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Opened 6 years ago
Closed 6 years ago
#2669 closed defect (fixed)
Problem with hacked code: bond rotater is None
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | VR | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.17763 ChimeraX Version: 0.91 (2019-11-15) Description Hi Tom, Here is the error related to Bond rotation in VR you asked about. The message is: Error processing trigger "new frame": AttributeError: 'NoneType' object has no attribute 'moving_side' File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side See log for complete Python traceback. Best, Józef Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.91 (2019-11-15) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open D:\data\Projects\TycACOM\COMDBv2-TycB1C\cluster4_1.pdb Summary of feedback from opening D:\data\Projects\TycACOM\COMDBv2-TycB1C\cluster4_1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_58w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_58.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster4_1.pdb #1 --- Chain | Description A | No description available B | No description available > select /A:28 9 atoms, 8 bonds, 1 model selected > select up 66 atoms, 67 bonds, 1 model selected > select up 4468 atoms, 4553 bonds, 1 model selected > select clear > mlp Map values for surface "cluster4_1.pdb_A SES surface": minimum -25.66, mean -3.762, maximum 24.7 Map values for surface "cluster4_1.pdb_B SES surface": minimum -24.06, mean -3.679, maximum 21.58 > transparency 50 target s > select :lys,arg,asp,glu 1114 atoms, 1038 bonds, 1 model selected > show sel atoms > select /b 205 atoms, 207 bonds, 1 model selected > hide sel surfaces > hide sel cartoons > show sel atoms > vr true started SteamVR rendering VR mode bond rotation > torsion /B:14@HN,N,CA,CB -2.92 move large Traceback (most recent call last): File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 614, in next_frame self.process_controller_events() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 642, in process_controller_events self.process_controller_buttons() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 659, in process_controller_buttons hc.process_event(e) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2213, in process_event self._dispatch_event(m, event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2217, in _dispatch_event mode.pressed(hand_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3025, in pressed self._click(hand_button_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3034, in _click m.vr_press(e) File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side AttributeError: 'NoneType' object has no attribute 'moving_side' Error processing trigger "new frame": AttributeError: 'NoneType' object has no attribute 'moving_side' File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side See log for complete Python traceback. > vr false > vr true started SteamVR rendering > torsion /B:14@HN,N,CA,CB -146.41 move large VR mode label > label #1/B:14 color yellow bgColor dimgray size 64 height 0.7 > label #1/B:13 color yellow bgColor dimgray size 64 height 0.7 > label #1/B:12 color yellow bgColor dimgray size 64 height 0.7 > label #1/B:11 color yellow bgColor dimgray size 64 height 0.7 VR mode bond rotation > torsion /B:12@N,CA,C,O 85.73 > torsion /B:13@N,CA,C,O -27.01 move large > torsion /B:13@N,CA,C,O -39.38 move large Traceback (most recent call last): File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 614, in next_frame self.process_controller_events() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 642, in process_controller_events self.process_controller_buttons() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 659, in process_controller_buttons hc.process_event(e) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2213, in process_event self._dispatch_event(m, event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2217, in _dispatch_event mode.pressed(hand_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3025, in pressed self._click(hand_button_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3034, in _click m.vr_press(e) File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side AttributeError: 'NoneType' object has no attribute 'moving_side' Error processing trigger "new frame": AttributeError: 'NoneType' object has no attribute 'moving_side' File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side See log for complete Python traceback. > vr true > vr false > vr true started SteamVR rendering > torsion /B:11@CA /B:11@N /B:10@C /B:10@CA -100.73 > torsion /B:12@N,CA,CB,CG -162.51 move large > torsion /B:12@N,CA,C,O 50.93 > torsion /B:12@N,CA,C,O 89.84 > torsion /B:11@N,CA,C,O 3.15 > torsion /B:12@N,CA,C,O 77.84 > torsion /B:12@N,CA,C,O 62.99 > show sel surfaces > torsion /B:12@N,CA,C,O 56.03 > vr false > close session > open D:\data\Projects\TycACOM\TycB3COM-TycB1C-nonative-complex-manual-from- cluster4.cxs format session opened ChimeraX session > select up 4673 atoms, 4760 bonds, 2 models selected > select up 4673 atoms, 4760 bonds, 3 models selected > vr true started SteamVR rendering VR mode label > label #2/B:12 color yellow bgColor dimgray size 64 height 0.7 > label #2/B:11 color yellow bgColor dimgray size 64 height 0.7 > select :lys,arg,asp,glu 1114 atoms, 1038 bonds, 2 models selected > show sel atoms > label delete residues VR mode bond rotation > torsion #2/B:14@HN,N,CA,CB -32.81 move large > torsion #2/B:14@CB,CA,N,HN -33.02 > vr false > close session > open D:/data/Projects/TycACOM/COMDBv2-TycB1C/cluster4_1.pdb Summary of feedback from opening D:/data/Projects/TycACOM/COMDBv2-TycB1C/cluster4_1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_58w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_58.