sequence.residues out of range

[rmattoo@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Volumes/Rayees_T5/ctSAGA_proc/ctSAGA Model build/ctTra1_chimeraX.cxs"

Opened ctSAGA_job123_3p58A_zflip.mrc as #1, grid size 480,480,480, pixel 1.02,
shown at level 0.00491, step 2, values float32  
Opened ctSAGA_job123_3p58A_zflip.mrc gaussian as #2, grid size 480,480,480,
pixel 1.02, shown at level 0.00212, step 1, values float32  
Opened ctSAGA_job123_3p58A_zflip.mrc gaussian as #3, grid size 480,480,480,
pixel 1.02, shown at level 0.00242, step 1, values float32  
Opened composite_map.ccp4 as #6, grid size 360,360,360, pixel 1.04, shown at
level 4.36, step 1, values float32  
Opened cryosparc_P21_J118_007_volume_map_sharp_zflip.mrc as #7, grid size
360,360,360, pixel 1.04, shown at level 0.549, step 1, values float32  
Opened cryosparc_P21_J118_007_volume_map_sharp_zflip.mrc as #10, grid size
360,360,360, pixel 1.04, shown at level 0.28, step 2, values float32  
Log from Wed May 3 22:19:52 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Volumes/Rayees_T5/ctSAGA_proc/ctSAGA_Maps/ctSAGA_job123_3p58A_zflip.mrc

Opened ctSAGA_job123_3p58A_zflip.mrc as #1, grid size 480,480,480, pixel 1.02,
shown at level 0.00491, step 2, values float32  

> volume guass #1 sdev 2

Expected a density maps specifier or a keyword  

> volume gaussian #1 sDev 2

Opened ctSAGA_job123_3p58A_zflip.mrc gaussian as #2, grid size 480,480,480,
pixel 1.02, shown at step 1, values float32  

> volume #2 level 0.001649

> volume #2 level 0.002119

> volume gaussian #1 sDev 3

Opened ctSAGA_job123_3p58A_zflip.mrc gaussian as #3, grid size 480,480,480,
pixel 1.02, shown at step 1, values float32  

> volume #3 level 0.0005095

> volume #3 level 0.0005424

> volume #3 level 0.002423

> volume gaussian #1 sDev 4

Opened ctSAGA_job123_3p58A_zflip.mrc gaussian as #4, grid size 480,480,480,
pixel 1.02, shown at step 1, values float32  

> volume #4 level 0.001535

> volume #4 level 0.000505

> volume #4 level 0.00173

> open
> /Volumes/Rayees_T5/ctSAGA_proc/Phenix_SBgrid/CombineFocusedMaps_296/composite_map.pdb

Summary of feedback from opening
/Volumes/Rayees_T5/ctSAGA_proc/Phenix_SBgrid/CombineFocusedMaps_296/composite_map.pdb  
---  
warning | Ignored bad PDB record found on line 31182  
  
Chain information for composite_map.pdb #5  
---  
Chain | Description  
A | No description available  
  

> open
> /Volumes/Rayees_T5/ctSAGA_proc/Phenix_SBgrid/CombineFocusedMaps_296/composite_map.ccp4

Opened composite_map.ccp4 as #6, grid size 360,360,360, pixel 1.04, shown at
level 2.67, step 2, values float32  

> volume #6 step 1

> volume #6 level 5.433

> hide #!4 models

> hide #5 models

> show #5 models

> volume #6 level 3.473

> open
> "/Volumes/Rayees_T5/ctSAGA_proc/ctSAGA_Maps/combined_sessions_021821/ctSAGA_Tra1/NU
> Refinement
> Tra1/Subtracted_maps/cryosparc_P21_J118_007_volume_map_sharp_zflip.mrc"

Opened cryosparc_P21_J118_007_volume_map_sharp_zflip.mrc as #7, grid size
360,360,360, pixel 1.04, shown at level 0.28, step 2, values float32  

