Opened 3 days ago

Last modified 44 hours ago

#19364 feedback defect

ChimeraX tools not starting and other problems

Reported by: chrisz@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Platform Version:
Keywords: Cc: chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Hi, I am an industry user of ChimeraX, and I've been using it for about 4 years. I am now at Vividion Therapeutics, where our IT performs routine updates of our windows systems. After a recent update I am having problems with ChimeraX. IT has ruled out some things they suspected on our end such as permissions, etc. When I launch ChimeraX now, the only thing that shows up is the main window. I have to manually launch the command line interface, the log, the models, and the toolbar under the "Tools" dropdown. These things then all function normally except for the Log. A window for the Log pops up, but there is no actual log that populates when I execute commands, which is a problem for me when I am performing measurements and the results pop up in the log. The only other thing that I can find that is wrong is my models don't center themselves properly when I enter command "view" or save an image. I'm not sure what is wrong, but I would love to return to having a working Log. Do these probelms seem familiar at all? Are there any suggestions for something we can do on our end to fix this? Thanks a lot, Chris

Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_sphere_SAR.cxs

Log from Thu Sep 25 15:05:58 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_oligomer_2.cxs

Log from Fri Sep 19 09:41:54 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_oligomer.cxs

Log from Wed Sep 17 14:41:08 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open P:/UserFolders/ChrisZ/MYD88/Xray/Refine_8/MyD88_refine_8.pdb

Chain information for MyD88_refine_8.pdb #1  
---  
Chain | Description  
A | No description available  
  

> close session

> open
> P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_refine_11-coot-0_no_H_w_water.pdb

Chain information for MyD88_refine_11-coot-0_no_H_w_water.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open 4dom

4dom title:  
Crystal Structure of the TIR-domain of Human Myeloid Differentiation Primary
Response protein (MyD88) [more info...]  
  
Chain information for 4dom #2  
---  
Chain | Description | UniProt  
A | Myeloid differentiation primary response protein MyD88 | MYD88_HUMAN 157-296  
  
1 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> 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 MyD88_refine_11-coot-0_no_H_w_water.pdb, chain A (#1) with 4dom,
chain A (#2), sequence alignment score = 712.2  
RMSD between 137 pruned atom pairs is 0.529 angstroms; (across all 141 pairs:
0.840)  
  

> set bgColor white

> graphics silhouettes true

> lighting soft

> dssp

Computing secondary structure  
[Repeated 1 time(s)]

> open 7beq

7beq title:  
MicroED structure of the MyD88 TIR domain higher-order assembly [more info...]  
  
Chain information for 7beq #3  
---  
Chain | Description | UniProt  
A | Myeloid differentiation primary response protein MyD88 | MYD88_HUMAN 155-296  
  

> open 7ber

7ber title:  
SFX structure of the MyD88 TIR domain higher-order assembly (solved, rebuilt
and refined using an identical protocol to the MicroED structure of the MyD88
TIR domain higher-order assembly) [more info...]  
  
Chain information for 7ber #4  
---  
Chain | Description | UniProt  
A | Myeloid differentiation primary response protein MyD88 | MYD88_HUMAN 155-296  
  

> open 7l6w

7l6w title:  
SFX structure of the MyD88 TIR domain higher-order assembly [more info...]  
  
Chain information for 7l6w #5  
---  
Chain | Description | UniProt  
A | Myeloid differentiation primary response protein MyD88 | MYD88_HUMAN 159-296  
  
42 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> log metadata #4

Metadata for 7ber #4  
---  
Title | SFX structure of the MyD88 TIR domain higher-order assembly (solved, rebuilt and refined using an identical protocol to the MicroED structure of the MyD88 TIR domain higher-order assembly)  
Citation | Clabbers, M.T.B., Holmes, S., Muusse, T.W., Vajjhala, P.R., Thygesen, S.J., Malde, A.K., Hunter, D.J.B., Croll, T.I., Flueckiger, L., Nanson, J.D., Rahaman, M.H., Aquila, A., Hunter, M.S., Liang, M., Yoon, C.H., Zhao, J., Zatsepin, N.A., Abbey, B., Sierecki, E., Gambin, Y., Stacey, K.J., Darmanin, C., Kobe, B., Xu, H., Ve, T. (2021). MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography. Nat Commun, 12, 2578-2578. PMID: 33972532. DOI: 10.1038/s41467-021-22590-6  
Gene source | Homo sapiens (human)  
Experimental method | X-ray diffraction  
Resolution | 2.3Å  
  
> open 8s78

Summary of feedback from opening 8s78 fetched from pdb  
---  
note | Fetching compressed mmCIF 8s78 from http://files.rcsb.org/download/8s78.cif  
  
8s78 title:  
MicroED Structure of TLR2 TIR domain-induced MyD88 TIR domain higher-order
assembly [more info...]  
  
Chain information for 8s78 #6  
---  
Chain | Description | UniProt  
A | Myeloid differentiation primary response protein MyD88 | MYD88_HUMAN 154-296  
  

> open 4eo7

4eo7 title:  
Crystal structure of the TIR domain of human myeloid differentiation primary
response protein 88. [more info...]  
  
Chain information for 4eo7 #7  
---  
Chain | Description | UniProt  
A | Myeloid differentiation primary response protein MyD88 | MYD88_HUMAN 157-296  
  
Non-standard residues in 4eo7 #7  
---  
MG — magnesium ion  
  
50 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> close #3-7

> open 7beq

7beq title:  
MicroED structure of the MyD88 TIR domain higher-order assembly [more info...]  
  
Chain information for 7beq #3  
---  
Chain | Description | UniProt  
A | Myeloid differentiation primary response protein MyD88 | MYD88_HUMAN 155-296  
  

> ui tool show "Crystal Contacts"

> crystalcontacts #3

6 pairs of asymmetric units of 7beq contact at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
         6     0      0      0 -1  0      0         1
         4     0      3      0  0  0      0         1
         4     0      0      0  1  0      0         1
         2     0      3      0  0  1      0         1
         2     0      3      0 -1  1      0         1
         2     0      3      0 -1  0      0         1
    

  

> hide #2 models

> hide #1 models

> open 7ber

7ber title:  
SFX structure of the MyD88 TIR domain higher-order assembly (solved, rebuilt
and refined using an identical protocol to the MicroED structure of the MyD88
TIR domain higher-order assembly) [more info...]  
  
Chain information for 7ber #5  
---  
Chain | Description | UniProt  
A | Myeloid differentiation primary response protein MyD88 | MYD88_HUMAN 155-296  
  

> crystalcontacts #5

5 pairs of asymmetric units of 7ber contact at distance 3.0 A

    
    
      Atoms  MTRIX  SMTRY   Unit cell  MTRIXref  Copies
         5     0      1      0  0  0      0         1
         3     0      0      0 -1  0      0         1
         2     0      3      0  0  1      0         1
         2     0      3      0 -1  1      0         1
         2     0      0      0  1  0      0         1
    

  

> select add #6

5665 atoms, 5795 bonds, 690 residues, 6 models selected  

> ui mousemode right "translate selected models"

> view matrix models #6,1,0,0,-24.3,0,1,0,23.715,0,0,1,88.715

> close #6

> select add #5

1133 atoms, 1159 bonds, 138 residues, 1 model selected  

> select subtract #5

Nothing selected  

> close #5

> show #4:280 atoms

> ui mousemode right select

Drag select of 71 residues  

> select up

782 atoms, 795 bonds, 98 residues, 2 models selected  

> select up

2266 atoms, 2318 bonds, 276 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #4.2,-1,1.2246e-16,5.5511e-17,38.136,0,1,-1.6762e-16,-13.391,0,0,-1,40.86,#4.6,-1,1.2246e-16,5.5511e-17,38.136,0,1,-1.6762e-16,-44.401,0,0,-1,40.86

> view matrix models
> #4.2,-1,1.2246e-16,5.5511e-17,39.832,0,1,-1.6762e-16,-14.778,0,0,-1,50.905,#4.6,-1,1.2246e-16,5.5511e-17,39.832,0,1,-1.6762e-16,-45.788,0,0,-1,50.905

> view matrix models
> #4.2,-1,1.2246e-16,5.5511e-17,33.091,0,1,-1.6762e-16,-15.604,0,0,-1,50.258,#4.6,-1,1.2246e-16,5.5511e-17,33.091,0,1,-1.6762e-16,-46.614,0,0,-1,50.258

