Clipper: math range error

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-14.0-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:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
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  
Updating list of available bundles failed: [Errno 60] Operation timed out  
2024-06-19 10:29:55,818 WARNING Retrying (Retry(total=2, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x158680490>: Failed to establish a new connection: [Errno 60] Operation timed
out')':
/cxservices/api/v1/chimerax/updates?uuid=afa5d20e-b034-59d3-ab8f-b8841e7e277c&OS=macosx&OSVersion=14.0&ChimeraXVersion=1.6.1  
2024-06-19 10:31:10,843 WARNING Retrying (Retry(total=1, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x15863ba90>: Failed to establish a new connection: [Errno 60] Operation timed
out')':
/cxservices/api/v1/chimerax/updates?uuid=afa5d20e-b034-59d3-ab8f-b8841e7e277c&OS=macosx&OSVersion=14.0&ChimeraXVersion=1.6.1  
2024-06-19 10:32:25,851 WARNING Retrying (Retry(total=0, connect=None,
read=None, redirect=None, status=None)) after connection broken by
'NewConnectionError('<urllib3.connection.HTTPConnection object at
0x14ffc7e20>: Failed to establish a new connection: [Errno 60] Operation timed
out')':
/cxservices/api/v1/chimerax/updates?uuid=afa5d20e-b034-59d3-ab8f-b8841e7e277c&OS=macosx&OSVersion=14.0&ChimeraXVersion=1.6.1  

> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-apo/cryosparc/P5/J1755-C2/cryosparc_P28_J1755_006_volume_map.mrc
> format mrc

Opened cryosparc_P28_J1755_006_volume_map.mrc as #1, grid size 336,336,336,
pixel 1.07, shown at level 0.0323, step 2, values float32  

> ui mousemode right "map eraser"

> volume erase #1 center 230.16,167.42,177.56 radius 57.205

Opened cryosparc_P28_J1755_006_volume_map.mrc copy as #3, grid size
336,336,336, pixel 1.07, shown at step 1, values float32  

> volume #3 level 0.0623

> volume erase #3 center 243.3,228.34,176.6 radius 57.116

> save /Users/whenriques/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-apo/cryosparc/P5/J1755-C2/J1755-cas3-for-local-
> refine.mrc models #3

> close #2

> close session

> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-bound/phenix/J1222-local-
> refine/J1222-local-refine.ccp4 format ccp4

Opened J1222-local-refine.ccp4 as #1, grid size 270,270,270, pixel 1.67, shown
at level 0.183, step 2, values float32  

> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-bound/phenix/J1222-local-
> refine/RealSpaceRefine_1_chains_corrected_Jerry/prespacer_chains_corrected_refine1-23-joined.pdb

prespacer_chains_corrected_refine1-23-joined.pdb title:  
Alphafold monomer V2.0 prediction for crispr-associated nuclease/helicase CAS3
subtype I-F/ypest (Q02ML8) [more info...]  
  
Chain information for prespacer_chains_corrected_refine1-23-joined.pdb #2  
---  
Chain | Description | UniProt  
A | crispr-associated nuclease/helicase CAS3 subtype I-F/ypest | CAS3_PSEAB
1-1076  
C E | No description available |  
G | No description available |  
H | No description available |  
  

> volume #1 step 1

> volume #1 level 1.044

> lighting soft

> set bgColor white

> volume #1 level 0.7931

> isolde start

> set selectionWidth 4

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
prespacer_chains_corrected_refine1-23-joined.pdb title:  
Alphafold monomer V2.0 prediction for crispr-associated nuclease/helicase CAS3
subtype I-F/ypest (Q02ML8) [more info...]  
  
Chain information for prespacer_chains_corrected_refine1-23-joined.pdb  
---  
Chain | Description | UniProt  
2.2/A | crispr-associated nuclease/helicase CAS3 subtype I-F/ypest |
CAS3_PSEAB 1-1076  
2.2/C 2.2/E | No description available |  
2.2/G | No description available |  
2.2/H | No description available |  
  

> clipper associate #1 toModel #2

Opened J1222-local-refine.ccp4 as #2.1.1.1, grid size 270,270,270, pixel 1.67,
shown at step 1, values float32  

> select /C

5062 atoms, 5115 bonds, 324 residues, 1 model selected  

> isolde sim start /C

ISOLDE: started sim  

> isolde stepto #1

Selection contains no residues!  