> volume #7 step 1

> volume #7 level 0.4146

> hide #5 models

> hide #!7 models

> show #!7 models

> hide #!6 models

> hide #!7 models

> show #!7 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> volume #7 level 0.6072

> hide #!7 models

> show #!6 models

> volume #6 level 4.356

> show #!7 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> volume #7 level 0.5494

> volume #6 level 4.356

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> open
> /Volumes/Rayees_T5/ctSAGA_proc/Phenix_SBgrid/RealSpaceRefine_267/ctSaga_Tra1__real_space_refined_267.pdb

Chain information for ctSaga_Tra1__real_space_refined_267.pdb #8  
---  
Chain | Description  
A | No description available  
  

> hide #5 models

> show #!4 models

> show #!3 models

> close #4

> hide #!3 models

> ui tool show "Fit in Map"

> fitmap #6 inMap #7

Fit map composite_map.ccp4 in map
cryosparc_P21_J118_007_volume_map_sharp_zflip.mrc using 161938 points  
correlation = 0.9975, correlation about mean = 0.9891, overlap = 2.346e+06  
steps = 68, shift = 0.57, angle = 1.48 degrees  
  
Position of composite_map.ccp4 (#6) relative to
cryosparc_P21_J118_007_volume_map_sharp_zflip.mrc (#7) coordinates:  
Matrix rotation and translation  
0.99966880 0.02549381 0.00351455 -5.72447426  
-0.02550234 0.99967187 0.00240299 4.52285021  
-0.00345213 -0.00249182 0.99999094 0.62040268  
Axis -0.09467337 0.13474665 -0.98634694  
Axis point 171.60805098 224.76974430 0.00000000  
Rotation angle (degrees) 1.48131947  
Shift along axis 0.53946188  
  

> fitmap #8 inMap #7

Fit molecule ctSaga_Tra1__real_space_refined_267.pdb (#8) to map
cryosparc_P21_J118_007_volume_map_sharp_zflip.mrc (#7) using 30987 atoms  
average map value = 1.29, steps = 44  
shifted from previous position = 0.0367  
rotated from previous position = 0.0314 degrees  
atoms outside contour = 9454, contour level = 0.54944  
  
Position of ctSaga_Tra1__real_space_refined_267.pdb (#8) relative to
cryosparc_P21_J118_007_volume_map_sharp_zflip.mrc (#7) coordinates:  
Matrix rotation and translation  
0.99999993 -0.00037573 -0.00008111 0.10984312  
0.00037569 0.99999985 -0.00038987 0.02332928  
0.00008126 0.00038984 0.99999992 -0.10447577  
Axis 0.71208312 -0.14829350 0.68625554  
Axis point 0.00000000 273.40021614 60.90068150  
Rotation angle (degrees) 0.03136824  
Shift along axis 0.00306078  
  

> fitmap #8 inMap #7

Fit molecule ctSaga_Tra1__real_space_refined_267.pdb (#8) to map
cryosparc_P21_J118_007_volume_map_sharp_zflip.mrc (#7) using 30987 atoms  
average map value = 1.29, steps = 64  
shifted from previous position = 0.016  
rotated from previous position = 0.00416 degrees  
atoms outside contour = 9453, contour level = 0.54944  
  
Position of ctSaga_Tra1__real_space_refined_267.pdb (#8) relative to
cryosparc_P21_J118_007_volume_map_sharp_zflip.mrc (#7) coordinates:  
Matrix rotation and translation  
0.99999994 -0.00034796 -0.00004855 0.08924051  
0.00034794 0.99999988 -0.00033121 0.00746415  
0.00004866 0.00033119 0.99999994 -0.07946990  
Axis 0.68595351 -0.10066309 0.72064882  
Axis point -22.29323682 250.17716317 0.00000000  
Rotation angle (degrees) 0.02766408  
Shift along axis 0.00319359  
  

> open
> /Volumes/Rayees_T5/ctSAGA_proc/Phenix_SBgrid/RealSpaceRefine_295/phenixRSR_ctSAGA_Tra1_res1850_2450__J402_cutOut2_real_space_refined_295-coot-1.pdb

