Segger: 'NoneType' object has no attribute 'matrix'

[jackieliu0406@…]

The following bug report has been submitted:
Platform:        macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/TEST/Downloads/emd_15793.map

Opened emd_15793.map as #1, grid size 560,560,560, pixel 0.731, shown at level
0.264, step 4, values float32  

> volume #1 step 1

> open 8b0x

8b0x title:  
Translating 70S ribosome in the unrotated state (P and E, tRNAs) [more
info...]  
  
Chain information for 8b0x #2  
---  
Chain | Description | UniProt  
0 | 50S ribosomal protein L33 | RL33_ECOLI 1-55  
1 | 50S ribosomal protein L34 | RL34_ECOLI 1-46  
2 | 50S ribosomal protein L35 | RL35_ECOLI 1-65  
3 | 50S ribosomal protein L36 | RL36_ECOLI 1-38  
A | 16S rRNA |  
B | 30S ribosomal protein S2 | RS2_ECOLI 1-241  
C | 30S ribosomal protein S3 | RS3_ECOLI 1-233  
D | 30S ribosomal protein S4 | RS4_ECOLI 1-206  
E | 30S ribosomal protein S5 | RS5_ECOLI 1-167  
F | 30S ribosomal protein S6 | RS6_ECOLI 1-135  
G | 30S ribosomal protein S7 | RS7_ECOLI 1-179  
H | 30S ribosomal protein S8 | RS8_ECOLI 1-130  
I | 30S ribosomal protein S9 | RS9_ECOLI 1-130  
J | 30S ribosomal protein S10 | RS10_ECOLI 1-103  
K | 30S ribosomal protein S11 | RS11_ECOLI 1-130  
L | 30S ribosomal protein S12 | RS12_ECOLI 1-124  
M | 30S ribosomal protein S13 | RS13_ECOLI 1-118  
N | 30S ribosomal protein S14 | RS14_ECOLI 1-101  
O | 30S ribosomal protein S15 | RS15_ECOLI 1-89  
P | 30S ribosomal protein S16 | RS16_ECOLI 1-82  
Q | 30S ribosomal protein S17 | RS17_ECOLI 1-84  
R | 30S ribosomal protein S18 | RS18_ECOLI 1-75  
S | 30S ribosomal protein S19 | RS19_ECOLI 1-92  
T | 30S ribosomal protein S20 | RS20_ECOLI 1-87  
U | 30S ribosomal protein S21 | RS21_ECOLI 1-71  
X | mRNA |  
Z | P-site tRNA |  
a | 23S rRNA |  
b | 5S rRNA |  
c | 50S ribosomal protein L2 | RL2_ECOLI 1-273  
d | 50S ribosomal protein L3 | RL3_ECOLI 1-209  
e | 50S ribosomal protein L4 | RL4_ECOLI 1-201  
f | 50S ribosomal protein L5 | RL5_ECOLI 1-179  
g | 50S ribosomal protein L6 | RL6_ECOLI 1-177  
h | 50S ribosomal protein L9 | RL9_ECOLI 1-149  
i | 50S ribosomal protein L13 | RL13_ECOLI 1-142  
j | 50S ribosomal protein L14 | RL14_ECOLI 1-123  
k | 50S ribosomal protein L15 | RL15_ECOLI 1-144  
l | 50S ribosomal protein L16 | RL16_ECOLI 1-136  
m | 50S ribosomal protein L17 | RL17_ECOLI 1-127  
n | 50S ribosomal protein L18 | RL18_ECOLI 1-117  
o | 50S ribosomal protein L19 | RL19_ECOLI 1-115  
p | 50S ribosomal protein L20 | RL20_ECOLI 1-118  
q | 50S ribosomal protein L21 | RL21_ECOLI 1-103  
r | 50S ribosomal protein L22 | RL22_ECOLI 1-110  
s | 50S ribosomal protein L23 | RL23_ECOLI 1-100  
t | 50S ribosomal protein L24 | RL24_ECOLI 1-104  
u | 50S ribosomal protein L25 | RL25_ECOLI 1-94  
v | 50S ribosomal protein L27 | RL27_ECOLI 1-85  
w | 50S ribosomal protein L28 | RL28_ECOLI 1-78  
x | 50S ribosomal protein L29 | RL29_ECOLI 1-63  
y | 50S ribosomal protein L30 | RL30_ECOLI 1-59  
z | 50S ribosomal protein L32 | RL32_ECOLI 1-57  
  