> view matrix models
> #4.2,-1,1.2246e-16,5.5511e-17,33.179,0,1,-1.6762e-16,-15.518,0,0,-1,51.748,#4.6,-1,1.2246e-16,5.5511e-17,33.179,0,1,-1.6762e-16,-46.528,0,0,-1,51.748

> hide #4.5 cartoons

> ui mousemode right select

> select clear

> hide #4.5 atoms

Drag select of 743 residues, 7 atoms, 4 bonds  

> select up

6052 atoms, 970 bonds, 744 residues, 6 models selected  

> select up

6712 atoms, 6865 bonds, 818 residues, 6 models selected  

> color sel dark gray

Drag select of 828 residues, 15 atoms, 10 bonds  

> color sel dark gray

> show #2 models

> show #1 models

> matchmaker #1 to #4.5

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 7beq 0 -1 1 sym 3, chain A (#4.5) with
MyD88_refine_11-coot-0_no_H_w_water.pdb, chain A (#1), sequence alignment
score = 627.5  
RMSD between 87 pruned atom pairs is 1.056 angstroms; (across all 138 pairs:
5.036)  
  

> hide #2 models

Drag select of 18 residues  

> select clear

Drag select of 12 residues  

> ui mousemode right zoom

> color #4.6 forestgreen

> color #4.4 forestgreen

> 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 MyD88_refine_11-coot-0_no_H_w_water.pdb, chain A (#1) with 4dom,
chain A (#2), sequence alignment score = 712.2  
RMSD between 137 pruned atom pairs is 0.529 angstroms; (across all 141 pairs:
0.840)  
  

> show #2 models

> hide #2 models

> hide #4.2 cartoons

> hide #4.2 atoms

> hide #1 atoms

> show #1:LIG atoms

> show #1:280 atoms

> ui mousemode right select

> select clear

[Repeated 3 time(s)]

> show #4.2 cartoons

> hide #4.2 cartoons

> show #2 models

> hide #!4 models

> hide #3 models

> show #1:274 atoms

> show #2:280 atoms

> show #1 atoms

> ui tool show H-Bonds

> hbonds sel color #ffff00 showDist true reveal true log true

Atom specifier selects no atoms  

> select :LIG

23 atoms, 26 bonds, 1 residue, 1 model selected  

> hbonds sel color #ffff00 showDist true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 MyD88_refine_11-coot-0_no_H_w_water.pdb
    	2 4dom
    	3 7beq
    	4.1 7beq 0 -1 0 sym 0
    	4.2 7beq 0 0 0 sym 3
    	4.3 7beq 0 1 0 sym 0
    	4.4 7beq 0 0 1 sym 3
    	4.5 7beq 0 -1 1 sym 3
    	4.6 7beq 0 -1 0 sym 3
    
    11 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A CYS 274 SG  MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A LIG 301 O3  no hydrogen  3.857  N/A
    MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A ASP 275 N   MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A LIG 301 O3  no hydrogen  2.988  N/A
    MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A CYS 280 N   MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A LIG 301 O2  no hydrogen  3.016  N/A
    MyD88_refine_11-coot-0_no_H_w_water.pdb #1/C HOH 5 O     MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A LIG 301 N1  no hydrogen  2.811  N/A
    MyD88_refine_11-coot-0_no_H_w_water.pdb #1/C HOH 14 O    MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A LIG 301 O1  no hydrogen  2.877  N/A
    4dom #2/A ARG 288 NH2                                    MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A LIG 301 O2  no hydrogen  3.552  N/A
    4dom #2/A HOH 319 O                                      MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A LIG 301 N1  no hydrogen  3.247  N/A
    7beq 0 0 0 sym 3 #4.2/A CYS 274 SG                       MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A LIG 301 O3  no hydrogen  3.066  N/A
    7beq 0 0 0 sym 3 #4.2/A ASP 275 N                        MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A LIG 301 O3  no hydrogen  2.984  N/A
    7beq 0 -1 1 sym 3 #4.5/A CYS 274 SG                      MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A LIG 301 O3  no hydrogen  3.027  N/A
    7beq 0 -1 1 sym 3 #4.5/A ASP 275 N                       MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A LIG 301 O3  no hydrogen  3.124  N/A
    

  
11 hydrogen bonds found  

> open P:/UserFolders/ChrisZ/MYD88/Xray/Refine_12/MyD88_refine_12_287.pdb

Chain information for MyD88_refine_12_287.pdb #6  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

> hide #2 models

> view

> select :287

70 atoms, 60 bonds, 10 residues, 10 models selected  

> select #6:287

7 atoms, 6 bonds, 1 residue, 1 model selected  

"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."  

[Repeated 2 time(s)]

> open P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_refine_13-coot-0_water.pdb

Chain information for MyD88_refine_13-coot-0_water.pdb #7  
---  
Chain | Description  
A | No description available  
  

> hide #6 models

> select #7:287

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #7:301

23 atoms, 26 bonds, 1 residue, 1 model selected  

> ~select

Nothing selected  

> select ligand

69 atoms, 78 bonds, 3 residues, 3 models selected  

> select @287

Nothing selected  

> select :287

77 atoms, 66 bonds, 11 residues, 11 models selected  

> select ligand

69 atoms, 78 bonds, 3 residues, 3 models selected  

> ui tool show H-Bonds

> hbonds sel color #ffff00 showDist true interModel false reveal true log true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 MyD88_refine_11-coot-0_no_H_w_water.pdb
    	6 MyD88_refine_12_287.pdb
    	7 MyD88_refine_13-coot-0_water.pdb
    
    15 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A CYS 274 SG  MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A LIG 301 O3  no hydrogen  3.857  N/A
    MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A ASP 275 N   MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A LIG 301 O3  no hydrogen  2.988  N/A
    MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A CYS 280 N   MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A LIG 301 O2  no hydrogen  3.016  N/A
    MyD88_refine_11-coot-0_no_H_w_water.pdb #1/C HOH 5 O     MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A LIG 301 N1  no hydrogen  2.811  N/A
    MyD88_refine_11-coot-0_no_H_w_water.pdb #1/C HOH 14 O    MyD88_refine_11-coot-0_no_H_w_water.pdb #1/A LIG 301 O1  no hydrogen  2.877  N/A
    MyD88_refine_12_287.pdb #6/A CYS 274 SG                  MyD88_refine_12_287.pdb #6/A 287 301 O3                  no hydrogen  3.858  N/A
    MyD88_refine_12_287.pdb #6/A ASP 275 N                   MyD88_refine_12_287.pdb #6/A 287 301 O3                  no hydrogen  2.993  N/A
    MyD88_refine_12_287.pdb #6/A CYS 280 N                   MyD88_refine_12_287.pdb #6/A 287 301 O2                  no hydrogen  2.981  N/A
    MyD88_refine_12_287.pdb #6/A 287 301 N1                  MyD88_refine_12_287.pdb #6/C HOH 5 O                     no hydrogen  2.887  N/A
    MyD88_refine_12_287.pdb #6/C HOH 14 O                    MyD88_refine_12_287.pdb #6/A 287 301 O1                  no hydrogen  2.877  N/A
    MyD88_refine_13-coot-0_water.pdb #7/A CYS 274 SG         MyD88_refine_13-coot-0_water.pdb #7/A 287 301 O3         no hydrogen  3.857  N/A
    MyD88_refine_13-coot-0_water.pdb #7/A ASP 275 N          MyD88_refine_13-coot-0_water.pdb #7/A 287 301 O3         no hydrogen  2.995  N/A
    MyD88_refine_13-coot-0_water.pdb #7/A CYS 280 N          MyD88_refine_13-coot-0_water.pdb #7/A 287 301 O2         no hydrogen  2.987  N/A
    MyD88_refine_13-coot-0_water.pdb #7/A 287 301 N1         MyD88_refine_13-coot-0_water.pdb #7/C HOH 5 O            no hydrogen  2.899  N/A
    MyD88_refine_13-coot-0_water.pdb #7/C HOH 14 O           MyD88_refine_13-coot-0_water.pdb #7/A 287 301 O1         no hydrogen  2.883  N/A
    

