Opened 20 months ago

Closed 20 months ago

#14838 closed defect (not a bug)

savepos

Reported by: kamil.sekulski@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Command Line Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Savepos command does not work. It says "Unknown command: savepos"

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:/Users/kamsekul/Desktop/Projects/DBT/Structural_biology/X-ray/EV91489/2024-03-11_PRI005/05/Buster03/refine-
> coot-5.pdb

Summary of feedback from opening
C:/Users/kamsekul/Desktop/Projects/DBT/Structural_biology/X-ray/EV91489/2024-03-11_PRI005/05/Buster03/refine-
coot-5.pdb  
---  
warnings | Ignored bad PDB record found on line 5  
REMARK --------------------- added by autoBUSTER
-------------------------------  
  
Ignored bad PDB record found on line 6  
REMARK run at = Mon Mar 25 09:16:53 EDT 2024  
  
Ignored bad PDB record found on line 14  
REMARK Files used:  
  
Ignored bad PDB record found on line 15  
REMARK PDB = Buster03/pdbchk.pdb  
  
Ignored bad PDB record found on line 16  
REMARK MTZ = /mnt/c/Users/kamsekul/Desktop/Projects/DBT/Structura  
  
4 messages similar to the above omitted  
  
refine-coot-5.pdb title:  
\--- [more info...]  
  
Chain information for refine-coot-5.pdb #1  
---  
Chain | Description  
A | No description available  
B E | No description available  
C F | No description available  
D | No description available  
  
Non-standard residues in refine-coot-5.pdb #1  
---  
8AZ — (8AZ)  
IHP — (IHP)  
ZN — (ZN)  
  

> style stick

Changed 8465 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 1950 atom styles  

> nucleotides fill

> style nucleic stick

Changed 1950 atom styles  

> show atoms

> hide atoms

[Repeated 1 time(s)]

> show atoms

> hide cartoons

> show cartoons

> hide atoms

> open
> C:\Users\kamsekul\Desktop\Projects\DBT\Structural_biology\X-ray\EV91489\2024-03-04\12\refine4\refine.pdb
> format pdb

Summary of feedback from opening
C:\Users\kamsekul\Desktop\Projects\DBT\Structural_biology\X-ray\EV91489\2024-03-04\12\refine4\refine.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK --------------------- added by autoBUSTER
---------------------------------START  
  
Ignored bad PDB record found on line 2  
REMARK run at = Fri Mar 15 09:05:51 EDT 2024  
  
Ignored bad PDB record found on line 10  
REMARK Files used:  
  
Ignored bad PDB record found on line 11  
REMARK PDB = ./pdbchk.pdb  
  
Ignored bad PDB record found on line 12  
REMARK MTZ =
/mnt/c/Users/kamsekul/Desktop/Projects/DBT/Structural_biology/X-ray/EV91489/2024-03-04/12/staraniso_alldata-
unique.mtz  
  
3 messages similar to the above omitted  
  
Chain information for refine.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> open
> C:\Users\kamsekul\Desktop\Projects\DBT\Structural_biology\X-ray\EV91489\2024-03-11_PRI005\05\Buster03\refine-
> coot-5.pdb format pdb

Summary of feedback from opening
C:\Users\kamsekul\Desktop\Projects\DBT\Structural_biology\X-ray\EV91489\2024-03-11_PRI005\05\Buster03\refine-
coot-5.pdb  
---  
warnings | Ignored bad PDB record found on line 5  
REMARK --------------------- added by autoBUSTER
-------------------------------  
  
Ignored bad PDB record found on line 6  
REMARK run at = Mon Mar 25 09:16:53 EDT 2024  
  
Ignored bad PDB record found on line 14  
REMARK Files used:  
  
Ignored bad PDB record found on line 15  
REMARK PDB = Buster03/pdbchk.pdb  
  
Ignored bad PDB record found on line 16  
REMARK MTZ = /mnt/c/Users/kamsekul/Desktop/Projects/DBT/Structura  
  
4 messages similar to the above omitted  
  
refine-coot-5.pdb title:  
\--- [more info...]  
  
Chain information for refine-coot-5.pdb #3  
---  
Chain | Description  
A | No description available  
B E | No description available  
C F | No description available  
D | No description available  
  
Non-standard residues in refine-coot-5.pdb #3  
---  
8AZ — (8AZ)  
IHP — (IHP)  
ZN — (ZN)  
  

> open
> C:\Users\kamsekul\Desktop\Projects\DBT\Structural_biology\X-ray\EV91489\2024-03-04\12\refine4\refine.pdb
> format pdb

Summary of feedback from opening
C:\Users\kamsekul\Desktop\Projects\DBT\Structural_biology\X-ray\EV91489\2024-03-04\12\refine4\refine.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK --------------------- added by autoBUSTER
---------------------------------START  
  
Ignored bad PDB record found on line 2  
REMARK run at = Fri Mar 15 09:05:51 EDT 2024  
  
Ignored bad PDB record found on line 10  
REMARK Files used:  
  
Ignored bad PDB record found on line 11  
REMARK PDB = ./pdbchk.pdb  
  
Ignored bad PDB record found on line 12  
REMARK MTZ =
/mnt/c/Users/kamsekul/Desktop/Projects/DBT/Structural_biology/X-ray/EV91489/2024-03-04/12/staraniso_alldata-
unique.mtz  
  