Summary of feedback from opening
/Volumes/Rayees_T5/ctSAGA_proc/Phenix_SBgrid/RealSpaceRefine_295/phenixRSR_ctSAGA_Tra1_res1850_2450__J402_cutOut2_real_space_refined_295-coot-1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ARG A 13
TRP A 24 1 12  
Start residue of secondary structure not found: HELIX 2 2 GLU A 33 LEU A 36 1
4  
Start residue of secondary structure not found: HELIX 3 3 VAL A 40 ARG A 58 1
19  
Start residue of secondary structure not found: HELIX 4 4 HIS A 59 ALA A 65 1
7  
Start residue of secondary structure not found: HELIX 5 5 ARG A 66 ALA A 73 1
8  
39 messages similar to the above omitted  
  
Chain information for
phenixRSR_ctSAGA_Tra1_res1850_2450__J402_cutOut2_real_space_refined_295-coot-1.pdb
#4  
---  
Chain | Description  
A | No description available  
  

> hide #4 models

> show #4 models

> fitmap #4 inMap #7

Fit molecule
phenixRSR_ctSAGA_Tra1_res1850_2450__J402_cutOut2_real_space_refined_295-coot-1.pdb
(#4) to map cryosparc_P21_J118_007_volume_map_sharp_zflip.mrc (#7) using 4983
atoms  
average map value = 0.7772, steps = 56  
shifted from previous position = 1.66  
rotated from previous position = 1.15 degrees  
atoms outside contour = 1853, contour level = 0.54944  
  
Position of
phenixRSR_ctSAGA_Tra1_res1850_2450__J402_cutOut2_real_space_refined_295-coot-1.pdb
(#4) relative to cryosparc_P21_J118_007_volume_map_sharp_zflip.mrc (#7)
coordinates:  
Matrix rotation and translation  
0.99980698 0.01954246 -0.00202285 -3.81847037  
-0.01953382 0.99980036 0.00420351 2.96273050  
0.00210459 -0.00416318 0.99998912 -0.12196181  
Axis -0.20825846 -0.10273789 -0.97266301  
Axis point 152.93130971 190.40907933 0.00000000  
Rotation angle (degrees) 1.15099294  
Shift along axis 0.60947184  
  

> open
> /Volumes/Rayees_T5/ctSAGA_proc/Phenix_SBgrid/RealSpaceRefine_293/phenixRSR_ctSAGA_Tra1_res1_540__J403_cutOut1_real_space_refined_293.pdb

Chain information for
phenixRSR_ctSAGA_Tra1_res1_540__J403_cutOut1_real_space_refined_293.pdb #9  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Fit in Map"

> hide #!9 models

> show #!9 models

> fitmap #9 inMap #1

Fit molecule
phenixRSR_ctSAGA_Tra1_res1_540__J403_cutOut1_real_space_refined_293.pdb (#9)
to map ctSAGA_job123_3p58A_zflip.mrc (#1) using 3793 atoms  
average map value = -0.0002089, steps = 76  
shifted from previous position = 2.32  
rotated from previous position = 4.18 degrees  
atoms outside contour = 3793, contour level = 0.0049126  
  
Position of
phenixRSR_ctSAGA_Tra1_res1_540__J403_cutOut1_real_space_refined_293.pdb (#9)
relative to ctSAGA_job123_3p58A_zflip.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99748528 0.06371019 0.03105034 -14.12079599  
-0.06422475 0.99780934 0.01586531 9.68072288  
-0.02997153 -0.01781961 0.99939190 8.52495443  
Axis -0.23120896 0.41884623 -0.87812884  
Axis point 144.04272604 227.93059024 0.00000000  
Rotation angle (degrees) 4.17742244  
Shift along axis -0.16641944  
  

> fitmap #9 inMap #1

Fit molecule
phenixRSR_ctSAGA_Tra1_res1_540__J403_cutOut1_real_space_refined_293.pdb (#9)
to map ctSAGA_job123_3p58A_zflip.mrc (#1) using 3793 atoms  
average map value = -0.0002089, steps = 56  
shifted from previous position = 0.00612  
rotated from previous position = 0.0106 degrees  
atoms outside contour = 3793, contour level = 0.0049126  
  
