id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17297 Split molecule output arangarajan@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.26100 ChimeraX Version: 1.10.dev202504020144 (2025-04-02 01:44:35 UTC) Description when i save models to pdb , it is written out with several types of issues.. one i recently encountered is that each residue was written as a model and due to this i could not load this pdb into MOE. I encounter this type of error with written out only a single model or sel using save xxx.pdb sel t save xxx.pdb #2 i am not able to share the file due to confidentality issues. Log: UCSF ChimeraX version: 1.10.dev202504020144 (2025-04-02) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open D:/AR-9197-structure/PP_Class1/PP_Class1/6OLZ_fit178.pdb Summary of feedback from opening D:/AR-9197-structure/PP_Class1/PP_Class1/6OLZ_fit178.pdb --- warnings | Bad residue range for secondary structure: HELIX 36 36 GLU A 9 GLY A 177 1 169 Bad residue range for secondary structure: HELIX 37 37 ALA A 2 ASP A 206 1 205 Bad residue range for secondary structure: HELIX 55 55 PRO A 2 ALA A 148 1 147 Bad residue range for secondary structure: HELIX 59 59 THR A 7 PRO A 109 1 103 Bad residue range for secondary structure: HELIX 64 64 VAL A 2 LYS A 115 1 114 35 messages similar to the above omitted Chain information for 6OLZ_fit178.pdb #1 --- Chain | Description A | No description available A | No description available B | No description available B | No description available > open 6olz 6olz title: Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with PP tRNA [more info...] Chain information for 6olz #2 --- Chain | Description | UniProt A | Proprotein convertase subtilisin/kexin type 9 | PCSK9_HUMAN 0-25 A2 | 28S ribosomal RNA | A3 | 5.8S ribosomal RNA | A4 | 5S ribosomal RNA | AA | 60S ribosomal protein L8 | RL8_HUMAN 2-249 AB | 60S ribosomal protein L3 | RL3_HUMAN 2-395 AC | 60S ribosomal protein L4 | RL4_HUMAN 3-365 AD | 60S ribosomal protein L5 | RL5_HUMAN 4-297 AE | 60S ribosomal protein L6 | RL6_HUMAN 42-288 AF | 60S ribosomal protein L7 | RL7_HUMAN 15-248 AG | 60S ribosomal protein L7a | RL7A_HUMAN 29-262 AH | 60S ribosomal protein L9 | RL9_HUMAN 1-191 AI | 60S ribosomal protein L10 | RL10_HUMAN 3-213 AJ | 60S ribosomal protein L11 | RL11_HUMAN 9-177 AL | 60S ribosomal protein L13 | RL13_HUMAN 2-206 AM | 60S ribosomal protein L14 | RL14_HUMAN 2-140 AN | 60S ribosomal protein L15 | RL15_HUMAN 2-204 AO | 60S ribosomal protein L13a | RL13A_HUMAN 5-199 AP | 60S ribosomal protein L17 | RL17_HUMAN 2-154 AQ | 60S ribosomal protein L18 | RL18_HUMAN 2-188 AR | 60S ribosomal protein L19 | RL19_HUMAN 2-182 AS | 60S ribosomal protein L18a | RL18A_HUMAN 1-175 AT | 60S ribosomal protein L21 | RL21_HUMAN 2-158 AU | 60S ribosomal protein L22 | RL22_HUMAN 18-116 AV | 60S ribosomal protein L23 | Q9BTQ7_HUMAN 12-140 AW | 60S ribosomal protein L24 | RL24_HUMAN 2-122 AX | 60S ribosomal protein L23a | RL23A_HUMAN 39-155 AY | 60S ribosomal protein L26 | RL26_HUMAN 1-127 AZ | 60S ribosomal protein L27 | RL27_HUMAN 3-136 Aa | 60S ribosomal protein L27a | RL27A_HUMAN 2-148 Ab | 60S ribosomal protein L29 | RL29_HUMAN 2-119 Ac | 60S ribosomal protein L30 | RL30_HUMAN 7-109 Ad | 60S ribosomal protein L31 | RL31_HUMAN 18-123 Ae | 60S ribosomal protein L32 | RL32_HUMAN 2-130 Af | 60S ribosomal protein L35a | RL35A_HUMAN 2-110 Ag | 60S ribosomal protein L34 | RL34_HUMAN 2-115 Ah | 60S ribosomal protein L35 | RL35_HUMAN 2-123 Ai | 60S ribosomal protein L36 | RL36_HUMAN 5-101 Aj | 60S ribosomal protein L37 | RL37_HUMAN 2-85 Ak | 60S ribosomal protein L38 | RL38_HUMAN 2-70 Al | 60S ribosomal protein L39 | RL39_HUMAN 2-51 Am | 