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster4_1.pdb #1 --- Chain | Description A | No description available B | No description available > select /A:110 14 atoms, 14 bonds, 1 model selected > select up 212 atoms, 213 bonds, 1 model selected > select up 4468 atoms, 4553 bonds, 1 model selected > mlp sel Map values for surface "cluster4_1.pdb_A SES surface": minimum -25.66, mean -3.762, maximum 24.7 > transparency 50 target s > select :lys,arg,asp,glu 1114 atoms, 1038 bonds, 1 model selected > show sel atoms > select up 3868 atoms, 3920 bonds, 2 models selected > show sel atoms > hide sel cartoons > hide sel atoms > select /a 4468 atoms, 4553 bonds, 1 model selected > show sel cartoons > select /b 205 atoms, 207 bonds, 1 model selected > show sel atoms > select :lys,arg,asp,glu 1114 atoms, 1038 bonds, 1 model selected > show sel atoms > vr true started SteamVR rendering VR mode label > label #1/B:14 color yellow bgColor dimgray size 64 height 0.7 > label #1/B:19 color yellow bgColor dimgray size 64 height 0.7 > label #1/B:13 color yellow bgColor dimgray size 64 height 0.7 > label #1/B:12 color yellow bgColor dimgray size 64 height 0.7 > label #1/B:11 color yellow bgColor dimgray size 64 height 0.7 > select /b 205 atoms, 207 bonds, 1 model selected > show sel surfaces > transparency 50 target s > label delete residues VR mode bond rotation > torsion /B:13@N,CA,C,O -118.53 move large > torsion /B:12@N,CA,C,O 51.02 Traceback (most recent call last): File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 614, in next_frame self.process_controller_events() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 642, in process_controller_events self.process_controller_buttons() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 659, in process_controller_buttons hc.process_event(e) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2213, in process_event self._dispatch_event(m, event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2217, in _dispatch_event mode.pressed(hand_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3025, in pressed self._click(hand_button_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3034, in _click m.vr_press(e) File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side AttributeError: 'NoneType' object has no attribute 'moving_side' Error processing trigger "new frame": AttributeError: 'NoneType' object has no attribute 'moving_side' File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side See log for complete Python traceback. > vr false > vr true started SteamVR rendering > torsion /B:11@N,CA,C,O -76.76 Traceback (most recent call last): File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 614, in next_frame self.process_controller_events() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 642, in process_controller_events self.process_controller_buttons() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 659, in process_controller_buttons hc.process_event(e) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2213, in process_event self._dispatch_event(m, event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2217, in _dispatch_event mode.pressed(hand_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3025, in pressed self._click(hand_button_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3034, in _click m.vr_press(e) File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side AttributeError: 'NoneType' object has no attribute 'moving_side' Error processing trigger "new frame": AttributeError: 'NoneType' object has no attribute 'moving_side' File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side See log for complete Python traceback. > vr false > vr true started SteamVR rendering > torsion /B:12@HN,N,CA,CB 41.37 > torsion /B:12@HN,N,CA,CB 21.83 > torsion /B:12@N,CA,C,O 75.50 > torsion /B:12@N,CA,C,O 79.00 > torsion /B:11@HN,N,CA,CB -30.05 > torsion /B:13@CA /B:13@N /B:12@C /B:12@CA 158.61 > torsion /B:12@N,CA,C,O 89.29 > torsion /B:12@N,CA,C,O 77.12 VR mode minimize Missing atoms or parameterization needed by force field. All heavy atoms and hydrogens with standard names are required. Error with ignoreExternalBonds=False was No template found for residue 1 (MET). The set of atoms is similar to MET, but it is missing 8 hydrogen atoms. Error with ignoreExternalBonds=True was No template found for residue 1 (MET). The set of atoms is similar to MET, but it is missing 8 hydrogen atoms. Missing atoms or parameterization needed by force field. All heavy atoms and hydrogens with standard names are required. Error with ignoreExternalBonds=False was No template found for residue 1 (MET). The