help matchmaker: 'NoneType' object has no attribute 'split'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.9rc202411160247 (2024-11-16 02:47:39 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9rc202411160247 (2024-11-16)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open D:\Documents\Files\Downloads\1mbn.pdb format pdb

1mbn.pdb title:  
The stereochemistry of the protein myoglobin [more info...]  
  
Chain information for 1mbn.pdb #1  
---  
Chain | Description | UniProt  
A | myoglobin | MYG_PHYCA 1-153  
  
Non-standard residues in 1mbn.pdb #1  
---  
HEM — protoporphyrin IX containing Fe (HEME)  
OH — hydroxide ion  
  

> view

> select /A:64

10 atoms, 10 bonds, 1 residue, 1 model selected  

> color sel red

> show sel atoms

> select add #1

1260 atoms, 1290 bonds, 6 pseudobonds, 155 residues, 2 models selected  

> select subtract #1

Nothing selected  

> open D:/Documents/Files/Downloads/AlphaFod-
> heme/fold_2024_11_18_17_17_full_data_1.json

Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command structure option, for example  
  
open D:/Documents/Files/Downloads/AlphaFod-
heme/fold_2024_11_18_17_17_full_data_1.json structure #1  
  
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as  
  
open mole_channels.json format mole  

> open D:/Documents/Files/Downloads/AlphaFod-
> heme/fold_2024_11_18_17_17_model_1.cif

Summary of feedback from opening D:/Documents/Files/Downloads/AlphaFod-
heme/fold_2024_11_18_17_17_model_1.cif  
---  
note | Fetching CCD HEM from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/HEM/HEM.cif  
  
Chain information for fold_2024_11_18_17_17_model_1.cif #2  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> hide #!1 models

> view

> select /A:64

19 atoms, 18 bonds, 2 residues, 2 models selected  

> color (#!2 & sel) orange red

> show sel & #!2 atoms

> clear

Unknown command: clear  

> select clear

> select add #2

1266 atoms, 1296 bonds, 4 pseudobonds, 155 residues, 2 models selected  

> select subtract #2

Nothing selected  

> hide #!2 atoms

[Repeated 1 time(s)]

> show #!2 atoms

> undo

[Repeated 2 time(s)]

> select /A:64

19 atoms, 18 bonds, 2 residues, 2 models selected  

> hide sel & #!2 atoms

> color (#!2 & sel) cyan

> color (#!2 & sel) light sea green

> ui tool show "Color Actions"

> color (#!2 & sel) cornflower blue

> select add #2

1276 atoms, 1306 bonds, 4 pseudobonds, 156 residues, 3 models selected  

> close

> open D:\Documents\Files\Downloads\1mbn.pdb format pdb

1mbn.pdb title:  
The stereochemistry of the protein myoglobin [more info...]  
  
Chain information for 1mbn.pdb #1  
---  
Chain | Description | UniProt  
A | myoglobin | MYG_PHYCA 1-153  
  
Non-standard residues in 1mbn.pdb #1  
---  
HEM — protoporphyrin IX containing Fe (HEME)  
OH — hydroxide ion  
  

> select /A:64

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel red

> open D:/Documents/Files/Downloads/AlphaFod-
> heme/fold_2024_11_18_17_17_model_1.cif

Chain information for fold_2024_11_18_17_17_model_1.cif #2  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> hide #!1 models

> view

> select /A:65

12 atoms, 10 bonds, 2 residues, 2 models selected  

> show sel & #!2 atoms

> color (#!2 & sel) red

> show #!1 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> rmsd

Missing or invalid "atoms" argument: empty atom specifier  

> select clear

> rmsd

Missing or invalid "atoms" argument: empty atom specifier  

> rmsd #0:myoglobin C-alpha #1:myoglobin C-alpha

Expected a keyword  

> rmsd #0:myoglobin

Missing required "to" argument  

> rmsd #0:myoglobin C-alpha

Expected a keyword  

> rmsd #0:myoglobin c-alpha

Expected a keyword  

> show #!1 models

> matchmaker #2 to #1

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1mbn.pdb, chain A (#1) with fold_2024_11_18_17_17_model_1.cif,
chain A (#2), sequence alignment score = 762.3  
RMSD between 152 pruned atom pairs is 0.566 angstroms; (across all 153 pairs:
0.698)  
  

