -9.80300 31.79700 C 12.25000 -7.50000 30.03000 C 13.14900 -6.85800 29.09000 C 12.78400 -7.26500 27.65400 C 12.95400 -5.28800 29.24700 N 23.96300 -7.08000 22.71400 C 23.51300 -6.23000 23.79600 C 24.64200 -5.49100 24.55400 O 25.70000 -6.05300 24.86000 C 22.67400 -7.10900 24.70000 C 21.85100 -6.54900 25.84400 C 21.30600 -5.20100 25.53800 C 20.72500 -7.51800 26.08000 N 25.36500 -1.87800 27.32900 C 24.76800 -0.86400 28.17700 C 25.71900 0.32000 28.15400 O 26.87900 0.14000 28.43900 C 24.60700 -1.44900 29.57400 C 24.19900 -0.47200 30.60900 C 23.81200 -1.24900 31.83100 N 24.91500 -1.59700 32.68800 C 24.81000 -2.40200 33.74900 N 23.63900 -2.96600 34.09900 N 25.89400 -2.68000 34.46800 N 17.15600 2.39600 39.71300 C 18.22700 2.57400 38.75700 C 17.68300 2.85400 37.35200 O 16.54700 2.45800 37.05200 C 19.12400 1.35000 38.73000 C 18.52300 0.09900 38.09500 C 19.61400 -0.99800 37.92900 N 19.00400 -2.13000 37.23700 C 19.61600 -3.23200 36.84700 N 20.89100 -3.39500 37.07200 N 18.92400 -4.16100 36.17100 N 15.64700 1.95600 30.27400 C 14.96500 1.03700 31.22500 C 15.12200 1.57200 32.66900 O 16.26200 1.75500 33.13100 C 15.54900 -0.40500 31.09400 C 15.24700 -1.44300 32.20000 C 13.76000 -1.82300 32.21600 C 16.06900 -2.68700 32.01900 N 13.99600 0.99400 36.81700 C 13.49200 -0.02500 37.79500 C 13.43600 0.55600 39.19800 O 14.35200 1.27400 39.58900 C 14.43000 -1.25200 37.81700 C 14.26200 -2.11500 36.60500 C 15.60700 -2.67300 36.12500 O 16.54900 -1.90300 35.86800 O 15.70600 -3.88100 36.03600 O 9.47700 -4.97700 31.55400 C 22.05900 -5.25500 30.57100 C 21.75300 -6.14500 29.58200 C 21.20700 -4.81400 31.40400 C 20.41500 -6.60900 29.45800 C 19.92800 -5.19600 31.36400 O 19.07700 -4.59600 32.16500 C 19.49100 -6.09600 30.39600 C 23.30800 -4.74800 30.65700 C 19.74900 -3.63400 32.97500 O 24.27600 -5.08000 29.88200 O 23.35300 -3.85200 31.51100 O 18.13000 -6.58000 30.20500 O 9.28600 -2.26200 31.76200 LookupError: Could not find atom: [] on t.pdb 138 N 24.13000 -6.89000 35.03400 C 23.97400 -6.67300 33.59200 C 22.80900 -7.47800 33.00800 O 22.98600 -8.20700 32.04400 C 25.24100 -7.06500 32.85200 C 26.45000 -6.39800 33.43100 C 27.74400 -6.76700 32.71200 O 27.96600 -6.32100 31.56100 O 28.54200 -7.50300 33.33300 N 21.62000 -7.32500 33.57200 C 20.44600 -8.07800 33.08100 C 19.29300 -7.46700 33.85800 O 19.52200 -6.73000 34.81300 C 20.53300 -9.54600 33.52800 C 19.70400 -10.49400 32.66600 O 18.95000 -10.04600 31.81000 O 19.82000 -11.72000 32.82700 N 18.07400 -7.85000 33.47100 C 16.80400 -7.47800 34.13800 C 16.84600 -8.32400 35.44800 O 17.72900 -9.14600 35.58900 C 15.63200 -7.97500 33.28000 O 15.55500 -9.41200 33.36500 N 15.85900 -8.19200 36.35300 C 15.82300 -8.94900 37.59700 C 15.16700 -10.32500 37.51000 O 15.18400 -11.13600 38.44500 C 15.09100 -8.08800 38.65200 C 15.84100 -6.85000 39.04800 S 17.43400 -7.39700 39.80700 C 18.44700 -6.20800 38.85400 N 14.63200 -10.64900 36.34900 C 13.89600 -11.91700 36.23500 C 14.52000 -13.19400 36.78700 O 13.99100 -13.81300 37.72700 C 13.47900 -12.09600 34.79600 O 12.63300 -10.97600 34.44500 C 12.70700 -13.48700 34.61800 N 6.23200 0.91900 28.18900 C 5.83600 -0.32200 28.85000 C 6.07000 -0.16100 30.37200 O 7.19500 0.09400 30.81000 C 6.62700 -1.51200 28.27600 C 6.51400 -2.86100 29.07700 C 7.65700 -3.78200 28.74900 N 7.66800 -5.01100 29.49300 C 6.89200 -6.08100 29.31700 N 5.95000 -6.13000 28.36900 N 7.12800 -7.16300 30.09300 N 6.20100 -6.29300 38.85800 C 6.70700 -7.65200 38.84100 C 6.47400 -8.28200 40.19600 O 6.94100 -7.76700 41.18100 C 8.18100 -7.66600 38.56900 C 8.79600 -9.05600 38.26000 C 8.48000 -9.51500 36.85100 C 10.25900 -8.94000 38.22500 N 8.66300 -1.40000 36.89300 C 9.61600 -1.04000 35.86600 C 8.98100 -0.25000 34.72100 O 7.84300 -0.49300 34.39600 C 10.33400 -2.25100 35.31700 N 8.13100 -11.53800 31.19800 C 9.09400 -10.56100 31.72900 C 10.37200 -10.53500 30.91500 O 10.87700 -11.59100 30.45700 C 9.31600 -11.03600 33.14700 C 9.19400 -12.53500 33.05700 C 8.19400 -12.82300 31.93900 N 10.88300 -9.32300 30.74800 C 12.08500 -9.00300 29.98700 C 13.33800 -9.66000 30.59300 O 13.43200 -9.80300 31.79700 C 12.25000 -7.50000 30.03000 C 13.14900 -6.85800 29.09000 C 12.78400 -7.26500 