ribbon cross section: unsupported operand type(s) for *: 'float' and 'NoneType'

[ogahura@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.94 (2020-04-14)
Description
cartoon style modeh tube

Log:
UCSF ChimeraX version: 0.94.dev202004140658 (2020-04-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/ondrejgahura/Work/Lab Book/F1Fo/Model
> Building/Chimerax/Tb_Eg_Fo_membrane_working.cxs" format session

Log from Sun Apr 19 15:39:43 2020UCSF ChimeraX version: 0.94.dev202004140658
(2020-04-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/ondrejgahura/Work/Lab Book/F1Fo/Model
> Building/Models/Tb_Eg_Fo_membrane.cxs"

File not found: /Users/ondrejgahura/Work/Lab Book/F1Fo/Model
Building/Models/Tb_Eg_Fo_membrane.cxs  

> open2 "/Users/ondrejgahura/Work/Lab Book/F1Fo/Model
> Building/Chimerax/Tb_Eg_Fo_membrane.cxs"

Unable to restore "SchemesManager" object  

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 63, in pbg_update  
self._update_graphics()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 218, in _update_graphics  
d.positions = self._update_positions(pbonds, bond_atoms)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 231, in _update_positions  
axyz0, axyz1 = to_pbg*ba1.pb_scene_coords, to_pbg*ba2.pb_scene_coords  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 754, in pb_scene_coords  
v[i] = a.pb_scene_coord  
File "cymol.pyx", line 242, in
chimerax.atomic.cymol.CyAtom.pb_scene_coord.__get__  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
TypeError: Cannot multiply Place times "None"  
  
Error processing trigger "changes":  
TypeError: Cannot multiply Place times "None"  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
  
See log for complete Python traceback.  
  

> set bgColor white

> graphics silhouettes true

> lighting simple

> rename #1 Fo-membrane_built

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #!2 models

> show #1.13 models

> show #1.14 models

> show #1.15 models

> show #2.1 models

> show #!2.2 models

> show #!2.3 models

> show #!2.4 models

> show #1.7 models

> show #1.8 models

> show #1.9 models

> show #1.10 models

> show #1.11 models

> hide #1.7 models

> hide #1.8 models

> hide #1.9 models

> hide #1.10 models

> hide #1.11 models

> hide #1.12 models

> hide #1.13 models

> hide #1.14 models

> hide #1.15 models

> show #!2.5 models

> show #2.6 models

> show #!2.7 models

> close #2

> open 6tdv

Summary of feedback from opening 6tdv fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET #1 in chain F  
Atom H1 is not in the residue template for LEU #1 in chain L  
Atom H1 is not in the residue template for MET #1 in chain T  
Atom H1 is not in the residue template for MET #1 in chain f  
Atom H1 is not in the residue template for LEU #1 in chain l  
1 messages similar to the above omitted  
notes | Fetching compressed mmCIF 6tdv from
http://files.rcsb.org/download/6tdv.cif  
Fetching CCD CDL from http://ligand-expo.rcsb.org/reports/C/CDL/CDL.cif  
Fetching CCD LMT from http://ligand-expo.rcsb.org/reports/L/LMT/LMT.cif  
Fetching CCD LPP from http://ligand-expo.rcsb.org/reports/L/LPP/LPP.cif  
Fetching CCD TRT from http://ligand-expo.rcsb.org/reports/T/TRT/TRT.cif  
  
6tdv title:  
Cryo-EM structure of Euglena gracilis mitochondrial ATP synthase, membrane
region [more info...]  
  