Position of
phenixRSR_ctSAGA_Tra1_res1_540__J403_cutOut1_real_space_refined_293.pdb (#9)
relative to ctSAGA_job123_3p58A_zflip.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99749574 0.06353589 0.03107147 -14.10672219  
-0.06405266 0.99781940 0.01592817 9.64121828  
-0.02999171 -0.01787849 0.99939024 8.53245111  
Axis -0.23245693 0.41987471 -0.87730782  
Axis point 143.78638612 228.27403193 0.00000000  
Rotation angle (degrees) 4.16999745  
Shift along axis -0.15827696  
  

> help help:user

> hide #!7 models

> show #!7 models

> hide #!7 models

> hide #!6 models

> select #8 /A:1830-2450

4983 atoms, 5100 bonds, 621 residues, 1 model selected  

> hide #!9 models

> show #!9 models

> hide #4 models

> show #4 models

> hide #8 models

> show #8 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> delete atoms sel

> delete bonds sel

> hide #!9 models

> show #!9 models

> hide #4 models

> show #4 models

> select #8 /A:1-540

3964 atoms, 4052 bonds, 499 residues, 1 model selected  

> hide #!9 models

> show #!9 models

> hide #4 models

> show #4 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> show #!6 models

> hide #!6 models

> delete atoms sel

> delete bonds sel

> help help:user

[Repeated 2 time(s)]

> hide #!8 models

> show #!8 models

> hide #4 models

> show #4 models

> hide #!8 models

> show #!8 models

> hide #4 models

> show #4 models

> hide #!9 models

> show #!9 models

> combine #8 #4 #9 [close false] [modelId #10] [name mergedTra1]

Expected a keyword  

> combine #8|#4|#9 [close false] [modelId #10] [name mergedTra1]

Expected a keyword  

> combine [#8 #4 #9] [close false] [modelId #10] [name mergedTra1]

Expected a keyword  

> combine #8 & #4 & #9 [close false] [modelId #10] [name mergedTra1]

Expected a keyword  

> toolshed show

> cd "/Volumes/Rayees_T5/ctSAGA_proc/ctSAGA Model build"

Current working directory is: /Volumes/Rayees_T5/ctSAGA_proc/ctSAGA Model
build  

> save "/Volumes/Rayees_T5/ctSAGA_proc/ctSAGA Model build/ctTra1_chimeraX.cxs"
> includeMaps true

> hide #!8 models

> show #!8 models

> hide #4 models

> show #4 models

> combine #8 #4 #9 [close false] [modelId #10] [name mergedTra1]

Expected a keyword  

> hide #!9 models

> show #!9 models

> hide #!8 models

> show #!8 models

> hide #4 models

> show #4 models

> hide #!9 models

> show #!9 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> combine #8 #4 #9 [close false] [modelId #10] [name mergedTra1]

Expected a keyword  

> combine #8 #9 #4 close false modelId #10 name Merged_Tra1

Remapping chain ID 'A' in
phenixRSR_ctSAGA_Tra1_res1_540__J403_cutOut1_real_space_refined_293.pdb #9 to
'B'  
Remapping chain ID 'A' in
phenixRSR_ctSAGA_Tra1_res1850_2450__J402_cutOut2_real_space_refined_295-coot-1.pdb
#4 to 'C'  

> hide #4 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> open
> "/Volumes/Rayees_T5/ctSAGA_proc/ctSAGA_Maps/combined_sessions_021821/ctSAGA_Tra1/NU
> Refinement
> Tra1/Subtracted_maps/cryosparc_P21_J118_007_volume_map_sharp_zflip.mrc"

Opened cryosparc_P21_J118_007_volume_map_sharp_zflip.mrc as #10, grid size
360,360,360, pixel 1.04, shown at level 0.28, step 2, values float32  