60S ribosomal protein L40 | RL40_HUMAN 78-127 An | 60S ribosomal protein L41 | RL41_HUMAN 1-25 Ao | 60S ribosomal protein L36a | RL36A_HUMAN 2-106 Ap | 60S ribosomal protein L37a | RL37A_HUMAN 2-92 At | 60S ribosomal protein L28 | RL28_HUMAN 2-123 B1 | 18S ribosomal RNA | BA | 40S ribosomal protein SA | RSSA_HUMAN 5-219 BB | 40S ribosomal protein S3a | RS3A_HUMAN 22-233 BC | 40S ribosomal protein S2 | RS2_HUMAN 57-278 BD | 40S ribosomal protein S3 | RS3_HUMAN 2-221 BE | 40S ribosomal protein S4, Y isoform 1 | RS4Y1_HUMAN 2-258 BF | 40S ribosomal protein S5 | RS5_HUMAN 15-204 BG | 40S ribosomal protein S6 | RS6_HUMAN 1-232 BH | 40S ribosomal protein S7 | RS7_HUMAN 12-194 BI | 40S ribosomal protein S8 | RS8_HUMAN 2-208 BJ | 40S ribosomal protein S9 | RS9_HUMAN 2-180 BK | 40S ribosomal protein S10 | RS10_HUMAN 1-98 BL | 40S ribosomal protein S11 | RS11_HUMAN 6-158 BM | 40S ribosomal protein S12 | RS12_HUMAN 11-130 BN | 40S ribosomal protein S13 | RS13_HUMAN 2-150 BO | 40S ribosomal protein S14 | RS14_HUMAN 16-151 BP | 40S ribosomal protein S15 | RS15_HUMAN 12-131 BQ | 40S ribosomal protein S16 | RS16_HUMAN 8-146 BR | 40S ribosomal protein S17 | RS17_HUMAN 2-126 BS | 40S ribosomal protein S18 | RS18_HUMAN 4-142 BT | 40S ribosomal protein S19 | RS19_HUMAN 2-144 BU | 40S ribosomal protein S20 | RS20_HUMAN 20-116 BV | 40S ribosomal protein S21 | RS21_HUMAN 1-81 BW | 40S ribosomal protein S15a | RS15A_HUMAN 2-130 BX | 40S ribosomal protein S23 | RS23_HUMAN 2-140 BY | 40S ribosomal protein S24 | RS24_HUMAN 4-128 BZ | 40S ribosomal protein S25 | RS25_HUMAN 28-113 Ba | 40S ribosomal protein S26 | RS26_HUMAN 2-98 Bb | 40S ribosomal protein S27 | RS27_HUMAN 4-83 Bc | 40S ribosomal protein S28 | RS28_HUMAN 7-68 Bd | 40S ribosomal protein S29 | RS29_HUMAN 5-55 Be | 40S ribosomal protein S30 | E9PR30_HUMAN 3-57 Bf | Ubiquitin-40S ribosomal protein S27a | RS27A_HUMAN 79-151 Bg | Receptor of activated protein C kinase 1 | RACK1_HUMAN 2-315 Bv | tRNA | Bx | mRNA | Non-standard residues in 6olz #2 --- MG — magnesium ion MVM — N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide ZN — zinc ion > mmaker #2 to #1 Computing secondary structure [Repeated 1 time(s)] 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 6OLZ_fit178.pdb, chain A (#1) with 6olz, chain A2 (#2), sequence alignment score = 22099.1 RMSD between 3643 pruned atom pairs is 0.001 angstroms; (across all 3643 pairs: 0.001) > select #2 /Bv 1625 atoms, 1813 bonds, 77 pseudobonds, 78 residues, 3 models selected > ~select Nothing selected > split #2 Split 6olz (#2) into 82 models Chain information for 6olz A #2.1 --- Chain | Description A | No description available Chain information for 6olz A2 #2.2 --- Chain | Description A2 | No description available Chain information for 6olz A3 #2.3 --- Chain | Description A3 | No description available Chain information for 6olz A4 #2.4 --- Chain | Description A4 | No description available Chain information for 6olz AA #2.5 --- Chain | Description AA | No description available Chain information for 6olz AB #2.6 --- Chain | Description AB | No description available Chain information for 6olz AC #2.7 --- Chain | Description AC | No description available Chain information for 6olz AD #2.8 --- Chain | Description AD | No description available Chain information for 6olz AE #2.9 --- Chain | Description AE | No description available Chain information for 6olz AF #2.10 --- Chain | Description AF | No description available Chain information for 6olz AG #2.11 --- Chain | Description AG | No description available Chain information for 6olz AH #2.12 --- Chain | Description AH | No description available Chain information for 6olz AI #2.13 --- Chain | Description AI | No description available Chain information for 6olz AJ #2.14 --- Chain | Description AJ | No description available Chain information for 6olz AL #2.15 --- Chain | Description AL | No description available Chain information for 6olz AM #2.16 --- Chain | Description AM | No description available Chain information for 6olz AN #2.17 --- Chain | Description AN | No description available Chain information for 6olz AO #2.18 --- Chain | Description AO | No description available Chain information for 6olz AP #2.19 --- Chain | Description AP | No description available Chain information for 6olz AQ #2.20 --- Chain | Description AQ | No description available Chain information for 6olz AR #2.21 --- Chain | Description AR | No description available Chain information for 6olz AS #2.22 --- Chain | Description AS | No description available Chain information for 6olz AT #2.23 --- Chain | Description AT | No description available Chain information for 6olz AU #2.24 --- Chain | Description AU | No description available Chain information for 6olz AV #2.25 --- Chain | Description AV | No description available Chain information for 6olz AW #2.26 --- Chain | Description AW | No description available Chain information for 6olz AX #2.27 --- Chain | Description AX | No description available Chain information for 6olz AY #2.28 --- Chain | Description AY | No description available Chain information for 6olz AZ #2.29 --- Chain | Description AZ | No description available Chain information for 6olz Aa #2.30 --- Chain | Description Aa | No description available Chain information for 6olz Ab #2.31 --- Chain | Description Ab | No description available Chain information for 6olz Ac #2.32 --- Chain | Description Ac | No description available Chain information for 6olz Ad #2.33 --- Chain | Description Ad | No description available Chain information for 6olz Ae #2.34 --- Chain | Description Ae | No description available Chain information for 6olz Af #2.35 --- Chain | Description Af | No description available Chain information for 6olz Ag #2.36 --- Chain | Description Ag | No description available Chain information for 6olz Ah #2.37 --- Chain | Description Ah | No description available Chain information for 6olz Ai #2.38 --- Chain | Description Ai | No description available Chain information for 6olz Aj #2.39 --- Chain | Description Aj | No description available Chain information for 6olz Ak #2.40 --- Chain | Description Ak | No description available Chain information for 6olz Al #2.41 --- Chain | Description Al | No description available Chain information for 6olz Am #2.42 --- Chain | Description Am | No description available Chain information for 6olz An #2.43 --- Chain | Description An | No description available Chain information for 6olz Ao #2.44 --- Chain | Description Ao | No description available Chain information for 6olz Ap #2.45 --- Chain | Description Ap | No description available Chain information for 6olz At #2.46 --- Chain | Description At | No description available Chain information for 6olz B1 #2.47 --- Chain | Description B1 | No description available Chain information for 6olz BA #2.48 --- Chain | Description BA | No description available Chain information for 6olz BB #2.49 --- Chain | Description BB | No description available Chain information for 6olz BC #2.50 --- Chain | Description BC | No description available Chain information for 6olz BD #2.51 --- Chain | Description BD | No description available Chain information for 6olz BE #2.52 --- Chain | Description BE | No description available Chain information for 6olz BF #2.53 --- Chain | Description BF | No description available Chain information for 6olz BG #2.54 --- Chain | Description BG | No description available Chain information for 6olz BH #2.55 --- Chain | Description BH | No description available Chain information for 6olz BI #2.56 --- Chain | Description BI | No description available Chain information for 6olz BJ #2.57 --- Chain | Description BJ | No description available Chain information for 6olz BK #2.58 --- Chain | Description BK | No description available Chain information for 6olz BL #2.59 --- Chain | Description BL | No description available Chain information for 6olz BM #2.60 --- Chain | Description BM | No description available Chain information for 6olz BN #2.61 --- Chain | Description BN | No description available Chain information for 6olz BO #2.62 --- Chain | Description BO | No description available Chain information for 6olz BP #2.63 --- Chain | Description BP | No description available Chain information for 6olz BQ #2.64 --- Chain | Description BQ | No description available Chain information for 6olz BR #2.65 --- Chain | Description BR | No description available Chain information for 6olz BS #2.66 --- Chain | Description BS | No description available Chain information for 6olz BT #2.67 --- Chain | Description BT | No description available Chain information for 6olz BU #2.68 --- Chain | Description BU | No description available Chain information for 6olz BV #2.69 --- Chain | Description BV | No description available Chain information for 6olz BW #2.70 --- Chain | Description BW | No description available Chain information for 6olz BX #2.71 --- Chain | Description BX | No description available Chain information for 6olz BY #2.72 --- Chain | Description BY | No description available Chain information for 6olz BZ #2.73 --- Chain | Description BZ | No description available Chain information for 6olz Ba #2.74 --- Chain | Description Ba | No description available Chain information for 6olz Bb #2.75 --- Chain | Description Bb | No description available Chain information for 6olz Bc #2.76 --- Chain | Description Bc | No description available Chain information for 6olz Bd #2.77 --- Chain | Description Bd | No description available Chain information for 6olz Be #2.78 --- Chain | Description Be | No description available Chain information for 6olz Bf #2.79 --- Chain | Description Bf | No description available Chain information for 6olz Bg #2.80 --- Chain | Description Bg | No description available Chain information for 6olz Bv #2.81 --- Chain | Description Bv | No description available Chain information for 6olz Bx #2.82 --- Chain | Description Bx | No description available > select #2.81 1625 atoms, 1813 bonds, 77 pseudobonds, 78 residues, 3 models selected > select ~sel 426805 atoms, 458192 bonds, 5668 pseudobonds, 34738 residues, 108 models selected > hide sel target a > cartoon > select ~sel 1625 atoms, 1813 bonds, 77 pseudobonds, 78 residues, 3 models selected > hide > hide target c > select #2.81 1625 atoms, 1813 bonds, 77 pseudobonds, 78 residues, 3 models selected > show sel target c > save trna-for-fitted-AR-model.pdb selectedOnly true > close session > open ""C:/Users/Amith Rangarajan/Desktop/trna-for-fitted-AR-model.pdb"" Chain information for trna-for-fitted-AR-model.pdb #1 --- Chain | Description Bv | No description available Computing secondary structure > close session > open D:/AR-9197-structure/PP_Class1/PP_Class1/generate-6olz-model.cxc > open 6OLZ_fit178.pdb Summary of feedback from opening 6OLZ_fit178.pdb --- warnings | Bad residue range for secondary structure: HELIX 36 36 GLU A 9 GLY A 177 1 169 Bad residue range for secondary structure: HELIX 37 37 ALA A 2 ASP A 206 1 205 Bad residue range for secondary structure: HELIX 55 55 PRO