Chain information for 6tdv #2  
---  
Chain | Description  
A a | ATPTB1  
B b | ATPTB3  
D d | ATPTB6  
E e | ATPTB12  
F f | subunit a  
G g | subunit b  
H h | subunit d  
I i | subunit f  
J j | subunit i/j  
K k | subunit k  
L l | subunit 8  
M m | ATPEG1  
N n | ATPEG2  
O o | ATPEG3  
P p | ATPEG4  
Q q | ATPEG5  
R r | ATPEG6  
S s | ATPEG7  
T t | ATPEG8  
  
Non-standard residues in 6tdv #2  
---  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
LMT — dodecyl-β-D-maltoside  
LPP — 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate
(1,2-dipalmitoyl-Sn-glycero-3-phosphate; L-B,G-dipalmitoyl-A-phosphatidic acid
disodium salt; 3-Sn-phosphatidic acid; 1,2-dipalmitoyldisodium salt)  
TRT — fragment of triton X-100
(1-{2-[2-(2-methoxyethoxy)ethoxy]ethoxy}-4-(1,1,3,3-tetramethylbutyl)benzene)  
  
  

> select #2

95420 atoms, 96673 bonds, 3 pseudobonds, 2 models selected  

> style sel stick

Changed 95420 atom styles  

> show sel cartoons

> hide sel atoms

> hide #!2 models

> show #!2 models

> save2 "/Users/ondrejgahura/Work/Lab Book/F1Fo/Model
> Building/Chimerax/Tb_Eg_Fo_membrane.cxs"

> ui mousemode rightMode "translate selected models"

> hide #1.16 models

> show #1.16 models

> hide #1.16 models

> hide #!2 models

> show #1.16 models

> hide #1.16 models

> show #1.15 models

> hide #1.15 models

> hide #1.17 models

> show #1.15 models

> hide #1.15 models

> show #1.15 models

> show #1.17 models

> hide #1.15 models

> show #1.15 models

> hide #1.15 models

> save2 "/Users/ondrejgahura/Work/Lab Book/F1Fo/Model
> Building/Chimerax/Tb_Eg_Fo_membrane.cxs"

> ui mousemode rightMode select

> matchmaker #2 to #1.17

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker tryp_membrane_all_2.pdb, chain O (#1.17) with 6tdv, chain A (#2),
sequence alignment score = 316.7  
RMSD between 112 pruned atom pairs is 1.265 angstroms; (across all 354 pairs:
24.539)  
  

> show #!2 models

> hide #!2 models

> show #!2 models

> select clear

> show #1.16 models

> hide #1.16 models

> save2 "/Users/ondrejgahura/Work/Lab Book/F1Fo/Model
> Building/Chimerax/Tb_Eg_Fo_membrane_working.cxs"

> matchmaker #2/F to #1.17/G

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker tryp_membrane_all_2.pdb, chain G (#1.17) with 6tdv, chain F (#2),
sequence alignment score = 213.6  
RMSD between 22 pruned atom pairs is 1.420 angstroms; (across all 220 pairs:
11.831)  
  

> hide #1.17 models

> show #1.1 models

> hide #2

> ~ribbon #2

> ribbon #2/F

Drag select of 16 residues  

> select clear

> select #2/F:160

24 atoms, 23 bonds, 1 model selected  

> select up

56 atoms, 56 bonds, 1 model selected  

> select up

4761 atoms, 4826 bonds, 1 model selected  

> rainbow sel

> select clear

> show #1.8 models

> ribbon #1.8

> hide #1.8 models

> show #1.8 models

> select #1.8

820 atoms, 836 bonds, 1 model selected  
Alignment identifier is 1.8.L  

> select clear

> open2 "/Users/ondrejgahura/Work/Lab Book/F1Fo/Model
> Building/Models/Fo_membrane/Tb927.5.2930_ATPTB2_subunit-d.pdb"

Ignored bad PDB record found on line 110  
LINKR VAL E 8 LEU E 10 gap  
  

Ignored bad PDB record found on line 111  
LINKR ASN E 46 LYS E 49 gap  
  

Ignored bad PDB record found on line 112  
LINKR ALA E 55 LEU E 61 gap  
  

Ignored bad PDB record found on line 113  
LINKR LYS F 49 ASN F 53 gap  
  

Ignored bad PDB record found on line 114  
LINKR ARG M 218 ASP M 223 gap  
  

Ignored bad PDB record found on line 115  
LINKR VAL P 79 ILE P 169 gap  
  

Ignored bad PDB record found on line 116  
LINKR GLY T 101 VAL T 103 gap  
  

Ignored bad PDB record found on line 117  
LINKR PRO T 160 ALA T 163 gap  
  

Ignored bad PDB record found on line 118  
LINKR ARG U 90 TRP U 92 gap  
  

Ignored bad PDB record found on line 119  
LINKR GLY U 100 VAL U 102 gap  
  

Ignored bad PDB record found on line 120  
LINKR LEU U 141 GLU U 148 gap  
  

Tb927.5.2930_ATPTB2_subunit-d.pdb title:  
\--- [more info...]  
  
