id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
19364	ChimeraX tools not starting and other problems	chrisz@…	Eric Pettersen	"{{{
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

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    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
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    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
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    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
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    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
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    ChimeraX-Crystal: 1.0
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    ChimeraX-Dicom: 1.2.6
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    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
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    ChimeraX-NRRD: 1.2
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    imagecodecs: 2024.6.1
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    importlib_metadata: 8.0.0
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    ipykernel: 6.29.5
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    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
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    stack-data: 0.6.3
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    tcia_utils: 1.5.1
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    typing_extensions: 4.12.2
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    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
}}}
"	defect	feedback	normal		Platform				chimera-programmers				all	ChimeraX