> undo

> select /A:65

12 atoms, 10 bonds, 2 residues, 2 models selected  

> color (#!2 & sel) lime

> color (#!2 & sel) yellow

> show #!1 models

> select clear

> rmsd #2 to #1

Number of atoms from first atom spec (1266) differs from number in second
(1260)  

> rmsd #2/A:2-154@CA to #1/A:1-153@CA

RMSD between 153 atom pairs is 0.698  

> save D:/Documents/Files/Downloads/AlphaFod-heme/rsmd-predictedVsx-ray.cxs

> color #1 #aaffffff

> color #1 #aaff00ff

> color #1 #aa5500ff

> undo

[Repeated 2 time(s)]

> save D:/Documents/Files/Downloads/AlphaFod-heme/rsmd-predictedVsx-ray.cxs

> save D:/Documents/Files/Downloads/AlphaFod-heme/1mbn-pred.jpg width 699
> height 461 supersample 3

> view

> show atoms

> hide atoms

> undo

[Repeated 1 time(s)]

> ~hbonds

> hbonds reveal true

628 hydrogen bonds found  

> undo

[Repeated 4 time(s)]

> hide sel & #!2 cartoons

> show sel & #!2 cartoons

> ~hbonds

> show #!1 models

> hbonds sel reveal true

8 hydrogen bonds found  

> ~hbonds

> color #1 lime

> hide #!2 models

> show #!1 models

> undo

[Repeated 2 time(s)]

> hide #!2 models

> show #!1 models

> select /A:65

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #1/A:65

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:65

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/A:64

10 atoms, 10 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

5 hydrogen bonds found  

> style sel stick

Changed 10 atom styles  

> style sel stick

Changed 10 atom styles  

> hide #3 models

> show #3 models

> show #!2 models

> select #2/A:65

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel lime

> hide #!2 models

> view

> save D:/Documents/Files/Downloads/AlphaFod-heme/1mbn-hbond.jpg width 715
> height 461 supersample 3

> show #!2 models

> hide #3 models

> hide #!1 models

> hbonds sel reveal true

4 hydrogen bonds found  

> hbonds sel reveal true

4 hydrogen bonds found  

> select #2/A65

Nothing selected  

> select #2/A:65

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

4 hydrogen bonds found  

> hbonds sel reveal true

4 hydrogen bonds found  

> color sel yellow

> show #3 models

> select clear

> save D:/Documents/Files/Downloads/AlphaFod-heme/pred-hbond.jpg width 715
> height 461 supersample 3

> show #!1 models

> hide #3 models

> show #3 models

> select #1/A:64

10 atoms, 10 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

5 hydrogen bonds found  

> select clear

> save D:/Documents/Files/Downloads/AlphaFod-heme/1mbn-pred-hbond.jpg width
> 715 height 461 supersample 3

> open D:/Documents/Files/Downloads/charmm-
> gui-3169748070/gromacs/step5_input.pdb

Summary of feedback from opening D:/Documents/Files/Downloads/charmm-
gui-3169748070/gromacs/step5_input.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
156699 messages similar to the above omitted  
  
Chain information for step5_input.pdb #4  
---  
Chain | Description  
? | No description available  
  

> hide #1.1 models

> hide #!2 models

> hide #2.1 models

> hide #3 models

> view

Drag select of 1840 atoms, 17 residues, 1367 bonds  

> undo

> hide #4 models

> view

> hide #!1 models

> open D:/Documents/Files/Downloads/charmm-
> gui-3169748070/gromacs/step5_input.pdb

Summary of feedback from opening D:/Documents/Files/Downloads/charmm-
gui-3169748070/gromacs/step5_input.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
156699 messages similar to the above omitted  
  
Chain information for step5_input.pdb #5  
---  
Chain | Description  
? | No description available  
  

> view

> hide #5 models

> open D:/Documents/Files/Downloads/charmm-
> gui-3169748070/gromacs/step7_production.mdp

Unrecognized file suffix '.mdp'  

> open D:/Documents/Files/Downloads/charmm-gui-3169748070/step1_pdbreader.pdb

Summary of feedback from opening D:/Documents/Files/Downloads/charmm-
gui-3169748070/step1_pdbreader.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON NOV, 15.
2024. JOB  
  
Ignored bad PDB record found on line 2  
REMARK READ PDB, MANIPULATE STRUCTURE IF NEEDED, AND GENERATE TOPOLOGY FILE  
  
Ignored bad PDB record found on line 3  
REMARK DATE: 11/15/24 14: 9:54 CREATED BY USER: apache  
  