set of atoms is similar to MET, but it is missing 8 hydrogen atoms. Error with ignoreExternalBonds=True was No template found for residue 1 (MET). The set of atoms is similar to MET, but it is missing 8 hydrogen atoms. > addh Summary of feedback from adding hydrogens to cluster4_1.pdb #1 --- notes | No usable SEQRES records for cluster4_1.pdb (#1) chain A; guessing termini instead No usable SEQRES records for cluster4_1.pdb (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A MET 1, /B THR 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A HIS 452, /B ILE 22 444 hydrogen bonds /A HIS 452 is not terminus, removing H atom from 'C' /B ILE 22 is not terminus, removing H atom from 'C' 3021 hydrogens added > vr false > pwd Current working directory is: C:\ProgramData\ChimeraX > cd d:\data\Projects\TycACOM Current working directory is: d:\data\Projects\TycACOM > select 7694 atoms, 7781 bonds, 1 model selected > save TycBCOM-TycB1C-nonnative-version2.pdb selectedOnly true > close session > open D:/data/Projects/TycACOM/COMDBv2-TycCC1full/COMDBv2-TycCC1full/cluster2_1.pdb Summary of feedback from opening D:/data/Projects/TycACOM/COMDBv2-TycCC1full/COMDBv2-TycCC1full/cluster2_1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_127w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_127.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster2_1.pdb #1 --- Chain | Description A | No description available B | No description available > close session > open D:/data/Projects/TycACOM/TycACOMbun-TycCC1/cluster1_1.pdb Summary of feedback from opening D:/data/Projects/TycACOM/TycACOMbun- TycCC1/cluster1_1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_105w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_105.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster1_1.pdb #1 --- Chain | Description A | No description available B | No description available > close session > open D:/data/Projects/TycACOM/TycACOMbun-TycCC1/cluster2_1.pdb Summary of feedback from opening D:/data/Projects/TycACOM/TycACOMbun- TycCC1/cluster2_1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_151w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_151.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster2_1.pdb #1 --- Chain | Description A | No description available B | No description available > close session > open D:/data/Projects/TycACOM/TycACOMbun-TycCC1/cluster4_1.pdb Summary of feedback from opening D:/data/Projects/TycACOM/TycACOMbun- TycCC1/cluster4_1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_196w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_196.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster4_1.pdb #1 --- Chain | Description A | No description available B | No description available > select /A:335 10 atoms, 9 bonds, 1 model selected > select up 80 atoms, 80 bonds, 1 model selected > select up 4383 atoms, 4472 bonds, 1 model selected > mlp sel Map values for surface "cluster4_1.pdb_A SES surface": minimum -27.53, mean -3.487, maximum 24.6 > transparency 50 target s > select :lys,arg,asp,glu 1112 atoms, 1035 bonds, 1 model selected > show sel atoms > close session > open D:/data/Projects/TycACOM/TycACOMbun-TycCC1/cluster3_1.pdb Summary of feedback from opening D:/data/Projects/TycACOM/TycACOMbun- TycCC1/cluster3_1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_78w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_78.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster3_1.pdb #1 --- Chain | Description A | No description available B | No description available > close session > open D:/data/Projects/TycACOM/TycACOMbun-TycCC1/cluster1_1.pdb Summary of feedback from opening D:/data/Projects/TycACOM/TycACOMbun- TycCC1/cluster1_1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_105w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_105.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster1_1.pdb #1 --- Chain | Description A | No description available B | No description available > select /A:52 13 atoms, 12 bonds, 1 model selected > select up 118 atoms, 119 bonds, 1 model selected > select up 4383 atoms, 4472 bonds, 1 model selected > mlp sel Map values for surface "cluster1_1.pdb_A SES surface": minimum -27.59, mean -3.323, maximum 23.87 > select :lys,arg,asp,glu 1112 atoms, 1035 bonds, 1 model selected > show sel atoms > transparency 50 target s > select /B:6 8 atoms, 7 bonds, 1 model selected > select up 70 atoms, 71 bonds, 1 model selected > select up 253 atoms, 255 bonds, 1 model selected > show sel atoms > hide sel cartoons > show sel surfaces > transparency 50 target s > vr true started SteamVR rendering VR mode bond rotation > torsion /B:12@N,CA,C,O 96.54 > torsion /B:12@N,CA,C,O 111.76 > torsion /B:13@CA /B:13@N /B:12@C /B:12@CA 39.28 > torsion /B:12@N,CA,C,O 81.05 > vr false > close session > open D:/data/Projects/TycACOM/TycCC1-full-ISOLDE.pdb Summary of feedback from opening D:/data/Projects/TycACOM/TycCC1-full- ISOLDE.pdb --- warning | Ignored bad PDB record found on line 7148 END Chain information for TycCC1-full-ISOLDE.pdb #1 --- Chain | Description A | No description available > select /A:9 22 atoms, 21 bonds, 1 model selected > show sel atoms > toolshed show Rotamers > swapaa interactive