Add Charge: dictionary changed size during iteration

[ym337@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202101290040 (2021-01-29 00:40:04 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.dev202101290040 (2021-01-29)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5gup

Summary of feedback from opening 5gup fetched from pdb  
---  
warnings | Atom OG has no neighbors to form bonds with according to residue
template for SER /2:79  
Atom OG has no neighbors to form bonds with according to residue template for
SER /4:79  
  
5gup title:  
Cryo-EM structure of mammalian respiratory supercomplex I1III2IV1 [more
info...]  
  
Chain information for 5gup #1  
---  
Chain | Description  
0 Ab | Cytochrome b-c1 complex subunit 6, mitochondrial  
1 Ac | Cytochrome b-c1 complex subunit 9  
2 4 | Cytochrome b-c1 complex subunit Rieske, mitochondrial  
3 Ad | Cytochrome b-c1 complex subunit 10  
5 u | Cytochrome b-c1 complex subunit 1, mitochondrial  
6 v | Cytochrome b-c1 complex subunit 2, mitochondrial  
7 w | Cytochrome b  
8 x | Cytochrome c1, heme protein, mitochondrial  
9 y | Cytochrome b-c1 complex subunit 7  
A | Cytochrome c oxidase subunit 6C  
Aa z | Cytochrome b-c1 complex subunit 8  
Ae Af | Cytochrome b-c1 complex subunit Rieske transit peptide, mitochondrial  
Ag | Cytochrome c oxidase subunit 8B, mitochondrial  
Ah | Cytochrome c oxidase subunit 7A1, mitochondrial  
Ai | Cytochrome c oxidase subunit 7B, mitochondrial  
Aj | Cytochrome c oxidase subunit 7C, mitochondrial  
Ak | Cytochrome c oxidase subunit 1  
Al | Cytochrome c oxidase subunit 2  
Am | Cytochrome c oxidase subunit 3  
An | Cytochrome c oxidase subunit 4 isoform 1, mitochondrial  
Ao | Cytochrome c oxidase subunit 5A, mitochondrial  
Ap | Cytochrome c oxidase subunit 5B, mitochondrial  
Aq | Cytochrome c oxidase subunit 6A, mitochondrial  
Ar | Cytochrome c oxidase subunit 6B1  
B | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial  
C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial  
D | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial  
E | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial  
F | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial  
G | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial  
H | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial  
I | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial  
J | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial  
K R | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 12  
L | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 9, mitochondrial  
M | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 7  
N | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 5  
O X | Acyl carrier protein, mitochondrial  
P | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 2  
Q | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 6  
S | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 1  
T | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 3  
U | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial  
V | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 11  
W | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 13  
Y | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 2, mitochondrial  
Z | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 3  
a | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 5, mitochondrial  
b | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 6  
c | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 8, mitochondrial  
d | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 10  
e | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 11, mitochondrial  
f | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial  
g | NADH dehydrogenase [ubiquinone] 1 subunit C2  
h | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5  
i | NADH-ubiquinone oxidoreductase chain 2  
j | NADH-ubiquinone oxidoreductase chain 3  
k | NADH-ubiquinone oxidoreductase chain 4L  
l | NADH-ubiquinone oxidoreductase chain 5  
m | NADH-ubiquinone oxidoreductase chain 6  
n | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 1  
o | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 4  
p | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 9  
q | NADH-ubiquinone oxidoreductase chain 4  
r | NADH-ubiquinone oxidoreductase chain 1  
s | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 8  
t | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 7  
  
Non-standard residues in 5gup #1  
---  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
CU — copper (II) ion  
FES — FE2/S2 (inorganic) cluster  
FMN — flavin mononucleotide (riboflavin monophosphate)  
HEA — heme-A  
HEC — heme C  
HEM — protoporphyrin IX containing Fe (HEME)  
MG — magnesium ion  
NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate  
PEE — 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)  
PLX —
(9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2Λ~5~-aza-6Λ~5~-phosphaoctacosane-6,6,11-triol  
SF4 — iron/sulfur cluster  
ZMP — S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-
alanyl}amino)ethyl] tetradecanethioate  
ZN — zinc ion  
  