27.65400 C 12.95400 -5.28800 29.24700 N 23.96300 -7.08000 22.71400 C 23.51300 -6.23000 23.79600 C 24.64200 -5.49100 24.55400 O 25.70000 -6.05300 24.86000 C 22.67400 -7.10900 24.70000 C 21.85100 -6.54900 25.84400 C 21.30600 -5.20100 25.53800 C 20.72500 -7.51800 26.08000 N 25.36500 -1.87800 27.32900 C 24.76800 -0.86400 28.17700 C 25.71900 0.32000 28.15400 O 26.87900 0.14000 28.43900 C 24.60700 -1.44900 29.57400 C 24.19900 -0.47200 30.60900 C 23.81200 -1.24900 31.83100 N 24.91500 -1.59700 32.68800 C 24.81000 -2.40200 33.74900 N 23.63900 -2.96600 34.09900 N 25.89400 -2.68000 34.46800 N 17.15600 2.39600 39.71300 C 18.22700 2.57400 38.75700 C 17.68300 2.85400 37.35200 O 16.54700 2.45800 37.05200 C 19.12400 1.35000 38.73000 C 18.52300 0.09900 38.09500 C 19.61400 -0.99800 37.92900 N 19.00400 -2.13000 37.23700 C 19.61600 -3.23200 36.84700 N 20.89100 -3.39500 37.07200 N 18.92400 -4.16100 36.17100 N 15.64700 1.95600 30.27400 C 14.96500 1.03700 31.22500 C 15.12200 1.57200 32.66900 O 16.26200 1.75500 33.13100 C 15.54900 -0.40500 31.09400 C 15.24700 -1.44300 32.20000 C 13.76000 -1.82300 32.21600 C 16.06900 -2.68700 32.01900 N 13.99600 0.99400 36.81700 C 13.49200 -0.02500 37.79500 C 13.43600 0.55600 39.19800 O 14.35200 1.27400 39.58900 C 14.43000 -1.25200 37.81700 C 14.26200 -2.11500 36.60500 C 15.60700 -2.67300 36.12500 O 16.54900 -1.90300 35.86800 O 15.70600 -3.88100 36.03600 O 9.47700 -4.97700 31.55400 C 22.05900 -5.25500 30.57100 C 21.75300 -6.14500 29.58200 C 21.20700 -4.81400 31.40400 C 20.41500 -6.60900 29.45800 C 19.92800 -5.19600 31.36400 O 19.07700 -4.59600 32.16500 C 19.49100 -6.09600 30.39600 C 23.30800 -4.74800 30.65700 C 19.74900 -3.63400 32.97500 O 24.27600 -5.08000 29.88200 O 23.35300 -3.85200 31.51100 O 18.13000 -6.58000 30.20500 O 9.28600 -2.26200 31.76200 File ""C:\Users\Samaray\AppData\Local\UCSF\ChimeraX\1.8\Python311\site- packages\AaronTools\geometry.py"", line 1374, in find raise LookupError( See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 528.49 OpenGL renderer: NVIDIA GeForce RTX 2080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: en_US.cp1252 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: windows Manufacturer: System manufacturer Model: System Product Name OS: Microsoft Windows 10 Pro (Build 18362) Memory: 34,291,212,288 MaxProcessMemory: 137,438,953,344 CPU: 16 Intel(R) Core(TM) i9-9900KF CPU @ 3.60GHz OSLanguage: en-US Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2024.2.2 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57 ChimeraX-AtomicLibrary: 14.0.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.4 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.4 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8rc202405171936 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.3 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 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: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.16 ChimeraX-ModelPanel: 1.5 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: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.4 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 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-Segmentations: 3.0.3 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 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: 1.39 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.1 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 comtypes: 1.4.1 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.51.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 24.0 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.43 psutil: 5.9.8 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pywin32: 306 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 Send2Trash: 1.8.3 SEQCROW: 1.8.8 setuptools: 69.5.1 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 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: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.2 typing-extensions: 4.11.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 WMI: 1.5.1 }}} " defect assigned normal Third Party all ChimeraX