Non-standard residues in 8b0x #2  
---  
K — potassium ion  
MG — magnesium ion  
MS6 — (2S)-2-amino-4-(methylsulfanyl)butane-1-thiol  
ZN — zinc ion  
  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 139385 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> set bgColor white

> graphics silhouettes true

> lighting flat

> color zone #1 near /A,X,Z,a,b distance 2.5

> ui tool show "Side View"

> lighting full

> volume #1 step 2

> ui mousemode right zoom

> ui mousemode right "translate selected models"

> ui mousemode right zoom

> ui tool show "Segment Map"

Segmenting emd_15793.map, density threshold 0.264415  
Only showing 60 of 1146 regions.  
Showing 60 of 1146 region surfaces  
76202 watershed regions, grouped to 1146 regions  
Showing emd_15793.seg - 1146 regions, 60 surfaces  

> hide #3.60 models

> hide #3.59 models

> hide #3.58 models

> undo

> show #3.59 models

> show #3.60 models

> ui mousemode right select

> hide #3.60 models

> hide #3.59 models

> hide #3.58 models

> hide #3.57 models

> hide #3.56 models

> hide #3.55 models

> hide #3.53 models

> hide #3.54 models

> hide #3.52 models

> hide #3.51 models

> hide #3.50 models

> hide #3.49 models

> hide #3.48 models

> hide #3.47 models

> hide #3.25 models

> hide #3.26 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #3.1 models

> hide #3.2 models

> hide #3.3 models

> hide #3.4 models

> hide #3.5 models

> hide #3.6 models

> hide #3.7 models

> hide #3.8 models

> show #!3 models

> hide #!1 models

Drag select of 105818, 76 of 46360 triangles, 106060, 318 of 39120 triangles,
105760, 2039 of 31212 triangles, 90 residues, 95 shapes  

> select add #3

1274 atoms, 98 residues, 62 models selected  

> select subtract #3

1274 atoms, 98 residues, 1 model selected  

> show #3.1 models

Drag select of 105776, 15305 of 57480 triangles, 105753, 16073 of 59704
triangles, 105792, 10299 of 47804 triangles, 106056, 9379 of 44176 triangles,
11 atoms, 276 residues, 19 pseudobonds, 384 shapes  

> select add #3

4831 atoms, 19 pseudobonds, 331 residues, 63 models selected  

> close #3

> select add #2

151507 atoms, 151568 bonds, 7348 pseudobonds, 22062 residues, 4 models
selected  

> select subtract #2

Nothing selected  

> show #!1 models

Drag select of 1 emd_15793.map , 53 atoms, 718 residues, 105 pseudobonds, 1116
shapes  

> ui mousemode right select

> select clear

> ui mousemode right translate

> ui mousemode right zoom

Segmenting emd_15793.map, density threshold 0.264415  
Only showing 60 of 1146 regions.  
Showing 60 of 1146 region surfaces  
76202 watershed regions, grouped to 1146 regions  
Showing emd_15793.seg - 1146 regions, 60 surfaces  

> hide #!1 models

> hide #!2 models

> close #3

> show #!1 models

> show #!2 models

> ui tool show "Fit to Segments"

Simulating map res 4.000, grid 2.000  

> molmap #2 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Opened 8b0x map 4 as #3, grid size 122,134,145, pixel 2, shown at level 0.125,
step 1, values float32  
No segmentation chosen  

> show #!3 models

> hide #!3 models

> show #!3 models

Segmenting 8b0x map 4, density threshold 0.124931  
Showing 43 region surfaces  
13625 watershed regions, grouped to 43 regions  
Showing 8b0x map 4.seg - 43 regions, 43 surfaces  