sel ASP lib Dunbrack > swapaa #1/A:9 ASP criteria 1 Using Dunbrack library TycCC1-full-ISOLDE.pdb #1/A LYS 9: phi -154.2, psi 165.3 trans Applying ASP rotamer (chi angles: -156.9 -6.7) to TycCC1-full-ISOLDE.pdb #1/A ASP 9 > select 7135 atoms, 7224 bonds, 1 model selected > pwd Current working directory is: d:\data\Projects\TycACOM > save TycC1C_K9D.pdb selectedOnly true > mlp sel Map values for surface "TycCC1-full-ISOLDE.pdb_A SES surface": minimum -28.51, mean -2.517, maximum 24.7 > select up 7135 atoms, 7224 bonds, 2 models selected > transparency 50 target s > select :lys,arg,asp,glu 1547 atoms, 1476 bonds, 1 model selected > show sel atoms > open D:/data/Projects/TycACOM/C-COMbun-rand2/cluster1_1.pdb Summary of feedback from opening D:/data/Projects/TycACOM/C-COMbun- rand2/cluster1_1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_46w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_46.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster1_1.pdb #2 --- Chain | Description A | No description available B | No description available > mmaker #2 to #17 No 'to' model specified > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TycCC1-full-ISOLDE.pdb, chain A (#1) with cluster1_1.pdb, chain A (#2), sequence alignment score = 1245.9 RMSD between 185 pruned atom pairs is 1.312 angstroms; (across all 445 pairs: 3.736) > close #2 > open D:/data/Projects/TycACOM/C-COMbun-rand2/cluster1_1.pdb Summary of feedback from opening D:/data/Projects/TycACOM/C-COMbun- rand2/cluster1_1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_46w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_46.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster1_1.pdb #2 --- Chain | Description A | No description available B | No description available > open D:/data/Projects/TycACOM/C-COMbun-rand2/cluster1_2.pdb Summary of feedback from opening D:/data/Projects/TycACOM/C-COMbun- rand2/cluster1_2.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_40w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_40.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster1_2.pdb #3 --- Chain | Description A | No description available B | No description available > open D:/data/Projects/TycACOM/C-COMbun-rand2/cluster1_3.pdb Summary of feedback from opening D:/data/Projects/TycACOM/C-COMbun- rand2/cluster1_3.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_191w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_191.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster1_3.pdb #4 --- Chain | Description A | No description available B | No description available > open D:/data/Projects/TycACOM/C-COMbun-rand2/cluster1_4.pdb Summary of feedback from opening D:/data/Projects/TycACOM/C-COMbun- rand2/cluster1_4.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_91w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_91.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster1_4.pdb #5 --- Chain | Description A | No description available B | No description available > mmaker #2-5 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker TycCC1-full-ISOLDE.pdb, chain A (#1) with cluster1_1.pdb, chain A (#2), sequence alignment score = 1245.9 RMSD between 185 pruned atom pairs is 1.312 angstroms; (across all 445 pairs: 3.736) Matchmaker TycCC1-full-ISOLDE.pdb, chain A (#1) with cluster1_2.pdb, chain A (#3), sequence alignment score = 1218.5 RMSD between 181 pruned atom pairs is 1.306 angstroms; (across all 445 pairs: 3.770) Matchmaker TycCC1-full-ISOLDE.pdb, chain A (#1) with cluster1_3.pdb, chain A (#4), sequence alignment score = 1212.3 RMSD between 185 pruned atom pairs is 1.335 angstroms; (across all 445 pairs: 3.758) Matchmaker TycCC1-full-ISOLDE.pdb, chain A (#1) with cluster1_4.pdb, chain A (#5), sequence alignment score = 1176.5 RMSD between 185 pruned atom pairs is 1.279 angstroms; (across all 445 pairs: 3.712) > hide #5 models > hide #3 models > hide #2 models > close #2 > close #3 > close #5 > select #4/B:17 9 atoms, 8 bonds, 1 model selected > select up 86 atoms, 86 bonds, 1 model selected > select up 257 atoms, 259 bonds, 1 model selected > show sel atoms > hide sel cartoons > toolshed show Toolbar > vr true started SteamVR rendering Traceback (most recent call last): File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 614, in next_frame self.process_controller_events() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 642, in process_controller_events self.process_controller_buttons() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 659, in process_controller_buttons hc.process_event(e) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2213, in process_event self._dispatch_event(m, event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2217, in _dispatch_event mode.pressed(hand_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3025, in pressed self._click(hand_button_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3034, in _click m.vr_press(e) File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side AttributeError: 'NoneType' object has no attribute 'moving_side' Error processing trigger "new frame": AttributeError: 'NoneType' object has no attribute 'moving_side' File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side