> isolde stepto /C:1

> isolde stepto next

[Repeated 132 time(s)]

> isolde sim pause

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> close session

> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-bound/phenix/J1222-local-
> refine/RealSpaceRefine_1/trimmed-8flj-AFCas3_real_space_refined_001.pdb

Chain information for trimmed-8flj-AFCas3_real_space_refined_001.pdb #1  
---  
Chain | Description  
A | No description available  
C | No description available  
D | No description available  
K | No description available  
L | No description available  
M N | No description available  
  

> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-bound/phenix/J1222-local-
> refine/J1222-local-refine.ccp4

Opened J1222-local-refine.ccp4 as #2, grid size 270,270,270, pixel 1.67, shown
at level 0.183, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.425

> volume #2 level 0.6764

> volume #2 level 0.5686

> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-bound/phenix/J1222-local-
> refine/RealSpaceRefine_1_chains_corrected_Jerry/prespacer_chains_corrected_refine1-23-joined.pdb

prespacer_chains_corrected_refine1-23-joined.pdb title:  
Alphafold monomer V2.0 prediction for crispr-associated nuclease/helicase CAS3
subtype I-F/ypest (Q02ML8) [more info...]  
  
Chain information for prespacer_chains_corrected_refine1-23-joined.pdb #3  
---  
Chain | Description | UniProt  
A | crispr-associated nuclease/helicase CAS3 subtype I-F/ypest | CAS3_PSEAB
1-1076  
C E | No description available |  
G | No description available |  
H | No description available |  
  

> hide #!2 models

> hide #1 models

> show #1 models

> hide #1 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> volume #2 level 0.847

> show #1 models

Must have exactly two atoms selected!  

> hide #!2 models

> show #!3 models

> hide #1 models

> show #1 models

> hide #!3 models

> select *

Expected an objects specifier or a keyword  

> select

50418 atoms, 51276 bonds, 1 pseudobond, 3617 residues, 5 models selected  

> style sel & #1 stick

Changed 21737 atom styles  

> color sel & #1 byhetero

> select /A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,-1.8962,0,1,0,28.622,0,0,1,-11.628

> select #3/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> hide #1 models

> show #!3 models

> hide #!3 models

> show #1 models

> select #1/A:1

Nothing selected  

> select #1/A:100

Nothing selected  

> select #1/A:101

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:101@N

1 atom, 1 residue, 1 model selected  

> select #1/A:101@N #1/A:100@C

1 atom, 1 residue, 1 model selected  

> select #1/A:101@N #1/A:100@CA

1 atom, 1 residue, 1 model selected  

> select #1/A:101@N #1/M:100@CA

1 atom, 1 residue, 1 model selected  

> select #1/A:101@N #1/M:100

1 atom, 1 residue, 1 model selected  

> show #!3 models

> select #3/A:99-101

61 atoms, 60 bonds, 3 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> select
> #1/A:109-122,125-128,130-137,149-161,167-175,183-187,208-219,231-236,243-246,253-260,267-269,271-286,290-298,301-320,349-364,367-373,381-384,390-412,426-437,457-467,484-496,500-502,524-527,531-538,546-548,550-552,562-568,578-580,583-585,587-598,612-631,660-679,699-720,740-753,772-785,793-797,800-808,822-824,842-851,872-875,899-902,905-909,914-917,929-938,953-956,960-963,966-970,1008-1010,1030-1041,1045-1052

3553 atoms, 3579 bonds, 443 residues, 1 model selected  

> select #3/A:99-101

61 atoms, 60 bonds, 3 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> hide #!3 models

> select up

427 atoms, 430 bonds, 27 residues, 1 model selected  

> select #1/M:100

Nothing selected  

> select #1/M:99@O

1 atom, 1 residue, 1 model selected  
Must have exactly two atoms selected!  

> show #!3 models

> hide #1 models

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select up

109 atoms, 108 bonds, 6 residues, 1 model selected  

> select up

1631 atoms, 1642 bonds, 99 residues, 1 model selected  

> select #3/A:99-101

61 atoms, 60 bonds, 3 residues, 1 model selected  

> close #1

> close #3

> show #!2 models

> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-bound/phenix/J1222-local-
> refine/RealSpaceRefine_1/trimmed-8flj-
> AFCas3_real_space_refined_001-coot-0.pdb

Chain information for trimmed-8flj-AFCas3_real_space_refined_001-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
C | No description available  
D | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
  

> select #1/A:101@N #1/M:100@O

2 atoms, 2 residues, 1 model selected  

> style sel stick

Changed 2 atom styles  

> select add #2

2 atoms, 2 residues, 4 models selected  

> select subtract #2

2 atoms, 2 residues, 1 model selected  

> select add #1

21746 atoms, 22179 bonds, 1844 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #1