Chain information for step1_pdbreader.pdb #6  
---  
Chain | Description  
P | No description available  
  
Computing secondary structure  

> view

> hide #!6 models

> open D:/Documents/Files/Downloads/charmm-gui-3169748070/step2_orient.pdb

Summary of feedback from opening D:/Documents/Files/Downloads/charmm-
gui-3169748070/step2_orient.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK CALC TOPAREA = 1421.183  
  
Ignored bad PDB record found on line 2  
REMARK CALC BOTAREA = 1232.17108  
  
Ignored bad PDB record found on line 3  
REMARK CALC XMAX = 68.3374169  
  
Ignored bad PDB record found on line 4  
REMARK CALC XMIN = -36.680897  
  
Ignored bad PDB record found on line 5  
REMARK CALC YMAX = 42.1967391  
  
4 messages similar to the above omitted  
  
Chain information for step2_orient.pdb #7  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> hide #!7 models

> open D:/Documents/Files/Downloads/charmm-gui-3169748070/step3_packing.pdb

Summary of feedback from opening D:/Documents/Files/Downloads/charmm-
gui-3169748070/step3_packing.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON NOV, 15.
2024. JOB  
  
Ignored bad PDB record found on line 2  
REMARK GENERATES LIPID PACKING USING BIG SPHERES  
  
Ignored bad PDB record found on line 3  
REMARK DATE: 11/15/24 14:22:32 CREATED BY USER: apache  
  
Chain information for step3_packing.pdb #8  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> hide #!8 models

> show #!8 models

> hide #!8 models

> open D:/Documents/Files/Downloads/charmm-gui-3169748070/step4.3_ion.pdb

Summary of feedback from opening D:/Documents/Files/Downloads/charmm-
gui-3169748070/step4.3_ion.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON NOV, 15.
2024. JOB  
  
Ignored bad PDB record found on line 2  
REMARK GENERATES ION CONFORMATION USING MONTE-CARLO SIMULATION  
  
Ignored bad PDB record found on line 3  
REMARK DATE: 11/15/24 14:34:19 CREATED BY USER: apache  
  
Chain information for step4.3_ion.pdb #9  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> color #9 yellow

> undo

> view

> hide #!9 models

> open "D:/Documents/Files/Downloads/del_gq at1r/step4.3_ion (2).pdb"

Summary of feedback from opening D:/Documents/Files/Downloads/del_gq
at1r/step4.3_ion (2).pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON NOV, 16.
2024. JOB  
  
Ignored bad PDB record found on line 2  
REMARK GENERATES ION CONFORMATION USING MONTE-CARLO SIMULATION  
  
Ignored bad PDB record found on line 3  
REMARK DATE: 11/16/24 15:27:10 CREATED BY USER: apache  
  
Chain information for step4.3_ion (2).pdb #10  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> hide #10 models

> open "D:/Documents/Files/Downloads/del_gq at1r/step5_assembly.pdb"

Summary of feedback from opening D:/Documents/Files/Downloads/del_gq
at1r/step5_assembly.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON NOV, 16.
2024. JOB  
  
Ignored bad PDB record found on line 2  
REMARK INPUT GENERATION  
  
Ignored bad PDB record found on line 3  
REMARK DATE: 11/16/24 17:25: 3 CREATED BY USER: apache  
  
Ignored bad PDB record found on line 172328  
TER 172325 CLA 214  
  
Chain information for step5_assembly.pdb #11  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> color #11 #304396ff

> color #11 lime

> color #11 #ebfff1ff

> undo

[Repeated 2 time(s)]

> view

> select #11/A

Nothing selected  

> color #11 yellow

> view

> select protein

84354 atoms, 85340 bonds, 14 pseudobonds, 5279 residues, 15 models selected  

> color (#11 & sel) cyan

> select clear

> view

> save "D:/Documents/Files/Downloads/del_gq at1r/del_gq.jpg" width 715 height
> 461 supersample 3

> view

[Repeated 1 time(s)]

> save "D:/Documents/Files/Downloads/del_gq at1r/del_gq-top.jpg" width 715
> height 461 supersample 3

> open "D:/Documents/Files/Downloads/del_gq at1r/del_gq (2).pdb"

Summary of feedback from opening D:/Documents/Files/Downloads/del_gq
at1r/del_gq (2).pdb  
---  
warning | Ignored bad PDB record found on line 2575  
  