See log for complete Python traceback. > vr false > vr true started SteamVR rendering > torsion #4/B:15@HN,N,CA,CB 87.49 move large > torsion #4/B:15@N,CA,C,O -167.32 move large > torsion #4/B:14@N,CA,C,O 73.76 > torsion #4/B:14@N,CA,C,O -3.85 > torsion #4/B:14@CA #4/B:14@N #4/B:13@C #4/B:13@CA 134.22 > torsion #4/B:13@N,CA,C,O -85.54 > torsion #4/B:13@HN,N,CA,CB 61.83 Traceback (most recent call last): File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 614, in next_frame self.process_controller_events() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 642, in process_controller_events self.process_controller_buttons() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 659, in process_controller_buttons hc.process_event(e) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2213, in process_event self._dispatch_event(m, event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2217, in _dispatch_event mode.pressed(hand_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3025, in pressed self._click(hand_button_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3034, in _click m.vr_press(e) File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side AttributeError: 'NoneType' object has no attribute 'moving_side' Error processing trigger "new frame": AttributeError: 'NoneType' object has no attribute 'moving_side' File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side See log for complete Python traceback. > vr false > vr true started SteamVR rendering > torsion #4/B:13@N,CA,C,O -94.94 > torsion #4/B:13@CA #4/B:13@C #4/B:14@N #4/B:14@CA 136.52 move large > torsion #4/B:14@CA #4/B:14@N #4/B:13@C #4/B:13@CA 81.14 > torsion #4/B:12@HN,N,CA,CB -41.90 > torsion #4/B:12@CA #4/B:12@N #4/B:11@C #4/B:11@CA -160.48 > torsion #4/B:12@HN,N,CA,CB -55.97 > torsion #4/B:12@CA #4/B:12@N #4/B:11@C #4/B:11@CA -149.78 > torsion #4/B:11@N,CA,C,O 160.91 > torsion #4/B:11@CB,CA,N,HN -36.30 move large > torsion #4/B:11@CB,CA,N,HN -31.62 move large > torsion #4/B:11@HN,N,CA,CB -49.59 > vr false > select #4/a 4468 atoms, 4553 bonds, 1 model selected > delete sel > toolshed show ISOLDE > set selectionWidth 4 Chain information for TycCC1-full-ISOLDE.pdb --- Chain | Description 1.3/A | No description available Done loading forcefield Chain information for cluster1_3.pdb --- Chain | Description 2.3/B | No description available > select #4 Nothing selected > select #4 Nothing selected > select #4/b Nothing selected > select #2 257 atoms, 259 bonds, 8 models selected Bad residue number: 1 Adding hydrogens Summary of feedback from adding hydrogens to cluster1_3.pdb #2.3 --- notes | No usable SEQRES records for cluster1_3.pdb (#2.3) chain B; guessing termini instead Chain-initial residues that are actual N termini: cluster1_3.pdb #2.3/B THR 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: cluster1_3.pdb #2.3/B ARG 27 19 hydrogen bonds cluster1_3.pdb #2.3/B ARG 27 is not terminus, removing H atom from 'C' 169 hydrogens added > view > hide #!2.3 models > show #!2.3 models > hide #!2 models > show #!2 models > select #2 426 atoms, 428 bonds, 13 models selected > close session Traceback (most recent call last): File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\isolde\openmm\openmm_interface.py", line 994, in _sim_end_cb self._pr_sim_end_cb() File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\isolde\openmm\openmm_interface.py", line 1050, in _pr_sim_end_cb restraints = self.position_restraint_mgr.get_restraints(self.sim_construct.all_atoms) File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\isolde\molobject.py", line 2022, in get_restraints return self._get_restraints(atoms) File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\isolde\molobject.py", line 1975, in _get_restraints num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret)) AttributeError: 'Position_Restraint_Mgr' object has no attribute '_c_pointer' Error processing trigger "sim terminated": AttributeError: 'Position_Restraint_Mgr' object has no attribute '_c_pointer' File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\isolde\molobject.py", line 1975, in _get_restraints num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret)) See log for complete Python traceback. > open d:\data\Projects\TycACOM\TycC1C_K9D.pdb format PDB Summary of feedback from opening d:\data\Projects\TycACOM\TycC1C_K9D.pdb --- warning | Ignored bad PDB record found on line 7136 END Chain information for TycC1C_K9D.pdb #1 --- Chain | Description A | No description available > close session > open D:/data/Projects/TycACOM/C-COMbun-rand2/cluster1_1.pdb Summary of feedback from opening D:/data/Projects/TycACOM/C-COMbun- rand2/cluster1_1.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_46w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_46.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster1_1.pdb #1 --- Chain | Description A | No description available B | No description available > open D:/data/Projects/TycACOM/C-COMbun-rand2/cluster1_2.pdb Summary of feedback from opening D:/data/Projects/TycACOM/C-COMbun- rand2/cluster1_2.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_40w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_40.