> save "/Volumes/Rayees_T5/ctSAGA_proc/ctSAGA Model build/Merged_Tra1.pdb"
> relModel #10

> hide #!10 models

> save "/Volumes/Rayees_T5/ctSAGA_proc/ctSAGA Model build/ctTra1_chimeraX.cxs"

——— End of log from Wed May 3 22:19:52 2023 ———

opened ChimeraX session  

> show #!9 models

> hide #!9 models

> show #!8 models

> show #!9 models

> show #4 models

> combine #8 #9 #4 close true modelId #11 name Merged_Tra1

Remapping chain ID 'A' in
phenixRSR_ctSAGA_Tra1_res1_540__J403_cutOut1_real_space_refined_293.pdb #9 to
'B'  
Remapping chain ID 'A' in
phenixRSR_ctSAGA_Tra1_res1850_2450__J402_cutOut2_real_space_refined_295-coot-1.pdb
#4 to 'C'  

> cd "/Volumes/Rayees_T5/ctSAGA_proc/ctSAGA Model build"

Current working directory is: /Volumes/Rayees_T5/ctSAGA_proc/ctSAGA Model
build  

> show #!7 models

> hide #!7 models

> show #!7 models

> show #!10 models

> close #10

> save "/Volumes/Rayees_T5/ctSAGA_proc/ctSAGA Model build/Merged2_Tra1.pdb"
> relModel #7

> hide #!7 models

> show #!6 models

> transparency #6.1 50

> hide #!6 models

> show #!6 models

> hide #!6 models

> ui tool show AlphaFold

> alphafold predict
> MATSLIEDVVKKLSVAETGTGNSLSERSLLVLPLMQVSCYTELKVKAEAACALRDSLDHYTAGPAYPAFLKKVMPVFIHILRQQPVFQTTGEQGHMQKLRNCILEILHRLPTSQTPPEHFEPYAHEIVDLLLELVRTDNEDNVILCVKILSDIMRHQHKIMSGKVQTFLNLIQELFEQLDKVVRDQLDNTSTTGPPGPPSTPGSTQSSFLPHQQSPRPGSPVTTGVTDFGADANQQANRLLPRGMYSFKVLAECPIIVVSIFQVHRSAVTPNVKAFVPLIKSALLCQAKAQDQAHREAAARGTIHIGVSPNIKNRAAFGDFITAQVKTMSFLAYLLRQYSSQLSDFLPHLPDIIVRLLRDCPRDKSSARKELFVAIRHIINFNFRKIFLPKIDELLDERTLVGDGLTVHETMRPLAYSMLADLIHHVRDQLSPEQIRKTVEVYTRNLQDNFPGTSFQTMSAKLLLNMAECIARLPNKVDARHYLIMILNAIADKFAAMNRQYPNAVKLSKQYAQQAAKNVPETYLADKENPPDWDEIDIFNATPIKISNPRDRAADPVVDNKFLFRNLMTGLKNTFYQLK
> directory /Users/rmattoo/Downloads/ChimeraX/AlphaFold/ctTra1_res_1_to_580