A 2 ALA A 148 1 147 Bad residue range for secondary structure: HELIX 59 59 THR A 7 PRO A 109 1 103 Bad residue range for secondary structure: HELIX 64 64 VAL A 2 LYS A 115 1 114 35 messages similar to the above omitted Chain information for 6OLZ_fit178.pdb #1 --- Chain | Description A | No description available A | No description available B | No description available B | No description available > open 6olz 6olz title: Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with PP tRNA [more info...] Chain information for 6olz #2 --- Chain | Description | UniProt A | Proprotein convertase subtilisin/kexin type 9 | PCSK9_HUMAN 0-25 A2 | 28S ribosomal RNA | A3 | 5.8S ribosomal RNA | A4 | 5S ribosomal RNA | AA | 60S ribosomal protein L8 | RL8_HUMAN 2-249 AB | 60S ribosomal protein L3 | RL3_HUMAN 2-395 AC | 60S ribosomal protein L4 | RL4_HUMAN 3-365 AD | 60S ribosomal protein L5 | RL5_HUMAN 4-297 AE | 60S ribosomal protein L6 | RL6_HUMAN 42-288 AF | 60S ribosomal protein L7 | RL7_HUMAN 15-248 AG | 60S ribosomal protein L7a | RL7A_HUMAN 29-262 AH | 60S ribosomal protein L9 | RL9_HUMAN 1-191 AI | 60S ribosomal protein L10 | RL10_HUMAN 3-213 AJ | 60S ribosomal protein L11 | RL11_HUMAN 9-177 AL | 60S ribosomal protein L13 | RL13_HUMAN 2-206 AM | 60S ribosomal protein L14 | RL14_HUMAN 2-140 AN | 60S ribosomal protein L15 | RL15_HUMAN 2-204 AO | 60S ribosomal protein L13a | RL13A_HUMAN 5-199 AP | 60S ribosomal protein L17 | RL17_HUMAN 2-154 AQ | 60S ribosomal protein L18 | RL18_HUMAN 2-188 AR | 60S ribosomal protein L19 | RL19_HUMAN 2-182 AS | 60S ribosomal protein L18a | RL18A_HUMAN 1-175 AT | 60S ribosomal protein L21 | RL21_HUMAN 2-158 AU | 60S ribosomal protein L22 | RL22_HUMAN 18-116 AV | 60S ribosomal protein L23 | Q9BTQ7_HUMAN 12-140 AW | 60S ribosomal protein L24 | RL24_HUMAN 2-122 AX | 60S ribosomal protein L23a | RL23A_HUMAN 39-155 AY | 60S ribosomal protein L26 | RL26_HUMAN 1-127 AZ | 60S ribosomal protein L27 | RL27_HUMAN 3-136 Aa | 60S ribosomal protein L27a | RL27A_HUMAN 2-148 Ab | 60S ribosomal protein L29 | RL29_HUMAN 2-119 Ac | 60S ribosomal protein L30 | RL30_HUMAN 7-109 Ad | 60S ribosomal protein L31 | RL31_HUMAN 18-123 Ae | 60S ribosomal protein L32 | RL32_HUMAN 2-130 Af | 60S ribosomal protein L35a | RL35A_HUMAN 2-110 Ag | 60S ribosomal protein L34 | RL34_HUMAN 2-115 Ah | 60S ribosomal protein L35 | RL35_HUMAN 2-123 Ai | 60S ribosomal protein L36 | RL36_HUMAN 5-101 Aj | 60S ribosomal protein L37 | RL37_HUMAN 2-85 Ak | 60S ribosomal protein L38 | RL38_HUMAN 2-70 Al | 60S ribosomal protein L39 | RL39_HUMAN 2-51 Am | 60S ribosomal protein L40 | RL40_HUMAN 78-127 An | 60S ribosomal protein L41 | RL41_HUMAN 1-25 Ao | 60S ribosomal protein L36a | RL36A_HUMAN 2-106 Ap | 60S ribosomal protein L37a | RL37A_HUMAN 2-92 At | 60S ribosomal protein L28 | RL28_HUMAN 2-123 B1 | 18S ribosomal RNA | BA | 40S ribosomal protein SA | RSSA_HUMAN 5-219 BB | 40S ribosomal protein S3a | RS3A_HUMAN 22-233 BC | 40S ribosomal protein S2 | RS2_HUMAN 57-278 BD | 40S ribosomal protein S3 | RS3_HUMAN 2-221 BE | 40S ribosomal protein S4, Y isoform 1 | RS4Y1_HUMAN 2-258 BF | 40S ribosomal protein S5 | RS5_HUMAN 15-204 BG | 40S ribosomal protein S6 | RS6_HUMAN 1-232 BH | 40S ribosomal protein S7 | RS7_HUMAN 12-194 BI | 40S ribosomal protein S8 | RS8_HUMAN 2-208 BJ | 40S ribosomal protein S9 | RS9_HUMAN 2-180 BK | 40S ribosomal protein S10 | RS10_HUMAN 1-98 BL | 40S ribosomal protein S11 | RS11_HUMAN 6-158 BM | 40S ribosomal protein S12 | RS12_HUMAN 11-130 BN | 40S ribosomal protein S13 | RS13_HUMAN 2-150 BO | 40S ribosomal protein S14 | RS14_HUMAN 16-151 BP | 40S ribosomal protein S15 | RS15_HUMAN 12-131 BQ | 40S ribosomal protein S16 | RS16_HUMAN 8-146 BR | 40S ribosomal protein S17 | RS17_HUMAN 2-126 BS | 40S ribosomal protein S18 | RS18_HUMAN 4-142 BT | 40S ribosomal protein S19 | RS19_HUMAN 2-144 BU | 40S ribosomal protein S20 | RS20_HUMAN 20-116 BV | 40S ribosomal protein S21 | RS21_HUMAN 1-81 BW | 40S ribosomal protein S15a | RS15A_HUMAN 2-130 BX | 40S ribosomal protein S23 | RS23_HUMAN 2-140 BY | 40S ribosomal protein S24 | RS24_HUMAN 4-128 BZ | 40S ribosomal protein S25 | RS25_HUMAN 28-113 Ba | 40S ribosomal protein S26 | RS26_HUMAN 2-98 Bb | 40S ribosomal protein S27 | RS27_HUMAN 4-83 Bc | 40S ribosomal protein S28 | RS28_HUMAN 7-68 Bd | 40S ribosomal protein S29 | RS29_HUMAN 5-55 Be | 40S ribosomal protein S30 | E9PR30_HUMAN 3-57 Bf | Ubiquitin-40S ribosomal protein S27a | RS27A_HUMAN 79-151 Bg | Receptor of activated protein C kinase 1 | RACK1_HUMAN 2-315 Bv | tRNA | Bx | mRNA | Non-standard residues in 6olz #2 --- MG — magnesium ion MVM — N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide ZN — zinc ion > mmaker #2 to #1 Computing secondary structure [Repeated 1 time(s)] 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 6OLZ_fit178.pdb, chain A (#1) with 6olz, chain A2 (#2), sequence alignment score = 22099.1 RMSD between 3643 pruned atom pairs is 0.001 angstroms; (across all 3643 pairs: 0.001) > save 6olz-rotated-for-AR-fitted-model.pdb #2 executed generate-6olz-model.cxc OpenGL version: 3.3.0 NVIDIA 560.94 OpenGL renderer: NVIDIA GeForce RTX 4070 Laptop GPU/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: en_US.cp1252 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: windows Manufacturer: LENOVO Model: 83DF OS: Microsoft Windows 11 Home (Build 26100) Memory: 34,070,192,128 MaxProcessMemory: 137,438,953,344 CPU: 32 Intel(R) Core(TM) i9-14900HX OSLanguage: en-US Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 asttokens: 3.0.0 auditwheel: 6.3.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.2.1 build: 1.2.2.post1 certifi: 2025.1.31 cftime: 1.6.4.post1 charset-normalizer: 3.4.1 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.1 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.5 ChimeraX-AtomicLibrary: 14.1.13 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 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: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.dev202504020144 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.5.3 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.8 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 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-MutationScores: 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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.7 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: 1.1.2 ChimeraX-ProfileGrids: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 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: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.4.10 contourpy: 1.3.1 coverage: 7.8.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.13 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.56.0 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h5py: 3.13.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.7 pluggy: 1.5.0 prompt_toolkit: 3.0.50 psutil: 7.0.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.3.5 pytest-cov: 6.1.0 python-dateutil: 2.9.0.post0 pytz: 2025.2 pywin32: 310 pyzmq: 26.3.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 75.8.2 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.13.0 tzdata: 2025.2 urllib3: 2.3.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.13 WMI: 1.5.1 }}} " defect closed normal Input/Output not a bug all ChimeraX