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster1_2.pdb #2 --- Chain | Description A | No description available B | No description available > open D:/data/Projects/TycACOM/C-COMbun-rand2/cluster1_3.pdb Summary of feedback from opening D:/data/Projects/TycACOM/C-COMbun- rand2/cluster1_3.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_191w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_191.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster1_3.pdb #3 --- Chain | Description A | No description available B | No description available > open D:/data/Projects/TycACOM/C-COMbun-rand2/cluster1_4.pdb Summary of feedback from opening D:/data/Projects/TycACOM/C-COMbun- rand2/cluster1_4.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_91w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_91.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 30 messages similar to the above omitted Chain information for cluster1_4.pdb #4 --- Chain | Description A | No description available B | No description available > mmaker #2-4 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker cluster1_1.pdb, chain A (#1) with cluster1_2.pdb, chain A (#2), sequence alignment score = 2247.8 RMSD between 445 pruned atom pairs is 0.395 angstroms; (across all 452 pairs: 0.737) Matchmaker cluster1_1.pdb, chain A (#1) with cluster1_3.pdb, chain A (#3), sequence alignment score = 2271.2 RMSD between 446 pruned atom pairs is 0.423 angstroms; (across all 452 pairs: 1.350) Matchmaker cluster1_1.pdb, chain A (#1) with cluster1_4.pdb, chain A (#4), sequence alignment score = 2212.4 RMSD between 445 pruned atom pairs is 0.428 angstroms; (across all 452 pairs: 1.016) > close #1-2 > close #4 > select /A:81 8 atoms, 7 bonds, 1 model selected > select up 46 atoms, 45 bonds, 1 model selected > select up 4468 atoms, 4553 bonds, 1 model selected > show sel surfaces > mlp sel Map values for surface "cluster1_3.pdb_A SES surface": minimum -25.32, mean -3.568, maximum 24.69 > toolshed show "Side View" > select /B:20 10 atoms, 9 bonds, 1 model selected > select up 86 atoms, 86 bonds, 1 model selected > select up 257 atoms, 259 bonds, 1 model selected > show sel atoms > hide sel cartoons > show sel surfaces > transparency 50 target s > select :lys,arg,asp,glu 1123 atoms, 1046 bonds, 1 model selected > show sel atoms > vr true started SteamVR rendering VR mode zoom Traceback (most recent call last): File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 614, in next_frame self.process_controller_events() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 642, in process_controller_events self.process_controller_buttons() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 659, in process_controller_buttons hc.process_event(e) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2213, in process_event self._dispatch_event(m, event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2217, in _dispatch_event mode.pressed(hand_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3025, in pressed self._click(hand_button_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3034, in _click m.vr_press(e) File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side AttributeError: 'NoneType' object has no attribute 'moving_side' Error processing trigger "new frame": AttributeError: 'NoneType' object has no attribute 'moving_side' File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side See log for complete Python traceback. > vr false > vr true started SteamVR rendering > torsion /B:12@N,CA,C,O -118.43 Traceback (most recent call last): File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 614, in next_frame self.process_controller_events() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 642, in process_controller_events self.process_controller_buttons() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 659, in process_controller_buttons hc.process_event(e) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2213, in process_event self._dispatch_event(m, event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2217, in _dispatch_event mode.pressed(hand_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3025, in pressed self._click(hand_button_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3034, in _click m.vr_press(e) File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side AttributeError: 'NoneType' object has no attribute 'moving_side' Error processing trigger "new frame": AttributeError: 'NoneType' object has no attribute 'moving_side' File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side See log for complete Python traceback. > vr false > vr true started SteamVR rendering > torsion /B:13@CA /B:13@N /B:12@C /B:12@CA -115.69 > torsion /B:12@N,CA,C,O 172.03 > torsion /B:13@CA /B:13@N /B:12@C /B:12@CA -80.66 > torsion /B:12@HN,N,CA,CB 23.18 > torsion /B:12@HN,N,CA,CB 43.92 > torsion /B:12@HN,N,CA,CB 63.75 > torsion /B:12@HN,N,CA,CB -43.96 > torsion /B:12@N,CA,C,O 98.93 > torsion /B:12@HN,N,CA,CB -47.85 > torsion /B:12@N,CA,C,O 23.97 > torsion /B:10@N,CA,C,O 77.12 > torsion /B:10@N,CA,C,O 148.60 > torsion /B:13@N,CA,C,O 169.23 > torsion /B:13@N,CA,C,O 158.18 Traceback (most recent call last): File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 