3 messages similar to the above omitted  
  
Chain information for refine.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> ui tool show "Model Panel"

> hide #!1 models

> hide #!3 models

> hide #!2 models

> hide #!4 models

> show #!4 models

> nucleotides #!4 atoms

> style nucleic & #!4 stick

Changed 975 atom styles  

> nucleotides #!4 fill

> style nucleic & #!4 stick

Changed 975 atom styles  

> nucleotides #!4 fill

> style nucleic & #!4 stick

Changed 975 atom styles  

> nucleotides #!4 tube/slab shape box

> nucleotides #!4 ladder

> nucleotides #!4 tube/slab shape box

> select #4/C:19

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

485 atoms, 541 bonds, 23 residues, 1 model selected  

> select up

4029 atoms, 4202 bonds, 432 residues, 1 model selected  

> select down

485 atoms, 541 bonds, 23 residues, 1 model selected  

> select clear

> select #4/A:544

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

> select up

47 atoms, 47 bonds, 6 residues, 1 model selected  

> select up

3017 atoms, 3079 bonds, 384 residues, 1 model selected  

> set bgColor white

> color sel #ffaa7fff

> color sel #fea97fff

> color sel #f8a57cff

> color sel #f4a27aff

> color sel #e89a74ff

> color sel #f3a279ff

> select clear

> select #4/C:17

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

485 atoms, 541 bonds, 23 residues, 1 model selected  

> select up

4029 atoms, 4202 bonds, 432 residues, 1 model selected  

> select down

485 atoms, 541 bonds, 23 residues, 1 model selected  

> color sel #55ff7fff

> color sel #55aaffff

> color sel #55a9feff

> color sel #52a5f7ff

> select clear

> select #4/B:8

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

> select up

490 atoms, 546 bonds, 23 residues, 1 model selected  

> color sel cornflower blue

> color sel #53a7faff

> select clear

> select #4/A:545

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

> select up

47 atoms, 47 bonds, 6 residues, 1 model selected  

> select up

3017 atoms, 3079 bonds, 384 residues, 1 model selected  

> color sel #ffaa00ff

> color sel #ffaa7fff

> color sel #f1a078ff

> color sel #ee9e77ff

> color sel #dd936eff

> color sel #e69973ff

> select clear

> lighting simple

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting shadows false

> lighting shadows true

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

[Repeated 2 time(s)]

> lighting full

[Repeated 2 time(s)]

> lighting soft

[Repeated 1 time(s)]

> lighting simple

[Repeated 1 time(s)]

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true

> lighting shadows false

> lighting flat

[Repeated 1 time(s)]

> show sel atoms

[Repeated 1 time(s)]

> style sel stick

Changed 22 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 22 atom styles  

> select clear

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

[Repeated 1 time(s)]

> lighting full

[Repeated 1 time(s)]

> lighting soft

[Repeated 1 time(s)]

> lighting simple

[Repeated 1 time(s)]

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true

> lighting shadows false

> lighting flat

[Repeated 1 time(s)]

> lighting simple

[Repeated 1 time(s)]

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

[Repeated 1 time(s)]

> lighting full

[Repeated 1 time(s)]

> lighting soft

[Repeated 1 time(s)]

> lighting flat

[Repeated 1 time(s)]

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting simple

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting simple

[Repeated 1 time(s)]

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

[Repeated 2 time(s)]

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting flat

[Repeated 1 time(s)]

> lighting soft

[Repeated 1 time(s)]

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

[Repeated 1 time(s)]

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

[Repeated 1 time(s)]

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting full

[Repeated 1 time(s)]

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

[Repeated 1 time(s)]

> lighting simple

> lighting flat

> lighting full

> lighting flat

[Repeated 1 time(s)]

> lighting soft

> lighting flat

[Repeated 1 time(s)]

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting simple

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting full

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting flat

[Repeated 1 time(s)]

> graphics silhouettes false

> lighting flat

> graphics silhouettes false

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting flat

> save
> C:/Users/kamsekul/Desktop/Projects/DBT/Structural_biology/X-ray/EV91489/2024-03-11_PRI005/EV91489_R002_1.jpg
> width 1341 height 819 supersample 3

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting flat

[Repeated 1 time(s)]

> lighting shadows true intensity 0.5

> lighting shadows false

> save
> C:/Users/kamsekul/Desktop/Projects/DBT/Structural_biology/X-ray/EV91489/2024-03-11_PRI005/EV91489_R002_2.jpg
> width 1341 height 819 supersample 3

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true

> lighting shadows false

> lighting full

[Repeated 2 time(s)]

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> lighting full

[Repeated 3 time(s)]

> lighting soft

[Repeated 1 time(s)]

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes true

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting flat

[Repeated 1 time(s)]

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting simple

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting flat

[Repeated 1 time(s)]

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

[Repeated 1 time(s)]

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> graphics silhouettes false