21746 atoms, 22179 bonds, 1844 residues, 1 model selected  

> select add #2

21746 atoms, 22179 bonds, 1844 residues, 4 models selected  

> select subtract #2

21746 atoms, 22179 bonds, 1844 residues, 1 model selected  

> hide #!2 models

> show sel atoms

> style sel stick

Changed 21746 atom styles  

> select #1/A:101@N #1/M:100@O

2 atoms, 2 residues, 1 model selected  

> ui tool show "Change Chain IDs"

> changechains sel M A

Cannot reassign chain ID to only part of polymeric chain (/M)  

> changechains sel A Q

Cannot reassign chain ID to only part of polymeric chain (/A)  

> changechains sel M A

Cannot reassign chain ID to only part of polymeric chain (/M)  

> changechains sel M A

Cannot reassign chain ID to only part of polymeric chain (/M)  

> changechains sel A

Cannot reassign chain ID to only part of polymeric chain (/M)  

> help help:user/tools/changechains.html

Cannot change to an empty ID  
[Repeated 1 time(s)]

> changechains sel A,C,D,K,L,M,N A,C,E,H,G,A,B

Cannot reassign chain ID to only part of polymeric chain (/M)  

> changechains sel A,C,D,K,L,M,N A,C,E,H,G,A,B

Cannot reassign chain ID to only part of polymeric chain (/M)  

> changechains sel A,C,D,K,L,M,N A,C,E,H,G,A,B

Cannot reassign chain ID to only part of polymeric chain (/M)  
Select exactly one bond first!  

> changechains sel A,C,D,K,L,M,N A,C,E,H,G,A,B

Cannot reassign chain ID to only part of polymeric chain (/M)  

> changechains A,C,D,K,L,M,N A,C,E,H,G,A,B

Chain IDs of 1844 residues changed  

> select /A

9364 atoms, 9563 bonds, 1076 residues, 1 model selected  

> save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-prespacer-bound/phenix/J1222-local-
> refine/RealSpaceRefine_1/trimmed-8flj-
> AFCas3_real_space_refined_001-coot-0-cas23-joined-chains-renamed.pdb
> relModel #2

> set bgColor white

> view matrix models #1,1,0,0,6.8419,0,1,0,6.4336,0,0,1,13.102

> select /C

4188 atoms, 4233 bonds, 303 residues, 1 model selected  

> select #1/C

4188 atoms, 4233 bonds, 303 residues, 1 model selected  

> show sel surfaces

> set bgColor white

> graphics silhouettes true

> lighting shadows true

> lighting soft fillDirection -.1,.1,-.25 fillIntensity 0.1 direction -0, .1,
> -.2 intensity 0.2 multiShadow 128

> material specularReflectivity 0.1

> cartoon style protein xsection oval modeHelix default

> hide atoms

> show cartoons

> color #2/g,h #f69320ff

> color #1,2,3/a:1-94/b:1-94 #d799c4

> color #1,2,3/a:95-end/b:95-end #6d8fc9ff

> color #1,2,3/f,e #c2b59bff

> color #1,2,3/c,d #9c857a

> color #1/g:1-27/h:1-27 #f69320ff

> color #1/g:28-end/h:28-56 #92278f

> color #1/i/h:57-end #939598

> color #1/m,k #d91b5d

> color #1/l,j #a51e23

> select /G

854 atoms, 922 bonds, 27 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> select add #1

21746 atoms, 22180 bonds, 1844 residues, 1 model selected  

> view matrix models #1,1,0,0,6.8411,0,1,0,6.4326,0,0,1,13.1

> open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
> complex/cryoem/cas1-2-3-apo/phenix/J411-alphafold/RealSpaceRefine_17_chains_updated/apo-
> Refinement17-chains-corrected-renamed.cif

Summary of feedback from opening
/Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration-
complex/cryoem/cas1-2-3-apo/phenix/J411-alphafold/RealSpaceRefine_17_chains_updated/apo-
Refinement17-chains-corrected-renamed.cif  
---  
warnings | Atom H1 is not in the residue template for ARG /A:95  
Atom H1 is not in the residue template for TYR /C:115  
Atom H1 is not in the residue template for TYR /D:115  
Atom H1 is not in the residue template for TYR /E:115  
Atom H1 is not in the residue template for TYR /F:115  
  
Chain information for apo-Refinement17-chains-corrected-renamed.cif #3  
---  
Chain | Description  
A B | No description available  
C D E F | No description available  
  
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/mouse_modes/mousemodes.py", line 650, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 732, in wheel  
self.zoom(delta_z, stereo_scaling = not event.alt_down())  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 336, in zoom  
self.far_clip.plane_point = self.far_clip_point(new_origin, vd*distance,
distance)  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 299, in far_clip_point  
return origin +
view_vec*(1+self.adjusted_clip_multiplier(self._clip_multiplier, dist))  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 296, in
adjusted_clip_multiplier  
return 1-(1-mult)*exp(-dist*self._clip_exponent_multiplier)  
OverflowError: math range error  
  
