addh slow

[Tristan Croll]

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:
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    beautifulsoup4: 4.12.3
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    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

[Eric Pettersen]

You are not hallucinating. Adding hydrogens to 7mq8 on my Mac using ChimeraX 1.5 took 34 seconds whereas with the daily build it took 476 seconds. Will investigate.

[Eric Pettersen]

Some recent-ish code in Residue.add_atom() to possibly adjust missing-structure pseudobonds when atoms got added was really slowing down hydrogen addition for large structures.

Fix: ​https://github.com/RBVI/ChimeraX/commit/c5ede1f962a8c3dec750cfa581ab38f42d7fc7ff