> lighting shadows false

> lighting shadows true

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> save
> C:/Users/kamsekul/Desktop/Projects/DBT/Structural_biology/X-ray/EV91489/2024-03-11_PRI005/EV91489_R002_3.jpg
> width 1341 height 819 supersample 3

> set bgColor gray

> set bgColor #80808000

> set bgColor gray

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> set bgColor gray

> set bgColor #80808000

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> set bgColor white

> set bgColor #ffffff00

> ui tool show "Side View"

[Repeated 1 time(s)]

> view

[Repeated 1 time(s)]

> view orient

> view

> view orient

[Repeated 1 time(s)]

> view

[Repeated 1 time(s)]

> ui tool show "Side View"

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\kamsekul/Desktop\movie1.mp4

Movie saved to C:\Users\kamsekul/Desktop\movie1.mp4  
  

> cd
> C:/Users/kamsekul/Desktop/Projects/DBT/Structural_biology/X-ray/EV91489/2024-03-11_PRI005

Current working directory is:
C:\Users\kamsekul\Desktop\Projects\DBT\Structural_biology\X-ray\EV91489\2024-03-11_PRI005  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\kamsekul/Desktop\movie2.mp4

Movie saved to C:\Users\kamsekul/Desktop\movie2.mp4  
  

> cd
> C:/Users/kamsekul/Desktop/Projects/DBT/Structural_biology/X-ray/EV91489/2024-03-11_PRI005

Current working directory is:
C:\Users\kamsekul\Desktop\Projects\DBT\Structural_biology\X-ray\EV91489\2024-03-11_PRI005  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\kamsekul/Desktop\movie3.mp4

Movie saved to C:\Users\kamsekul/Desktop\movie3.mp4  
  

> lighting flat

[Repeated 2 time(s)]

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

[Repeated 1 time(s)]

> undo

[Repeated 7 time(s)]

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\kamsekul/Desktop\movie4.mp4

Movie saved to C:\Users\kamsekul/Desktop\movie4.mp4  
  

> save
> C:/Users/kamsekul/Desktop/Projects/DBT/Structural_biology/X-ray/EV91489/2024-03-11_PRI005/ADAR2_RNA.glb

> rock z 5 136 center 0,0,0 coordinateSystem 0

Invalid "coordinateSystem" argument: invalid coordinate-system  

> rock z 5 136 center 0,0,0 coordinateSystem 1

Invalid "coordinateSystem" argument: invalid coordinate-system  

> rock z 5 136 center 0,0,0

[Repeated 1 time(s)]

> rock z 0 136 center 0,0,0

[Repeated 2 time(s)]

> rock z 10 136 center 0,0,0

> rock z 10 180 center 0,0,0

> rock z 10 360 center 0,0,0

> rock z -5 180 center 0,0,0

> rock z -5 180 center 180,0,0

> rock z -5 180 center 0,180,0

> rock z 180 180 center 0,180,0

> rock z 20 180 center 0,180,0

[Repeated 1 time(s)]

> rock z 10 180 center 0,90,0

> rock z 10 180 center 0,180,0

> rock z 10 180 center 0,0,0

> rock z 10 180 center 0,45,0

> rock z 10 180 center 45,0,0

> rock z 10 180 center 0,0,45

> rock y 10 180 center 0,0,0

> rock y 15 180 center 0,0,0

> rock y 20 180 center 0,0,0

> rock y 20 250 center 0,0,0

[Repeated 3 time(s)]

> save
> C:/Users/kamsekul/Desktop/Projects/DBT/Structural_biology/X-ray/EV91489/2024-03-11_PRI005/EV91489_R002.gif
> width 1341 height 819 supersample 3

> save
> C:/Users/kamsekul/Desktop/Projects/DBT/Structural_biology/X-ray/EV91489/2024-03-11_PRI005/ADAR2_RNA_rock.glb

> rock y 20 250 center 0,0,0

> rock y 20 250 center 0,0,0 cycle 68

> rock y 20 250 center 0,0,0 cycle 120

> rock y 20 250 center 0,0,0 cycle 200

[Repeated 1 time(s)]

> save
> C:/Users/kamsekul/Desktop/Projects/DBT/Structural_biology/X-ray/EV91489/2024-03-11_PRI005/ADAR2_RNA_rock.glb

> save
> C:/Users/kamsekul/Desktop/Projects/DBT/Structural_biology/X-ray/EV91489/2024-03-11_PRI005/adar2.wrl

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\kamsekul/Desktop\movie5.mp4

Movie saved to C:\Users\kamsekul/Desktop\movie5.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\kamsekul/Desktop\movie6.mp4

Movie saved to C:\Users\kamsekul/Desktop\movie6.mp4  
  

> rock y 20 250 center 0,0,0 cycle 200

> ui tool show "Selection Inspector"

> rock y 20 250 center 0,0,0 cycle 200

[Repeated 1 time(s)]

> movie encode C:/Users/kamsekul/Desktop/ADAR2_rock.mp4

No frames have been recorded  

> movie record

> rock y 20 250 center 0,0,0 cycle 200

> movie encode C:/Users/kamsekul/Desktop/ADAR2_rock.mp4

Movie saved to C:/Users/kamsekul/Desktop/ADAR2_rock.mp4  
  

> open "C:/Users/kamsekul/OneDrive -
> Evotec/CPS-3976_02_A/03-Validation/refine-coot-0-val.pdb"

Summary of feedback from opening C:/Users/kamsekul/OneDrive -
Evotec/CPS-3976_02_A/03-Validation/refine-coot-0-val.pdb  
---  
warnings | Ignored bad PDB record found on line 5  
REMARK --------------------- added by autoBUSTER
-------------------------------  
  
Ignored bad PDB record found on line 6  
REMARK run at = Wed Feb 7 09:28:40 EST 2024  
  
Ignored bad PDB record found on line 13  
REMARK Files used:  
  
Ignored bad PDB record found on line 14  
REMARK PDB = ./pdbchk.pdb  
  
Ignored bad PDB record found on line 15  
REMARK MTZ = /mnt/c/Users/kamsekul/Desktop/Projects/DBT/Structura  
  
43 messages similar to the above omitted  
  
refine-coot-0-val.pdb title:  
That ACTS on RNA (HADAR2) bound to inositol hexakisphosphat [more info...]  
  
Chain information for refine-coot-0-val.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Non-standard residues in refine-coot-0-val.pdb #5  
---  
IHP — (IHP)  
SO4 — (SO4)  
ZN — (ZN)  
  

> select #5/A:405

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

> select up

191 atoms, 193 bonds, 22 residues, 1 model selected  

> select up

1175 atoms, 1193 bonds, 150 residues, 1 model selected  

> select up

1221 atoms, 1238 bonds, 156 residues, 1 model selected  

> select up

2942 atoms, 2998 bonds, 376 residues, 1 model selected  

> select up

2979 atoms, 3034 bonds, 378 residues, 1 model selected  

> select up

6373 atoms, 5973 bonds, 1250 residues, 1 model selected  

> select down

2979 atoms, 3034 bonds, 378 residues, 1 model selected  

> ui tool show "Model Panel"

> hide target m

[Repeated 1 time(s)]

> show #!5 models

> show #!4 models

> select add #5

6373 atoms, 5973 bonds, 4 pseudobonds, 1250 residues, 2 models selected  

> select subtract #5

Nothing selected  

> select add #5

6373 atoms, 5973 bonds, 4 pseudobonds, 1250 residues, 2 models selected  

> select subtract #5

Nothing selected  

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> hide #!4 models

> show #!4 models

> select #5/A:600

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

> select up

53 atoms, 55 bonds, 6 residues, 1 model selected  

> select up

1767 atoms, 1805 bonds, 226 residues, 1 model selected  

> select up

1827 atoms, 1865 bonds, 235 residues, 1 model selected  

> select up

2942 atoms, 2998 bonds, 376 residues, 1 model selected  

> matchmaker #5 to #4

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 refine.pdb, chain A (#4) with refine-coot-0-val.pdb, chain A (#5),
sequence alignment score = 1769  
RMSD between 342 pruned atom pairs is 0.678 angstroms; (across all 365 pairs:
1.438)  
  

> select clear

> select #5/B:561

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select up

72 atoms, 73 bonds, 9 residues, 1 model selected  

> select up

1491 atoms, 1526 bonds, 190 residues, 1 model selected  

> select up

1498 atoms, 1532 bonds, 191 residues, 1 model selected  

> select up

1644 atoms, 1679 bonds, 210 residues, 1 model selected  

> select up

1695 atoms, 1732 bonds, 216 residues, 1 model selected  

> select up

2778 atoms, 2832 bonds, 354 residues, 1 model selected  

> select up

2832 atoms, 2887 bonds, 361 residues, 1 model selected  

> select up

2869 atoms, 2923 bonds, 363 residues, 1 model selected  

> select up

6373 atoms, 5973 bonds, 1250 residues, 1 model selected  

> select down

2869 atoms, 2923 bonds, 363 residues, 1 model selected  

> select down

2832 atoms, 2887 bonds, 361 residues, 1 model selected  

> select up

2869 atoms, 2923 bonds, 363 residues, 1 model selected  

> view #2 clip false

[Repeated 1 time(s)]

> show #!2 target m

> hide #!2 target m

> close #2

> delete sel

> select clear

> select up

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

> select up

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

> select up

525 atoms, 16 bonds, 509 residues, 1 model selected  

> select down

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

> select up

525 atoms, 16 bonds, 509 residues, 1 model selected  

> select down

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

> delete sel

> select #5/C:116@O

1 atom, 1 residue, 1 model selected  

> select up

520 atoms, 12 bonds, 508 residues, 1 model selected  

> delete sel

> color #5 #55ff7fff

> color #5 #ffff7fff

> color #5 yellow

> color #5 #ffda20ff

> color #5 #fff829ff

> color #5 #ffdd1dff

> color #5 #f1d11bff

> color #5 #ccb117ff

> color #5 #ddc019ff

> color #5 #ffaaffff

> color #5 #aaff7fff

> color #5 yellow

> color #5 #ffff7fff

> color #5 #fdff6eff

> color #5 #d6ff65ff

> color #5 #fffa5eff

> color #5 #eae556ff

> color #5 #ded952ff

> color #5 #beba46ff

> color #5 #ded952ff

> color #5 #d6d14fff

> morph #5,4 frames 40

models have different number of chains, 1 (Morph - refine-coot-0-val.pdb #/A)
and 3 (refine.pdb #4/A,refine.pdb #4/B,refine.pdb #4/C)  

> select clear

> select #4/A:474

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

> select up

265 atoms, 272 bonds, 34 residues, 1 model selected  

> select up

3017 atoms, 3079 bonds, 384 residues, 1 model selected  

> select up

3054 atoms, 3115 bonds, 386 residues, 1 model selected  

> select up

4029 atoms, 4202 bonds, 432 residues, 1 model selected  

> select down

3054 atoms, 3115 bonds, 386 residues, 1 model selected  

> select down

3017 atoms, 3079 bonds, 384 residues, 1 model selected  

> select up

3054 atoms, 3115 bonds, 386 residues, 1 model selected  

> log metadata #5

Metadata for refine-coot-0-val.pdb #5  
---  
Title | That ACTS on RNA (HADAR2) bound to inositol hexakisphosphat  
Non-standard residues | IHP — (IHP)  
ZN — (ZN)  
Experimental method | X-ray diffraction  
Resolution | 2.24Å  
  
> log chains #5

Chain information for refine-coot-0-val.pdb #5  
---  
Chain | Description  
A | No description available  
  

> log metadata #5

Metadata for refine-coot-0-val.pdb #5  
---  
Title | That ACTS on RNA (HADAR2) bound to inositol hexakisphosphat  
Non-standard residues | IHP — (IHP)  
ZN — (ZN)  
Experimental method | X-ray diffraction  
Resolution | 2.24Å  
  
> log chains #5

Chain information for refine-coot-0-val.pdb #5  
---  
Chain | Description  
A | No description available  
  

> view #5 clip false

> show #!5 target m

[Repeated 1 time(s)]

> hide #!5 target m

> close #5

> show #4.1 models

> select add #4

4029 atoms, 4202 bonds, 1 pseudobond, 432 residues, 2 models selected  

> select subtract #4

Nothing selected  

> select add #4.1

1 pseudobond, 1 model selected  

> select subtract #4.1

Nothing selected  

> select add #4

4029 atoms, 4202 bonds, 1 pseudobond, 432 residues, 2 models selected  

> select subtract #4

Nothing selected  

> hide #4.1 models

> select add #4

4029 atoms, 4202 bonds, 1 pseudobond, 432 residues, 2 models selected  

> select clear

> undo

[Repeated 9 time(s)]

> select clear

> open "C:/Users/kamsekul/OneDrive -
> Evotec/CPS-3976_02_A/03-Validation/refine-coot-0-val.pdb"

Summary of feedback from opening C:/Users/kamsekul/OneDrive -
Evotec/CPS-3976_02_A/03-Validation/refine-coot-0-val.pdb  
---  
warnings | Ignored bad PDB record found on line 5  
REMARK --------------------- added by autoBUSTER
-------------------------------  
  
Ignored bad PDB record found on line 6  
REMARK run at = Wed Feb 7 09:28:40 EST 2024  
  
Ignored bad PDB record found on line 13  
REMARK Files used:  
  
Ignored bad PDB record found on line 14  
REMARK PDB = ./pdbchk.pdb  
  
Ignored bad PDB record found on line 15  
REMARK MTZ = /mnt/c/Users/kamsekul/Desktop/Projects/DBT/Structura  
  
43 messages similar to the above omitted  
  
refine-coot-0-val.pdb title:  
That ACTS on RNA (HADAR2) bound to inositol hexakisphosphat [more info...]  
  
Chain information for refine-coot-0-val.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Non-standard residues in refine-coot-0-val.pdb #2  
---  
IHP — (IHP)  
SO4 — (SO4)  
ZN — (ZN)  
  

> matchmaker #2 to #4

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 refine.pdb, chain A (#4) with refine-coot-0-val.pdb, chain A (#2),
sequence alignment score = 1769  
RMSD between 342 pruned atom pairs is 0.678 angstroms; (across all 365 pairs:
1.438)  
  

> select #2/B:571

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

> select up

120 atoms, 123 bonds, 15 residues, 1 model selected  

> select up

1491 atoms, 1526 bonds, 190 residues, 1 model selected  

> select up

1498 atoms, 1532 bonds, 191 residues, 1 model selected  

> select up

1644 atoms, 1679 bonds, 210 residues, 1 model selected  

> select up

1695 atoms, 1732 bonds, 216 residues, 1 model selected  

> select up

2778 atoms, 2832 bonds, 354 residues, 1 model selected  

> select up

2832 atoms, 2887 bonds, 361 residues, 1 model selected  

> select up

2869 atoms, 2923 bonds, 363 residues, 1 model selected  

> select up

6373 atoms, 5973 bonds, 1250 residues, 1 model selected  

> select down

2869 atoms, 2923 bonds, 363 residues, 1 model selected  

> delete sel

> select up

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

> select up

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

> select up

525 atoms, 16 bonds, 509 residues, 1 model selected  

> delete sel

> color #2 #dceb59ff

> color #2 #c9eb58ff

> color #2 #adc84bff

> color #2 #b2ce4dff

> hide #!2 models

> hide #4.1 models

> show #4.1 models

> hide #!4 models

> show #!2 models

> color #2 #a1ce39ff

> color #2 #9fce30ff

> color #2 #b4ce30ff

> color #2 #cece38ff

> color #2 #bece31ff

> color #2 #cebd39ff

> color #2 #cec439ff

> hide #!2 atoms

> open "C:/Users/kamsekul/OneDrive -
> Evotec/CPS-3976_02_A/03-Validation/refine-coot-0-val.pdb"

Summary of feedback from opening C:/Users/kamsekul/OneDrive -
Evotec/CPS-3976_02_A/03-Validation/refine-coot-0-val.pdb  
---  
warnings | Ignored bad PDB record found on line 5  
REMARK --------------------- added by autoBUSTER
-------------------------------  
  
Ignored bad PDB record found on line 6  
REMARK run at = Wed Feb 7 09:28:40 EST 2024  
  
Ignored bad PDB record found on line 13  
REMARK Files used:  
  
Ignored bad PDB record found on line 14  
REMARK PDB = ./pdbchk.pdb  
  
Ignored bad PDB record found on line 15  
REMARK MTZ = /mnt/c/Users/kamsekul/Desktop/Projects/DBT/Structura  
  
43 messages similar to the above omitted  
  
refine-coot-0-val.pdb title:  
That ACTS on RNA (HADAR2) bound to inositol hexakisphosphat [more info...]  
  
Chain information for refine-coot-0-val.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Non-standard residues in refine-coot-0-val.pdb #5  
---  
IHP — (IHP)  
SO4 — (SO4)  
ZN — (ZN)  
  

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> select #5/B:630

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

> select up

101 atoms, 104 bonds, 11 residues, 1 model selected  

> select up

1491 atoms, 1526 bonds, 190 residues, 1 model selected  

> select up

1498 atoms, 1532 bonds, 191 residues, 1 model selected  

> select up

1644 atoms, 1679 bonds, 210 residues, 1 model selected  

> select up

1695 atoms, 1732 bonds, 216 residues, 1 model selected  

> select up

2778 atoms, 2832 bonds, 354 residues, 1 model selected  

> select up

2832 atoms, 2887 bonds, 361 residues, 1 model selected  

> select up

2869 atoms, 2923 bonds, 363 residues, 1 model selected  

> select up

6373 atoms, 5973 bonds, 1250 residues, 1 model selected  

> select down

2869 atoms, 2923 bonds, 363 residues, 1 model selected  

> delete sel

> select clear

> select #5/C:261@O

1 atom, 1 residue, 1 model selected  

> select up

525 atoms, 16 bonds, 509 residues, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

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

> select up

525 atoms, 16 bonds, 509 residues, 1 model selected  

> select down

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

> delete sel

> select clear

[Repeated 3 time(s)]

> select #5/C:168@O

1 atom, 1 residue, 1 model selected  

> select up

520 atoms, 12 bonds, 508 residues, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> delete sel

> select #5/C:261@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select #5/C:160@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select clear

> select #5/C:186@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select #5/C:117@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select clear

> select #5/C:116@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select #5/C:172@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select #5/C:121@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select clear

> select #5/C:104@O

1 atom, 1 residue, 1 model selected  

> select #5/C:201@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select clear

> select #5/C:104@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select #5/C:105@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select #5/C:137@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select clear

> select #5/C:129@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select #5/C:133@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select #5/C:126@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select clear

> select #5/C:122@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select clear

[Repeated 2 time(s)]

> select #5/C:132@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select #5/C:377@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select #5/C:773@O

1 atom, 1 residue, 1 model selected  

> select up

502 atoms, 12 bonds, 490 residues, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select up

502 atoms, 12 bonds, 490 residues, 1 model selected  

> delete sel

> color #5 #fada5cff

> color #5 #fae549ff

> color #5 #fabe45ff

> color #5 #fab640ff

> color #5 #faba52ff

> color #5 #ecfa4cff

> color #5 #d9fa61ff

> color #5 #5afa5aff

> color #5 #3ffab5ff

> color #5 #39fac3ff

> color #5 #4afae5ff

> color #5 #55fab5ff

> color #5 #45fa81ff

> color #5 #64fa89ff

> color #5 #53d072ff

> color #5 #4ab865ff

> color #5 #54d173ff

> color #5 #467bd1ff

> color #5 #4f9fd1ff

> color #5 #48b8d1ff

> color #5 #4bc6d1ff

> color #5 #58add1ff

> color #5 #aa55ffff

> color #5 #aa00ffff

> color #5 #aaaaffff

> color #5 #a1a1f1ff

> color #5 #9d9decff

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting flat

> color #!5 bynucleotide

> hide #!5 atoms

> show #!5 atoms

[Repeated 1 time(s)]

> hide #!5 atoms

> show #!5 atoms

> hide #!5 atoms

> show #!5 cartoons

> hide #!5 cartoons

[Repeated 1 time(s)]

> show #!5 cartoons

> show #!5 atoms

> undo

[Repeated 9 time(s)]

> show #!5 surfaces

> hide #!5 surfaces

> show #!5 cartoons

[Repeated 1 time(s)]

> show #!5 atoms

[Repeated 1 time(s)]

> hide #!5 models

> hide #5.2 models

> hide #5.1 models

> show #5.1 models

> hide #5.1 models

> show #5.1 models

> show #5.2 models

> hide #5.2 models

> show #5.2 models

> hide #5.2 models

> ui tool show "Model Panel"

> color bfactor #!5

2979 atoms, 378 residues, 1 surfaces, atom bfactor range 13.7 to 64.4  

> mlp #!5

Map values for surface "refine-coot-0-val.pdb_A SES surface": minimum -28.86,
mean -5.766, maximum 23.24  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp #!5

Map values for surface "refine-coot-0-val.pdb_A SES surface": minimum -28.86,
mean -5.766, maximum 23.24  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor #!5

2979 atoms, 378 residues, 1 surfaces, atom bfactor range 13.7 to 64.4  

> color bfactor #!5

2979 atoms, 378 residues, 1 surfaces, atom bfactor range 13.7 to 64.4  

> mlp #!5

Map values for surface "refine-coot-0-val.pdb_A SES surface": minimum -28.86,
mean -5.766, maximum 23.24  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp #!5

Map values for surface "refine-coot-0-val.pdb_A SES surface": minimum -28.86,
mean -5.766, maximum 23.24  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic #!5

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for refine-coot-0-val.pdb_A SES surface #5.2: minimum,
-11.94, mean 2.72, maximum 27.23  
To also show corresponding color key, enter the above coulombic command and
add key true  

> rainbow #!5

> color #!5 bypolymer

> color #!5 bychain

> color #!5 byhetero

[Repeated 1 time(s)]

> hide #!5 surfaces

> color #!5 byhetero

[Repeated 1 time(s)]

> color #!5 bychain

[Repeated 1 time(s)]

> color #!5 byhetero

> color #!5 bychain

> color #!5 byhetero

> color #!5 bypolymer

[Repeated 1 time(s)]

> color #!5 bychain

> color #!5 byhetero

> open "C:/Users/kamsekul/OneDrive -
> Evotec/CPS-3976_02_A/03-Validation/refine-coot-0-val.pdb"

Summary of feedback from opening C:/Users/kamsekul/OneDrive -
Evotec/CPS-3976_02_A/03-Validation/refine-coot-0-val.pdb  
---  
warnings | Ignored bad PDB record found on line 5  
REMARK --------------------- added by autoBUSTER
-------------------------------  
  
Ignored bad PDB record found on line 6  
REMARK run at = Wed Feb 7 09:28:40 EST 2024  
  
Ignored bad PDB record found on line 13  
REMARK Files used:  
  
Ignored bad PDB record found on line 14  
REMARK PDB = ./pdbchk.pdb  
  
Ignored bad PDB record found on line 15  
REMARK MTZ = /mnt/c/Users/kamsekul/Desktop/Projects/DBT/Structura  
  
43 messages similar to the above omitted  
  
refine-coot-0-val.pdb title:  
That ACTS on RNA (HADAR2) bound to inositol hexakisphosphat [more info...]  
  
Chain information for refine-coot-0-val.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Non-standard residues in refine-coot-0-val.pdb #6  
---  
IHP — (IHP)  
SO4 — (SO4)  
ZN — (ZN)  
  

> hide #5.2 models

> hide #!5 models

> hide #5.1 models

> select #6/A:331

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

> select up

124 atoms, 125 bonds, 17 residues, 1 model selected  

> select up

1175 atoms, 1193 bonds, 150 residues, 1 model selected  

> select up

1221 atoms, 1238 bonds, 156 residues, 1 model selected  

> select up

2942 atoms, 2998 bonds, 376 residues, 1 model selected  

> select up

2979 atoms, 3034 bonds, 378 residues, 1 model selected  

> select up

6373 atoms, 5973 bonds, 1250 residues, 1 model selected  

> select down

2979 atoms, 3034 bonds, 378 residues, 1 model selected  

> delete sel

> select #6/C:793@O4

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

525 atoms, 16 bonds, 509 residues, 1 model selected  

> select down

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

> select up

525 atoms, 16 bonds, 509 residues, 1 model selected  

> select down

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

> select up

525 atoms, 16 bonds, 509 residues, 1 model selected  

> delete sel

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!4 models

> hide #!4 models

> show #!4 models

> matchmaker #6 to #4

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 refine.pdb, chain A (#4) with refine-coot-0-val.pdb, chain B (#6),
sequence alignment score = 1706.6  
RMSD between 328 pruned atom pairs is 0.617 angstroms; (across all 355 pairs:
1.631)  
  

> hide #!4 models

> color #6 #aaaaffff

> color #6 #9999e6ff

> color #!6 byhetero

> show #!4 models

> color #6 #ffaaffff

> color #6 #aaaaffff

> color #6 #aa55ffff

> color #6 #aa00ffff

> color #6 #5500ffff

> color #6 #5555ffff

> color #6 #ff55ffff

> color #6 #aa55ffff

> color #6 #aa557fff

> color #6 #aaaaffff

> color #6 #9c9ceaff

> color #6 #7b7bb8ff

> hide #!4 models

> color #!6 byhetero

> show #!4 models

> hide #!4 models

> show #!4 models

> color #6 #3f3f5eff

> color #6 #5c5c8aff

> color #6 #9393dcff

> color #6 #8383c5ff

> color #6 #54547eff

> color #6 #6f6fa7ff

> color #6 #7070a8ff

> color #6 #7575afff

> color #6 #7373adff

> color #!4,6 byhetero

> save C:\Users\kamsekul/Desktop\image1.png supersample 3

> save C:\Users\kamsekul/Desktop\image2.png supersample 3

> movie record

> rock y 20 250 center 0,0,0 cycle 200

> rock y 20 250 center 0,0,0 cycle 100

> movie encode C:/Users/kamsekul/Desktop/ADAR2apo_RNA_rock.mp4

Movie saved to C:/Users/kamsekul/Desktop/ADAR2apo_RNA_rock.mp4  
  

> hide #4.1 models

> hide #!4 models

> save C:/Users/kamsekul/Desktop/ADAR2.cxs

> rock y 20 250 center 0,0,0 cycle 100

> rock y 20 250 center 0,0,0 cycle 150

> rock y 20 250 center 0,0,0 cycle 200

[Repeated 1 time(s)]

> movie record

> rock y 20 250 center 0,0,0 cycle 200

> movie encode C:/Users/kamsekul/Desktop/ADAR2_apo_rock.mp4

Movie saved to C:/Users/kamsekul/Desktop/ADAR2_apo_rock.mp4  
  

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> morph #2,6 frames 40

Computed 41 frame morph #7  

> coordset #7 1,41

> morph #2,6 frames 40

Computed 41 frame morph #8  

> coordset #8 1,41

> close #7

> close #8

> show #!6 models

> show #!5 models

> hide #!5 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!4 models

> hide #!4 models

> show #!4 models

> morph #4,6 frames 40

models have different number of chains, 3 (Morph - refine.pdb #/A,Morph -
refine.pdb #/B,Morph - refine.pdb #/C) and 1 (refine-coot-0-val.pdb #6/B)  

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

485 atoms, 541 bonds, 23 residues, 1 model selected  

> select up

4029 atoms, 4202 bonds, 432 residues, 1 model selected  

> select up

29786 atoms, 29949 bonds, 4135 residues, 6 models selected  

> select up

29786 atoms, 29949 bonds, 1 pseudobond, 4135 residues, 8 models selected  

> select up

29786 atoms, 29949 bonds, 1 pseudobond, 4135 residues, 8 models selected  

> select up

29786 atoms, 29949 bonds, 1 pseudobond, 4135 residues, 8 models selected  

> select up

29786 atoms, 29949 bonds, 1 pseudobond, 4135 residues, 8 models selected  

> show #!4 target m

> view #4 clip false

[Repeated 1 time(s)]

> log metadata #4

No models had metadata

> log chains #4

Chain information for refine.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> hide #!4 target m

[Repeated 1 time(s)]

> show #!4 target m

> mcopy #4 settings a

Missing required "to_atoms" argument  

> mcopy #4 toAtoms #7 settings a

[Repeated 1 time(s)]

> select clear

> combine #4 set a

Expected a keyword  

> combine #4 #8 set a

Expected a keyword  

> combine #4 dwa

Expected a keyword  

> select #4/C:17

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

485 atoms, 541 bonds, 23 residues, 1 model selected  

> select up

4029 atoms, 4202 bonds, 432 residues, 1 model selected  

> select down

485 atoms, 541 bonds, 23 residues, 1 model selected  

> select up

4029 atoms, 4202 bonds, 432 residues, 1 model selected  

> select down

485 atoms, 541 bonds, 23 residues, 1 model selected  

> fly.cmd

Unknown command: fly.cmd  

> hide #!4 models

> show #!4 models

> open quality.py

No such file/path: quality.py  

> preset apply int 1

No preset name matches 'apply int 1'  

> show ligand

> select clear

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!6 models

> show #!4 models

> show ligand

> hide #!4 models

> show ligand

> ~modeldisplay #4

Unknown command: ~modeldisplay #4  

> show #!6 models

> savepose apo

Unknown command: savepose apo  

> reset apo

Unknown command: reset apo  

> savepose

Unknown command: savepose  

> savepos apo

Unknown command: savepos apo  

> savepos adar2

Unknown command: savepos adar2  

> ~savepos adar2

Unknown command: ~savepos adar2  

> help help:user

> savepos

Unknown command: savepos  

> help help:devel

> ui tool show "Selection Inspector"

> help savepos

No help found for 'savepos'  

> savepos

Unknown command: savepos  

> ui windowfill toggle

[Repeated 1 time(s)]

> help help:contact.html




OpenGL version: 3.3.0 - Build 27.20.100.9664
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Latitude 5410
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 16,760,946,688
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-10310U CPU @ 1.70GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 20 months ago

Component: Unassigned → Command Line
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → savepos

comment:2 by Eric Pettersen, 20 months ago

Resolution: → not a bug
Status: accepted → closed

Hi Kamil,

"savepos" is a Chimera command, not a ChimeraX command. The ChimeraX equivalent is "view name <view-name>" and the equivalent to "reset" is "view <view-name>".

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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