Save X3D: numpy array used as boolean

[amendezt@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6rc202304252053 (2023-04-25 20:53:05 UTC)
Description
Trying to save p53 structure in format x3d 

Log:
UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/alfonsomt/Documents/Laboratorio/Infografias/p53/China_hCoV-19_phylo_20230307.cxs

Log from Thu Apr 27 09:24:57 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> set bgColor #ffffff00

Log from Wed Apr 26 14:37:38 2023UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/bioinformatica/Downloads/P53_1.pdb

Summary of feedback from opening /Users/bioinformatica/Downloads/P53_1.pdb  
---  
warnings | Ignored bad PDB record found on line 10318  
END  
  
Start residue of secondary structure not found: HELIX 1 1 GLN B 167 THR B 170
1 4  
Start residue of secondary structure not found: HELIX 2 2 PRO B 177 ARG B 181
1 5  
Start residue of secondary structure not found: HELIX 3 3 PRO B 278 GLU B 287
1 10  
Start residue of secondary structure not found: SHEET 1 1 1 ARG B 110 GLY B
112 0  
Start residue of secondary structure not found: SHEET 2 2 1 CYS B 124 SER B
127 0  
65 messages similar to the above omitted  
  
P53_1.pdb title:  
Tumor suppressor P53 complexed with DNA [more info...]  
  
Chain information for P53_1.pdb  
---  
Chain | Description  
1.9/A 1.9/B 1.9/C | P53 tumor suppressor  
1.1/B | P53 tumor suppressor  
1.2/B 1.4/B 1.7/B 1.8/B | P53 tumor suppressor  
1.3/B 1.5/B 1.6/B | P53 tumor suppressor  
1.9/D | No description available  
  

> ui mousemode right select

Drag select of 132 residues  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of 17 atoms, 110 residues, 4 pseudobonds, 13 bonds  
Drag select of 38 residues  
Drag select of 9 atoms, 139 residues, 1 pseudobonds, 8 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

> select clear

Drag select of 11 residues  
Drag select of 8 residues  

> ui mousemode right "translate selected models"

> ui mousemode right select

> select clear

> select

9564 atoms, 9432 bonds, 16 pseudobonds, 1292 residues, 14 models selected  

> color sel byhetero

> coulombic sel

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: P53_1.pdb #1.5/B SER 96 OG, P53_1.pdb #1.5/B LEU
289 OXT, P53_1.pdb #1.6/B SER 96 OG, P53_1.pdb #1.6/B LEU 289 OXT, P53_1.pdb
#1.1/B SER 96 OG, and 6 other atoms  

> color sel bychain

> ui mousemode right select

> select clear

> ui mousemode right select

Drag select of P53_1.pdb_A SES surface, 70598 of 88382 triangles, P53_1.pdb_B
SES surface, 56419 of 88366 triangles, P53_1.pdb_C SES surface, 68040 of 88170
triangles, P53_1.pdb_D SES surface, 80025 of 88172 triangles, 139 residues  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 15010 of 17442 triangles, 10 residues  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 94275 of 170986 triangles, 148
residues  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 17248 of 17430 triangles, 11 residues  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 139303 of 167568 triangles, 17 atoms,
182 residues, 4 pseudobonds, 13 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 73451 of 169976 triangles, 79 residues  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 11 residues  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 16983 of 17450 triangles, 11 residues  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 158434 of 167568 triangles, 17 atoms,
189 residues, 4 pseudobonds, 13 bonds  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 11 residues  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, P53_1.pdb_B SES surface, P53_1.pdb_B
SES surface, P53_1.pdb_B SES surface, P53_1.pdb_B SES surface, P53_1.pdb_B SES
surface, P53_1.pdb_B SES surface, P53_1.pdb_B SES surface, P53_1.pdb_A SES
surface, P53_1.pdb_B SES surface, P53_1.pdb_C SES surface, P53_1.pdb_D SES
surface, 52 atoms, 988 residues, 12 pseudobonds, 39 bonds  