614, in next_frame self.process_controller_events() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 642, in process_controller_events self.process_controller_buttons() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 659, in process_controller_buttons hc.process_event(e) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2213, in process_event self._dispatch_event(m, event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2217, in _dispatch_event mode.pressed(hand_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3025, in pressed self._click(hand_button_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3034, in _click m.vr_press(e) File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side AttributeError: 'NoneType' object has no attribute 'moving_side' Error processing trigger "new frame": AttributeError: 'NoneType' object has no attribute 'moving_side' File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side See log for complete Python traceback. > vr false > vr true started SteamVR rendering > torsion /B:14@N,CA,C,O 124.03 > torsion /B:14@N,CA,C,O 133.07 > torsion /B:14@N,CA,C,O 125.59 VR mode select > select /B:8@CA 1 atom, 1 model selected > select /B:8@CA 1 atom, 1 model selected > vr false > select /b 257 atoms, 259 bonds, 1 model selected > hide sel surfaces > select up 2 atoms, 1 bond, 1 model selected > select up 13 atoms, 12 bonds, 2 models selected > toolshed show Rotamers > swapaa interactive sel LYS lib Dunbrack > save session D:/data/Projects/TycACOM/TycACOM-TycB1C-complex-manual-from- cluster1.cxs > close session > open D:\data\Projects\TycACOM\TycACOM-TycB1C-complex-manual-from- cluster1.cxs format session opened ChimeraX session > select up 2 atoms, 1 bond, 1 model selected > select up 13 atoms, 12 bonds, 2 models selected > toolshed show Rotamers > swapaa interactive sel LYS lib Dunbrack > select 4725 atoms, 4812 bonds, 1 model selected > pwd Current working directory is: d:\data\Projects\TycACOM > save TycACOM-TycB1C-v3.pdb selectedOnly true > close session > open D:/data/Projects/TycACOM/TycACOM-TycB1C-v3.pdb Summary of feedback from opening D:/data/Projects/TycACOM/TycACOM- TycB1C-v3.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK FILENAME="complex_191w.pdb0" Ignored bad PDB record found on line 2 REMARK =============================================================== Ignored bad PDB record found on line 3 REMARK HADDOCK run for complex Ignored bad PDB record found on line 4 REMARK initial structure: complex_191.pdb Ignored bad PDB record found on line 5 REMARK final NOE weights: unambig 50 amb: 50 31 messages similar to the above omitted Chain information for TycACOM-TycB1C-v3.pdb #1 --- Chain | Description A | No description available B | No description available > select /A:23 9 atoms, 8 bonds, 1 model selected > select /A:10 12 atoms, 11 bonds, 1 model selected > select up 52 atoms, 52 bonds, 1 model selected > select up 4468 atoms, 4553 bonds, 1 model selected > mlp sel Map values for surface "TycACOM-TycB1C-v3.pdb_A SES surface": minimum -26.52, mean -3.558, maximum 26.83 > select /B:5 12 atoms, 12 bonds, 1 model selected > select up 65 atoms, 66 bonds, 1 model selected > select up 257 atoms, 259 bonds, 1 model selected > show sel atoms > hide sel cartoons > transparency 50 target s > select :lys,arg,asp,glu 1123 atoms, 1046 bonds, 1 model selected > show sel atoms > select up 2 atoms, 1 bond, 1 model selected > select up 13 atoms, 12 bonds, 1 model selected > toolshed show Rotamers > swapaa interactive sel LYS lib Dunbrack > show sel surfaces > transparency 50 target s > hide sel surfaces > swapaa #1/B:8 LYS criteria 3 retain false Using Dunbrack library TycACOM-TycB1C-v3.pdb #1/B LYS 8: phi -64.1, psi -29.4 trans Applying LYS rotamer (chi angles: -70.3 -179.1 -177.8 -64.9) to TycACOM- TycB1C-v3.pdb #1/B LYS 8 > addh Summary of feedback from adding hydrogens to TycACOM-TycB1C-v3.pdb #1 --- notes | No usable SEQRES records for TycACOM-TycB1C-v3.pdb (#1) chain A; guessing termini instead No usable SEQRES records for TycACOM-TycB1C-v3.pdb (#1) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A MET 1, /B THR 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A HIS 452, /B ARG 27 435 hydrogen bonds /A HIS 452 is not terminus, removing H atom from 'C' /B ARG 27 is not terminus, removing H atom from 'C' 3055 hydrogens added > select clear > select /B:1@CB 1 atom, 1 model selected > select up 2 atoms, 1 bond, 1 model selected > select up 16 atoms, 15 bonds, 2 models selected > select up 426 atoms, 428 bonds, 2 models selected > show sel surfaces > select up 7777 atoms, 7864 bonds, 2 models selected > select down 426 atoms, 428 bonds, 3 models selected > select /b 426 atoms, 428 bonds, 1 model selected > show sel surfaces > transparency 50 target s > vr true started SteamVR rendering VR mode bond rotation > torsion /B:12@HN,N,CA,CB -41.73 > torsion /B:12@HN,N,CA,CB -34.44 > show sel cartoons > open D:/data/Projects/TycACOM/TycAmodule-homology.pdb Summary of feedback from opening D:/data/Projects/TycACOM/TycAmodule- homology.