Chain information for del_gq (2).pdb #12  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> hide #11 models

> view

[Repeated 1 time(s)]

> save "D:/Documents/Files/Downloads/del_gq at1r/del_gq-predicted.jpg" width
> 715 height 461 supersample 3

> color #12 #1b6270ff

> color #12 #3a6470ff

> color #12 #276070ff

> color #12 #0c5a70ff

> color #12 #27706eff

> color #12 #17705aff

> color #12 #036170ff

> color #12 #155870ff

> color #12 #335e70ff

> color #12 #4d6b70ff

> color #12 #215e70ff

> color #12 #0f6870ff

> color #12 #21e2f4ff

> view

> save "D:/Documents/Files/Downloads/del_gq at1r/del_gq-predicted.jpg" width
> 715 height 461 supersample 3

> hide #12 models

> open "D:/Documents/Files/Downloads/del_gq at1r/step5_assembly.pdb"

Summary of feedback from opening D:/Documents/Files/Downloads/del_gq
at1r/step5_assembly.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V3.7 ON NOV, 16.
2024. JOB  
  
Ignored bad PDB record found on line 2  
REMARK INPUT GENERATION  
  
Ignored bad PDB record found on line 3  
REMARK DATE: 11/16/24 17:25: 3 CREATED BY USER: apache  
  
Ignored bad PDB record found on line 172328  
TER 172325 CLA 214  
  
Chain information for step5_assembly.pdb #13  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> hide #13 models

> open "D:/Documents/Files/Downloads/del_gq at1r/gromacs/step5_input (2).pdb"

Summary of feedback from opening D:/Documents/Files/Downloads/del_gq
at1r/gromacs/step5_input (2).pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
72319 messages similar to the above omitted  
  
Chain information for step5_input (2).pdb #14  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> view

> select protein

97471 atoms, 98661 bonds, 14 pseudobonds, 6230 residues, 18 models selected  

> color (#14 & sel) cyan

> select clear

> view

> save "D:/Documents/Files/Downloads/del_gq at1r/gromacs/step5-input.jpg"
> width 715 height 461 supersample 3

> open "D:/Documents/Files/Downloads/del_gq at1r/gromacs/step7_production
> (2).mdp"

Unrecognized file suffix '.mdp'  

> open "D:/Documents/Files/Downloads/del_gq at1r/gromacs/topol (2).top"

Unrecognized file suffix '.top'  

> open "D:/Documents/Files/Downloads/del_gq at1r/gromacs/step7_production.mdp"

Unrecognized file suffix '.mdp'  

> open "D:/Documents/Files/Downloads/del_gq at1r/gromacs/step5_input.psf"

Command cancelled by user  

> view

[Repeated 1 time(s)]

> open D:/Documents/Files/Downloads/production_500ns.pdb

Summary of feedback from opening
D:/Documents/Files/Downloads/production_500ns.pdb  
---  
warning | Ignored bad PDB record found on line 2  
REMARK THIS IS A SIMULATION BOX  
  
production_500ns.pdb title:  
Title [more info...]  
  
Chain information for production_500ns.pdb #15  
---  
Chain | Description  
? | No description available  
  
Non-standard residues in production_500ns.pdb #15  
---  
CLA — (CLA)  
HSD — (HSD)  
POT — (POT)  
SOPC — (sopc)  
  

> select protein

108651 atoms, 109966 bonds, 15 pseudobonds, 6906 residues, 20 models selected  

> color (#14#!15 & sel) cyan

> select clear

> show #14#!15 atoms

> hide #14 models

> undo

[Repeated 1 time(s)]

> hide #14 models

> hide #!15 atoms

> show #!15 atoms

> hide #!15 models

> open D:/Documents/Files/Downloads/step89c.pdb

Summary of feedback from opening D:/Documents/Files/Downloads/step89c.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK THIS IS A SIMULATION BOX  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
153369 messages similar to the above omitted  
  
step89c.pdb title:  
coordinates after constraining [more info...]  
  