  
15 hydrogen bonds found  

> save P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_oligomer.cxs

——— End of log from Wed Sep 17 14:41:08 2025 ———

opened ChimeraX session  

> open
> P:/UserFolders/ChrisZ/MYD88/Xray/9-18-25_MyD88_VVD-506287_coordinates.pdb

Chain information for 9-18-25_MyD88_VVD-506287_coordinates.pdb #8  
---  
Chain | Description  
A | No description available  
  

> matchmaker #2 to #8

Computing secondary structure  
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 9-18-25_MyD88_VVD-506287_coordinates.pdb, chain A (#8) with 4dom,
chain A (#2), sequence alignment score = 725.3  
RMSD between 137 pruned atom pairs is 0.547 angstroms; (across all 141 pairs:
0.851)  
  

> hide #!5 models

> hide #!7 models

> hide #5.1 models

> color #2 tomato

> show #2 models

> color #8 cornflowerblue

> color ligand byhetero

> ui mousemode right select

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide sel atoms

> color ligand dark orange

> color ligand byhetero

> color solvent byhetero

> select clear

> hide #8:1-290 atoms

> hide solvent

> hide #2 atoms

> show #8:280 atoms

> color #8:280 byhetero

> select #8/A:292@CB

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> open 7beq

7beq title:  
MicroED structure of the MyD88 TIR domain higher-order assembly [more info...]  
  
Chain information for 7beq #9  
---  
Chain | Description | UniProt  
A | Myeloid differentiation primary response protein MyD88 | MYD88_HUMAN 155-296  
  

> ,atch #9 to #8

Unknown command: ,atch #9 to #8  

> matchmaker #9 to #8

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 9-18-25_MyD88_VVD-506287_coordinates.pdb, chain A (#8) with 7beq,
chain A (#9), sequence alignment score = 651.4  
RMSD between 89 pruned atom pairs is 1.089 angstroms; (across all 138 pairs:
5.045)  
  

> color #9 forestgreen

"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."  

[Repeated 1 time(s)]

> save P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_oligomer_2.cxs

——— End of log from Fri Sep 19 09:41:54 2025 ———

opened ChimeraX session  

> show #!1 models

> show #!4 models

> view

> show #!5 models

> hide #!5 models

> hide #8 models

> hide #9 models

> show #3 models

> hide #2 models

> ui mousemode right select

Drag select of 798 atoms, 831 residues, 3 pseudobonds, 683 bonds  

> hide sel atoms

> color sel cornflowerblue

> show #1,3,4:274,280 atoms

> style sel sphere

Changed 6869 atom styles  

> cartoon suppressBackgroundDisplay true

Expected an atoms specifier or a keyword  

> cartoon suppressBackboneDisplay true

> select clear

> hide #3 models

> show #3 models

> hide #4.5/A cartoons

> hide #4.5/A atoms

> hide #4.2/A cartoons

> cartoon #4.2 suppressBackboneDisplay true

> hide #4.2/A atoms, cartoons

Drag select of 36 atoms, 830 residues  

> color color sel byhet

Invalid "color" argument: Expected a color or one of 'byatom', 'bychain',
'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer',
'fromatoms', 'fromcartoons', 'fromribbons', or 'random'  
Drag select of 19 residues  

> select up

291 atoms, 294 bonds, 34 residues, 1 model selected  

> select up

1190 atoms, 1221 bonds, 142 residues, 1 model selected  

> select up

1250 atoms, 1221 bonds, 202 residues, 1 model selected  

> color sel #ABC2ED

Drag select of 6 atoms, 54 residues  

> select up

563 atoms, 575 bonds, 66 residues, 1 model selected  

> select up

1133 atoms, 1159 bonds, 138 residues, 1 model selected  

> color sel #ABC2ED

Drag select of 76 residues  

> select up

811 atoms, 827 bonds, 97 residues, 1 model selected  

> select up

1133 atoms, 1159 bonds, 138 residues, 1 model selected  

> color sel #ABC2ED

Drag select of 36 atoms, 831 residues  

> color sel byhetero

> select #4.6/A:274@SG

1 atom, 1 residue, 1 model selected  

> color sel lime green

> select #1/A:274@SG

1 atom, 1 residue, 1 model selected  

> color sel lime green

> select #4.4/A:274@SG

1 atom, 1 residue, 1 model selected  

> color sel lime green

> select #4.1/A:274@SG

1 atom, 1 residue, 1 model selected  

> color sel lime green

> select #3/A:274@SG

1 atom, 1 residue, 1 model selected  

> color sel lime green

> select #4.3/A:274@SG

1 atom, 1 residue, 1 model selected  

> color sel lime green

> save P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_oligomer_2.cxs

> select clear

> show #3 surfaces

> show #4.3/A surfaces

> show #4.3/A transparency 50

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> transparency #4.3/A 20

> transparency #4.3/A 80

> transparency #4.3/A 70

> transparency #4.3/A 60

> hide #4.4 cartoons

> save P:/UserFolders/ChrisZ/MYD88/Xray/filament_2.png width 2000 height 2000
> supersample 3

> hide surfaces

> open
> P:/UserFolders/ChrisZ/MYD88/Xray/113972389_in38892v8_xP2110506287311_free.mtz

Summary of feedback from opening
P:/UserFolders/ChrisZ/MYD88/Xray/113972389_in38892v8_xP2110506287311_free.mtz  
---  
warnings | WARNING: multiple experimental reflection datasets found:  
(dataset) HKL_base,  
(dataset) IMEAN, SIGIMEAN,  
(dataset) I(+), SIGI(+), I(-), SIGI(-),  
(dataset) F, SIGF,  
(dataset) F(+), SIGF(+), F(-), SIGF(-),  
(dataset) DANO, SIGDANO  
Automatically choosing "(dataset) F, SIGF".  
No free flags detected in this dataset! Automatically generated a new random
set with 1988 free from 40240 observed reflections. You should save your data
to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Launching live xmap mgr took 1.6013085842132568 seconds.  
  
Opened (LIVE) 2mFo-DFc as #8.1.1.2, grid size 78,82,78, pixel
0.317,0.303,0.312, shown at level 0.879, step 1, values float32  
Opened (LIVE) mFo-DFc as #8.1.1.3, grid size 78,82,78, pixel
0.317,0.303,0.312, shown at level -0.23,0.23, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_25 as #8.1.1.4, grid size 78,82,78, pixel
0.317,0.303,0.312, shown at level 0.215, step 1, values float32  
Opened crystallographic dataset from
P:/UserFolders/ChrisZ/MYD88/Xray/113972389_in38892v8_xP2110506287311_free.mtz  
Found experimental reflection data:  
(dataset) F, SIGF  
Rwork: 0.2288; Rfree: 0.2324  
Generated maps:  
Reflection Data  
(LIVE) 2mFo-DFc  
(LIVE) mFo-DFc  
(LIVE) 2mFo-DFc_smooth_25  
Any unwanted maps may be safely closed via the Model panel.  

> hide #!8.1 models

> hide #!8 models

> show #4.4 cartoons

> lighting soft

> cofr false

Expected 3-tuple of numbers or a keyword  

> cofr showPivot false

> open 5uzb

Summary of feedback from opening 5uzb fetched from pdb  
---  
note | Fetching compressed mmCIF 5uzb from http://files.rcsb.org/download/5uzb.cif  
  
5uzb title:  
Cryo-EM structure of the MAL TIR domain filament [more info...]  
  