> show sel cartoons

> show sel atoms

> show sel cartoons

> show sel cartoons

> show sel atoms

> show sel cartoons

> transparency (#!1.1-9 & sel) 90

> ui mousemode right "translate selected models"

> ui mousemode right "translate selected atoms"

> ui mousemode right translate

> set bgColor white

> ui mousemode right select

> select clear

> select

9564 atoms, 9432 bonds, 16 pseudobonds, 1292 residues, 14 models selected  

> transparency (#!1.1-9 & sel) 90

> transparency (#!1.1-9 & sel) 70

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 63 atoms, 11 residues, 56 bonds  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 134541 of 169976 triangles, 817 atoms,
182 residues, 4 pseudobonds, 688 bonds  

> set bgColor gray

> set bgColor black

> set bgColor white

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 17264 of 17450 triangles, 63 atoms, 11
residues, 56 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 166570 of 170986 triangles, 930 atoms,
194 residues, 4 pseudobonds, 788 bonds  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 150274 of 167568 triangles, 900 atoms,
189 residues, 4 pseudobonds, 762 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 5996 of 17430 triangles, 23 atoms, 6
residues, 19 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 134629 of 167568 triangles, 861 atoms,
184 residues, 4 pseudobonds, 729 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 63 atoms, 11 residues, 56 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 77898 of 169976 triangles, 539 atoms,
120 residues, 2 pseudobonds, 461 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 12537 of 17450 triangles, 51 atoms, 10
residues, 44 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 104554 of 169976 triangles, 717 atoms,
165 residues, 4 pseudobonds, 606 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 14116 of 17450 triangles, 56 atoms, 10
residues, 50 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 16285 of 17442 triangles, 61 atoms, 11
residues, 54 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 163569 of 170260 triangles, 927 atoms,
193 residues, 4 pseudobonds, 781 bonds  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 63 atoms, 11 residues, 56 bonds  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 129556 of 167568 triangles,
P53_1.pdb_B SES surface, 485 of 17430 triangles, 823 atoms, 179 residues, 4
pseudobonds, 694 bonds  
Drag select of P53_1.pdb_B SES surface, 162685 of 167568 triangles,
P53_1.pdb_B SES surface, 990 atoms, 205 residues, 4 pseudobonds, 840 bonds  

> color (#!1.6,8 & sel) orange

> transparency (#!1.6,8 & sel) 80

> ui mousemode right select

> select clear

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 123477 of 170260 triangles, 771 atoms,
166 residues, 4 pseudobonds, 654 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 25136 of 169976 triangles, 118 atoms,
41 residues, 1 pseudobonds, 97 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 62181 of 170260 triangles, 399 atoms,
92 residues, 3 pseudobonds, 347 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 159760 of 169976 triangles, 899 atoms,
191 residues, 4 pseudobonds, 761 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 25367 of 167568 triangles, 119 atoms,
35 residues, 103 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 16499 of 17430 triangles, 62 atoms, 11
residues, 56 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

> select clear

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 4923 of 17430 triangles, 16 atoms, 5
residues, 12 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 107494 of 167568 triangles, 684 atoms,
146 residues, 4 pseudobonds, 581 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 68886 of 170986 triangles, 497 atoms,
118 residues, 1 pseudobonds, 421 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 7439 of 17442 triangles, 29 atoms, 9
residues, 24 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 15325 of 17430 triangles, 58 atoms, 11
residues, 53 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 87376 of 169976 triangles, 561 atoms,
123 residues, 2 pseudobonds, 477 bonds  
Drag select of P53_1.pdb_B SES surface, 6756 of 17450 triangles, 24 atoms, 6
residues, 20 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 65654 of 169976 triangles, 351 atoms,
88 residues, 293 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 6992 of 17450 triangles, 25 atoms, 5
residues, 23 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 16949 of 17612 triangles, 63 atoms, 11
residues, 56 bonds  

> ui mousemode right "translate selected models"

> ui mousemode right select

> select clear

Drag select of P53_1.pdb_B SES surface, 166298 of 169976 triangles,
P53_1.pdb_B SES surface, 996 atoms, 205 residues, 4 pseudobonds, 843 bonds  

> color (#!1.5,7 & sel) orange

> transparency (#!1.5,7 & sel) 90

> transparency (#!1.5,7 & sel) 80

Drag select of P53_1.pdb_B SES surface, 163549 of 170260 triangles,
P53_1.pdb_B SES surface, 983 atoms, 205 residues, 4 pseudobonds, 832 bonds  

> color (#!1.3-4 & sel) orange

> transparency (#!1.3-4 & sel) 80

Drag select of P53_1.pdb_B SES surface, 146878 of 170986 triangles,
P53_1.pdb_B SES surface, 16241 of 17442 triangles, 915 atoms, 191 residues,
776 bonds  

> color (#!1.1-2 & sel) orange

> transparency (#!1.1-2 & sel) 80

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 81532 of 170986 triangles, 536 atoms,
114 residues, 4 pseudobonds, 455 bonds  

> color (#!1.1 & sel) orange

> select clear

> save /Users/bioinformatica/Downloads/Propuesta_1_P53.cxs

> save /Users/bioinformatica/Downloads/Propuesta_1.1_P53.bmp width 15360
> height 8640 supersample 3

> open /Users/bioinformatica/Downloads/DNA_1.pdb

Summary of feedback from opening /Users/bioinformatica/Downloads/DNA_1.pdb  
---  
warning | Ignored bad PDB record found on line 1036  
END  
  
DNA_1.pdb title:  
Structure of A B-DNA dodecamer. Conformation and dynamics [more info...]  
  
Chain information for DNA_1.pdb #2  
---  
Chain | Description  
A B | DNA (5'-D(*CP*GP*CP*GP*ap*ap*TP*TP*CP*GP*CP*G)- 3')  
  

> ui mousemode right select

> select #2/A#2/B

566 atoms, 544 bonds, 104 residues, 1 model selected  

> ui mousemode right "translate selected models"

> select #2/A#2/B

566 atoms, 544 bonds, 104 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 5696 of 170986 triangles, 11 atoms, 6
residues, 9 bonds  

> color (#!1.1 & sel) orange

> save "/Users/bioinformatica/Downloads/Proyecto Chimera P53.cxs"

> ui mousemode right select

> select clear

> save /Users/bioinformatica/Downloads/Proyecto_Chimera_P53.cxs

——— End of log from Wed Apr 26 14:37:38 2023 ———

opened ChimeraX session  

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 63 atoms, 11 residues, 56 bonds  

> ui mousemode right "rotate selected models"

> view matrix models
> #1.4,0.21777,0.63544,-0.74081,150.09,-0.94711,-0.045726,-0.31763,-20.993,-0.23571,0.7708,0.59187,110.3

> turn

> view matrix models
> #1.4,-0.25362,0.91819,-0.30431,164.34,-0.9151,-0.12579,0.38311,-70.637,0.31349,0.37564,0.87214,41.134

> turn

[Repeated 2 time(s)]

> view matrix models
> #1.4,-0.22288,0.94334,-0.24584,162.26,-0.92377,-0.12382,0.36239,-68.973,0.31142,0.30786,0.89902,33.409

> view matrix models
> #1.4,-0.11878,0.95433,-0.27413,161.82,-0.90546,0.00919,0.42434,-61.01,0.40748,0.29862,0.86301,31.806

> view matrix models
> #1.4,-0.13675,0.87202,-0.46999,166.38,-0.90689,0.080688,0.41357,-53.791,0.39856,0.48278,0.77979,53.834

> turn

> view matrix models
> #1.4,0.13162,0.71036,-0.69142,156.61,-0.91267,0.35907,0.19518,-15.259,0.38692,0.60535,0.69559,70.367

> turn

[Repeated 2 time(s)]

> view matrix models
> #1.4,-0.35364,0.67537,-0.64716,165.36,-0.93272,-0.30678,0.18953,-75.241,-0.070533,0.67065,0.73842,87.535

> turn

> view matrix models
> #1.4,-0.5234,0.73904,-0.42412,163.11,-0.83183,-0.33528,0.44233,-95.795,0.1847,0.58431,0.79023,68.922

> view matrix models
> #1.4,-0.41781,0.74042,-0.52651,166.11,-0.89806,-0.24883,0.36273,-81.202,0.13756,0.62439,0.7689,75.262

> view matrix models
> #1.4,-0.46459,0.66994,-0.57908,164.17,-0.87354,-0.23951,0.42374,-84.685,0.14518,0.70271,0.6965,86.472

> turn

[Repeated 4 time(s)]

> view matrix models
> #1.4,-0.62347,0.44884,-0.64017,152.31,-0.76185,-0.16477,0.62645,-93.163,0.17569,0.87829,0.44468,116.48

> turn

[Repeated 3 time(s)]

> view matrix models
> #1.4,-0.67921,0.34193,-0.64944,144.75,-0.71724,-0.12146,0.68616,-94.063,0.15573,0.93184,0.32774,128.88

> turn

[Repeated 1 time(s)]

> view matrix models
> #1.4,-0.72798,0.3215,-0.60554,141.76,-0.67772,-0.20399,0.70646,-104,0.1036,0.92467,0.36639,127.51

> ui mousemode right "move picked models"

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 63 atoms, 11 residues, 56 bonds  

> ui mousemode right "move picked models"

> view matrix models
> #1.2,0.37199,0.64796,-0.66466,-16.104,-0.92254,0.17887,-0.34195,-7.8912,-0.10268,0.74038,0.6643,-5.0434

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 17428 of 17430 triangles, 63 atoms, 11
residues, 56 bonds  

> ui mousemode right "move picked models"

> view matrix models
> #1.8,-0.12284,-0.52283,0.84354,89.023,0.062133,0.84426,0.53233,102.77,-0.99048,0.1178,-0.071224,56.197

> ui mousemode right select

Drag select of P53_1.pdb_B SES surface, 17586 of 17612 triangles, 63 atoms, 11
residues, 56 bonds  

> ui mousemode right "move picked models"

> view matrix models
> #1.4,-0.72798,0.3215,-0.60554,139.19,-0.67772,-0.20399,0.70646,-133.31,0.1036,0.92467,0.36639,129.41

> ui mousemode right select

[Repeated 2 time(s)]Drag select of P53_1.pdb_B SES surface, 17172 of 17450
triangles, 63 atoms, 11 residues, 56 bonds  

> ui mousemode right "move picked models"

> view matrix models
> #1.7,0.96201,0.097447,-0.25504,41.81,-0.22282,-0.25963,-0.93965,144.45,-0.15778,0.96078,-0.22805,81.968

> ui mousemode right "move picked models"

> view matrix models
> #1.1,-0.048666,0.98891,0.14029,5.0729,-0.4281,-0.14756,0.8916,-10.185,0.90242,-0.016669,0.43054,7.4088

> view matrix models
> #1.6,0.3285,0.77755,0.53619,-53.155,-0.29045,-0.45703,0.84069,67.865,0.89874,-0.4319,0.07571,26.047

> view matrix models
> #1.5,-0.27196,-0.81489,0.51184,90.332,0.71162,0.18774,0.67701,-64.658,-0.64779,0.54836,0.52884,96.243

> view matrix models
> #1.3,-0.85829,0.20075,0.47227,35.275,-0.29483,0.56036,-0.774,49.642,-0.42002,-0.80355,-0.42176,54.996

> view matrix models
> #1.2,0.37199,0.64796,-0.66466,0.90387,-0.92254,0.17887,-0.34195,-6.0687,-0.10268,0.74038,0.6643,10.22

> view matrix models
> #1.8,-0.12284,-0.52283,0.84354,90.726,0.062133,0.84426,0.53233,76.405,-0.99048,0.1178,-0.071224,59.133

> view matrix models
> #1.7,0.96201,0.097447,-0.25504,20.169,-0.22282,-0.25963,-0.93965,140.02,-0.15778,0.96078,-0.22805,62.659

> view matrix models
> #1.4,-0.72798,0.3215,-0.60554,134.43,-0.67772,-0.20399,0.70646,-104.46,0.1036,0.92467,0.36639,123.58

> ui mousemode right "rotate selected models"

> view matrix models
> #1.7,0.94308,0.14177,-0.30084,22.979,-0.26471,-0.2276,-0.93708,142.4,-0.20132,0.96338,-0.17712,63.349

> view matrix models
> #1.7,0.93793,0.15481,-0.31035,23.441,-0.27313,-0.22178,-0.93606,142.88,-0.21374,0.96273,-0.16573,63.891

> ui mousemode right select

Drag select of P53_1.pdb_A SES surface, 87866 of 88382 triangles, P53_1.pdb_B
SES surface, 86145 of 88366 triangles, P53_1.pdb_C SES surface, 87038 of 88170
triangles, P53_1.pdb_D SES surface, 88157 of 88172 triangles, 1911 atoms, 168
residues, 1787 bonds  

> ui mousemode right "rotate selected models"

> view matrix models
> #1.9,-0.96104,0.031717,-0.27459,83.957,0.27578,0.17725,-0.94474,48.542,0.018706,-0.98366,-0.17909,49.057

> ui mousemode right select

> save C:/Users/manu_/Documents/1_IMAG.cxs

——— End of log from Thu Apr 27 09:24:57 2023 ———

opened ChimeraX session  

> select ::name="HOH"

300 atoms, 300 residues, 8 models selected  

> show sel atoms

> delete atoms sel

> delete bonds sel

> save
> /Users/alfonsomt/Documents/Laboratorio/Infografias/p53/China_hCoV-19_phylo_20230307.cxs

> save /Users/alfonsomt/Documents/Laboratorio/Infografias/p53/p53_alone.x3d

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 109, in save  
return save_x3d(session, path, **kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 1042, in save_x3d  
m.x3d_needs(x3d_scene)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1381, in x3d_needs  
d.x3d_needs(x3d_scene)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 750, in x3d_needs  
super().x3d_needs(x3d_scene)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1381, in x3d_needs  
d.x3d_needs(x3d_scene)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1388, in x3d_needs  
if any_transp and self.vertex_colors:  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1388, in x3d_needs  
if any_transp and self.vertex_colors:  
  
See log for complete Python traceback.  
  

> select

9264 atoms, 9432 bonds, 16 pseudobonds, 992 residues, 14 models selected  

> hide sel atoms

> save /Users/alfonsomt/Documents/Laboratorio/Infografias/p53/p53_alone.x3d

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 109, in save  
return save_x3d(session, path, **kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 1042, in save_x3d  
m.x3d_needs(x3d_scene)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1381, in x3d_needs  
d.x3d_needs(x3d_scene)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 750, in x3d_needs  
super().x3d_needs(x3d_scene)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1381, in x3d_needs  
d.x3d_needs(x3d_scene)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1388, in x3d_needs  
if any_transp and self.vertex_colors:  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1388, in x3d_needs  
if any_transp and self.vertex_colors:  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-18.8.6
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac mini
      Model Identifier: Macmini8,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 3.2 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0)
      OS Loader Version: 540.120.3~22

Software:

    System Software Overview:

      System Version: macOS 12.6.5 (21G531)
      Kernel Version: Darwin 21.6.0
      Time since boot: 2:44

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.4
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6rc202304252053
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

[pett]

Reported by Alfonso Méndez Tenorio

[Greg Couch]

Fixed in the daily build and the 1.6 release candidate as of tomorrow. Thanks for using the X3D output. Please let me know if there any issues with the X3D output. I suspect you are the only one using X3D output right now.