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2019-08-01 Time 13:49:08 GMT Daylight Time +0100 (1564663748.34 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : C:\Users\fagec\Desktop\B4E_refine\XDS_ASCII_scaled1_R3toH3_2.4A.mtz 41 messages similar to the above omitted Chain information for TycAmodule-homology.pdb #2 --- Chain | Description | No description available > select #2 16925 atoms, 17110 bonds, 1 model selected VR mode translate selected models > show sel atoms > hide sel atoms > show sel atoms > hide sel cartoons VR mode bond rotation VR mode translate selected models VR mode bond rotation > torsion #2:1061@H,N,CA,HA -120.04 move large > show sel cartoons > hide sel cartoons > torsion #2:1060@H #2:1060@N #2:1059@C #2:1059@CA -102.70 move large > torsion #2:1061@H,N,CA,HA 116.26 move large Traceback (most recent call last): File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 614, in next_frame self.process_controller_events() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 642, in process_controller_events self.process_controller_buttons() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 659, in process_controller_buttons hc.process_event(e) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2213, in process_event self._dispatch_event(m, event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2217, in _dispatch_event mode.pressed(hand_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3025, in pressed self._click(hand_button_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3034, in _click m.vr_press(e) File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side AttributeError: 'NoneType' object has no attribute 'moving_side' Error processing trigger "new frame": AttributeError: 'NoneType' object has no attribute 'moving_side' File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side See log for complete Python traceback. > vr false > vr true started SteamVR rendering > torsion #2:1066@O,C,CA,N -133.77 VR mode translate selected models > show sel cartoons > hide sel cartoons VR mode bond rotation > torsion #2:1060@H #2:1060@N #2:1059@C #2:1059@CA 1.80 move large > torsion #2:1059@H,N,CA,HA 177.97 move large > torsion #2:1059@H #2:1059@N #2:1058@C #2:1058@CA 37.62 move large > torsion #2:1058@HB2,CB,CA,N -74.12 > torsion #2:1058@N,CA,C,O 21.61 move large > torsion #2:1051@H #2:1051@N #2:1050@C #2:1050@CA 94.49 move large VR mode tug > vr false > close #2 > vr true started SteamVR rendering > ui mousemode rightMode "bond rotation" VR mode bond rotation Traceback (most recent call last): File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 614, in next_frame self.process_controller_events() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 642, in process_controller_events self.process_controller_buttons() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 659, in process_controller_buttons hc.process_event(e) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2213, in process_event self._dispatch_event(m, event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2217, in _dispatch_event mode.pressed(hand_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3025, in pressed self._click(hand_button_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3034, in _click m.vr_press(e) File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side AttributeError: 'NoneType' object has no attribute 'moving_side' Error processing trigger "new frame": AttributeError: 'NoneType' object has no attribute 'moving_side' File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side See log for complete Python traceback. > vr false > vr true started SteamVR rendering Traceback (most recent call last): File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py", line 130, in invoke return self._func(self._name, data) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 614, in next_frame self.process_controller_events() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 642, in process_controller_events self.process_controller_buttons() File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 659, in process_controller_buttons hc.process_event(e) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2213, in process_event self._dispatch_event(m, event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 2217, in _dispatch_event mode.pressed(hand_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3025, in pressed self._click(hand_button_event) File "D:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 3034, in _click m.vr_press(e) File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side AttributeError: 'NoneType' object has no attribute 'moving_side' Error processing trigger "new frame": AttributeError: 'NoneType' object has no attribute 'moving_side' File "D:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\bond_rot\mouse_rot.py", line 85, in vr_press atom1 = br.moving_side See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 418.91 OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → VR |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problem with hacked code: bond rotater is None |
comment:2 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Fixed.
The error happened when the VR button is pressed and the cone does not point at a bond. The new code to allow rotating either side of a bond was not checking for the case where no bond was picked.