OverflowError: math range error  
  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 296, in
adjusted_clip_multiplier  
return 1-(1-mult)*exp(-dist*self._clip_exponent_multiplier)  
  
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/mouse_modes/mousemodes.py", line 650, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 732, in wheel  
self.zoom(delta_z, stereo_scaling = not event.alt_down())  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 336, in zoom  
self.far_clip.plane_point = self.far_clip_point(new_origin, vd*distance,
distance)  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 299, in far_clip_point  
return origin +
view_vec*(1+self.adjusted_clip_multiplier(self._clip_multiplier, dist))  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 296, in
adjusted_clip_multiplier  
return 1-(1-mult)*exp(-dist*self._clip_exponent_multiplier)  
OverflowError: math range error  
  
OverflowError: math range error  
  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 296, in
adjusted_clip_multiplier  
return 1-(1-mult)*exp(-dist*self._clip_exponent_multiplier)  
  
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/mouse_modes/mousemodes.py", line 650, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 732, in wheel  
self.zoom(delta_z, stereo_scaling = not event.alt_down())  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 336, in zoom  
self.far_clip.plane_point = self.far_clip_point(new_origin, vd*distance,
distance)  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 299, in far_clip_point  
return origin +
view_vec*(1+self.adjusted_clip_multiplier(self._clip_multiplier, dist))  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 296, in
adjusted_clip_multiplier  
return 1-(1-mult)*exp(-dist*self._clip_exponent_multiplier)  
OverflowError: math range error  
  
OverflowError: math range error  
  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 296, in
adjusted_clip_multiplier  
return 1-(1-mult)*exp(-dist*self._clip_exponent_multiplier)  
  
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/mouse_modes/mousemodes.py", line 650, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 732, in wheel  
self.zoom(delta_z, stereo_scaling = not event.alt_down())  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 336, in zoom  
self.far_clip.plane_point = self.far_clip_point(new_origin, vd*distance,
distance)  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 299, in far_clip_point  
return origin +
view_vec*(1+self.adjusted_clip_multiplier(self._clip_multiplier, dist))  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 296, in
adjusted_clip_multiplier  
return 1-(1-mult)*exp(-dist*self._clip_exponent_multiplier)  
OverflowError: math range error  
  
OverflowError: math range error  
  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 296, in
adjusted_clip_multiplier  
return 1-(1-mult)*exp(-dist*self._clip_exponent_multiplier)  
  
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/mouse_modes/mousemodes.py", line 650, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 732, in wheel  
self.zoom(delta_z, stereo_scaling = not event.alt_down())  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 336, in zoom  
self.far_clip.plane_point = self.far_clip_point(new_origin, vd*distance,
distance)  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 299, in far_clip_point  
return origin +
view_vec*(1+self.adjusted_clip_multiplier(self._clip_multiplier, dist))  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 296, in
adjusted_clip_multiplier  
return 1-(1-mult)*exp(-dist*self._clip_exponent_multiplier)  
OverflowError: math range error  
  
OverflowError: math range error  
  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 296, in
adjusted_clip_multiplier  
return 1-(1-mult)*exp(-dist*self._clip_exponent_multiplier)  
  
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/mouse_modes/mousemodes.py", line 650, in _wheel_event  
f.wheel(MouseEvent(event))  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/std_modes.py", line 732, in wheel  
self.zoom(delta_z, stereo_scaling = not event.alt_down())  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 336, in zoom  
self.far_clip.plane_point = self.far_clip_point(new_origin, vd*distance,
distance)  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 299, in far_clip_point  
return origin +
view_vec*(1+self.adjusted_clip_multiplier(self._clip_multiplier, dist))  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 296, in
adjusted_clip_multiplier  
return 1-(1-mult)*exp(-dist*self._clip_exponent_multiplier)  
OverflowError: math range error  
  
OverflowError: math range error  
  
File "/Users/whenriques/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/clipper/mousemodes.py", line 296, in
adjusted_clip_multiplier  
return 1-(1-mult)*exp(-dist*self._clip_exponent_multiplier)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1
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: MacBookPro17,1
      Model Number: MJ123LL/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.1.1
      OS Loader Version: 10151.1.1

Software:

    System Software Overview:

      System Version: macOS 14.0 (23A344)
      Kernel Version: Darwin 23.0.0
      Time since boot: 11 days, 21 hours, 17 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        BenQ GW2760HS:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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-Clipper: 0.21.0
    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-ISOLDE: 1.6.0
    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
    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