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  

> show #!7 models

> hide #!7 models

> show #!6 models

> hide #!6 models

> cartoon style #11 modeHelix tube

> undo

> hide #!11 models

> show #!11 models

> bond help

Missing or invalid "atoms" argument: invalid atoms specifier  

> bond #11 /C:2450 /A:2451 reasonable true

Created 11 bonds  

> bond #11 /A:1829 /A:1830 reasonable true

Created 0 bonds  

> bond #11 /A:1829-1830 reasonable true

Created 0 bonds  

> bond #11 /A:1829 & 1830 reasonable true

Expected a keyword  

> bond #11 /A:1829|1830 reasonable true

Expected a keyword  

> bond #11 /A:1829:1830 reasonable true

Created 0 bonds  

> bond #11 /A:1829-1830 reasonable true

Created 0 bonds  

> bond #11 /A:1829 to 1830 reasonable true

Expected a keyword  

> bond #11 /A:1829 & 1830 reasonable true

Expected a keyword  

> alphafold predict
> MATSLIEDVVKKLSVAETGTGNSLSERSLLVLPLMQVSCYTELKVKAEAACALRDSLDHYTAGPAYPAFLKKVMPVFIHILRQQPVFQTTGEQGHMQKLRNCILEILHRLPTSQTPPEHFEPYAHEIVDLLLELVRTDNEDNVILCVKILSDIMRHQHKIMSGKVQTFLNLIQELFEQLDKVVRDQLDNTSTTGPPGPPSTPGSTQSSFLPHQQSPRPGSPVTTGVTDFGADANQQANRLLPRGMYSFKVLAECPIIVVSIFQVHRSAVTPNVKAFVPLIKSALLCQAKAQDQAHREAAARGTIHIGVSPNIKNRAAFGDFITAQVKTMSFLAYLLRQYSSQLSDFLPHLPDIIVRLLRDCPRDKSSARKELFVAIRHIINFNFRKIFLPKIDELLDERTLVGDGLTVHETMRPLAYSMLADLIHHVRDQLSPEQIRKTVEVYTRNLQDNFPGTSFQTMSAKLLLNMAECIARLPNKVDARHYLIMILNAIADKFAAMNRQYPNAVKLSKQYAQQAAKNVPETYLADKENPPDWDEIDIFNATPIKISNPRDRAADPVVDNKFLFRNLMTGLKNTFYQLK
> directory /Users/rmattoo/Downloads/ChimeraX/AlphaFold/ctTra1_res_1_to_580

Running AlphaFold prediction  

> bond #11 /A:1829|1830 reasonable true

Expected a keyword  

> bond #11 /A:1829 and 1830 reasonable true

Expected a keyword  

> bond #11 /A:1829 reasonable true

Created 0 bonds  

> bond #11 /A:1829-1830 reasonable true

Created 0 bonds  

> bond #11 /A:1829-1830 reasonable false

Created 189 bonds  

> bond #11 /B:540 /A:541 reasonable true

Created 0 bonds  

> bond #11 /B:540 /A:541 reasonable false

Created 153 bonds  

> alphafold predict
> MATSLIEDVVKKLSVAETGTGNSLSERSLLVLPLMQVSCYTELKVKAEAACALRDSLDHYTAGPAYPAFLKKVMPVFIHILRQQPVFQTTGEQGHMQKLRNCILEILHRLPTSQTPPEHFEPYAHEIVDLLLELVRTDNEDNVILCVKILSDIMRHQHKIMSGKVQTFLNLIQELFEQLDKVVRDQLDNTSTTGPPGPPSTPGSTQSSFLPHQQSPRPGSPVTTGVTDFGADANQQANRLLPRGMYSFKVLAECPIIVVSIFQVHRSAVTPNVKAFVPLIKSALLCQAKAQDQAHREAAARGTIHIGVSPNIKNRAAFGDFITAQVKTMSFLAYLLRQYSSQLSDFLPHLPDIIVRLLRDCPRDKSSARKELFVAIRHIINFNFRKIFLPKIDELLDERTLVGDGLTVHETMRPLAYSMLADLIHHVRDQLSPEQIRKTVEVYTRNLQDNFPGTSFQTMSAKLLLNMAECIARLPNKVDARHYLIMILNAIADKFAAMNRQYPNAVKLSKQYAQQAAKNVPETYLADKENPPDWDEIDIFNATPIKISNPRDRAADPVVDNKFLFRNLMTGLKNTFYQLK
> directory /Users/rmattoo/Downloads/ChimeraX/AlphaFold/ctTra1_res_1_to_580

