id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15840 addh slow Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22631 ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Perhaps it's just been a while since I did anything with something so large, but adding hydrogens to 7mq8 seems to take an unusually long time (almost 17 minutes to add 226,148 hydrogens). Out of curiosity I ran it with the Python profiler, which shows that about 90% of the time is going into struct_edit.add_atom() taking about 4ms per call, which feels surprising (is each addition triggering some callback that could be deferred to the end in cases like this?): from chimerax.core.commands import run command = ""time addh"" %prun -s cumulative run(session, command) 78127107 function calls (78109096 primitive calls) in 1003.590 seconds Ordered by: cumulative time ncalls tottime percall cumtime percall filename:lineno(function) 15/1 0.000 0.000 1003.702 1003.702 {built-in method builtins.exec} 2/1 0.000 0.000 1003.702 1003.702 run.py:27(run) 2/1 0.001 0.000 1003.702 1003.702 cli.py:3116(run) 1 0.000 0.000 1003.672 1003.672 time.py:25(time) 1 0.016 0.016 1003.403 1003.403 cmd.py:35(cmd_addh) 1 0.058 0.058 1003.283 1003.283 cmd.py:165(hbond_add_hydrogens) 1 4.599 4.599 990.889 990.889 hbond.py:39(add_hydrogens) 149426 0.703 0.000 918.421 0.006 hbond.py:899(_attach_hydrogens) 149426 1.136 0.000 917.718 0.006 cmd.py:890(add_altloc_hyds) 226527 1.922 0.000 916.529 0.004 cmd.py:924(new_hydrogen) 226839 887.754 0.004 908.497 0.004 struct_edit.py:42(add_atom) 156988 0.372 0.000 36.244 0.000 bond_geom.py:47(bond_positions) 100553 2.637 0.000 28.751 0.000 bond_geom.py:152(tetra_pos) 1 1.107 1.107 13.887 13.887 hbond.py:318(find_hbonds) 34100 0.531 0.000 11.850 0.000 bond_geom.py:235(angle_pos) 120411 1.225 0.000 11.089 0.000 plane.py:43(__init__) 19858 3.555 0.000 9.543 0.000 cmd.py:778(find_rotamer_nearest) 226839 2.101 0.000 9.391 0.000 struct_edit.py:160(add_bond) 144687 0.521 0.000 7.970 0.000 acceptor_geom.py:12(acc_syn_anti) 903884 1.750 0.000 7.486 0.000 matrix.py:438(normalize_vector) 43851 0.123 0.000 7.133 0.000 place.py:190(inverse) 55520 0.695 0.000 7.104 0.000 bond_geom.py:122(planar_pos) 43851 0.878 0.000 6.636 0.000 matrix.py:131(invert_matrix) 226526 2.177 0.000 6.307 0.000 cmd.py:1029(_h_name) 1 0.037 0.037 5.787 5.787 cmd.py:201(post_add) 244971 1.019 0.000 5.576 0.000 molc.py:173(get_prop) 43851 5.116 0.000 5.517 0.000 linalg.py:492(inv) 1 1.317 1.317 5.338 5.338 cmd.py:441(_prep_add) 174032 0.166 0.000 5.157 0.000 acceptor_geom.py:70(test_phi_psi) 120530 0.652 0.000 4.534 0.000 common_geom.py:17(test_phi) 987477 2.500 0.000 4.473 0.000 linalg.py:2383(norm) Log: > isolde shorthand Initialising ISOLDE-specific command aliases: Alias Equivalent full command ------------------------------------------------- st isolde step {arguments} aw isolde add water {arguments} awsf isolde add water {arguments} sim false al isolde add ligand {arguments} aa isolde add aa $1 sel {arguments} ht isolde mod his sel {arguments} so setattr sel atoms occupancy {arguments} ab isolde adjust bfactors {arguments} ss isolde sim start sel rt isolde release torsions sel {arguments} rd isolde release distances sel {arguments} ra rd; rt pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color {arguments} bychain; color {arguments} byhet cs clipper set contourSensitivity {arguments} UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7mq8 format mmcif fromDatabase pdb 7mq8 title: Cryo-EM structure of the human SSU processome, state pre-A1 [more info...] Chain information for 7mq8 #1 --- Chain | Description | UniProt L0 | 5'ETS rRNA | L1 | 18S rRNA | L2 | U3 snoRNA | L3 | 40S ribosomal protein S18 | L4 | 40S ribosomal protein S4, X isoform | RS4X_HUMAN 1-263 L5 | 40S ribosomal protein S5 | RS5_HUMAN 1-204 L6 | 40S ribosomal protein S6 | RS6_HUMAN 1-249 L7 | 40S ribosomal protein S7 | RS7_HUMAN 1-194 L8 | 40S ribosomal protein S8 | RS8_HUMAN 1-208 L9 | 40S ribosomal protein S9 | RS9_HUMAN 1-194 LA | 40S ribosomal protein S12 | RS12_HUMAN 1-132 LC | 40S ribosomal protein S16 | RS16_HUMAN 1-146 LD | 40S ribosomal protein S11 | RS11_HUMAN 1-158 LF | 40S ribosomal protein S24 | RS24_HUMAN 1-133 LG | 40S ribosomal protein S28 | RS28_HUMAN 1-69 LH | WD repeat-containing protein 75 | WDR75_HUMAN 1-830 LI | Nucleolar protein 11 | LJ | U3 small nucleolar RNA-associated protein 15 homolog | UTP15_HUMAN 1-518 LK LL | WD repeat-containing protein 43 | WDR43_HUMAN 1-677 LM | HEAT repeat-containing protein 1 | HEAT1_HUMAN 1-2144 LN | U3 small nucleolar RNA-associated protein 4 homolog | UTP4_HUMAN 1-686 LO | Periodic tryptophan protein 2 homolog | PWP2_HUMAN 1-919 LP | U3 small nucleolar RNA-associated protein 6 homolog | UTP6_HUMAN 1-597 LQ | WD repeat-containing protein 3 | WDR3_HUMAN 1-943 LR | Transducin beta-like protein 3 | TBL3_HUMAN 1-808 LS | U3 small nucleolar RNA-associated protein 18 homolog | UTP18_HUMAN 1-556 LT | WD repeat-containing protein 36 | WDR36_HUMAN 1-951 LU | DDB1- and CUL4-associated factor 13 | DCA13_HUMAN 1-445 LW | WD repeat-containing protein 46 | WDR46_HUMAN 1-610 LZ | U3 small nucleolar ribonucleoprotein protein IMP3 | IMP3_HUMAN 1-184 N0 | 5'ETS rRNA | NA | U3 small nucleolar ribonucleoprotein protein MPP10 | MPP10_HUMAN 1-681 NB | Something about silencing protein 10 | SAS10_HUMAN 1-479 NC | Neuroguidin | NGDN_HUMAN 1-315 ND | Nucleolar protein 7 | NOL7_HUMAN 1-257 NE | Uncharacterized protein C1orf131 | CA131_HUMAN 1-293 NF | 40S ribosomal protein S13 | RS13_HUMAN 1-151 NG | 40S ribosomal protein S14 | RS14_HUMAN 1-151 NH | Nucleolar protein 6 | NOL6_HUMAN 1-1146 NI | Ribosomal RNA-processing protein 7 homolog A | RRP7A_HUMAN 1-280 NJ NK | RNA cytidine acetyltransferase | NAT10_HUMAN 1-1025 NM | 40S ribosomal protein S3a | RS3A_HUMAN 1-264 NN | Protein AATF | AATF_HUMAN 1-560 NO | 40S ribosomal protein S15a | RS15A_HUMAN 1-130 NQ | 40S ribosomal protein S27 | RS27_HUMAN 1-84 NR | RRP12-like protein | NT | Ubiquitin-40S ribosomal protein S27a | NU | 40S ribosomal protein S17 | RS17_HUMAN 1-135 NW | Nucleolar protein 10 | NOL10_HUMAN 1-688 NY | KRR1 small subunit processome component homolog | KRR1_HUMAN 1-381 SA | Nucleolar protein 56 | NOP56_HUMAN 1-594 SB | Nucleolar protein 58 | NOP58_HUMAN 1-529 SC SD | rRNA 2'-O-methyltransferase fibrillarin | FBRL_HUMAN 1-321 SE SF | NHP2-like protein 1 | NH2L1_HUMAN 1-128 SG | U3 small nucleolar RNA-interacting protein 2 | U3IP2_HUMAN 1-475 SH | RNA 3'-terminal phosphate cyclase-like protein | RCL1_HUMAN 1-373 SI | Ribosome biogenesis protein BMS1 homolog | SJ SK | Ribosomal RNA small subunit methyltransferase NEP1 | NEP1_HUMAN 1-244 SL | rRNA-processing protein FCF1 homolog | FCF1_HUMAN 1-198 SM | U3 small nucleolar ribonucleoprotein protein IMP4 | IMP4_HUMAN 1-291 SP | Small subunit processome component 20 homolog | UTP20_HUMAN 1-2785 SQ | Deoxynucleotidyltransferase terminal-interacting protein 2 | TDIF2_HUMAN 1-756 SR | 40S ribosomal protein S23 | RS23_HUMAN 1-143 SS | U3 small nucleolar RNA-associated protein 14 homolog A | UT14A_HUMAN 1-771 ST | Nucleolar protein 14 | SU | Nucleolar complex protein 4 homolog | SW | RNA-binding protein PNO1 | PNO1_HUMAN 1-252 SX | Unassigned peptides | SY | Probable U3 small nucleolar RNA-associated protein 11 | UTP11_HUMAN 1-253 SZ | Bystin | Non-standard residues in 7mq8 #1 --- ATP — adenosine-5'-triphosphate GTP — guanosine-5'-triphosphate MG — magnesium ion SAH — S-adenosyl-L-homocysteine ZN — zinc ion 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > ui tool show Shell 0.01s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. > time addh > addh Summary of feedback from adding hydrogens to 7mq8 #1 --- warnings | Not adding hydrogens to /L0 G 431 P because it is missing heavy-atom bond partners Not adding hydrogens to /L1 A 2 P because it is missing heavy-atom bond partners Not adding hydrogens to /L2 G 3 P because it is missing heavy-atom bond partners Not adding hydrogens to /L3 UNK 88 CB because it is missing heavy-atom bond partners Not adding hydrogens to /L3 UNK 89 CB because it is missing heavy-atom bond partners 1738 messages similar to the above omitted Unknown hybridization for atom (P) of residue type N; not adding hydrogens to it The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /LQ PRO 341 N; /LT PRO 810 N; /NJ PRO 349 N; /NJ PRO 803 N; /LM PRO 1242 N; /NK PRO 349 N; /NJ PRO 806 N; /SU PRO 505 N; /NK PRO 803 N; /NK PRO 806 N; /NH PRO 284 N; /LM PRO 750 N; /NI PRO 100 N notes | Termini for 7mq8 (#1) chain L0 determined from SEQRES records Termini for 7mq8 (#1) chain L1 determined from SEQRES records Termini for 7mq8 (#1) chain L2 determined from SEQRES records Termini for 7mq8 (#1) chain L3 determined from SEQRES records Termini for 7mq8 (#1) chain L4 determined from SEQRES records 70 messages similar to the above omitted Chain-initial residues that are actual N termini: /L6 MET 1, /LF MET 1, /LI UNK 8, /LP MET 1, /LU MET 1, /NJ MET 1, /NK MET 1, /NR UNK 74, /SB MET 1, /SM MET 1, /SU UNK 7, /SX UNK 689, /SY MET 1, /SZ UNK 130 Chain-initial residues that are not actual N termini: /L3 SER 2, /L4 ALA 2, /L5 PRO 15, /L6 GLU 91, /L7 ILE 8, /L7 SER 119, /L8 GLY 2, /L8 GLU 151, /L9 LYS 11, /LA VAL 11, /LC GLY 5, /LD ALA 2, /LG GLN 7, /LH ILE 7, /LH THR 692, /LH ASN 716, /LH ASP 803, /LI PRO 165, /LI LEU 189, /LI LYS 205, /LI ASN 242, /LI GLY 262, /LI CYS 286, /LI GLN 310, /LI PRO 396, /LI SER 577, /LJ ALA 2, /LJ ASN 343, /LK PRO 463, /LL CYS 9, /LL GLN 93, /LL LYS 331, /LL ASP 456, /LL LYS 594, /LM THR 2, /LM SER 1202, /LM VAL 1368, /LM ALA 1438, /LM GLN 1457, /LM SER 1507, /LM GLY 1545, /LM GLU 1598, /LM GLU 1662, /LM VAL 1889, /LM ARG 1932, /LM PHE 1979, /LM LYS 2013, /LM ASP 2059, /LN GLY 2, /LN ALA 638, /LO LYS 2, /LO LYS 271, /LP SER 213, /LP GLN 296, /LP LEU 346, /LQ LYS 5, /LQ PRO 261, /LQ PRO 341, /LQ GLU 377, /LQ PRO 403, /LQ ARG 