Chain information for 5uzb #10  
---  
Chain | Description | UniProt  
A B C D E F G H I J K L M N | Toll/interleukin-1 receptor domain-containing adapter protein | TIRAP_HUMAN 79-221  
  

> hide #10 atoms

> show #10/A cartoons

> matchmaker #10/A to #4.6

Computing secondary structure  
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 7beq 0 -1 0 sym 3, chain A (#4.6) with 5uzb, chain A (#10),
sequence alignment score = 179.1  
RMSD between 78 pruned atom pairs is 1.146 angstroms; (across all 129 pairs:
4.190)  
  

> color #10/A dark orange

> hide #4.6 cartoons

> hide #4.6 atoms

> hide #!4 models

> show #!4 models

> hide #1 cartoons

> hide #1 atoms

> show #4 cartoons

> hide #4.6/A cartoons

> hide #4.2/A cartoons

> hide #4.5/A cartoons

> show #4.2/A cartoons

> color #4.2/A cornflowerblue

> show #4.2/A:274,280 atoms

> select #4.2/A

1133 atoms, 1159 bonds, 138 residues, 1 model selected  

> style sel sphere

Changed 1133 atom styles  

> color #4.2/A byhetero

> select #4.2/A:274@SG

1 atom, 1 residue, 1 model selected  

> color sel lime green

> show #10/A surfaces

> show 4.2/A surface

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #4.2/A surfaces

> shotransparency #4.2/A 60

Unknown command: shotransparency #4.2/A 60  

> transparency #4.2/A 60

> select clear

> transparency #4.2/A 50

> transparency #4.2/A 70

> save P:/UserFolders/ChrisZ/MYD88/Xray/mal_filament.png width 2000 height
> 2000 supersample 3

> save P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_oligomer_3.cxs

> close session

Deleting Crystallographic maps(113972389_in38892v8_xP2110506287311_free.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_25  

> open
> P:/UserFolders/ChrisZ/MYD88/Xray/9-18-25_MyD88_VVD-506287_coordinates.pdb

Chain information for 9-18-25_MyD88_VVD-506287_coordinates.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open P:/UserFolders/ChrisZ/MYD88/Xray/Refine_24/MyD88_refine_24.mtz

Summary of feedback from opening
P:/UserFolders/ChrisZ/MYD88/Xray/Refine_24/MyD88_refine_24.mtz  
---  
warning | WARNING: multiple experimental reflection datasets found:  
(Original-experimental-data-mapped-to-asu) I-obs, SIGI-obs,  
(Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered  
Automatically choosing "(Experimental-data-used-in-refinement) F-obs-filtered,
SIGF-obs-filtered".  
notes | Launching live xmap mgr took 1.2749474048614502 seconds.  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 78,82,78, pixel
0.317,0.303,0.312, shown at level 0.875, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 78,82,78, pixel
0.317,0.303,0.312, shown at level -0.228,0.228, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_25 as #1.1.1.4, grid size 78,82,78, pixel
0.317,0.303,0.312, shown at level 0.213, step 1, values float32  
Opened (STATIC) (Model-structure-factors-(all-solvent-and-scales-included))
F-model, PHIF-model as #1.1.1.5, grid size 78,82,78, pixel 0.317,0.303,0.312,
shown at level -1.02,1.02, step 1, values float32  
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT, PH2FOFCWT as #1.1.1.6,
grid size 78,82,78, pixel 0.317,0.303,0.312, shown at level 0.868, step 1,
values float32  
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT_no_fill, PH2FOFCWT_no_fill
as #1.1.1.7, grid size 78,82,78, pixel 0.317,0.303,0.312, shown at level
0.868, step 1, values float32  
Opened (STATIC) (Fourier-map-coefficients) FOFCWT, PHFOFCWT as #1.1.1.8, grid
size 78,82,78, pixel 0.317,0.303,0.312, shown at level -0.436,0.436, step 1,
values float32  
Chain information for 9-18-25_MyD88_VVD-506287_coordinates.pdb  
---  
Chain | Description  
1.2/A | No description available  
  
Opened crystallographic dataset from
P:/UserFolders/ChrisZ/MYD88/Xray/Refine_24/MyD88_refine_24.mtz  
Found experimental reflection data:  
(Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered  
Rwork: 0.2279; Rfree: 0.2451  
Generated maps:  
Reflection Data  
(LIVE) 2mFo-DFc  
(LIVE) mFo-DFc  
(LIVE) 2mFo-DFc_smooth_25  
(STATIC) (Model-structure-factors-(all-solvent-and-scales-included)) F-model,
PHIF-model  
(STATIC) (Fourier-map-coefficients) 2FOFCWT, PH2FOFCWT  
(STATIC) (Fourier-map-coefficients) 2FOFCWT_no_fill, PH2FOFCWT_no_fill  
(STATIC) (Fourier-map-coefficients) FOFCWT, PHFOFCWT  
Any unwanted maps may be safely closed via the Model panel.  

> view #1:280

> hide #!1.1.1.8 models

> hide #!1.1.1.7 models

> hide #!1.1.1.6 models

> hide #!1.1.1.5 models

> hide #!1.1.1.4 models

> hide #!1.1.1.3 models

> hide #!1.1.1.2 models

> show #!1.1.1.2 models

> hide #!1.1.1.2 models

> show #!1.1.1.2 models

> hide #!1.1.1.2 models

> show #!1.1.1.3 models

> hide #!1.1.1.3 models

> show #!1.1.1.4 models

> hide #!1.1.1.4 models

> show #!1.1.1.5 models

> hide #!1.1.1.5 models

> show #!1.1.1.6 models

> hide #!1.1.1.6 models

> show #!1.1.1.7 models

> hide #!1.1.1.7 models

> show #!1.1.1.8 models

> ui tool show "Volume Viewer"

> volume #1.1.1.8 level -0.4361 level 0.5642

> volume #1.1.1.8 level -0.5706 level 0.5642

> volume #1.1.1.8 style surface

> transparency #1.1.1.8 50

> transparency #1.1.1.8 70

> color #1/A cornflowerblue

> color #1/A byhetero

> hide solvent

> ui tool show "Side View"

> volume #1.1.1.8 level -0.5706 level 0.6155

> hide cartoons

> color ligand dark orange

> color ligand byhetero

> cofr showPivot false

> volume #1.1.1.8 level -0.5706 level 0.5706

> save P:/UserFolders/ChrisZ/MYD88/Xray/omit_map_1.png width 2000 height 2000
> supersample 3

> view :301

> hide #!1.1.1.8 models

> show #!1.1.1.2 models

> color #1.1.1.2 dark gray

> show solvent

> volume #1.1.1.2 level 0.6052

> view :301

> select clear

[Repeated 1 time(s)]

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 13 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.9, grid size 78,82,78, pixel
0.317,0.303,0.312, shown at level 0.566, step 1, values float32  
Done loading forcefield  

> 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  

> select clear

> isolde start

> set selectionWidth 4

Done loading forcefield  

> 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  

> close session

Deleting Crystallographic maps(MyD88_refine_24.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_25  
Deleting (LIVE) MDFF potential  

> open
> P:/UserFolders/ChrisZ/MYD88/Xray/9-18-25_MyD88_VVD-506287_coordinates.pdb

Chain information for 9-18-25_MyD88_VVD-506287_coordinates.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open P:/UserFolders/ChrisZ/MYD88/Xray/Refine_24/MyD88_refine_24.mtz

Summary of feedback from opening
P:/UserFolders/ChrisZ/MYD88/Xray/Refine_24/MyD88_refine_24.mtz  
---  
warning | WARNING: multiple experimental reflection datasets found:  
(Original-experimental-data-mapped-to-asu) I-obs, SIGI-obs,  
(Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered  
Automatically choosing "(Experimental-data-used-in-refinement) F-obs-filtered,
SIGF-obs-filtered".  
notes | Launching live xmap mgr took 1.657564640045166 seconds.  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 78,82,78, pixel
0.317,0.303,0.312, shown at level 0.878, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 78,82,78, pixel
0.317,0.303,0.312, shown at level -0.229,0.229, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_25 as #1.1.1.4, grid size 78,82,78, pixel
0.317,0.303,0.312, shown at level 0.214, step 1, values float32  
Opened (STATIC) (Model-structure-factors-(all-solvent-and-scales-included))
F-model, PHIF-model as #1.1.1.5, grid size 78,82,78, pixel 0.317,0.303,0.312,
shown at level -1.02,1.02, step 1, values float32  
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT, PH2FOFCWT as #1.1.1.6,
grid size 78,82,78, pixel 0.317,0.303,0.312, shown at level 0.868, step 1,
values float32  
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT_no_fill, PH2FOFCWT_no_fill
as #1.1.1.7, grid size 78,82,78, pixel 0.317,0.303,0.312, shown at level
0.868, step 1, values float32  
Opened (STATIC) (Fourier-map-coefficients) FOFCWT, PHFOFCWT as #1.1.1.8, grid
size 78,82,78, pixel 0.317,0.303,0.312, shown at level -0.436,0.436, step 1,
values float32  
Chain information for 9-18-25_MyD88_VVD-506287_coordinates.pdb  
---  
Chain | Description  
1.2/A | No description available  
  
Opened crystallographic dataset from
P:/UserFolders/ChrisZ/MYD88/Xray/Refine_24/MyD88_refine_24.mtz  
Found experimental reflection data:  
(Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered  
Rwork: 0.2279; Rfree: 0.2461  
Generated maps:  
Reflection Data  
(LIVE) 2mFo-DFc  
(LIVE) mFo-DFc  
(LIVE) 2mFo-DFc_smooth_25  
(STATIC) (Model-structure-factors-(all-solvent-and-scales-included)) F-model,
PHIF-model  
(STATIC) (Fourier-map-coefficients) 2FOFCWT, PH2FOFCWT  
(STATIC) (Fourier-map-coefficients) 2FOFCWT_no_fill, PH2FOFCWT_no_fill  
(STATIC) (Fourier-map-coefficients) FOFCWT, PHFOFCWT  
Any unwanted maps may be safely closed via the Model panel.  

> color #1.2 cornflowerblue

> color #1.2 byhetero

> clipper spotlight radius 20

> view :301

> hide #!1.1.1.3 models

> hide #!1.1.1.4 models

> hide #!1.1.1.5 models

> hide #!1.1.1.6 models

> hide #!1.1.1.7 models

> hide #!1.1.1.8 models

> hide #1.3 models

> show #1.3 models

> hide #1.3 models

> hide #!1.1.1.2 models

> hide #!1.1.1.1 models

> show #!1.1.1.1 models

> show #!1.1.1.2 models

> hide #!1.1.1.1 models

> ui tool show "Volume Viewer"

> color #1.1.1.2 dark gray

> volume #1.1.1.2 level 0.6463

> volume #1.1.1.2 level 0.6161

> hide #1.2 cartoons

> cofr showPivot false

> color ligand dark orange

> color ligand byhetero

> movie record

> turn y 2 180

> wait 180

> movie encode C:\ProgramData\ChimeraX\movie1.mp4

Movie saved to C:\ProgramData\ChimeraX\movie1.mp4  
  

> rock

> stop

Unknown or unsupported skia image format  

> clipper spotlight radius 15

> clipper spotlight radius 13

> select clear

> clipper spotlight radius 15

> select clear

> volume #1.1.1.2 level 0.5559

> volume #1.1.1.2 level 0.586

> cofr showPivot false

> rock 50

Expected an axis vector or a keyword  

> rock y 50

> stop

> rock y 60 60

> rock y 60 200

> rock y 60 2 cycle forever

Invalid "cycle" argument: Expected an integer  

> rock y 60 2 cycle 10

> rock y 60 200 cycle 10

> rock y 60

> stop

> rock y 60 60

> rock y 60 30 cycle 10

> rock y 60 cycle 200

> stop

> rock y 60 cycle 200

> stop

> rock y 60 cycle 200

> stop

> rock y 60 200 cycle 200

> ; rock y 60 400 cycle 200; movie

Incomplete command: movie  

> movie, rock y 60 400 cycle 200, movie

Unknown command: movie, rock y 60 400 cycle 200, movie  

> movie record

> rock y 60 400 cycle 200

> movie stop

> clipper spotlight radius 16

> clipper spotlight radius 17

> cofr showPivot false

> movie record

> rock y 60 400 cycle 200

> movie stop

> movie encode P:/UserFolders/ChrisZ/MYD88/Xray/movie_1

Unrecognized movie file suffix movie_1, use *.avi, *.webm, *.wmv, *.mov,
*.ogv, *.png, *.mp4  

> movie record

> rock y 60 400 cycle 200

> movie stop

> movie encode P:/UserFolders/ChrisZ/MYD88/Xray/movie_1.mov

Movie encoding failed because no images were recorded.  

> movie record

> rock y 60 400 cycle 200

> movie encode P:/UserFolders/ChrisZ/MYD88/Xray/movie_1.mov

Movie saved to P:/UserFolders/ChrisZ/MYD88/Xray/movie_1.mov  
  

> movie record

> rock y 60 400 cycle 200

> movie encode P:/UserFolders/ChrisZ/MYD88/Xray/movie_1.mov

Movie encoding failed because no images were recorded.  

> movie record

> rock y 60 400 cycle 200

> movie encode P:/UserFolders/ChrisZ/MYD88/Xray/movie_1.mp4

Movie encoding failed because no images were recorded.  

> movie record

> rock y 60 400 cycle 200

> wait 400

> movie encode P:/UserFolders/ChrisZ/MYD88/Xray/movie_1.mp4

Movie saved to P:/UserFolders/ChrisZ/MYD88/Xray/movie_1.mp4  
  

> hide :gol

> movie record

> rock y 60 400 cycle 200

> wait 400

> movie encode P:/UserFolders/ChrisZ/MYD88/Xray/movie_1.mp4

Movie saved to P:/UserFolders/ChrisZ/MYD88/Xray/movie_1.mp4  
  

> volume #1.1.1.2 level 0.586

> movie record

> rock y 60 400 cycle 200

> wait 400

> movie encode P:/UserFolders/ChrisZ/MYD88/Xray/movie_2.mp4

Movie saved to P:/UserFolders/ChrisZ/MYD88/Xray/movie_2.mp4  
  

> save P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_movie.cxs

> hide #!1.1 models

> lighting soft

> hide #!1 models

> show #!1 models

> hide #!1.1.1 models

> hide #!1.1.1.2 models

> show #1.2 cartoons

> graphics silhouettes false

> graphics silhouettes true

> show #1.2 cartoons

> close session

Deleting Crystallographic maps(MyD88_refine_24.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_25  

> open
> P:/UserFolders/ChrisZ/MYD88/Xray/9-18-25_MyD88_VVD-506287_coordinates.pdb

Chain information for 9-18-25_MyD88_VVD-506287_coordinates.pdb #1  
---  
Chain | Description  
A | No description available  
  

> lighting soft

> color #1 cornflowerblue

> color ligand dark orange

> color byhetero

> hide :gol

> view

> show #1 surfaces

> hide surfaces

> hide :276,286,273,253,250 atoms

> show surfaces

> hide surfaces

> show :288 atoms

> hide :288 atoms

> hide :276,286,273,253,250,285 atoms

> hide :276,286,273,253,250,285,279 atoms

> show :251 atoms

> hide :251 atoms

> show :281 atoms

> hide :281 atoms

> show :272 atoms

> select ligand

29 atoms, 31 bonds, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #ffff00 interModel false intraRes false reveal true log
> true
    
    
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 9-18-25_MyD88_VVD-506287_coordinates.pdb
    
    6 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A CYS 274 SG  /A 287 301 O3  no hydrogen  3.841  N/A
    /A ASP 275 N   /A 287 301 O3  no hydrogen  3.005  N/A
    /A CYS 280 N   /A 287 301 O2  no hydrogen  2.966  N/A
    /A 287 301 N1  /C HOH 5 O     no hydrogen  2.887  N/A
    /A GOL 302 O3  /A TYR 276 O   no hydrogen  2.880  N/A
    /C HOH 14 O    /A 287 301 O1  no hydrogen  2.905  N/A
    

  
6 hydrogen bonds found  

> hide :gol

> hbonds sel color #ffff00 reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 9-18-25_MyD88_VVD-506287_coordinates.pdb
    
    6 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A CYS 274 SG  /A 287 301 O3  no hydrogen  3.841  N/A
    /A ASP 275 N   /A 287 301 O3  no hydrogen  3.005  N/A
    /A CYS 280 N   /A 287 301 O2  no hydrogen  2.966  N/A
    /A 287 301 N1  /C HOH 5 O     no hydrogen  2.887  N/A
    /A GOL 302 O3  /A TYR 276 O   no hydrogen  2.880  N/A
    /C HOH 14 O    /A 287 301 O1  no hydrogen  2.905  N/A
    

  
6 hydrogen bonds found  

> hide :gol

> select /C:14@O

1 atom, 1 residue, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

23 atoms, 26 bonds, 1 residue, 1 model selected  

> select /C:14@O

1 atom, 1 residue, 1 model selected  

> select /C:5@O

1 atom, 1 residue, 1 model selected  

> select ligand, /C:14,5

Expected an objects specifier or a keyword  

> select ligand,/C:14,5

Expected an objects specifier or a keyword  

> select /C:14@O

1 atom, 1 residue, 1 model selected  

> hbonds sel color #ffff00 dashes 6 reveal true retainCurrent true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 9-18-25_MyD88_VVD-506287_coordinates.pdb
    
    2 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /C HOH 14 O  /A ALA 292 O   no hydrogen  2.781  N/A
    /C HOH 14 O  /A 287 301 O1  no hydrogen  2.905  N/A
    

  
2 hydrogen bonds found  

> select /C:5@O

1 atom, 1 residue, 1 model selected  

> hbonds sel color #ffff00 dashes 6 reveal true retainCurrent true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 9-18-25_MyD88_VVD-506287_coordinates.pdb
    
    3 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A 287 301 N1  /C HOH 5 O    no hydrogen  2.887  N/A
    /C HOH 5 O     /A LEU 252 O  no hydrogen  3.094  N/A
    /C HOH 5 O     /A THR 272 O  no hydrogen  2.668  N/A
    

  
3 hydrogen bonds found  

> cartoon :280,275,272,252,292 suppressBackboneDisplay false

> save P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_hbonds.cxs

> hide #1.2 models

> show #1.2 models

> show #1 surfaces

> hide #1.2 models

> select /A:253@CA

1 atom, 1 residue, 1 model selected  

> select clear

> hide #1 surfaces

> show #1 surfaces

> hide #1 surfaces

> ui mousemode right "tape measure"

> marker segment #2 position -9.342,-1.314,-5.991 toPosition
> -9.148,-1.292,-1.208 color yellow radius 0.1 label 4.787 labelHeight 0.4787
> labelColor yellow

> marker segment #2 position -10.81,-1.459,-5.92 toPosition
> -10.57,-3.177,-2.82 color yellow radius 0.1 label 3.552 labelHeight 0.3552
> labelColor yellow

> marker segment #2 position -10.51,1.128,-8.487 toPosition -10.02,-0.9,-10.48
> color yellow radius 0.1 label 2.887 labelHeight 0.2887 labelColor yellow

> show #1 surfaces

> marker delete #2

> hide #1 surfaces

> marker segment #2 position -9.342,-1.314,-5.991 toPosition
> -7.696,-1.255,-2.979 color yellow radius 0.1 label 3.433 labelHeight 0.3433
> labelColor yellow

> marker segment #2 position -10.81,-1.459,-5.92 toPosition
> -10.57,-3.177,-2.82 color yellow radius 0.1 label 3.552 labelHeight 0.3552
> labelColor yellow

> show #1 surfaces

> hide #2.1 models

> view

> hide #1 surfaces

> show :250 atoms

> show surfaces

> hide #1 surfaces

> marker delete #2

> ui mousemode right select

> select /C:42@O

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select /C:50@O

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> show #1.2 models

> cartoon :250 suppressBackboneDisplay false

> save P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_287_Hbonds_3.png width 2000
> height 2000 supersample 3

> hbonds sel color #ffff00 dashes 6 showDist true reveal true retainCurrent
> true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 9-18-25_MyD88_VVD-506287_coordinates.pdb
    
    1 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /C HOH 50 O  /A ASN 278 O  no hydrogen  2.706  N/A
    

  
1 hydrogen bonds found  

> hide sel

> hbonds sel color #ffff00 dashes 6 reveal true retainCurrent true log true

Atom specifier selects no atoms  

> hide #!1.2 models

> show #!1.2 models

> hbonds sel color #ffff00 dashes 6 reveal true retainCurrent true log true

Atom specifier selects no atoms  

> select ligand

29 atoms, 31 bonds, 2 residues, 1 model selected  

> hbonds sel color #ffff00 dashes 6 reveal true retainCurrent true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 9-18-25_MyD88_VVD-506287_coordinates.pdb
    
    6 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A CYS 274 SG  /A 287 301 O3  no hydrogen  3.841  N/A
    /A ASP 275 N   /A 287 301 O3  no hydrogen  3.005  N/A
    /A CYS 280 N   /A 287 301 O2  no hydrogen  2.966  N/A
    /A 287 301 N1  /C HOH 5 O     no hydrogen  2.887  N/A
    /A GOL 302 O3  /A TYR 276 O   no hydrogen  2.880  N/A
    /C HOH 14 O    /A 287 301 O1  no hydrogen  2.905  N/A
    

  
6 hydrogen bonds found  

> hide :gol

> hide #1.2.1 models

> select clear

> save P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_287_Hbonds_3.png width 2000
> height 2000 supersample 3

> hide #!1.2 models

> show #!1.2 models

> select /C:50@O

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> save P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_287_Hbonds_3.png width 2000
> height 2000 supersample 3

> show surfaces #1

Expected ',' or a keyword  

> show #1 surfaces

> hide #!1.2 models

> hide #1 surfaces

> ui mousemode right "tape measure"

> marker segment #2 position -9.342,-1.314,-5.991 toPosition
> -7.696,-1.255,-2.979 color yellow radius 0.1 label 3.433 labelHeight 0.3433
> labelColor yellow

> marker segment #2 position -10.81,-1.459,-5.92 toPosition
> -10.57,-3.177,-2.82 color yellow radius 0.1 label 3.552 labelHeight 0.3552
> labelColor yellow

> view

[Repeated 1 time(s)]

> show #1 surfaces

> hide #2.1 models

> save P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_287_Hbonds_4.png width 2000
> height 2000 supersample 3

> show #2.1 models

> hide #2.1 models

> save P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_hbonds.cxs

> hide #!2 models

> hide #!1.1 models

> ui mousemode right select

> select #1/A:301@C10

1 atom, 1 residue, 1 model selected  

> select #1/A:301@C11

1 atom, 1 residue, 1 model selected  

> select #1/A:301@C12

1 atom, 1 residue, 1 model selected  

> color sel pale green

> select #1/A:301@C11

1 atom, 1 residue, 1 model selected  

> select #1/A:301@C11

1 atom, 1 residue, 1 model selected  

> select #1/A:301@C11

1 atom, 1 residue, 1 model selected  

> color sel pale green

> select #1/A:301@C10

1 atom, 1 residue, 1 model selected  

> color sel pale green

> select #1/A:301@C9

1 atom, 1 residue, 1 model selected  

> color sel pale green

> select #1/A:301@C8

1 atom, 1 residue, 1 model selected  

> color sel pale green

> select #1/A:301@C13

1 atom, 1 residue, 1 model selected  

> color sel pale green

> select #1/A:301@C14

1 atom, 1 residue, 1 model selected  

> color sel pale green

> select #1/A:301@C6

1 atom, 1 residue, 1 model selected  

> color sel medium purple

> select #1/A:301@C5

1 atom, 1 residue, 1 model selected  

> color sel medium purple

> select #1/A:301@C4

1 atom, 1 residue, 1 model selected  

> color sel medium purple

> select #1/A:301@C3

1 atom, 1 residue, 1 model selected  

> color sel medium purple

> select #1/A:301@C7

1 atom, 1 residue, 1 model selected  

> color sel medium purple

> select #1/A:301@C2

1 atom, 1 residue, 1 model selected  

> color sel medium purple

> select #1/A:301@C1

1 atom, 1 residue, 1 model selected  

> color sel coral

> select #1/A:301@C15

1 atom, 1 residue, 1 model selected  

> color sel coral

> select #1/A:301@C17

1 atom, 1 residue, 1 model selected  

> color sel light salmon

> select #1/A:301@C1

1 atom, 1 residue, 1 model selected  

> color sel light salmon

> select #1/A:301@C15

1 atom, 1 residue, 1 model selected  

> color sel light salmon

> select #1/A:301@C16

1 atom, 1 residue, 1 model selected  

> color sel light salmon

> select #1/A:301@S1

1 atom, 1 residue, 1 model selected  

> show #1 surfaces

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue 287+CYS (net charge +0) with am1-bcc
method  
287+CYS: number of electrons (269) + formal charge (+0) is odd; cannot compute
charges for radical species using AM1-BCC method  

> select #1:1-300

1241 atoms, 1180 bonds, 4 pseudobonds, 229 residues, 2 models selected  

> select #1:1-290

1197 atoms, 1135 bonds, 3 pseudobonds, 223 residues, 2 models selected  

> select

1274 atoms, 1214 bonds, 10 pseudobonds, 235 residues, 7 models selected  

> coulombic sel & #!1

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 9-18-25_MyD88_VVD-506287_coordinates.pdb_A SES surface
#1.1: minimum, -13.08, mean 0.56, maximum 10.03  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select clear

> select ligand

29 atoms, 31 bonds, 2 residues, 1 model selected  

> style sel sphere

Changed 29 atom styles  

> size byattribute

Missing or invalid "attrName" argument: Expected a text string  

> size atomRadius

Missing "atomRadius" keyword's argument  

> size atomRadius 0

Atom radius must be greater than 0.  

> size atomRadius +0

Changed 1274 atom radii  

> size atomRadius default

Changed 1274 atom radii  

> size sel atomRadius default

Changed 29 atom radii  

> sphere sel

Unknown command: sphere sel  

> size atomRadius default style sphere

Expected a keyword  

> style sel stick

Changed 29 atom styles  

> show sel surfaces

> hide sel surfaces

> style sel ball

Changed 29 atom styles  

> style sel stick

Changed 29 atom styles  

> ui tool show "Render/Select by Attribute"

> size sel default

Expected a keyword  

> size sel atomRadius default

Changed 29 atom radii  

> style sel sphere

Changed 29 atom styles  

> select clear

> select #1/C:14@O

1 atom, 1 residue, 1 model selected  

> size sel atomRadius default

Changed 1 atom radii  

> select #1/C:25@O

1 atom, 1 residue, 1 model selected  

> size sel atomRadius default

Changed 1 atom radii  

> select #1/C:5@O

1 atom, 1 residue, 1 model selected  

> size sel atomRadius default

Changed 1 atom radii  

> select #1/C:14@O

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> select #1/C:25@O

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> select #1/C:5@O

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> select clear

> open P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_VVD-506287_prepared_covbond.pdb

MyD88_VVD-506287_prepared_covbond.pdb title:  
9-18-25_MyD88_VVD-506287_coordinates - prepared [more info...]  
  
Chain information for MyD88_VVD-506287_prepared_covbond.pdb #3  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in MyD88_VVD-506287_prepared_covbond.pdb #3  
---  
287 — (287)  
GOL — (GOL)  
  
Computing secondary structure  

> matchmaker #3 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 9-18-25_MyD88_VVD-506287_coordinates.pdb, chain A (#1) with
MyD88_VVD-506287_prepared_covbond.pdb, chain A (#3), sequence alignment score
= 742.8  
RMSD between 141 pruned atom pairs is 0.000 angstroms; (across all 141 pairs:
0.000)  
  

> hide #!1 models

> show #3 surfaces

> select #3/C:50@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> size sel atomRadius default

Changed 3 atom radii  

> select #3/C:5@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> size sel atomRadius default

Changed 3 atom radii  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> size sel atomRadius default

Changed 3 atom radii  

> select #3 ligand

Expected a keyword  

> select #3:ligand

Nothing selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

44 atoms, 47 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 44 atom styles  

> select #3/C:14@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 3 atom styles  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 3 atom styles  

> select #3/C:5@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 3 atom styles  

> hide #!3 models

> show #!1 models

> show #3/C atoms

> show #!3 models

> hide #!3 models

> select add #3

2413 atoms, 2433 bonds, 153 residues, 1 model selected  

> select subtract #3

1 model selected  

> show #3/C atoms

> hide #1/C atoms

> show #3/C atoms

> show #!3 models

> hide #3 surfaces

> select #3/C:50@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #3/C:61@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #3/C:63@O

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #3/A:301@C2

1 atom, 1 residue, 1 model selected  

> color sel medium purple

> select #3/A:301@C5

1 atom, 1 residue, 1 model selected  

> color sel medium purple

> select #3/A:301@C1

1 atom, 1 residue, 1 model selected  

> color sel light salmon

> select clear

> select #1/A:301@C3

1 atom, 1 residue, 1 model selected  

> color sel medium slate blue

> color sel medium purple

> select clear

> save P:/UserFolders/ChrisZ/MYD88/Xray/MyD88_sphere_SAR.cxs

——— End of log from Thu Sep 25 15:05:58 2025 ———

opened ChimeraX session  

> color ligand dark orange

> color ligand byhetero

> save P:/UserFolders/ChrisZ/MYD88/Xray/orange_sphere.png width 2000 height
> 2000 supersample 3

"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY2:" "The operation
completed successfully."  

"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY3:" "The operation
completed successfully."  

"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY2:" "The operation
completed successfully."  

"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY3:" "The operation
completed successfully."  

"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY2:" "The operation
completed successfully."  

"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY3:" "The operation
completed successfully."  

"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."  

[Repeated 8 time(s)]

> close session

> open 1mjs

1mjs title:  
MH2 domain of transcriptional factor SMAD3 [more info...]  
  
Chain information for 1mjs #1  
---  
Chain | Description | UniProt  
A | SMAD 3 | SMAD3_HUMAN 228-424  
  

> view

> open 1u7f

1u7f title:  
Crystal Structure of the phosphorylated Smad3/Smad4 heterotrimeric complex
[more info...]  
  
Chain information for 1u7f #2  
---  
Chain | Description | UniProt  
A C | Mothers against decapentaplegic homolog 3 | SMAD3_HUMAN 228-425  
B | Mothers against decapentaplegic homolog 4 | SMAD4_HUMAN 314-552  
  
51 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> color #1 bychain

> color #2 bychain

> matchmaker #1 to #2/A

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 1u7f, chain A (#2) with 1mjs, chain A (#1), sequence alignment
score = 971.4  
RMSD between 154 pruned atom pairs is 0.732 angstroms; (across all 178 pairs:
2.178)  
  

> color #1 cornflowerblue

> hide #1 cartoons

> show #1/A,C:227,236,255,282,285,419,424 atoms

> hide #1/A,C:227,236,255,282,285,419,424 atoms

> show #2/A,C:227,236,255,282,285,419,424 atoms

> ui mousemode right select

Drag select of 16 atoms, 188 residues, 12 bonds  

> select up

1946 atoms, 1988 bonds, 243 residues, 1 model selected  

> select up

3127 atoms, 3206 bonds, 394 residues, 1 model selected  

> select clear

> show #2/A,C:227,236,255,282,285,419,424 spheres

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  
Drag select of 31 atoms, 318 residues, 23 bonds  
Drag select of 15 atoms, 142 residues, 11 bonds  

> select up

1605 atoms, 1635 bonds, 203 residues, 1 model selected  

> select up

3127 atoms, 3206 bonds, 394 residues, 1 model selected  

> style sel sphere

Changed 3127 atom styles  

> color byhetero

> select clear

> show #2/A,C:227,236,255,282,285,419,421,424 atoms

> open 1u7v

1u7v title:  
Crystal Structure of the phosphorylated Smad2/Smad4 heterotrimeric complex
[more info...]  
  
Chain information for 1u7v #3  
---  
Chain | Description | UniProt  
A C | Mothers against decapentaplegic homolog 2 | SMAD2_HUMAN 270-467  
B | Mothers against decapentaplegic homolog 4 | SMAD4_HUMAN 314-549  
  

> matchmaker #2 to #3

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 1u7v, chain B (#3) with 1u7f, chain B (#2), sequence alignment
score = 1153.7  
RMSD between 186 pruned atom pairs is 0.235 angstroms; (across all 193 pairs:
1.942)  
  

> hide #3 cartoons

> hide pbonds

> show pbonds

> hide labels

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> label delete pbonds

> hide #3 pbonds

Drag select of 1 atoms  

> hide sel

> color #2/A,C cornflowerblue

> color #2/B tomato

> lighting soft

> color #2/A,C:227,236,255,282,285,419,424 magenta

> color #2/A,C:421 byhetero

> color #2/C #ABC2ED

> color #2/C cornflowerblue

> color #2/A #ABC2ED

> color #2/A,C:227,236,255,282,285,419,424 magenta

> color #2/A,C:421 byhetero

> color #2/A:227,236,255,282,285,419,424 violet

> color #2/A:227,236,255,282,285,419,424 pale violet red

> color #2/A:227,236,255,282,285,419,424 light pink

> color #2/A:227,236,255,282,285,419,424 pink

> color #2/A:227,236,255,282,285,419,424 light pink

> color #2/A:227,236,255,282,285,419,424 hot pink

> color #2/C:227,236,255,282,285,419,424 dark orange

> color #2/C:227,236,255,282,285,419,424 magenta

> color #2/A:227,236,255,282,285,419,424 light pink

> color #2/C:227,236,255,282,285,419,424 violet

> color #2/A:227,236,255,282,285,419,424 pink

> color #2/A:227,236,255,282,285,419,424 light pink

> color #2/C:227,236,255,282,285,419,424 forestgreen

> color #2/C:227,236,255,282,285,419,424 violet

> save P:/UserFolders/ChrisZ/SMAD3/trimer_spheres.png width 2000 height 2000
> supersample 3

[Repeated 1 time(s)]

> sphere size #2/A,C:227,236,255,282,285,419,424 0.5

Unknown command: sphere size #2/A,C:227,236,255,282,285,419,424 0.5  

> select #2/A,C:227,236,255,282,285,419,424

82 atoms, 70 bonds, 12 residues, 1 model selected  

> style sel stick

Changed 82 atom styles  

> select clear

> view

> save P:/UserFolders/ChrisZ/SMAD3/trimer_sticks.png width 2000 height 2000
> supersample 3

> select #2/A,C:227,236,255,282,285,419,424

82 atoms, 70 bonds, 12 residues, 1 model selected  

> style sel ball

Changed 82 atom styles  

> style sel sphere

Changed 82 atom styles  

> sphere size 0.5

Unknown command: sphere size 0.5  

> size sel atomRadius -.5

Changed 82 atom radii  

> select clear

> view

> select #2/A,C:227,236,255,282,285,419,424

82 atoms, 70 bonds, 12 residues, 1 model selected  

> size sel atomRadius +.5

Changed 82 atom radii  

> size sel atomRadius -.6

Changed 82 atom radii  

> select clear

> view

> save P:/UserFolders/ChrisZ/SMAD3/trimer_spheres.png width 2000 height 2000
> supersample 3

"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."  

[Repeated 16 time(s)]

QWindowsWindow::setGeometry: Unable to set geometry 405x269+569+395 (frame:
421x308+561+364) on QWidgetWindow/"QDockWidgetClassWindow" on "DELL P2422H
(1)". Resulting geometry: 599x269+569+395 (frame: 615x308+561+364) margins: 8,
31, 8, 8 minimum size: 399x118 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=524303, y=524326), mintrack=POINT(x=415, y=157)))  

> view

> hide cartoons

> hide atoms

> open 3ts8

Summary of feedback from opening 3ts8 fetched from pdb  
---  
note | Fetching compressed mmCIF 3ts8 from http://files.rcsb.org/download/3ts8.cif  
  
3ts8 title:  
Crystal structure of a multidomain human p53 tetramer bound to the natural
CDKN1A(p21) p53-response element [more info...]  
  
Chain information for 3ts8 #4  
---  
Chain | Description | UniProt  
A B C D | Cellular tumor antigen p53 | P53_HUMAN 94-291 321-356  
K | CDKN1A(p21) sense strand |   
L | CDKN1A(p21) anti-sense strand |   
  
Non-standard residues in 3ts8 #4  
---  
ZN — zinc ion  
  
Drag select of 8621 atoms, 71 pseudobonds  

> hide sel atoms

> show #4 cartoons

> select clear

> color #4 bychain

> select clear

> show #4:277 spheres

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #4:277 atoms

Drag select of 76 residues  
Drag select of 73 residues  

> select clear

QWindowsWindow::setGeometry: Unable to set geometry 593x378+3650+545 (frame:
609x417+3642+514) on QWidgetWindow/"QDockWidgetClassWindow" on "DELL P2422H
(2)". Resulting geometry: 605x378+3647+548 (frame: 621x417+3639+517) margins:
8, 31, 8, 8 minimum size: 399x118 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=524303, y=524326), mintrack=POINT(x=415, y=157)))  

> ui windowfill toggle

> view

> hide #4

> hide #4 cartoons

> show #2 cartoons

> view

> select #2/A,C:227,236,255,282,285,419,424

82 atoms, 70 bonds, 12 residues, 1 model selected  

> show sel atoms

> select #2/A,C:227,236,255,282,285,419,421 atoms

Expected a keyword  

> show #2/A,C:227,236,255,282,285,419,421 atoms

> select clear

> hide #2/A,B cartoons

> hide #2/A,B atoms

> select #2/C:421@SG

1 atom, 1 residue, 1 model selected  

> select #2/C:422

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #2/C:420

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

> select #2/C:422

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #2/C:420

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

> select clear

> select #2/C:423

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

> select #2/C:424@CB

1 atom, 1 residue, 1 model selected  

> select clear

> select #2/C:424@CB

1 atom, 1 residue, 1 model selected  

> show #2/A,B cartoons

> hide #2/A,B atoms

> show #2/A,B cartoons

> hide #2/A,B cartoons

> select up

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select clear

> show #2/A,B cartoons

> show #3 cartoons

> hide #3 cartoons

> hide #2/A,B cartoons

QWindowsWindow::setGeometry: Unable to set geometry 605x378+1197+354 (frame:
627x434+1186+309) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 599x361+1200+368 (frame:
621x417+1189+323) margins: 11, 45, 11, 11 minimum size: 399x118 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=621, y=233)))  




OpenGL version: 3.3.0 - Build 32.0.101.6987
OpenGL renderer: Intel(R) Graphics
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 7450
OS: Microsoft Windows 11 Enterprise (Build 26100)
Memory: 33,427,021,824
MaxProcessMemory: 137,438,953,344
CPU: 14 Intel(R) Core(TM) Ultra 7 165U
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    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: 1.58.8
    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: 3.0.0
    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-Clipper: 0.24.0
    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: 1.9
    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-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    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: 1.5.18
    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-PhenixUI: 1.3.7
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    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: 3.5.6
    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: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    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
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1
    zipp: 3.19.2

Change History (5)

comment:1 by Eric Pettersen, 3 days ago

Cc: chimera-programmers added
Component: Unassigned → Platform
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → ChimeraX tools not starting and other problems

comment:2 by Eric Pettersen, 3 days ago

Status: accepted → feedback

Hi Christopher,

It's highly suspicious that these problems started happening after your system was upgraded. You ask IT to ensure that the driver for your graphics card is up to date and that your machine is using that driver. You should also remove the folder that ChimeraX uses to store configuration information in case that got corrupted somehow. Normally you would use the "info path" command to report the folder name, but since your log isn't working you can't do that. It should be <your home folder>\AppData\Local\UCSF\ChimeraX. If you remove that folder, ChimeraX will revert to the configuration it had when it was initially installed (it will forget recently used file, etc.)
Let me know if any of that helps.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by chrisz@…, 2 days ago

Hi Eric,
Thanks for the suggestion. I found the ChimeraX configuration information file you pointed out and deleted it. When I reopened ChimeraX I could see that it was sort of reset. I saw the "Get Started" screen and ISOLDE was gone. However, no luck, when I reinitialized ChimeraX it is still in the same state as it was before-with no Log. I can ask my IT department about the graphics card/driver. Any other suggestions? Thanks so much for the help, I appreciate it.
Chris Zerio

Last edited 44 hours ago by Tom Goddard (previous) (diff)

comment:4 by Greg Couch, 45 hours ago

Where there any other changes made since ChimeraX worked? From the error "Unable to set geometry 593x378+3650+545", it looks like it trying to place the window on a very large secondary display. Were you using that before? So it could be that your laptop is underpowered for that setup.

Another possibility it is a bug in the Qt interface toolkit that ChimeraX uses. Newer versions of ChimeraX use newer versions of the toolkit, so try ChimeraX 1.10.1 or a daily build to see if they behave better.

comment:5 by Tom Goddard, 44 hours ago

If the ChimeraX log is blank that is because it is a Qt html panel you will also likely see that the file history thumbnails in the graphics area when you start ChimeraX won't appear because that is a Qt html panel, and also the ChimeraX Help viewer won't work. Qt uses Chromium to display html and each html panel is rendered by a separate process. That evidently is not working. It could be a security issue that Qt starts these subprocesses to render html and it may be blocked on your computer. Or it could be that there are missing libraries on your system that prevent Qt html from working. I don't have a good idea about how to diagnose these Windows computer system problems.

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