> hide #3.1 models

> show #3.1 models

> hide #3.1 models

> hide #!4 models

> show #!4 models

> hide #4.10 models

> close #4

> hide #!3 models

> close #3

> show #!1 models

> hide #!1 models

> show #!1 models

Segmenting emd_15793.map, density threshold 0.264415  
Showing 1146 region surfaces  
76202 watershed regions, grouped to 1146 regions  
Showing emd_15793.seg - 1146 regions, 1146 surfaces  

> hide #!1 models

> close #3

> log metadata #2

Metadata for 8b0x #2  
---  
Title | Translating 70S ribosome in the unrotated state (P and E, tRNAs)  
Citations | Fromm, S.A., O'Connor, K.M., Purdy, M., Bhatt, P.R., Loughran, G.,
Atkins, J.F., Jomaa, A., Mattei, S. (2023). The translating bacterial ribosome
at 1.55 angstrom resolution generated by cryo-EM imaging services. Nat Commun,
14, 1095-1095. PMID: 36841832. DOI: 10.1038/s41467-023-36742-3  
Fromm, S.A., O'Connor, K.M., Purdy, M., Bhatt, P.R., Loughran, G., Atkins,
J.F., Jomaa, A., Mattei, S. (2022). The translating bacterial ribosome at 1.55
angstrom resolution by open access cryo-EM. Biorxiv. DOI:
10.1101/2022.08.30.505838  
Non-standard residues | K — potassium ion  
MG — magnesium ion  
MS6 — (2S)-2-amino-4-(methylsulfanyl)butane-1-thiol  
ZN — zinc ion  
Source (natural) | Escherichia coli B  
CryoEM Map | EMDB 15793 — open map  
Experimental method | Electron microscopy  
Resolution | 1.55Å  
  
> ui mousemode right translate

> show #!1 models

Segmenting emd_15793.map, density threshold 0.264415  
Only showing 60 of 76202 regions.  
Showing 60 of 76202 region surfaces  
76202 watershed regions, grouped to 76202 regions  
Showing emd_15793.seg - 76202 regions, 60 surfaces  

> hide #!1 models

> close #3

> show #!1 models

Segmenting emd_15793.map, density threshold 0.264415  
Showing 5 region surfaces  
76202 watershed regions, grouped to 5 regions  
Showing emd_15793.seg - 5 regions, 5 surfaces  

> hide #!2 models

> show #!2 models

> hide #!1 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  

> hide #!2 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  

> show #!2 models

Grouped 5 regions  

> select add #3

2 models selected  

> select subtract #3

Nothing selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  
Opened emd_15793_masked as #4, grid size 560,560,560, pixel 0.731, shown at
step 1, values float32  
Top score: 0.99996, z-score: 158.93629 (avg: 0.2771, stdev: 0.0045)  

> select add #3

2 models selected  

> select subtract #3

Nothing selected  

> close #3

> show #!1 models

> ui tool show "Segment Map"

No segmentation chosen  
[Repeated 1 time(s)]Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2233, in FitMapToSelRGroup  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  
Simulating map res 4.000, grid 2.000  

> molmap #2 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Opened 8b0x map 4 as #3, grid size 122,134,145, pixel 2, shown at level 0.125,
step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 3012, in FitMapToRGroups  
tvol = self.MapVolume ( fmap )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  
No symmetry detected for emd_15793.map  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 3012, in FitMapToRGroups  
tvol = self.MapVolume ( fmap )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  

> show #!3 models

> hide #!3 models

> show #!3 models

Simulating map res 4.000, grid 2.000  

> molmap #2 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Opened 8b0x map 4 as #4, grid size 122,134,145, pixel 2, shown at level 0.125,
step 1, values float32  

> close #4

> close #3

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 289, in _fit  
self.Fit()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 1335, in Fit  
func()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 3012, in FitMapToRGroups  
tvol = self.MapVolume ( fmap )  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
AttributeError: 'NoneType' object has no attribute 'matrix'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/segger/fit_dialog.py", line 2735, in MapVolume  
mm = fmap.data.matrix()  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

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: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGP3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 10151.61.4

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 27 days, 8 hours, 8 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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: 2.2.5
    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: 1.6.1
    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

[Eric Pettersen]

Reported by Songzhe Liu

[Tom Goddard]

Fixed in ChimeraX 1.7.