537, /LQ THR 753, /LQ ASN 793, /LQ SER 923, /LR PHE 11, /LR ASN 464, /LS ALA 62, /LS LYS 138, /LS ASP 215, /LT ARG 64, /LT SER 735, /LT PRO 810, /LW GLN 95, /LW SER 603, /LZ VAL 2, /NA GLU 355, /NA SER 468, /NA ILE 674, /NB ALA 407, /NC GLU 189, /ND ASN 169, /NE PHE 166, /NE LYS 253, /NE GLY 269, /NF GLY 2, /NG GLU 25, /NH GLU 76, /NI PRO 18, /NJ GLN 89, /NJ ASP 178, /NJ LEU 228, /NJ LEU 423, /NJ ALA 457, /NJ GLY 602, /NJ GLU 669, /NJ GLY 762, /NK ASP 91, /NK SER 231, /NK ALA 457, /NK GLY 602, /NK GLU 682, /NK GLY 762, /NM THR 10, /NM GLU 245, /NN ALA 509, /NO VAL 2, /NQ PRO 2, /NT LYS 92, /NU ARG 5, /NW ASN 7, /NW ILE 43, /NW LEU 230, /NY GLY 39, /NY LYS 264, /SA VAL 2, /SA LYS 90, /SA HIS 353, /SC ASN 85, /SC LYS 131, /SD ARG 78, /SD LYS 131, /SE ALA 4, /SF VAL 6, /SG GLU 73, /SG PHE 103, /SG LYS 194, /SH HIS 6, /SI SER 49, /SI THR 369, /SI UNK 625, /SI ALA 664, /SI PRO 687, /SI HIS 727, /SI GLU 844, /SJ ARG 41, /SK ARG 41, /SL THR 7, /SP LYS 2, /SP GLU 492, /SP ARG 672, /SP GLU 787, /SP LYS 906, /SP ILE 1292, /SP ASN 1325, /SP PHE 1446, /SP ILE 1772, /SP ASP 1815, /SP ARG 1958, /SP ASP 2050, /SP LYS 2077, /SQ PHE 548, /SQ THR 593, /SR ALA 35, /SS ASN 121, /SS LEU 217, /SS LEU 664, /ST SER 29, /ST THR 493, /ST GLU 679, /ST GLN 787, /SU UNK 158, /SU PRO 203, /SU LYS 241, /SW GLU 73, /SY GLN 133, /SY GLN 185 Chain-final residues that are actual C termini: /L3 UNK 116, /L4 GLY 263, /L5 ARG 204, /LM PHE 2144, /LN THR 686, /LP LEU 597, /LQ THR 943, /LS PHE 556, /LU LYS 445, /LZ ALA 184, /NA LEU 681, /NB LYS 479, /NO PHE 130, /NR UNK 1029, /SE VAL 128, /SF VAL 128, /SH LYS 373, /SJ ILE 244, /SK ILE 244, /SL PHE 198, /SW PHE 252, /SX UNK 1472, /SY ARG 253 Chain-final residues that are not actual C termini: /L6 SER 78, /L6 SER 235, /L7 ILE 100, /L7 GLN 193, /L8 LYS 125, /L8 LYS 206, /L9 GLY 181, /LA CYS 130, /LC LYS 143, /LD ALA 148, /LF ARG 104, /LG LEU 68, /LH LYS 671, /LH ARG 703, /LH LYS 759, /LH ILE 827, /LI VAL 161, /LI MET 183, /LI LEU 195, /LI ILE 234, /LI VAL 255, /LI GLY 277, /LI LEU 303, /LI VAL 360, /LI SER 515, /LI LEU 718, /LJ ARG 318, /LJ MET 494, /LK THR 580, /LL PRO 69, /LL PRO 322, /LL ALA 413, /LL THR 580, /LL SER 604, /LM GLU 1166, /LM ASP 1361, /LM VAL 1428, /LM PHE 1454, /LM LYS 1472, /LM SER 1537, /LM LEU 1595, /LM GLN 1653, /LM ASP 1876, /LM LYS 1924, /LM ASN 1970, /LM THR 2007, /LM ALA 2055, /LN PRO 623, /LO ARG 239, /LO ARG 880, /LP PHE 200, /LP GLU 283, /LP LYS 339, /LQ LEU 223, /LQ HIS 332, /LQ SER 373, /LQ ASN 395, /LQ GLU 526, /LQ ALA 721, /LQ LYS 782, /LQ PHE 917, /LR SER 457, /LR LYS 789, /LS ARG 111, /LS GLU 198, /LT GLN 721, /LT GLN 806, /LT SER 948, /LW LEU 540, /LW VAL 609, /NA GLU 463, /NA LEU 599, /NC THR 282, /ND LYS 252, /NE ASP 236, /NE SER 261, /NE SER 288, /NF VAL 150, /NG THR 140, /NH SER 1141, /NI MET 251, /NJ GLN 77, /NJ GLU 174, /NJ PRO 221, /NJ ASN 414, /NJ GLN 434, /NJ ILE 585, /NJ CYS 658, /NJ THR 751, /NJ ALA 913, /NK LYS 61, /NK PRO 221, /NK GLN 434, /NK ARG 596, /NK PRO 657, /NK LEU 752, /NK ALA 913, /NM GLY 233, /NM ALA 253, /NN GLN 550, /NQ GLN 83, /NT CYS 149, /NU GLY 64, /NW LEU 14, /NW CYS 216, /NW THR 358, /NY PHE 246, /NY ILE 329, /SA SER 86, /SA LYS 340, /SA GLU 412, /SB SER 440, /SC SER 126, /SC PRO 317, /SD SER 126, /SD LYS 318, /SG GLU 99, /SG LYS 189, /SG PRO 468, /SI ASP 355, /SI GLY 