Running AlphaFold prediction  

> alphafold predict
> MATSLIEDVVKKLSVAETGTGNSLSERSLLVLPLMQVSCYTELKVKAEAACALRDSLDHYTAGPAYPAFLKKVMPVFIHILRQQPVFQTTGEQGHMQKLRNCILEILHRLPTSQTPPEHFEPYAHEIVDLLLELVRTDNEDNVILCVKILSDIMRHQHKIMSGKVQTFLNLIQELFEQLDKVVRDQLDNTSTTGPPGPPSTPGSTQSSFLPHQQSPRPGSPVTTGVTDFGADANQQANRLLPRGMYSFKVLAECPIIVVSIFQVHRSAVTPNVKAFVPLIKSALLCQAKAQDQAHREAAARGTIHIGVSPNIKNRAAFGDFITAQVKTMSFLAYLLRQYSSQLSDFLPHLPDIIVRLLRDCPRDKSSARKELFVAIRHIINFNFRKIFLPKIDELLDERTLVGDGLTVHETMRPLAYSMLADLIHHVRDQLSPEQIRKTVEVYTRNLQDNFPGTSFQTMSAKLLLNMAECIARLPNKVDARHYLIMILNAIADKFAAMNRQYPNAVKLSKQYAQQAAKNVPETYLADKENPPDWDEIDIFNATPIKISNPRDRAADPVVDNKFLFRNLMTGLKNTFYQLK
> directory /Users/rmattoo/Downloads/ChimeraX/AlphaFold/ctTra1_res_1_to_580

Running AlphaFold prediction  

> alphafold predict
> MATSLIEDVVKKLSVAETGTGNSLSERSLLVLPLMQVSCYTELKVKAEAACALRDSLDHYTAGPAYPAFLKKVMPVFIHILRQQPVFQTTGEQGHMQKLRNCILEILHRLPTSQTPPEHFEPYAHEIVDLLLELVRTDNEDNVILCVKILSDIMRHQHKIMSGKVQTFLNLIQELFEQLDKVVRDQLDNTSTTGPPGPPSTPGSTQSSFLPHQQSPRPGSPVTTGVTDFGADANQQANRLLPRGMYSFKVLAECPIIVVSIFQVHRSAVTPNVKAFVPLIKSALLCQAKAQDQAHREAAARGTIHIGVSPNIKNRAAFGDFITAQVKTMSFLAYLLRQYSSQLSDFLPHLPDIIVRLLRDCPRDKSSARKELFVAIRHIINFNFRKIFLPKIDELLDERTLVGDGLTVHETMRPLAYSMLADLIHHVRDQLSPEQIRKTVEVYTRNLQDNFPGTSFQTMSAKLLLNMAECIARLPNKVDARHYLIMILNAIADKFAAMNRQYPNAVKLSKQYAQQAAKNVPETYLADKENPPDWDEIDIFNATPIKISNPRDRAADPVVDNKFLFRNLMTGLKNTFYQLK
> directory /Users/rmattoo/Downloads/ChimeraX/AlphaFold/ctTra1_res_1_to_580

Running AlphaFold prediction  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!11 models

> volume #1 level 0.006195

> volume #1 step 1

> volume #1 level 0.009362

> show #!7 models

> vop add #7 onGrid #1

Opened cryosparc_P21_J118_007_volume_map_sharp_zflip.mrc resampled as #4, grid
size 480,480,480, pixel 1.02, shown at step 1, values float32  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!1 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!1 models

> show #!7 models

> hide #!7 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> close #4

> show #!7 models

> volume add #7 onGrid #1

Opened cryosparc_P21_J118_007_volume_map_sharp_zflip.mrc resampled as #4, grid
size 480,480,480, pixel 1.02, shown at step 1, values float32  

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!7 models

> hide #!7 models

> close #4

AlphaFold prediction finished  
Results in /Users/rmattoo/Downloads/ChimeraX/AlphaFold/ctTra1_res_1_to_580  

> open
> /Users/rmattoo/Downloads/ChimeraX/AlphaFold/ctTra1_res_1_to_580/best_model.pdb

Chain information for best_model.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/rmattoo/Downloads/ChimeraX/AlphaFold/ctTra1_res_1_to_580/best_model.pdb

Chain information for best_model.pdb #8  
---  
Chain | Description  
A | No description available  
  