> open 9539 fromDatabase emdb

Summary of feedback from opening 9539 fetched from emdb  
---  
note | Fetching compressed map 9539 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-9539/map/emd_9539.map.gz  
  
Opened emdb 9539 as #2, grid size 480,480,480, pixel 1.08, shown at level
0.0349, step 2, values float32  

> oulombic #1 surface #2

Unknown command: oulombic #1 surface #2  

> coulombic #1 surfaces #2

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/2 SER 79  
/3 GLU 12  
/3 MET 23  
/4 SER 79  
/6 TYR 55  
/6 GLU 452  
/8 MET 289  
/Aa LYS 82  
/Ad GLU 12  
/Ad ILE 18  
/Ad MET 23  
/Ae SER 6  
/Ae LEU 34  
/Ae PHE 49  
/Af ARG 27  
/Af LEU 34  
/Af PHE 49  
/Ah PHE 1  
/Ah GLU 7  
/B GLU 119  
/B LYS 329  
/B GLN 456  
/C LYS 56  
/C GLU 57  
/C THR 58  
/C HIS 60  
/C TRP 61  
/C LYS 62  
/C ASN 67  
/C ASP 68  
/C VAL 69  
/C ASP 70  
/C PRO 71  
/C PRO 72  
/C LYS 73  
/C ASP 74  
/C THR 75  
/C LEU 76  
/C VAL 77  
/C SER 78  
/C ASN 79  
/C ARG 323  
/D THR 43  
/D ARG 44  
/D GLN 123  
/D VAL 159  
/D TYR 160  
/D LYS 161  
/D ASN 164  
/D TRP 165  
/D GLU 167  
/D ASN 180  
/D ASP 190  
/D GLU 215  
/D GLU 240  
/D GLU 250  
/E ASN 48  
/E PRO 49  
/E ASP 50  
/E THR 51  
/E ASP 54  
/E PRO 218  
/E ARG 219  
/F PRO 75  
/F VAL 76  
/F SER 77  
/F GLU 78  
/F VAL 79  
/F SER 81  
/F ARG 82  
/F VAL 83  
/F ILE 84  
/F SER 85  
/F ASN 101  
/F LEU 102  
/F ASP 103  
/F LYS 104  
/F GLU 105  
/F THR 106  
/F LYS 107  
/F THR 108  
/F THR 110  
/F CYS 111  
/F TYR 113  
/F CYS 114  
/F LEU 116  
/F GLN 117  
/F PHE 118  
/G ASN 30  
/G LYS 428  
/G VAL 429  
/G LEU 431  
/G ILE 432  
/G SER 434  
/G PRO 435  
/G VAL 436  
/G ASP 437  
/G ASP 443  
/G ASP 447  
/G SER 448  
/G PRO 449  
/G LYS 450  
/G ILE 451  
/G LEU 452  
/G GLN 453  
/G ASP 454  
/G ILE 455  
/G SER 457  
/G ASN 459  
/G HIS 460  
/G GLN 464  
/G ARG 483  
/G GLN 498  
/G ARG 501  
/G LEU 502  
/G GLU 660  
/G ASN 663  
/G TYR 664  
/G PHE 665  
/G GLN 666  
/G GLN 667  
/G ASN 669  
/G GLU 670  
/G LEU 671  
/G SER 672  
/G LYS 673  
/G LEU 674  
/G VAL 675  
/G ASN 676  
/G GLN 677  
/G GLN 678  
/G LEU 679  
/G LEU 680  
/G ASP 682  
/G GLU 716  
/H LYS 51  
/H ARG 212  
/I SER 61  
/I ASP 105  
/I ASP 107  
/I ARG 216  
/J LYS 58  
/J LEU 59  
/J ASP 60  
/K MET 1  
/K GLU 2  
/K LEU 3  
/K VAL 4  
/K GLN 5  
/K VAL 6  
/K LEU 7  
/K ARG 8  
/K ARG 9  
/K LEU 11  
/K GLN 12  
/K GLN 13  
/K VAL 14  
/K SER 15  
/K HIS 17  
/K LEU 20  
/K ARG 21  
/K TYR 23  
/K LEU 24  
/K ARG 25  
/K VAL 26  
/K LEU 27  
/K PHE 28  
/K ARG 29  
/K ASN 31  
/K ASP 32  
/K VAL 33  
/K ARG 34  
/K VAL 35  
/K THR 37  
/K LEU 38  
/K VAL 39  
/K GLU 41  
/K ASP 42  
/K LYS 43  
/K TYR 44  
/K ASN 46  
/K LYS 47  
/K TYR 48  
/K TYR 49  
/K GLU 50  
/K ASP 51  
/K ASN 52  
/K LYS 53  
/K GLN 54  
/K PHE 55  
/K PHE 56  
/K ARG 58  
/K HIS 59  
/K ARG 60  
/K TRP 61  
/K VAL 62  
/K ILE 63  
/K TYR 64  
/K THR 65  
/K THR 66  
/K GLU 67  
/K MET 68  
/K ASN 69  
/K ARG 71  
/K ASP 72  
/K THR 73  
/K PHE 74  
/K TRP 75  
/K ASP 76  
/K VAL 77  
/K MET 81  
/K HIS 91  
/K CYS 92  
/K MET 93  
/K THR 94  
/K ASP 95  
/K ASP 96  
/K PRO 97  
/L LEU 40  
/L ILE 41  
/L ARG 85  
/L VAL 130  
/L LYS 175  
/L ARG 212  
/L LYS 233  
/L GLU 234  
/L GLU 311  
/L LYS 370  
/L VAL 375  
/L ASN 376  
/M ARG 6  
/M ARG 18  
/M ASP 19  
/M LEU 20  
/M GLN 21  
/M LYS 23  
/M LEU 24  
/M GLN 25  
/M LEU 26  
/M ARG 27  
/M TYR 28  
/M GLN 29  
/M GLU 30  
/M ILE 31  
/M MET 70  
/M SER 71  
/M SER 72  
/M GLN 73  
/M LYS 74  
/M GLU 91  
/M LEU 113  
/N LEU 5  
/N GLU 62  
/N LYS 66  
/N LYS 67  
/N ILE 116  
/O PRO 72  
/O PRO 73  
/O ASP 94  
/O PRO 95  
/O GLU 96  
/O LYS 97  
/O LEU 98  
/O LYS 106  
/O ASP 150  
/O LYS 151  
/O LYS 152  
/O ASP 153  
/O GLU 156  
/Q VAL 17  
/Q LYS 18  
/Q LYS 69  
/Q PRO 76  
/Q PRO 128  
/R TYR 127  
/R SER 128  
/R THR 129  
/R THR 130  
/R ARG 131  
/R LYS 132  
/R LYS 133  
/R ILE 134  
/R GLN 135  
/R GLU 136  
/R TRP 137  
/R VAL 138  
/R PRO 139  
/R PRO 140  
/R SER 141  
/R THR 142  
/R PRO 143  
/R TYR 144  
/S ASP 70  
/T ARG 4  
/T ILE 5  
/T LYS 10  
/T ASN 62  
/T LEU 84  
/U LEU 47  
/U GLU 49  
/U ARG 50  
/U THR 51  
/U THR 52  
/U ARG 53  
/U LYS 54  
/U LEU 55  
/U THR 56  
/U GLU 57  
/U THR 58  
/U SER 59  
/U LYS 60  
/U VAL 61  
/U ILE 62  
/U THR 63  
/U VAL 64  
/U ASP 65  
/U ASN 67  
/U ILE 68  
/U CYS 69  
/U SER 70  
/U LYS 72  
/U ARG 74  
/U LEU 75  
/U ARG 77  
/U GLU 78  
/U ILE 79  
/U GLU 81  
/U LYS 82  
/U LEU 83  
/U LEU 85  
/U ARG 86  
/U HIS 87  
/U PHE 88  
/U PRO 89  
/U GLU 90  
/U GLU 117  
/U LYS 118  
/U THR 155  
/U GLN 157  
/U GLU 162  
/U GLU 187  
/U GLU 199  
/U LEU 201  
/U HIS 204  
/U VAL 205  
/U VAL 206  
/U VAL 207  
/U TYR 208  
/U VAL 209  
/U ASP 210  
/U VAL 211  
/U PRO 212  
/U VAL 213  
/U PRO 214  
/U GLU 215  
/U ILE 216  
/U GLN 217  
/U SER 218  
/U ARG 219  
/U ILE 220  
/U GLN 221  
/U LYS 222  
/U LYS 223  
/U ASN 225  
/U PRO 226  
/U HIS 227  
/U GLU 228  
/U MET 229  
/U LYS 230  
/U ILE 231  
/U GLN 237  
/U ASP 238  
/U ASN 241  
/U LYS 244  
/U LYS 245  
/U LEU 248  
/U PRO 249  
/U GLU 250  
/U MET 251  
/U SER 252  
/U GLU 253  
/U LYS 254  
/U CYS 255  
/U GLU 256  
/U VAL 257  
/U LEU 258  
/U ARG 295  
/U ASP 327  
/U GLN 331  
/U LYS 332  
/U GLU 347  
/U ASP 348  
/U VAL 349  
/U ASP 351  
/U LYS 352  
/U LEU 356  
/U LYS 357  
/V GLN 79  
/V GLU 82  
/V LYS 83  
/V VAL 141  
/W LYS 7  
/W ARG 27  
/W MET 98  
/W LYS 99  
/W ASP 100  
/W GLU 108  
/W THR 144  
/X PRO 72  
/X PRO 73  
/X LYS 106  
/X ASP 150  
/X LYS 151  
/X LYS 152  
/X ASP 153  
/X GLU 156  
/Y HIS 39  
/Y ILE 40  
/Y GLU 41  
/Y ARG 43  
/Y TYR 44  
/Y ARG 45  
/Y GLN 46  
/Y GLN 49  
/Y LEU 50  
/Y TRP 74  
/Y HIS 75  
/Y ASP 76  
/Y SER 77  
/Y ASP 78  
/Y VAL 80  
/Y LEU 81  
/Y HIS 83  
/Y PHE 84  
/Y PRO 85  
/Y TYR 86  
/Y PRO 87  
/Y ASP 88  
/Y PRO 89  
/Y SER 90  
/Y GLN 91  
/Y TRP 92  
/Y THR 93  
/Y ASP 94  
/Y GLU 95  
/Y GLU 96  
/Y LEU 97  
/Z SER 12  
/Z LYS 13  
/Z MET 14  
/Z GLU 15  
/Z LEU 16  
/Z LYS 23  
/Z GLU 25  
/Z GLU 30  
/Z GLU 34  
/Z ARG 39  
/Z LEU 41  
/Z ARG 42  
/Z ASP 43  
/Z TRP 51  
/Z ASN 59  
/Z ASN 60  
/Z LYS 69  
/Z LYS 72  
/Z GLU 89  
/a LYS 52  
/a ILE 101  
/a GLU 103  
/a VAL 106  
/a GLU 111  
/a LYS 114  
/a ARG 123  
/a ASN 189  
/b ASP 7  
/b GLU 8  
/b LYS 9  
/b ARG 11  
/b LEU 12  
/b GLN 13  
/b GLN 14  
/b ARG 16  
/b GLU 17  
/b LYS 24  
/b ASP 25  
/b GLU 27  
/b SER 29  
/b PRO 30  
/b ARG 31  
/b GLU 32  
/b PRO 33  
/b VAL 34  
/b LEU 35  
/b PRO 36  
/b PRO 37  
/b LYS 49  
/b PHE 50  
/b LEU 51  
/b GLN 52  
/b ASP 53  
/b PRO 56  
/b TRP 57  
/b LYS 58  
/b ASN 59  
/b VAL 60  
/b ILE 61  
/b TYR 62  
/b LYS 63  
/b THR 64  
/b TYR 65  
/b ARG 66  
/b HIS 67  
/b ARG 103  
/b ILE 104  
/b PHE 105  
/b PRO 106  
/b ASP 108  
/b THR 109  
/b ILE 110  
/b LEU 111  
/b GLU 112  
/b THR 113  
/b GLU 115  
/b VAL 116  
/b ILE 117  
/b PRO 118  
/b LEU 119  
/b MET 120  
/b LYS 121  
/b GLU 122  
/b PHE 123  
/b PRO 124  
/b ASP 125  
/b GLN 126  
/c LYS 34  
/c ASP 35  
/c MET 36  
/c TYR 41  
/c LYS 43  
/c GLU 46  
/c GLU 47  
/c ARG 58  
/c VAL 59  
/c GLU 60  
/c ASP 61  
/c GLU 63  
/c ASP 67  
/c ASP 68  
/c ASP 74  
/c ASP 80  
/c ARG 81  
/c GLU 85  
/c GLU 103  
/c PHE 134  
/c GLU 148  
/c GLN 154  
/c PRO 155  
/c VAL 156  
/c PRO 158  
/c LYS 159  
/c GLN 160  
/c TYR 161  
/c PRO 162  
/c TYR 163  
/c ASN 164  
/c ASP 165  
/c LEU 166  
/c TYR 167  
/c LEU 168  
/c GLU 169  
/c ARG 170  
/c ASP 173  
/c PRO 174  
/c THR 175  
/c LYS 176  
/c GLU 177  
/c PRO 178  
/c GLU 179  
/c PRO 180  
/c VAL 181  
/d SER 4  
/d TRP 5  
/d ASP 6  
/d LYS 7  
/d ASP 8  
/d VAL 9  
/d TYR 10  
/d GLU 12  
/d ARG 15  
/d ARG 16  
/d THR 17  
/d PRO 18  
/d PRO 20  
/d PRO 22  
/d GLN 23  
/d THR 24  
/d SER 25  
/d LEU 26  
/d PRO 27  
/d ASN 28  
/d VAL 30  
/d THR 31  
/d TYR 32  
/d LEU 33  
/d THR 34  
/d LYS 35  
/d ILE 36  
/d PHE 37  
/d ASP 38  
/d LEU 39  
/d LEU 40  
/d VAL 41  
/d ASP 42  
/d ARG 43  
/d PRO 44  
/d VAL 45  
/d THR 46  
/d LEU 47  
/d ARG 49  
/d GLU 50  
/d PHE 51  
/d ILE 52  
/d GLU 53  
/d GLN 54  
/d GLN 55  
/d HIS 56  
/d LYS 58  
/d ASN 59  
/d GLU 67  
/d GLN 134  
/d GLU 166  
/d LYS 168  
/d LYS 171  
/d GLU 172  
/e ARG 54  
/e LEU 55  
/e GLN 56  
/e GLU 57  
/e ASP 58  
/e PRO 59  
/e ASP 60  
/e PRO 61  
/e GLU 62  
/e ASP 63  
/e GLU 64  
/e ARG 129  
/e GLU 130  
/e ASN 132  
/e LEU 134  
/f ASP 40  
/f ASN 73  
/g GLU 113  
/g ARG 122  
/h ILE 87  
/h LYS 88  
/h GLU 89  
/h LYS 91  
/h TYR 92  
/h THR 93  
/h PRO 94  
/h PRO 95  
/h PRO 96  
/h HIS 97  
/h HIS 98  
/h LEU 99  
/h LYS 101  
/h GLU 102  
/h ASP 103  
/h PRO 104  
/h ARG 105  
/i LYS 321  
/i ASN 347  
/j ARG 48  
/j PHE 51  
/k TYR 89  
/k GLN 91  
/k ASN 92  
/k LEU 95  
/k LEU 96  
/k GLN 97  
/l MET 1  
/l ASN 2  
/l LYS 434  
/l TYR 604  
/l HIS 605  
/l GLU 606  
/m TYR 105  
/m TYR 106  
/m LEU 108  
/m LYS 109  
/m GLU 110  
/m GLU 111  
/m GLU 112  
/m VAL 113  
/m GLU 114  
/m LYS 118  
/m PHE 119  
/m ASN 175  
/n ASN 3  
/n VAL 4  
/n LEU 5  
/n GLN 6  
/n ILE 7  
/n VAL 8  
/n LYS 34  
/n LYS 46  
/n ARG 47  
/n GLU 48  
/n LEU 49  
/o SER 2  
/o PHE 3  
/o LYS 7  
/o ASP 19  
/o GLU 22  
/o SER 41  
/o GLU 61  
/o GLU 118  
/o LYS 120  
/o LEU 121  
/o ASP 122  
/o GLN 123  
/o TYR 129  
/p SER 4  
/p TYR 9  
/p GLU 84  
/p SER 85  
/p LYS 138  
/p LEU 140  
/p GLN 141  
/p GLU 142  
/p GLU 143  
/p THR 144  
/p PRO 149  
/p ARG 150  
/p THR 151  
/p GLU 152  
/p LEU 154  
/p PRO 155  
/p PRO 156  
/p ARG 158  
/p LYS 159  
/p GLU 160  
/p MET 179  
/q MET 1  
/q TYR 459  
/r SER 318  
/s ILE 4  
/s VAL 5  
/s GLU 6  
/s GLU 80  
/s GLU 84  
/s LYS 130  
/s GLU 139  
/s GLU 149  
/s GLU 153  
/s GLU 155  
/s MET 172  
/t HIS 4  
/t LEU 5  
/t ARG 7  
/t ARG 8  
/t TYR 9  
/t LEU 10  
/t ASP 12  
/t ARG 21  
/t MET 22  
/t PRO 23  
/t THR 24  
/t PHE 25  
/t PRO 26  
/t PRO 27  
/t ASP 28  
/t TYR 29  
/t PHE 31  
/t PRO 32  
/t GLU 33  
/t ARG 34  
/t LYS 35  
/t GLU 36  
/t ARG 37  
/t GLU 38  
/t MET 39  
/t VAL 40  
/t THR 42  
/t GLN 43  
/t GLN 44  
/t GLU 45  
/t MET 46  
/t ASN 47  
/t ASP 48  
/t MET 52  
/t LEU 53  
/t GLN 54  
/t ASP 57  
/t GLN 65  
/t LYS 68  
/t LYS 70  
/t ARG 71  
/t ASP 72  
/t SER 73  
/t PHE 74  
/t PRO 75  
/t ASN 76  
/t PHE 77  
/t LEU 78  
/t GLU 83  
/t GLN 84  
/t ASP 86  
/t GLU 103  
/t GLU 105  
/t ARG 107  
/t LYS 112  
/t LYS 113  
/t GLU 116  
/t GLN 117  
/t ARG 118  
/t GLU 119  
/t GLU 121  
/t MET 122  
/t ARG 124  
/u THR 322  
/u HIS 323  
/v TYR 55  
/v GLU 452  
/x MET 289  

Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/coulombic/cmd.py", line 96, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/coulombic/coulombic.py", line 86, in assign_charges  
add_charges(session, charged_residues, method=charge_method, status=status)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/add_charge/charge.py", line 19, in add_charges  
uncharged_res_types = add_standard_charges(session, residues, status=status,
query_user=query_user,  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/add_charge/charge.py", line 176, in add_standard_charges  
for res_type, residues in uncharged_res_types.items():  
RuntimeError: dictionary changed size during iteration  
  
RuntimeError: dictionary changed size during iteration  
  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/add_charge/charge.py", line 176, in add_standard_charges  
for res_type, residues in uncharged_res_types.items():  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.11
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2.8 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Memory: 16 GB
      Boot ROM Version: 426.0.0.0.0
      SMC Version (system): 2.32f21

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H512)
      Kernel Version: Darwin 19.6.0
      Time since boot: 9 minutes

Graphics/Displays:

    Intel Iris Pro Graphics 6200:

      Chipset Model: Intel Iris Pro Graphics 6200
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1622
      Revision ID: 0x000a
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: ('en_US', 'UTF-8')
PySide2 version: 5.15.2
Qt version: 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.0
    backcall: 0.2.0
    biopython: 1.78
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.3.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.11.1
    ChimeraX-AtomicLibrary: 1.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.4
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202101290040
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.0.2
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.4
    ChimeraX-PDB: 2.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StrudelScore: 0.1
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.6
    ChimeraX-uniprot: 2.1
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.0
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.5.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    mrcfile: 1.2.0
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.2
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.8
    pandas: 1.2.0
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 20.3.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.8
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PySide2: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2020.5
    pyzmq: 20.0.0
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    recordtype: 1.3
    requests: 2.24.0
    scipy: 1.5.2
    Send2Trash: 1.5.0
    SEQCROW: 0.23
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    shiboken2: 5.15.2
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    stripy: 2.0.3
    suds-jurko: 0.6
    tables: 3.6.1
    threed-strudel: 0.3
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0