402, /SI UNK 631, /SI GLN 683, /SI GLY 695, /SI THR 760, /SI GLY 1276, /SM THR 290, /SP GLN 474, /SP GLU 662, /SP ASN 776, /SP GLY 871, /SP PRO 1282, /SP THR 1313, /SP ALA 1435, /SP THR 1690, /SP SER 1797, /SP GLY 1938, /SP GLU 2032, /SP VAL 2066, /SP VAL 2238, /SQ ALA 582, /SQ ALA 744, /SR ARG 142, /SS LYS 209, /SS LYS 250, /SS VAL 737, /ST ASP 488, /ST SER 665, /ST LYS 772, /ST ARG 852, /SU LEU 153, /SU VAL 195, /SU ARG 221, /SU PHE 513, /SY LEU 126, /SY GLN 175, /SZ SER 423 Chain-initial residues that are not actual 5' termini: /L0 G 431, /L1 A 2, /L2 G 3 Missing OXT added to C-terminal residue /L3 UNK 116 Missing OXT added to C-terminal residue /L5 ARG 204 Missing OXT added to C-terminal residue /LM PHE 2144 Missing OXT added to C-terminal residue /LQ THR 943 Missing OXT added to C-terminal residue /LS PHE 556 6 messages similar to the above omitted 24047 hydrogen bonds Adding 'H' to /L3 SER 2 Adding 'H' to /L4 ALA 2 Adding 'H' to /L6 GLU 91 Adding 'H' to /L7 ILE 8 Adding 'H' to /L7 SER 119 149 messages similar to the above omitted /L6 SER 235 is not terminus, removing H atom from 'C' /L7 GLN 193 is not terminus, removing H atom from 'C' /L8 LYS 206 is not terminus, removing H atom from 'C' /L9 GLY 181 is not terminus, removing H atom from 'C' /LA CYS 130 is not terminus, removing H atom from 'C' 43 messages similar to the above omitted /L0 C 1435 is not terminus, removing H atom from O3' /L1 A 1860 is not terminus, removing H atom from O3' 226148 hydrogens added command time 1004 seconds draw time 1.925 seconds OpenGL version: 3.3.0 NVIDIA 555.85 OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: en_GB.cp1252 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: windows Manufacturer: HP Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC OS: Microsoft Windows 11 Pro (Build 22631) Memory: 34,007,068,672 MaxProcessMemory: 137,438,953,344 CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz OSLanguage: en-GB 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: 2024.6.2 cftime: 1.6.4 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: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 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: 1.2.7 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-Clipper: 0.23.1 ChimeraX-ColorActions: 1.0.5 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: 1.8 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: 1.2.4 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-ISOLDE: 1.8 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: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 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: 1.13.5 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: 3.0.15 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: 1.16.5 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: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 4.53.0 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: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 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: 24.1 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: 3.0.47 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: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 WMI: 1.5.1 }}} " defect closed normal Performance fixed all ChimeraX