Chain information for step89c.pdb #16  
---  
Chain | Description  
? | No description available  
  
Non-standard residues in step89c.pdb #16  
---  
CLA — (CLA)  
HSD — (HSD)  
POT — (POT)  
SOPC — (sopc)  
  

> select protein

119831 atoms, 121264 bonds, 16 pseudobonds, 7582 residues, 22 models selected  

> color (#!16 & sel) cyan

> select clear

> view

> show #12 models

> hide #!16 models

> select add #12

2573 atoms, 2641 bonds, 317 residues, 1 model selected  

> select subtract #12

Nothing selected  

> show #11 models

> hide #12 models

> show #12 models

> hide #12 models

> view

[Repeated 1 time(s)]

> hide #11 models

> show #14 models

> view

[Repeated 1 time(s)]

> save "D:/Documents/Files/Downloads/del_gq at1r/del_gq-top2.jpg" width 715
> height 461 supersample 3

> hide #14 models

> open "D:/Documents/Files/Downloads/full_gq at1r/full_gq.pdb"

Chain information for full_gq.pdb #17  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Computing secondary structure  

> view

> color #17 cyan

> view

> save "D:/Documents/Files/Downloads/full_gq at1r/full_gq.jpg" width 715
> height 461 supersample 3

> hide #17 models

> select add #15

253374 atoms, 190801 bonds, 1 pseudobond, 63374 residues, 2 models selected  

> select subtract #15

Nothing selected  

> show #!15 models

> view

> md movie

Unknown command: md movie  

> toolshed show

Downloading bundle MolecularDynamicsViewer-1.6-py3-none-any.whl  
Installed MolecularDynamicsViewer (1.6)  

QWebEngineUrlScheme::registerScheme: Too late to register scheme "kmd"  

> md movie

Unknown command: md movie  

> hide #!15 models

> open D:/Documents/Files/Downloads/step5_input.gro

Chain information for Generated by CHARMM-GUI FF-Converter #18  
---  
Chain | Description  
? | No description available  
  

> select protein

136870 atoms, 138564 bonds, 16 pseudobonds, 8976 residues, 24 models selected  

> color (#18 & sel) cyan

> select clear

> md movie

Unknown command: md movie  

> view

> open D:/Documents/Files/Downloads/production.xtc

Couldn't allocate enough memory for coords  

> hide #18 models

> show #18 models

> show #17 models

> hide #18 models

> view

> select #17/B

2963 atoms, 3020 bonds, 359 residues, 1 model selected  

> color sel orange

> select clear

> select #17/A:319-400

315 atoms, 323 bonds, 41 residues, 1 model selected  

> color sel red

> select clear

> select #17/A:1-9

68 atoms, 67 bonds, 9 residues, 1 model selected  

> color sel red

> select clear

> view

[Repeated 1 time(s)]

> save "D:/Documents/Files/Downloads/full_gq at1r/full_gq2.jpg" width 715
> height 461 supersample 3

> hide #17 models

> show #!1 models

> show #!2 models

> show #2.1 models

> show #1.1 models

> show #3 models

> view

> hide #!1 models

> hide #1.1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> hide #2.1 models

> hide #3 models

> show #17 models

> hide #17 models

> show #17 models

> hide #17 models

> show #17 models

> view

> hide #17 models

> show #17 models

> hide #17 models

> open "D:/Documents/Files/Downloads/production_500ns (2).pdb"

Summary of feedback from opening D:/Documents/Files/Downloads/production_500ns
(2).pdb  
---  
warning | Ignored bad PDB record found on line 2  
REMARK THIS IS A SIMULATION BOX  
  
production_500ns (2).pdb title:  
Title [more info...]  
  
Chain information for production_500ns (2).pdb #19  
---  
Chain | Description  
? | No description available  
  
Non-standard residues in production_500ns (2).pdb #19  
---  
CLA — (CLA)  
HSD — (HSD)  
POT — (POT)  
SOPC — (sopc)  
  
Computing secondary structure  

> view

> open D:/Documents/Files/Downloads/production_500ns_pbc.pdb

Summary of feedback from opening
D:/Documents/Files/Downloads/production_500ns_pbc.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
production_500ns_pbc.pdb title:  
Title [more info...]  
  
Chain information for production_500ns_pbc.pdb #20  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in production_500ns_pbc.pdb #20  
---  
CLA — (CLA)  
HSD — (HSD)  
POT — (POT)  
SOPC — (sopc)  
  
Computing secondary structure  

> hide #19 models

> select protein

147414 atoms, 149244 bonds, 16 pseudobonds, 9610 residues, 26 models selected  

> color (#20 & sel) cyan

> select clear

> open "D:/Documents/Files/Downloads/del_gq at1r/del_gq (2).pdb"

Summary of feedback from opening D:/Documents/Files/Downloads/del_gq
at1r/del_gq (2).pdb  
---  
warning | Ignored bad PDB record found on line 2575  
  
Chain information for del_gq (2).pdb #21  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> hide #21 models

> open "D:/Documents/Files/Downloads/del_gq at1r/gromacs/step5_input.pdb"

Summary of feedback from opening D:/Documents/Files/Downloads/del_gq
at1r/gromacs/step5_input.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
72319 messages similar to the above omitted  
  
Chain information for step5_input.pdb #22  
---  
Chain | Description  
? | No description available  
  
Computing secondary structure  

> hide #20 models

> close #21

> select protein

152686 atoms, 154584 bonds, 16 pseudobonds, 9927 residues, 27 models selected  

> color (#22 & sel) yellow

> color (#22 & sel) cyan

> select clear

> hide #22 models

> show #20 models

> select protein

152686 atoms, 154584 bonds, 16 pseudobonds, 9927 residues, 27 models selected  

> color (#20 & sel) yellow

> select clear

> close #4-5

> hide #20 models

> close #6,10-14,17-19#7-9,15-16

> show #20 models

> show #22 models

> ui tool show Matchmaker

> matchermaker #20 to #22

Unknown command: matchermaker #20 to #22  

>

Missing command  

>

Missing command  

> close #3

> select add #20

172324 atoms, 134832 bonds, 37877 residues, 1 model selected  

> select subtract #20

Nothing selected  

>

Missing command  

>

Missing command  

>

Missing command  

> hide #22 models

>

Missing command  

> show #22 models

> ui tool show Matchmaker

No reference and/or match structure/chain chosen  

>

Missing command  

>

Missing command  

> ui tool show Matchmaker

>

Missing command  

> hide #20 models

> hide #22 models

> show #!1 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> show #!2 models

> show #1.1 models

> show #2.1 models

> save D:/Documents/Files/Downloads/AlphaFod-heme/sumperimposed.pdb

> close #1-2

> show #20 models

> show #22 models

> ui tool show Matchmaker

>

Missing command  

>

Missing command  

>

Missing command  

>

Missing command  

>

Missing command  

> select #22/?

5486 atoms, 5340 bonds, 531 residues, 1 model selected  

> select clear

> view

[Repeated 1 time(s)]

> save "D:/Documents/Files/Downloads/del_gq at1r/del_gq supermimposed.jpg"
> width 715 height 461 supersample 3

> show atoms

> hide atoms

>

Missing command  

>

Missing command  

> ui tool show Matchmaker

>

Missing command  

>

Missing command  

> view 22

Expected an objects specifier or a view name or a keyword  

> view 1

Expected an objects specifier or a view name or a keyword  

> view #1

No objects specified.  

> view #22

> view #20

> info

2 models  
#20, production_500ns_pbc.pdb, shown  
172324 atoms, 134832 bonds, 37877 residues, 1 chains
(A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z,0,1,2,3,4,5,6,7,8,9,
)  
#22, step5_input.pdb, shown  
172324 atoms, 134830 bonds, 37877 residues, 1 chains ( ,C ,3 )  

> select clear

>

Missing command  

>

Missing command  

> select #22/A

Nothing selected  

> select #22

172324 atoms, 134830 bonds, 37877 residues, 1 model selected  

> select #20

172324 atoms, 134832 bonds, 37877 residues, 1 model selected  

> sel to sel

Missing command  

> select to select

Missing command  

>

Missing command  

> select clear

> help matchmaker

Traceback (most recent call last):  
File "D:\ChimeraX 1.9rc202411160247\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "D:\ChimeraX 1.9rc202411160247\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.9rc202411160247\bin\Lib\site-
packages\chimerax\help_viewer\cmd.py", line 81, in help  
url = cli.command_url(cmd_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\ChimeraX 1.9rc202411160247\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3350, in command_url  
return _get_help_url(cmd.command_name.split())  
^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'split'  
  
AttributeError: 'NoneType' object has no attribute 'split'  
  
File "D:\ChimeraX 1.9rc202411160247\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3350, in command_url  
return _get_help_url(cmd.command_name.split())  
^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.2127
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: Latitude 7490
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 17,052,217,344
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8350U CPU @ 1.70GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 2.4.1
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9rc202411160247
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.11
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.3.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.8
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    MolecularDynamicsViewer: 1.6
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
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    pytz: 2024.2
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    sfftk-rw: 0.8.1
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    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
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    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1