Chain information for Tb927.5.2930_ATPTB2_subunit-d.pdb #4  
---  
Chain | Description  
C | No description available  
L | No description available  
  

> close #1.8

> rename #4 id #1.8

> dssp #1.8

> select #1.8

2020 atoms, 2050 bonds, 6 pseudobonds, 2 models selected  
Alignment identifier is 1.8.L  
Alignment identifier is 1.8.C  

> select clear

> select clear

> select clear

> hide #!1.8 models

> open2 "/Users/ondrejgahura/Work/Lab Book/F1Fo/Model
> Building/Models/Peripheral stalk_small_mask/ATPTB2_periph_stalk.pdb"

End residue of secondary structure not found: HELIX 6 6 MET A 264 TRP A 266 1
3  

Start residue of secondary structure not found: HELIX 7 7 PRO A 268 GLU A 275
1 8  

Start residue of secondary structure not found: HELIX 8 8 GLY A 282 TRP A 286
1 5  

Start residue of secondary structure not found: HELIX 10 10 THR A 332 VAL A
344 1 13  

ATPTB2_periph_stalk.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) ATPTB2 [more info...]  
  
Chain information for ATPTB2_periph_stalk.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> dssp #5

> select #5

2545 atoms, 2592 bonds, 2 pseudobonds, 2 models selected  
Alignment identifier is 5.A  
Alignment identifier is 5.B  

> select clear

Drag select of  

> show #!1.8 models

> select #5

2545 atoms, 2592 bonds, 2 pseudobonds, 2 models selected  

> rainbow sel

> hide #!5 models

> show #!5 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!5 models

> hide #!1.8 models

> show #!2 models

> ribbon #2

> ~ribbon #2

> ribbon #2/F

> open 6B2Z

Summary of feedback from opening 6B2Z fetched from pdb  
---  
note | Fetching compressed mmCIF 6b2z from
http://files.rcsb.org/download/6b2z.cif  
  
6b2z title:  
Cryo-EM structure of the dimeric FO region of yeast mitochondrial ATP synthase
[more info...]  
  
Chain information for 6b2z #6  
---  
Chain | Description  
0 1 2 3 4 5 6 7 8 9 B C D E F G H I J K | ATP synthase subunit c,
mitochondrial  
A L | ATP synthase protein 8  
M a | ATP synthase subunit a  
N b | ATP synthase subunit b  
O d | ATP synthase subunit d, mitochondrial  
P e | ATP synthase subunit e, mitochondrial  
Q f | ATP synthase subunit f, mitochondrial  
R g | ATP synthase subunit g  
S i | ATP synthase subunit j, mitochondrial  
T k | ATP synthase subunit k, mitochondrial  
  
  

> hide #1.1 models

> show #1.1 models

> open 6B2Z to #1.1

Missing filename suffix to  

> matchmaker #6/a to #1.1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker subunit-a.pdb, chain G (#1.1) with 6b2z, chain a (#6), sequence
alignment score = 282.1  
RMSD between 84 pruned atom pairs is 1.132 angstroms; (across all 216 pairs:
8.649)  
  

> select #6

21436 atoms, 21822 bonds, 1 model selected  

> style sel stick

Changed 21436 atom styles  

> hide sel atoms

> show sel cartoons

> ~ribbon #6

> ribbon #6/a

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> hide #6 models

> hide #!2 models

> show #1.16 models

> hide #1.16 models

> show #1.17 models

> hide #1.17 models

> show #1.17 models

> hide #1.17 models

> ribbon #2/P

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

Drag select of  

> select #1.2/k:105

8 atoms, 7 bonds, 1 model selected  

> select clear

> ribbon #2/K

> ~ribbon #2/P

> hide #1.2 models

> show #1.10 models

> hide #1.10 models

> show #1.10 models

> hide #1.10 models

> show #1.10 models

> hide #!2 models

> ribbon #6/K

> ~ribbon #6/K

> ribbon #6/k

> show #6 models

> show #!5 models

> hide #!5 models

> show #!2 models

> hide #!2 models

> select #6/a

1971 atoms, 2023 bonds, 1 model selected  
Alignment identifier is 6.a  

> select clear

> select clear

> select clear

> select clear

> show sel cartoons

> show sel atoms

> color sel byhetero

> select clear

> select #1.1/G:228

10 atoms, 9 bonds, 1 model selected  

> show sel atoms

> select clear

Expected a models specifier or a keyword  

> save 6b2z_Sc-su-a models #6/a

Missing filename suffix 6b2z_Sc-su-a  

> save 6b2z_Sc-su-a.pdb models #6/a

Unknown command: home  

> pwd

Current working directory is: /Users/ondrejgahura/Desktop  
Drag select of  

> hide #1.10 models

> hide #6 models

> show #6 models

> ~ribbon #6/k

> lighting simple

> toolshed show "Side View"

> save2 /Users/ondrejgahura/Work/Publications/TbATPS_structure/Pre-figures/su-
> a_Tb_Sc.jpg width 791 height 517 supersample 3

> select #6/a:223@CD

1 atom, 1 model selected  
Alignment identifier is 1.1.G  

> split #6

Chain information for 6b2z 0 #6.1  
---  
Chain | Description  
0 | No description available  
  
Chain information for 6b2z 1 #6.2  
---  
Chain | Description  
1 | No description available  
  
Chain information for 6b2z 2 #6.3  
---  
Chain | Description  
2 | No description available  
  
Chain information for 6b2z 3 #6.4  
---  
Chain | Description  
3 | No description available  
  
Chain information for 6b2z 4 #6.5  
---  
Chain | Description  
4 | No description available  
  
Chain information for 6b2z 5 #6.6  
---  
Chain | Description  
5 | No description available  
  
Chain information for 6b2z 6 #6.7  
---  
Chain | Description  
6 | No description available  
  
Chain information for 6b2z 7 #6.8  
---  
Chain | Description  
7 | No description available  
  
Chain information for 6b2z 8 #6.9  
---  
Chain | Description  
8 | No description available  
  
Chain information for 6b2z 9 #6.10  
---  
Chain | Description  
9 | No description available  
  
Chain information for 6b2z A #6.11  
---  
Chain | Description  
A | No description available  
  
Chain information for 6b2z B #6.12  
---  
Chain | Description  
B | No description available  
  
Chain information for 6b2z C #6.13  
---  
Chain | Description  
C | No description available  
  
Chain information for 6b2z D #6.14  
---  
Chain | Description  
D | No description available  
  
Chain information for 6b2z E #6.15  
---  
Chain | Description  
E | No description available  
  
Chain information for 6b2z F #6.16  
---  
Chain | Description  
F | No description available  
  
Chain information for 6b2z G #6.17  
---  
Chain | Description  
G | No description available  
  
Chain information for 6b2z H #6.18  
---  
Chain | Description  
H | No description available  
  
Chain information for 6b2z I #6.19  
---  
Chain | Description  
I | No description available  
  
Chain information for 6b2z J #6.20  
---  
Chain | Description  
J | No description available  
  
Chain information for 6b2z K #6.21  
---  
Chain | Description  
K | No description available  
  
Chain information for 6b2z L #6.22  
---  
Chain | Description  
L | No description available  
  
Chain information for 6b2z M #6.23  
---  
Chain | Description  
M | No description available  
  
Chain information for 6b2z N #6.24  
---  
Chain | Description  
N | No description available  
  
Chain information for 6b2z O #6.25  
---  
Chain | Description  
O | No description available  
  
Chain information for 6b2z P #6.26  
---  
Chain | Description  
P | No description available  
  
Chain information for 6b2z Q #6.27  
---  
Chain | Description  
Q | No description available  
  
Chain information for 6b2z R #6.28  
---  
Chain | Description  
R | No description available  
  
Chain information for 6b2z S #6.29  
---  
Chain | Description  
S | No description available  
  
Chain information for 6b2z T #6.30  
---  
Chain | Description  
T | No description available  
  
Chain information for 6b2z a #6.31  
---  
Chain | Description  
a | No description available  
  
Chain information for 6b2z b #6.32  
---  
Chain | Description  
b | No description available  
  
Chain information for 6b2z d #6.33  
---  
Chain | Description  
d | No description available  
  
Chain information for 6b2z e #6.34  
---  
Chain | Description  
e | No description available  
  
Chain information for 6b2z f #6.35  
---  
Chain | Description  
f | No description available  
  
Chain information for 6b2z g #6.36  
---  
Chain | Description  
g | No description available  
  
Chain information for 6b2z i #6.37  
---  
Chain | Description  
i | No description available  
  
Chain information for 6b2z k #6.38  
---  
Chain | Description  
k | No description available  
  
Split 6b2z (#6) into 38 models  

> hide #6.31 models

> show #6.31 models

> save 6b2z_Sc-su-a.pdb models #6.31

> cartoon style modeHelix tube

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1535, in
_update_graphics_if_needed  
s[i]._update_graphics_if_needed()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 297, in
_update_graphics_if_needed  
self._create_ribbon_graphics()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 550, in _create_ribbon_graphics  
ribbons_drawing.compute_ribbons(self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 576, in compute_ribbons  
_make_ribbon_graphics(structure, self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 127, in _make_ribbon_graphics  
xsection = xs_mgr.xs_helix_tube  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 1988, in xs_helix_tube  
self._xs_helix_tube = self._make_xs(self.STYLE_ROUND, scale)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 2023, in _make_xs  
return _xsection_round(scale, param['sides'], param['faceted'])  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 2147, in _xsection_round  
coords = circle * array(scale)  
TypeError: unsupported operand type(s) for *: 'float' and 'NoneType'  
  
Error processing trigger "graphics update":  
TypeError: unsupported operand type(s) for *: 'float' and 'NoneType'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 2147, in _xsection_round  
coords = circle * array(scale)  
  
See log for complete Python traceback.  
  

> cartoon style modeHelix tube

> select clear

> cartoon style modeHelix tube

> cartoon style modeHelix tube

> hide #6.31 models

> show #6.31 models

> save2 "/Users/ondrejgahura/Work/Lab Book/F1Fo/Model
> Building/Chimerax/Tb_Eg_Fo_membrane_working.cxs"

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1535, in
_update_graphics_if_needed  
s[i]._update_graphics_if_needed()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 297, in
_update_graphics_if_needed  
self._create_ribbon_graphics()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 550, in _create_ribbon_graphics  
ribbons_drawing.compute_ribbons(self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 576, in compute_ribbons  
_make_ribbon_graphics(structure, self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 127, in _make_ribbon_graphics  
xsection = xs_mgr.xs_helix_tube  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 1988, in xs_helix_tube  
self._xs_helix_tube = self._make_xs(self.STYLE_ROUND, scale)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 2023, in _make_xs  
return _xsection_round(scale, param['sides'], param['faceted'])  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 2147, in _xsection_round  
coords = circle * array(scale)  
TypeError: unsupported operand type(s) for *: 'float' and 'NoneType'  
  
Error processing trigger "graphics update":  
TypeError: unsupported operand type(s) for *: 'float' and 'NoneType'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/ribbon.py", line 2147, in _xsection_round  
coords = circle * array(scale)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.16
OpenGL renderer: Intel HD Graphics 4000 OpenGL Engine
OpenGL vendor: Intel Inc.

[Eric Pettersen]

Reported by Ondrej Gahura

[Tom Goddard]

Fixed.

The helix tube radius is normally calculated for each helix. Optimization of that code about 3 weeks ago broke that and gave every helix tube radius 2. Probably this error was caused by opening an older session which had the per-helix radius mode. I've made the per-helix radius display work again.