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> hide #4 models

> show #4 models

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> hide #8 models

> hide #4 models

> show #8 models

> show #4 models

> hide #4 models

> hide #8 models

> close #8

> show #4 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> mmaker #4 to #11

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2918, in run  
result = ci.function(session, *args, optional=optional,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3457, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Applications/ChimeraX-1.5.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-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 696, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 367, in match  
score, s1, s2 = align(session, rseq, mseq,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 68, in align  
score, seqs = NeedlemanWunsch.nw(ref, match,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 50, in nw  
"".join([s1.ss_type(i) or ' ' for i in range(len(s1))]),  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 50, in
<listcomp>  
"".join([s1.ss_type(i) or ' ' for i in range(len(s1))]),  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1185, in ss_type  
r = self.residue_at(loc)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at  
return convert.residue_or_none(f(self._c_pointer, index))  
IndexError: vector  
  
IndexError: vector  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at  
return convert.residue_or_none(f(self._c_pointer, index))  
  
See log for complete Python traceback.  
  

> hide #!11 models

> show #!11 models

> mmaker #4 to #11

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2918, in run  
result = ci.function(session, *args, optional=optional,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3457, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Applications/ChimeraX-1.5.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-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 696, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 367, in match  
score, s1, s2 = align(session, rseq, mseq,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 68, in align  
score, seqs = NeedlemanWunsch.nw(ref, match,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 50, in nw  
"".join([s1.ss_type(i) or ' ' for i in range(len(s1))]),  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 50, in
<listcomp>  
"".join([s1.ss_type(i) or ' ' for i in range(len(s1))]),  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1185, in ss_type  
r = self.residue_at(loc)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at  
return convert.residue_or_none(f(self._c_pointer, index))  
IndexError: vector  
  
IndexError: vector  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at  
return convert.residue_or_none(f(self._c_pointer, index))  
  
See log for complete Python traceback.  
  

> open
> /Users/rmattoo/Downloads/ChimeraX/AlphaFold/ctTra1_res_1_to_580/best_model.pdb

Chain information for best_model.pdb #8  
---  
Chain | Description  
A | No description available  
  

> hide #8 models

> show #8 models

> hide #4 models

> mmaker #8 to #11

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2918, in run  
result = ci.function(session, *args, optional=optional,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3457, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
File
"/Applications/ChimeraX-1.5.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-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 696, in cmd_match  
ret_vals = match(session, pairing, match_items, matrix, alg, gap_open,
gap_extend,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 367, in match  
score, s1, s2 = align(session, rseq, mseq,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/match.py", line 68, in align  
score, seqs = NeedlemanWunsch.nw(ref, match,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 50, in nw  
"".join([s1.ss_type(i) or ' ' for i in range(len(s1))]),  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 50, in
<listcomp>  
"".join([s1.ss_type(i) or ' ' for i in range(len(s1))]),  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1185, in ss_type  
r = self.residue_at(loc)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at  
return convert.residue_or_none(f(self._c_pointer, index))  
IndexError: vector  
  
IndexError: vector  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1151, in residue_at  
return convert.residue_or_none(f(self._c_pointer, index))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.10.12
OpenGL renderer: AMD Radeon Pro 555X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2.2 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0)
      OS Loader Version: 577~129

Software:

    System Software Overview:

      System Version: macOS 13.3.1 (a) (22E772610a)
      Kernel Version: Darwin 22.4.0
      Time since boot: 1 day, 1 hour, 21 minutes

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
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    Radeon Pro 555X:

      Chipset Model: Radeon Pro 555X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00e3
      ROM Revision: 113-C980AL-075
      VBIOS Version: 113-C97501P-005
      EFI Driver Version: 01.A1.075
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        SyncMaster:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: HCGS501068  
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    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
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    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: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

[Eric Pettersen]

Hi Rayees,

Thanks for reporting this problem. I cannot reproduce it here. Can you reproduce it? If so, is there any chance you could provide a session file saved just before the error occurs? I don't think there is any need to include the maps in the session (which will greatly increase the session size) since I don't think they're involved with the problem.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab