The following bug report has been submitted:
Platform: Linux-5.14.0-570.28.1.el9_6.x86_64-x86_64-with-glibc2.34
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /data/C3Modeling/ChimeraX/C3_Models_Maps.cxs
Opened J94_EMReady.mrc as #3, grid size 360,360,360, pixel 0.887, shown at
level 3.13, step 1, values float32
Opened J94_EMReady.mrc zone as #4, grid size 25,26,27, pixel 0.887, shown at
level 2.7, step 1, values float32
Opened J119_EMReady.mrc as #6, grid size 360,360,360, pixel 0.887, shown at
level 2.99, step 1, values float32
Opened J58_002_volume_map.mrc as #7, grid size 360,360,360, pixel 0.887, shown
at level 0.0273, step 1, values float32
Opened J59_002_volume_map.mrc as #8, grid size 360,360,360, pixel 0.887, shown
at level 0.0227, step 1, values float32
Log from Thu Jul 31 12:08:46 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open C3_Models_Maps.cxs
Opened J94_EMReady.mrc as #3, grid size 360,360,360, pixel 0.887, shown at
level 3.13, step 1, values float32
Opened J94_EMReady.mrc zone as #4, grid size 25,26,27, pixel 0.887, shown at
level 2.7, step 1, values float32
Log from Thu Jul 31 11:23:53 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open EC9TEFM_Models_Maps.cxs
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened EC13_map.mrc as #2, grid size 384,384,384, pixel 0.73, shown at level
0.0174, step 1, values float32
restore_snapshot for "Redust" returned None
restore_snapshot for "ZoneColor" returned None
[Repeated 1 time(s)]Log from Thu Dec 26 20:14:27 2024UCSF ChimeraX version:
1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "D:\\\Temiakov Lab\\\KH Cryo-
> EM\\\IC_modeling\\\ChimeraX\\\EC9-TEFM\\\EC9TEFM_Models_Maps.cxs"
Opened EC13_map.mrc as #4, grid size 384,384,384, pixel 0.73, shown at level
0.0174, step 1, values float32
Opened EC8_map.mrc as #2, grid size 384,384,384, pixel 0.73, shown at level
0.0174, step 1, values float32
Log from Sun Nov 17 21:45:19 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> C:\\\Users\\\kherb\\\Desktop\\\ChimeraX\\\EC13\\\EC8_EC13_Models_Maps.cxs
Opened EC13_map.mrc as #4, grid size 384,384,384, pixel 0.73, shown at level
0.0174, step 1, values float32
Opened EC8_map.mrc as #2, grid size 384,384,384, pixel 0.73, shown at level
0.0174, step 1, values float32
Log from Tue Oct 15 12:06:28 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\\\Users\\\krh021\\\Desktop\\\ChimeraX\\\EC8_EC13_Models_Maps.cxs
Opened EC13_map.mrc as #4, grid size 384,384,384, pixel 0.73, shown at level
0.0174, step 1, values float32
Opened EC8_map.mrc as #2, grid size 384,384,384, pixel 0.73, shown at level
0.0174, step 1, values float32
Log from Mon Oct 14 15:36:43 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\\\Users\\\krh021\\\Desktop\\\ChimeraX\\\EC8_EC13_Models_Maps.cxs
Opened EC13_map.mrc as #4, grid size 384,384,384, pixel 0.73, shown at level
0.0174, step 1, values float32
Opened EC8_map.mrc as #2, grid size 384,384,384, pixel 0.73, shown at level
0.0174, step 1, values float32
Log from Fri Sep 27 16:57:34 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\\\Users\\\krh021\\\Desktop\\\ChimeraX\\\EC8_EC13_Models_Maps.cxs
Opened IC0_map.mrc as #2, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened IC3_map.mrc as #4, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Log from Fri Sep 27 15:53:32 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\\\Users\\\krh021\\\Desktop\\\ChimeraX\\\IC_Models_Maps.cxs
Opened J781.mrc as #4, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J792.mrc as #3, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened 6erp_map2.mrc as #6, grid size 117,115,117, pixel 1.24,1.23,1.23, shown
at level 0.044, step 1, values float32
Opened J792 Clipped as #16, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J781 Clipped as #17, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J792 zone as #13, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J781 zone as #15, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J781.mrc zone as #11, grid size 384,384,384, pixel 0.751, shown at
level 0.0174, step 1, values float32
Opened J792.mrc zone as #9, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Log from Wed Sep 11 17:48:32 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\\\Users\\\krh021\\\Desktop\\\ChimeraX\\\IC3\\\IC3_PDB.cxs
Opened J781.mrc as #4, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J792.mrc as #3, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened 6erp_map2.mrc as #6, grid size 117,115,117, pixel 1.24,1.23,1.23, shown
at level 0.044, step 1, values float32
Opened J792 Clipped as #16, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J781 Clipped as #17, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J792 zone as #13, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J781 zone as #15, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J781.mrc zone as #11, grid size 384,384,384, pixel 0.751, shown at
level 0.0174, step 1, values float32
Opened J792.mrc zone as #9, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Log from Tue Sep 10 16:34:01 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\\\Users\\\krh021\\\Desktop\\\ChimeraX\\\IC3\\\IC3_PDB.cxs
Opened J781.mrc as #4, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J792.mrc as #3, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened 6erp_map2.mrc as #6, grid size 117,115,117, pixel 1.24,1.23,1.23, shown
at level 0.044, step 1, values float32
Opened J792 Clipped as #16, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J781 Clipped as #17, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J792 zone as #13, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J781 zone as #15, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J781.mrc zone as #11, grid size 384,384,384, pixel 0.751, shown at
level 0.0174, step 1, values float32
Opened J792.mrc zone as #9, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Log from Fri Aug 23 15:56:25 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\\\Users\\\krh021\\\Desktop\\\ChimeraX\\\IC_PDB.cxs
Opened J781 as #4, grid size 384,384,384, pixel 0.751, shown at level 0.0174,
step 1, values float32
Opened J792 as #3, grid size 384,384,384, pixel 0.751, shown at level 0.0174,
step 1, values float32
Opened 6erp_map2.mrc as #6, grid size 117,115,117, pixel 1.24,1.23,1.23, shown
at level 0.044, step 1, values float32
Opened IC3_J1043_map_locres.mrc as #7, grid size 384,384,384, pixel 0.751,
shown at level 6.47, step 2, values float32
Opened IC0_J1044_map_locres.mrc as #8, grid size 384,384,384, pixel 0.751,
shown at level 6.98, step 2, values float32
Opened J792 copy as #9, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J781 copy as #10, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J792 copy as #16, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J781 copy as #17, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J792 zone as #13, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J781 zone as #15, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Log from Fri Aug 23 12:03:12 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open C:\\\Users\\\krh021\\\Desktop\\\ChimeraX\\\IC_LocalRes.cxs
Opened J781 as #4, grid size 384,384,384, pixel 0.751, shown at level 0.0174,
step 1, values float32
Opened J792 as #3, grid size 384,384,384, pixel 0.751, shown at level 0.0174,
step 1, values float32
Opened 6erp_map2.mrc as #6, grid size 117,115,117, pixel 1.24,1.23,1.23, shown
at level 0.044, step 1, values float32
Opened IC3_J1043_map_locres.mrc as #7, grid size 384,384,384, pixel 0.751,
shown at level 6.47, step 2, values float32
Opened IC0_J1044_map_locres.mrc as #8, grid size 384,384,384, pixel 0.751,
shown at level 6.98, step 2, values float32
Opened J792 copy as #9, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J781 copy as #10, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J781 zone as #15, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J792 zone as #13, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J792 copy as #16, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Opened J781 copy as #17, grid size 384,384,384, pixel 0.751, shown at level
0.0174, step 1, values float32
Log from Fri Aug 23 11:39:06 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> surface cap false
Log from Tue Aug 20 14:24:19 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> surface cap false
Log from Tue Aug 20 14:15:31 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> surface cap false
Log from Sun Aug 18 23:50:44 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> surface cap false
Log from Sun Aug 18 23:04:58 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> surface cap false
Log from Sun Aug 18 19:51:27 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:\\\IC_Modelling\\\ChimeraX\\\IC_PDB_2.cxs
Opened J781 as #4, grid size 384,384,384, pixel 0.751, shown at level 0.0181,
step 1, values float32
Opened J792 as #3, grid size 384,384,384, pixel 0.751, shown at level 0.00198,
step 2, values float32
Log from Sun Aug 18 16:48:10 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:\IC_Modelling\ChimeraX\IC_PDB_2.cxs format session
Opened J781 as #4, grid size 384,384,384, pixel 0.751, shown at level 0.0181,
step 1, values float32
Opened J792 as #3, grid size 384,384,384, pixel 0.751, shown at level 0.00198,
step 2, values float32
Log from Sun Aug 18 13:15:51 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:\IC_Modelling\ChimeraX\IC_PDB_2.cxs format session
Opened J781 as #4, grid size 384,384,384, pixel 0.751, shown at level 0.0181,
step 1, values float32
Opened J792 as #3, grid size 384,384,384, pixel 0.751, shown at level 0.00198,
step 2, values float32
Log from Sat Aug 17 13:00:45 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:\\\IC_Modelling\\\ChimeraX\\\IC_PDB_2.cxs
Log from Sat Aug 17 12:19:07 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open D:/IC_Modelling/Models/Open/mtIC_J781_rsr_V6.pdb
Chain information for mtIC_J781_rsr_V6.pdb #1
---
Chain | Description
A | No description available
B | No description available
E | No description available
N | No description available
R | No description available
T | No description available
> select #*/A
1615 atoms, 1646 bonds, 192 residues, 1 model selected
> color sel red
> select #*/B
2632 atoms, 2697 bonds, 324 residues, 1 model selected
> color sel dodger blue
> select #*/E:122-355
1699 atoms, 1722 bonds, 2 pseudobonds, 211 residues, 2 models selected
> color sel teal
> select #*/E:356-643
2325 atoms, 2380 bonds, 288 residues, 1 model selected
> color sel #ACA9A9
> select #*/E:605-623
161 atoms, 165 bonds, 19 residues, 1 model selected
> color sel medium orchid
> select #*/E:643-1230
4465 atoms, 4580 bonds, 1 pseudobond, 564 residues, 2 models selected
> color sel spring green
> select #*/E:711-790
432 atoms, 439 bonds, 1 pseudobond, 56 residues, 2 models selected
> color sel goldenrod
> select #*/E:954-1044
753 atoms, 766 bonds, 91 residues, 1 model selected
> color sel plum
> select #*/T
1005 atoms, 1123 bonds, 50 residues, 1 model selected
> color sel blue
> select #*/R
68 atoms, 76 bonds, 3 residues, 1 model selected
> color sel red
> select #*/N
1035 atoms, 1164 bonds, 50 residues, 1 model selected
> color sel cyan
> select clear
> set bgColor white
> lighting simple
> lighting soft
> lighting full
[Repeated 1 time(s)]
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select /A:162
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:162-170
79 atoms, 80 bonds, 9 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> hide sel surfaces
> show sel cartoons
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 79 atom styles
> style sel sphere
Changed 79 atom styles
> style sel ball
Changed 79 atom styles
> select add #1
14839 atoms, 15385 bonds, 3 pseudobonds, 1681 residues, 2 models selected
> select subtract #1
Nothing selected
> nucleotides atoms
> style nucleic stick
Changed 2108 atom styles
> ui mousemode right select
> select /N:37@C6
1 atom, 1 residue, 1 model selected
> select /N:38@C1'
1 atom, 1 residue, 1 model selected
> ui mousemode right translate
> select add #1
14839 atoms, 15385 bonds, 3 pseudobonds, 1681 residues, 2 models selected
> select subtract #1
Nothing selected
> hide cartoons
> show cartoons
> hide atoms
> dssp
[Repeated 1 time(s)]
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> sequence chain /B
Alignment identifier is 1/B
> sequence chain /E
Alignment identifier is 1/E
> sequence chain /N
Alignment identifier is 1/N
> sequence chain /R
Alignment identifier is 1/R
> sequence chain /T
Alignment identifier is 1/T
> select /N:1
17 atoms, 18 bonds, 1 residue, 1 model selected
> select /N
1035 atoms, 1164 bonds, 50 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 1035 atom styles
> style sel stick
Changed 1035 atom styles
> show sel atoms
> color sel byhetero
> select /A/E
10099 atoms, 10325 bonds, 3 pseudobonds, 1254 residues, 2 models selected
> hide sel
> hide sel cartoons
> open D:/IC_Modelling/Models/Closed/mtIC_J792_rsr_V5.pdb
Summary of feedback from opening
D:/IC_Modelling/Models/Closed/mtIC_J792_rsr_V5.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER A 56 GLN A 71 1 16
End residue of secondary structure not found: HELIX 2 2 THR A 77 GLU A 90 1 14
Start residue of secondary structure not found: HELIX 3 3 ASP A 93 GLN A 120 1
28
Start residue of secondary structure not found: HELIX 4 4 PRO A 123 LEU A 151
1 29
Start residue of secondary structure not found: HELIX 5 5 ALA A 161 ARG A 169
1 9
Start residue of secondary structure not found: HELIX 6 6 PRO A 178 ASN A 191
1 14
Start residue of secondary structure not found: HELIX 7 7 ASP A 194 VAL A 225
1 32
Chain information for mtIC_J792_rsr_V5.pdb #2
---
Chain | Description
A | No description available
B | No description available
E | No description available
N | No description available
T | No description available
> select #*/A
3230 atoms, 3292 bonds, 384 residues, 2 models selected
> color sel red
> select #*/B
5267 atoms, 5398 bonds, 648 residues, 2 models selected
> color sel dodger blue
> select #*/E:122-355
3367 atoms, 3413 bonds, 4 pseudobonds, 419 residues, 4 models selected
> color sel teal
> select #*/E:356-643
4642 atoms, 4752 bonds, 576 residues, 2 models selected
> color sel #ACA9A9
> select #*/E:605-623
322 atoms, 330 bonds, 38 residues, 2 models selected
> color sel medium orchid
> select #*/E:643-1230
8954 atoms, 9185 bonds, 2 pseudobonds, 1131 residues, 4 models selected
> color sel spring green
> select #*/E:711-790
888 atoms, 903 bonds, 2 pseudobonds, 115 residues, 4 models selected
> color sel goldenrod
> select #*/E:954-1044
1506 atoms, 1532 bonds, 182 residues, 2 models selected
> color sel plum
> select #*/T
2010 atoms, 2247 bonds, 100 residues, 2 models selected
> color sel blue
> select #*/R
68 atoms, 76 bonds, 3 residues, 1 model selected
> color sel red
> select #*/N
2070 atoms, 2328 bonds, 100 residues, 2 models selected
> color sel cyan
> select clear
> hide cartoons
> hide atoms
> show cartoons
> dssp
> select */N/R/T
Expected an objects specifier or a keyword
> select *:/N/R/T
Expected an objects specifier or a keyword
> select /N/R/T
4148 atoms, 4651 bonds, 203 residues, 2 models selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 4148 atom styles
> style sel stick
Changed 4148 atom styles
> style sel sphere
Changed 4148 atom styles
> style sel ball
Changed 4148 atom styles
> color sel byhetero
> style sel stick
Changed 4148 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 4148 atom styles
> nucleotides sel ladder
> nucleotides sel tube/slab shape box
> nucleotides sel fill
> style nucleic & sel stick
Changed 4148 atom styles
> hide #!2 models
> nucleotides sel & #!1 fill
> style nucleic & sel & #!1 stick
Changed 2108 atom styles
> nucleotides sel & #!1 atoms
> style nucleic & sel & #!1 stick
Changed 2108 atom styles
> show #!2 models
> nucleotides sel atoms
> style nucleic & sel stick
Changed 4148 atom styles
> hide sel cartoons
> select add #1
16879 atoms, 17673 bonds, 3 pseudobonds, 1781 residues, 3 models selected
> select add #2
29598 atoms, 30685 bonds, 6 pseudobonds, 3359 residues, 4 models selected
> select subtract #2
14839 atoms, 15385 bonds, 3 pseudobonds, 1681 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> save D:/IC_Modelling/ChimeraX/IC_PDB_2.cxs includeMaps true
——— End of log from Sat Aug 17 12:19:07 2024 ———
opened ChimeraX session
> open D:/IC_Modelling/PyMOL/DeepEM_highRes_J781.mrc
> D:/IC_Modelling/PyMOL/DeepEM_highRes_J792.mrc
Opened DeepEM_highRes_J781.mrc as #3.1, grid size 384,384,384, pixel 0.751,
shown at level 0.0023, step 2, values float32
Opened DeepEM_highRes_J792.mrc as #3.2, grid size 384,384,384, pixel 0.751,
shown at level 0.00198, step 2, values float32
> hide #!2 models
> show #!2 models
> hide #!2 models
> view #3.1 clip false
> hide #!3.2 target m
> show #!3.2 target m
> hide #!3.1 target m
> show #!1 target m
> hide #!3.2 target m
> hide #!3 models
> rename #3.1 #
> rename #3.1 J781
> rename #3.1 renumber #4 J781
Expected a keyword
> rename #3.1 renumber 4
Expected a keyword
> rename #3.1 renumber #4
Expected a keyword
> rename #3.1 renumber 4
Expected a keyword
> rename #3.1 renumber '4'
Expected a keyword
> hide #!3.1 models
> hide #!3.2 models
> hide #!3 models
> color #/A red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #/A red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color fromcartoons #/A, red
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color fromcartoons #/A red
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color bymodel #/A red
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #1/A#2/A
3230 atoms, 3292 bonds, 384 residues, 2 models selected
> color (#!2 & sel) red
> select #*/A color sel red
Expected a keyword
> select #*/A, color sel red
Expected a keyword
> select #*/A, color red
Expected a keyword
> select #*/A, color
3230 atoms, 3292 bonds, 384 residues, 2 models selected
> select #*/A, red color
Expected a keyword
> select #*/A, color white
Expected a keyword
> select #*/A, color
3230 atoms, 3292 bonds, 384 residues, 2 models selected
> select #*/A
3230 atoms, 3292 bonds, 384 residues, 2 models selected
> color white
> undo
> select #*/A
3230 atoms, 3292 bonds, 384 residues, 2 models selected
> color sel white
> select #*/E:122-355
3367 atoms, 3413 bonds, 4 pseudobonds, 419 residues, 4 models selected
> color sel deepteal
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select add #2
16458 atoms, 17022 bonds, 5 pseudobonds, 1889 residues, 4 models selected
> select add #1
29598 atoms, 30685 bonds, 6 pseudobonds, 3359 residues, 4 models selected
> select subtract #1
14759 atoms, 15300 bonds, 3 pseudobonds, 1678 residues, 2 models selected
> select subtract #2
Nothing selected
> select #*/B
5267 atoms, 5398 bonds, 648 residues, 2 models selected
> color sequential l#007FFF
Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword
> undo
> select #*/B
5267 atoms, 5398 bonds, 648 residues, 2 models selected
> color sequential l#007FFF
Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword
> select clear
> undo
[Repeated 1 time(s)]
> select #*/A
3230 atoms, 3292 bonds, 384 residues, 2 models selected
> color sel red
> select #*/B
5267 atoms, 5398 bonds, 648 residues, 2 models selected
> color sel #007FFF
> select #*/E:122-355
3367 atoms, 3413 bonds, 4 pseudobonds, 419 residues, 4 models selected
> color sel #199999
> select #*/E:356-643
4642 atoms, 4752 bonds, 576 residues, 2 models selected
> color sel #B2B2B2
> select #*/E:588-605
256 atoms, 260 bonds, 36 residues, 2 models selected
> color sel #FF9999
> select #*/E:605-623
322 atoms, 330 bonds, 38 residues, 2 models selected
> color sel #BF00BF
> select #*/E:643-1230
8954 atoms, 9185 bonds, 2 pseudobonds, 1131 residues, 4 models selected
> color sel #00FF7F
> select #*/E:711-790
888 atoms, 903 bonds, 2 pseudobonds, 115 residues, 4 models selected
> color sel #FFB233
> select #*/E:954-1044
1506 atoms, 1532 bonds, 182 residues, 2 models selected
> color sel #FFA5D8
> select #*/T
2010 atoms, 2247 bonds, 100 residues, 2 models selected
> color sel blue
> select #*/R
68 atoms, 76 bonds, 3 residues, 1 model selected
> color sel red
> select #*/N
2070 atoms, 2328 bonds, 100 residues, 2 models selected
> color sel cyan
> select clear
> hide #!2 models
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> show #!1 models
> select add #2
15794 atoms, 16464 bonds, 3 pseudobonds, 1728 residues, 3 models selected
> select subtract #2
1035 atoms, 1164 bonds, 50 residues, 1 model selected
> select add #1
14839 atoms, 15385 bonds, 3 pseudobonds, 1681 residues, 2 models selected
> select subtract #1
Nothing selected
> select #2/E:1-355,x-x
1668 atoms, 1691 bonds, 2 pseudobonds, 208 residues, 2 models selected
> show #!2 models
> hide #!1 models
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> select ~sel & ##selected
13091 atoms, 13609 bonds, 1 pseudobond, 1470 residues, 2 models selected
> select #2/E:1-355
1668 atoms, 1691 bonds, 2 pseudobonds, 208 residues, 2 models selected
> measure rotation #1/E:1004-1018 toModel #2/E:1004-1018
Position of mtIC_J781_rsr_V6.pdb #1 relative to mtIC_J792_rsr_V5.pdb #2
coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
Rotation angle is near zero (0 degrees)
> hide #!2 models
> show #!2 models
> show #!1 models
> measure rotation #1/E:954-1044 toModel #2/E:954-1044
Position of mtIC_J781_rsr_V6.pdb #1 relative to mtIC_J792_rsr_V5.pdb #2
coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
Rotation angle is near zero (0 degrees)
> select add #2
14759 atoms, 15300 bonds, 3 pseudobonds, 1678 residues, 2 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> nucleotides atoms
> style nucleic stick
Changed 4148 atom styles
> hide cartoons
> hide atoms
> show cartoons
> color bypolymer
> undo
> color bychain
> undo
> color byhetero
> coulombic
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
mtIC_J781_rsr_V6.pdb #1/E HIS 597
mtIC_J781_rsr_V6.pdb #1/E ARG 598
mtIC_J792_rsr_V5.pdb #2/E LYS 595
mtIC_J792_rsr_V5.pdb #2/E HIS 597
mtIC_J792_rsr_V5.pdb #2/E ARG 598
Using Amber 20 recommended default charges and atom types for standard
residues
[Repeated 1 time(s)]Coulombic values for mtIC_J781_rsr_V6.pdb_A SES surface
#1.2: minimum, -17.98, mean 2.39, maximum 15.61
Coulombic values for mtIC_J781_rsr_V6.pdb_B SES surface #1.3: minimum, -14.83,
mean 0.88, maximum 17.14
Coulombic values for mtIC_J781_rsr_V6.pdb_E SES surface #1.4: minimum, -15.87,
mean 1.09, maximum 21.13
Coulombic values for mtIC_J781_rsr_V6.pdb_N SES surface #1.5: minimum, -25.86,
mean -11.61, maximum -2.38
Coulombic values for mtIC_J781_rsr_V6.pdb_R SES surface #1.6: minimum, -19.17,
mean -5.82, maximum 0.41
Coulombic values for mtIC_J781_rsr_V6.pdb_T SES surface #1.7: minimum, -22.23,
mean -11.62, maximum -1.70
Coulombic values for mtIC_J792_rsr_V5.pdb_A SES surface #2.2: minimum, -13.73,
mean 2.82, maximum 20.06
Coulombic values for mtIC_J792_rsr_V5.pdb_B SES surface #2.3: minimum, -12.13,
mean 0.84, maximum 17.00
Coulombic values for mtIC_J792_rsr_V5.pdb_E SES surface #2.4: minimum, -17.06,
mean 1.06, maximum 18.18
Coulombic values for mtIC_J792_rsr_V5.pdb_N SES surface #2.5: minimum, -27.89,
mean -11.44, maximum -2.22
Coulombic values for mtIC_J792_rsr_V5.pdb_T SES surface #2.6: minimum, -22.31,
mean -11.52, maximum -1.41
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!2 models
> select #1/A/E
10099 atoms, 10325 bonds, 3 pseudobonds, 1254 residues, 2 models selected
> hide sel
> hide cartoons sel
Expected ',' or a keyword
> hide cartoon, sel
Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'
> hide cartoons
> select
29598 atoms, 30685 bonds, 6 pseudobonds, 3359 residues, 9 models selected
> select subtract #3.2
29598 atoms, 30685 bonds, 6 pseudobonds, 3359 residues, 18 models selected
> select add #3
29598 atoms, 30685 bonds, 6 pseudobonds, 3359 residues, 20 models selected
> select subtract #3.1
29598 atoms, 30685 bonds, 6 pseudobonds, 3359 residues, 18 models selected
> select add #3
29598 atoms, 30685 bonds, 6 pseudobonds, 3359 residues, 20 models selected
> select subtract #3
29598 atoms, 30685 bonds, 6 pseudobonds, 3359 residues, 15 models selected
> select subtract #2
14839 atoms, 15385 bonds, 3 pseudobonds, 1681 residues, 13 models selected
> select subtract #1
6 models selected
> select #1/A/E
10099 atoms, 10325 bonds, 3 pseudobonds, 1254 residues, 2 models selected
> hide sel surfaces
> undo
[Repeated 6 time(s)]
> show sel & #!1 surfaces
> mlp sel & #!1
Map values for surface "mtIC_J781_rsr_V6.pdb_A SES surface": minimum -27.69,
mean -3.617, maximum 24.22
Map values for surface "mtIC_J781_rsr_V6.pdb_B SES surface": minimum -26.68,
mean -3.654, maximum 25.28
Map values for surface "mtIC_J781_rsr_V6.pdb_E SES surface": minimum -28.26,
mean -3.424, maximum 23.51
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel & #!1 surfaces
> undo
[Repeated 1 time(s)]
> show sel & #!1 surfaces
> select subtract #1
14759 atoms, 15300 bonds, 3 pseudobonds, 1678 residues, 18 models selected
> select add #1
29598 atoms, 30685 bonds, 6 pseudobonds, 3359 residues, 14 models selected
> select clear
> select add #1
14839 atoms, 15385 bonds, 3 pseudobonds, 1681 residues, 2 models selected
> select #1/A/E
10099 atoms, 10325 bonds, 3 pseudobonds, 1254 residues, 2 models selected
> hide sel surfaces
> select clear
> mlp #!1
Map values for surface "mtIC_J781_rsr_V6.pdb_A SES surface": minimum -27.69,
mean -3.617, maximum 24.22
Map values for surface "mtIC_J781_rsr_V6.pdb_B SES surface": minimum -26.68,
mean -3.654, maximum 25.28
Map values for surface "mtIC_J781_rsr_V6.pdb_E SES surface": minimum -28.26,
mean -3.424, maximum 23.51
To also show corresponding color key, enter the above mlp command and add key
true
> select ~sel & ##selected
Nothing selected
> select #1/N/R/T
2108 atoms, 2363 bonds, 103 residues, 1 model selected
> hide sel surfaces
> select ~sel & ##selected
12731 atoms, 13022 bonds, 3 pseudobonds, 1578 residues, 2 models selected
> select #1/E
8484 atoms, 8679 bonds, 3 pseudobonds, 1062 residues, 2 models selected
> hide sel surfaces
> ui tool show "Color Key"
> ui mousemode right "color key"
> ui mousemode right translate
> mlp sel
Map values for surface "mtIC_J781_rsr_V6.pdb_E SES surface": minimum -28.26,
mean -3.424, maximum 23.51
To also show corresponding color key, enter the above mlp command and add key
true
> ui tool show "Color Actions"
> ui tool show "Render/Select by Attribute"
> select add #1
14839 atoms, 15385 bonds, 3 pseudobonds, 1681 residues, 3 models selected
> rename #3.2 J792
> rename #3 ""
> rename #3.1 id #3
> rename #3.1 id #4
Cannot place models under an overlay models (#4)
> close #4
> rename #3.1 id #4
> rename #3.2 id #3
> rename #3 id #5
> rename #5.2 id #3
> show #5 models
> close #5
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide sel surfaces
> show sel atoms
> show #!2 models
> select add #2
29598 atoms, 30685 bonds, 6 pseudobonds, 3359 residues, 10 models selected
> hide sel surfaces
> hide sel atoms
> show sel cartoons
> hide #!2 models
> hide #!1 models
> select subtract #1
14759 atoms, 15300 bonds, 3 pseudobonds, 1678 residues, 13 models selected
> select subtract #2
5 models selected
> show #!1 models
> show #!4 models
> volume #4 step 1
> volume #4 level 0.07357
> volume #4 level 0.05773
> volume #4 level 0.02606
> volume #4 level 0.002296
> volume #4 level 0.01814
> volume #4 style mesh
> volume #4 style image
> volume #4 style surface
> volume #4 style image region 0,0,191,383,383,191 step 1 showOutlineBox true
> volume #4 region 0,0,0,383,383,383 step 1
> volume #4 style surface region 0,0,0,383,383,383 step 1
> volume #!4 showOutlineBox false
> volume #!4 showOutlineBox true
> volume #!4 showOutlineBox false
> transparency #1.2-7#4.1 50
> vop gaussian #4 sdev 2.25
Opened J781 gaussian as #5, grid size 384,384,384, pixel 0.751, shown at step
1, values float32
> close #5
> volume #4 change image level -0.0001477,0 level 0.002205,0.8 level 2.108,1
> surface dust #4 size 7.51
> color zone #4 near #1 distance 4.51
> select #*/E:122-355
3367 atoms, 3413 bonds, 4 pseudobonds, 419 residues, 4 models selected
> color sel #199999
> select #*/E:356-643
4642 atoms, 4752 bonds, 576 residues, 2 models selected
> color sel #B2B2B2
> select #*/E:588-605
256 atoms, 260 bonds, 36 residues, 2 models selected
> color sel #FF9999
> select #*/E:605-623
322 atoms, 330 bonds, 38 residues, 2 models selected
> color sel #BF00BF
> select #*/E:643-1230
8954 atoms, 9185 bonds, 2 pseudobonds, 1131 residues, 4 models selected
> color sel #00FF7F
> select #*/E:711-790
888 atoms, 903 bonds, 2 pseudobonds, 115 residues, 4 models selected
> color sel #FFB233
> select #*/E:954-1044
1506 atoms, 1532 bonds, 182 residues, 2 models selected
> color sel #FFA5D8
> select #*/T
2010 atoms, 2247 bonds, 100 residues, 2 models selected
> color sel blue
> select #*/R
68 atoms, 76 bonds, 3 residues, 1 model selected
> color sel red
> select #*/N
2070 atoms, 2328 bonds, 100 residues, 2 models selected
> color sel cyan
> select #*/A
3230 atoms, 3292 bonds, 384 residues, 2 models selected
> color sel red
> select #*/B
5267 atoms, 5398 bonds, 648 residues, 2 models selected
> color sel #007FFF
> select clear
> color zone #4 near #1 distance 4.51
> transparency #1.2-7#4.1 0
> transparency #1.2-7#4.1 50
> volume #!4 style mesh
> hide #!1 models
> volume #!4 hide
> volume show
> save D:/IC_Modelling/ChimeraX/IC_PDB_2.cxs includeMaps true
——— End of log from Sat Aug 17 13:00:45 2024 ———
opened ChimeraX session
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ~##num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ~##num_residues #3d60ffff; transparency 50
> mousemode rightMode clip
> mousemode alt rightMode "contour level"
> mousemode alt leftMode "translate selected models"
> mousemode shift leftMode "rotate selected models"
> mousemode alt control leftMode "pick blobs"
> alias cofron cofr centerofview showpivot 7,0.25
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 volume unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; volume zone ~##num_residues nearAtoms sel
> minimalBounds true range 15; close #10000
> alias map_unsphere volume unzone ~##num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ~##num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ~##num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> alias helix setattr $1 res is_helix true
> alias strand setattr $1 res is_strand true
> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false
> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode ~/Desktop/rock_movie.mp4; stop
> alias open_vseries "open browse vseries true"
> buttonpanel Shortcuts rows 3 columns 5
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr
> radius 1"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
> buttonpanel Shortcuts add reset_mouse command "mousemode alt right contour ;
> mousemode right clip ; mousemode alt left 'translate selected models' ;
> mousemode shift left 'rotate selected models' ; mousemode alt control left
> 'pick blobs'; help https://github.com/olibclarke/chimerax-
> trimmings/blob/main/default_mousemodes.md"
> buttonpanel Shortcuts add previous_model command prevmodel
> buttonpanel Shortcuts add next_model command nextmodel
> runscript C:\Users\kherb\Documents\ChimeraX\chimerax_startup.py
FYI: command is replacing existing command: "nextmodel"
FYI: command is replacing existing command: "prevmodel"
> save D:/IC_Modelling/ChimeraX/IC_PDB_2.cxs includeMaps true
——— End of log from Sun Aug 18 13:15:51 2024 ———
opened ChimeraX session
> buttonpanels
Unknown command: buttonpanels
> buttonpanel
Missing or invalid "title" argument: Expected a text string
> runscript C:\Users\kherb\Documents\ChimeraX\chimerax_startup.py
FYI: command is replacing existing command: "nextmodel"
FYI: command is replacing existing command: "prevmodel"
> save D:/IC_Modelling/ChimeraX/IC_PDB_2.cxs includeMaps true
——— End of log from Sun Aug 18 16:48:10 2024 ———
opened ChimeraX session
> color_ic
> buttonpanel Shortcuts rows 2 columns 4
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add cootmode_mesh command cootmode_mesh
> buttonpanel Shortcuts add previous_model command prevmodel
> buttonpanel Shortcuts add next_model command nextmodel
> runscript C:\Users\kherb\Documents\ChimeraX\chimerax_startup.py
FYI: command is replacing existing command: "nextmodel"
FYI: command is replacing existing command: "prevmodel"
> cootmode
> surface cap false
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> hide #!4 models
> show #!1 models
> volume #4 style mesh
> volume #3 style mesh
> surface style mesh
> cootmode_mesh
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> cootmode
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> cootmode_mesh
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> set bgColor white
> set bgColor #ffffff00
> surface cap false
> surface style solid
> lighting soft
> graphics silhouettes true
> style cartoon;
Expected a keyword
> set bgColor white
> surface cap false
> surface style solid
> lighting soft
> graphics silhouettes true
> style cartoon; ~rib
Expected a keyword
> set bgColor white
> surface cap true
[Repeated 1 time(s)]
> surface style solid
> lighting soft
> graphics silhouettes true
> style cartoon;
Expected a keyword
> set bgColor white
> surface cap false
[Repeated 1 time(s)]
> surface style solid
> lighting soft
> graphics silhouettes true
> style cartoon;
Expected a keyword
> show #!1 cartoons
> hide #!1 atoms
> set bgColor white
> surface cap true
[Repeated 1 time(s)]
> surface style solid
> lighting soft
> graphics silhouettes true
> style cartoon; view; hide atoms, show cartoon
Expected a keyword
> set bgColor white
> surface cap true
> surface style solid
> lighting soft
> graphics silhouettes true
> view
> hide atoms, show cartoon
Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'
> set bgColor white
> surface cap true
> surface style solid
> lighting soft
> graphics silhouettes true
> view
> hide atoms, show cartoons
Missing or invalid "what" argument: Should be one of 'atoms', 'bonds',
'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces'
> set bgColor white
> surface cap true
> surface style solid
> lighting soft
> graphics silhouettes true
> view
> hide atoms
> show cartoons
> set bgColor white
> surface cap true
> surface style solid
> lighting soft
> graphics silhouettes true
> view
> hide atoms
> show cartoons
> default_mol_display
> cootmode
> set bgColor transparent
> surface cap false
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> cootmode_mesh
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> default_mol_display
> ~display
> ribbon
> rainbow chains palette rdylbu-5
> lighting soft
> hide volumes;
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ~display
> ribbon
> rainbow chains palette rdylbu-5
> lighting soft
> hide map
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ~display
> ribbon
> rainbow chains palette rdylbu-5
> lighting soft
> hide volume
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #!4 models
> show #!4 models
> ~display
> ribbon
> rainbow chains palette rdylbu-5
> lighting soft
> volume hide
> ~display
> ribbon
> rainbow chains palette rdylbu-5
> lighting soft
> volume hide
> set bgColor white
> set bgColor #ffffff00
> ~display
> ribbon
> rainbow chains palette rdylbu-5
> lighting soft
> volume hide
> set bgColor white
> surface cap false
> ~display
> ribbon
> rainbow chains palette rdylbu-5
> lighting soft
> volume hide
> set bgColor white
> surface cap true
[Repeated 1 time(s)]
> ~display
> ribbon
> rainbow chains palette rdylbu-5
> lighting soft
> volume hide
> set bgColor white
> surface cap false
[Repeated 1 time(s)]
> cofr
Center of rotation: 143 125.07 143.98 center of view
> cofr centerOfView
> unclip
Unknown command: unclip
> clip 0
Expected a keyword
> clip off
> graphics silhouettes true
> cootmode_mesh
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> cootmode
> set bgColor transparent
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> cootmode_mesh
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> default_mol_display
> hide #!3 models
> hide #!4 models
> set bgColor white
> set bgColor #ffffff00
> clip off
> graphics silhouettes true
> set bgColor black
> set bgColor transparent
> surface cap false
> surface style mesh
> lighting flat
> graphics silhouettes false
> style stick
Changed 29598 atom styles
> ~ribbon
> color ##num_residues gold
> color byhetero
> display
> ~display @H*
> style ions ball
Changed 0 atom styles
> style solvent ball
Changed 0 atom styles
> size ballScale 0.2
Changed 2 ball scales
> size stickRadius 0.07
Changed 30685 bond radii
> transparency 50
> cofr centerOfView
> clip near -10 far 10 position cofr
> color ~##num_residues cornflower blue
> cootmode_mesh
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> undo
[Repeated 9 time(s)]
> default_mol_display
> lighting soft
> view
> set bgColor white
> set bgColor #ffffff00
> hide #!3 models
> hide #!4 models
> graphics silhouettes true
> set bgColor black
> set bgColor transparent
> surface cap false
> surface style mesh
> lighting flat
> graphics silhouettes false
> style stick
Changed 29598 atom styles
> ~ribbon
> color ##num_residues gold
> color byhetero
> display
> ~display @H*
> style ions ball
Changed 0 atom styles
> style solvent ball
Changed 0 atom styles
> size ballScale 0.2
Changed 2 ball scales
> size stickRadius 0.07
Changed 30685 bond radii
> cofr centerOfView
> clip near -10 far 10 position cofr
> color ~##num_residues #3d60ffff
> transparency 50
> cootmode_mesh
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> cootmode
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> cootmode_mesh
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> cootmode
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> cootmode_mesh
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> cootmode
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> cootmode_mesh
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> default_mol_display
> save D:/IC_Modelling/ChimeraX/IC_PDB_2.cxs includeMaps true
——— End of log from Sun Aug 18 19:51:27 2024 ———
opened ChimeraX session
> default_mol_display
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> alias cootmode set bgColor black; surface cap false; surface style mesh;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07;cofr centerofview;
> clip near -10 far 10 position cofr; color ~##num_residues #3d60ffff;
> transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft; volume hide; set bgColor white; cofr centerofview; clip off;
> graphics silhouettes true
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> alias helix setattr $1 res is_helix true
> alias strand setattr $1 res is_strand true
> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false
> alias color_ic color #*/E:122-355 #199999; color #*/E:356-643 #B2B2B2; color
> #*/E:588-605 #FF9999; color #*/E:605-623 #BF00BF; color #*/E:643-1230
> #00FF7F; color #*/E:711-790 #FFB233; color #*/E:954-1044 #FFA5D8; color #*/T
> blue; color #*/R red; color #*/N cyan; color #*/A red; color #*/B #007FFF
> buttonpanel Shortcuts rows 2 columns 4
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add previous_model command prevmodel
> buttonpanel Shortcuts add next_model command nextmodel
> runscript C:\Users\kherb\Documents\ChimeraX\chimerax_startup.py
FYI: command is replacing existing command: "nextmodel"
FYI: command is replacing existing command: "prevmodel"
> default_mol_display
> set bgColor #ffffff00
> cootmode
> set bgColor transparent
Changed 29598 atom styles
Changed 0 atom styles
[Repeated 1 time(s)]Changed 2 ball scales
Changed 30685 bond radii
> default_mol_display
> set bgColor #ffffff00
> ca_trace #1/N/R/T
Changed 2108 atom styles
Changed 30685 bond radii
Changed 6 pseudobond radii
> select #1/N/R/T
2108 atoms, 2363 bonds, 97 pseudobonds, 103 residues, 2 models selected
> show sel cartoons
> cartoon style (#!1 & sel & coil) xsection oval
> cartoon style (#!1 & sel) xsection barbell modeHelix default
> cartoon style (#!1 & sel) xsection oval modeHelix default
> cartoon style (#!1 & sel) modeHelix tube sides 20
> undo
> ~display $1
> hide $1
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> color ~E:122-355 #199999
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> ~colordef /E:122-355 #199999
> color delete /E:122-355 #199999
Expected fewer arguments
> ~colordef #/E:122-355 #199999
> color delete #/E:122-355 #199999
Expected fewer arguments
> color #/E:122-355 #199999
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #*/E:122-355 #199999
> show #!2 models
> hide #!1 models
> show #!1 models
> color #*/E:122-355 #199999
> hide #!2 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!1 models
> color #*/E:122-355 #199999
> select up
14839 atoms, 15385 bonds, 1681 residues, 4 models selected
> select up
14839 atoms, 15385 bonds, 3 pseudobonds, 1681 residues, 8 models selected
> select up
14839 atoms, 15385 bonds, 3 pseudobonds, 1681 residues, 8 models selected
> select up
29598 atoms, 30685 bonds, 3 pseudobonds, 3359 residues, 13 models selected
> select up
29598 atoms, 30685 bonds, 6 pseudobonds, 3359 residues, 19 models selected
> select down
29598 atoms, 30685 bonds, 3 pseudobonds, 3359 residues, 18 models selected
> select down
14839 atoms, 15385 bonds, 3 pseudobonds, 1681 residues, 13 models selected
> select down
3 pseudobonds, 7 models selected
> ~colordef #/E:122-355 #199999
> color delete #/E:122-355 #199999
Expected fewer arguments
> color #/E:122-355 #199999
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color $1/E:122-355 #199999
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color ~$1/E:122-355 #199999
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color $1/E:122-355 #199999
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> ~ribbon $1
> cartoon hide $1
Expected an atoms specifier or a keyword
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> ~ribbon $1
> cartoon hide $1
Expected an atoms specifier or a keyword
> hide #!2 models
> show #!2 models
> ~ribbon $1
> cartoon hide $1
Expected an atoms specifier or a keyword
> $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp @P&nucleic&$1; style $1
> stick; size stickradius 0.1; size pseudobondradius 0.1
Expected fewer arguments
> ~display
> ribbon
> rainbow chains palette rdylbu-5
> lighting soft
> volume hide
> set bgColor white
> cofr centerOfView
> clip off
> graphics silhouettes true
> alias color_ic color $1/E:122-355 #199999; color $1/E:356-643 #B2B2B2; color
> $1/E:588-605 #FF9999; color $1/E:605-623 #BF00BF; color $1/E:643-1230
> #00FF7F; color $1/E:711-790 #FFB233; color $1/E:954-1044 #FFA5D8; color $1/T
> blue; color $1/R red; color $1/N cyan; color $1/A red; color $1/B #007FFF
> color_ic #1
>
Missing or invalid first argument: Expected a text string
> color_ic #2
> hide #!2 models
> hide #!1 models
> show #!1 models
> select add #1
14839 atoms, 15385 bonds, 3 pseudobonds, 1681 residues, 2 models selected
> select subtract #1
6 models selected
> nucrib
Unknown command: nucrib
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6
> #1
Expected fewer arguments
> nucrib
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> select #1/N/R/T
2108 atoms, 2363 bonds, 103 residues, 1 model selected
> show sel atoms
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> alias cootmode set bgColor black; surface cap false; surface style mesh;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07;cofr centerofview;
> clip near -10 far 10 position cofr; color ~##num_residues #3d60ffff;
> transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft; volume hide; set bgColor white; cofr centerofview; clip off;
> graphics silhouettes true
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> alias helix setattr $1 res is_helix true
> alias strand setattr $1 res is_strand true
> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false
> alias color_ic color $1/E:122-355 #199999; color $1/E:356-643 #B2B2B2; color
> $1/E:588-605 #FF9999; color $1/E:605-623 #BF00BF; color $1/E:643-1230
> #00FF7F; color $1/E:711-790 #FFB233; color $1/E:954-1044 #FFA5D8; color $1/T
> blue; color $1/R red; color $1/N cyan; color $1/A red; color $1/B #007FFF
> alias color_ec color $1/E:122-355 #199999; color $1/E:356-643 #B2B2B2; color
> $1/E:588-605 #FF9999; color $1/E:605-623 #BF00BF; color $1/E:643-1230
> #00FF7F; color $1/E:711-790 #FFB233; color $1/E:954-1044 #FFA5D8; color $1/T
> blue; color $1/R red; color $1/N cyan; color $1/A/B #B24C66
> buttonpanel Shortcuts rows 2 columns 4
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add previous_model command prevmodel
> buttonpanel Shortcuts add next_model command nextmodel
> runscript C:\Users\kherb\Documents\ChimeraX\chimerax_startup.py
FYI: command is replacing existing command: "nextmodel"
FYI: command is replacing existing command: "prevmodel"
> save D:/IC_Modelling/ChimeraX/IC_PDB_2.cxs includeMaps true
> open D:/IC_Modelling/Models/Open/mtIC_J781_rsr_V6.pdb
Chain information for mtIC_J781_rsr_V6.pdb #5
---
Chain | Description
A | No description available
B | No description available
E | No description available
N | No description available
R | No description available
T | No description available
> hide #!1 models
> default_mol_display
> color_ic #6
> color_ic #5
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> close #1
> rename #5 id #1
> save D:/IC_Modelling/ChimeraX/IC_PDB_2.cxs includeMaps true
——— End of log from Sun Aug 18 23:04:58 2024 ———
opened ChimeraX session
> camera ortho
> cofr centerOfView
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
> alias cootmode set bgColor black; surface cap false; surface style mesh;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07;cofr centerofview;
> clip near -10 far 10 position cofr; color ~##num_residues #3d60ffff;
> transparency 50
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft; volume hide; set bgColor white; cofr centerofview; clip off;
> graphics silhouettes true
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias selbetween ks ri
> alias helix setattr $1 res is_helix true
> alias strand setattr $1 res is_strand true
> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false
> alias color_ic color $1/E:122-355 #199999; color $1/E:356-643 #B2B2B2; color
> $1/E:588-605 #FF9999; color $1/E:605-623 #BF00BF; color $1/E:643-1230
> #00FF7F; color $1/E:711-790 #FFB233; color $1/E:954-1044 #FFA5D8; color $1/T
> blue; color $1/R red; color $1/N cyan; color $1/A red; color $1/B #007FFF
> alias color_ec color $1/E:122-355 #199999; color $1/E:356-643 #B2B2B2; color
> $1/E:588-605 #FF9999; color $1/E:605-623 #BF00BF; color $1/E:643-1230
> #00FF7F; color $1/E:711-790 #FFB233; color $1/E:954-1044 #FFA5D8; color $1/T
> blue; color $1/R red; color $1/N cyan; color $1/A/B #B24C66
> buttonpanel Shortcuts rows 2 columns 4
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add previous_model command prevmodel
> buttonpanel Shortcuts add next_model command nextmodel
> runscript C:\Users\kherb\Documents\ChimeraX\chimerax_startup.py
FYI: command is replacing existing command: "nextmodel"
FYI: command is replacing existing command: "prevmodel"
> save D:/IC_Modelling/ChimeraX/IC_PDB_2.cxs includeMaps true
> nubric
Unknown command: nubric
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6
> nucrib
> select #1/N/R/T
2108 atoms, 2364 bonds, 103 residues, 1 model selected
> show sel atoms
> nucleotides sel ladder
> color sel bynucleotide
> undo
> nucleotides sel tube/slab shape ellipsoid
> nucleotides sel tube/slab shape box
> nucleotides sel fill
> style nucleic & sel stick
Changed 2108 atom styles
> nucleotides sel ladder
> define axis
Axis 'root #/axis' centered at [144.89054199 152.99878053 127.5712724 ] with
direction [-0.11302511 -0.42209342 0.899479 ], radius 26.8925, and length
139.347
> select #0:994, sel #0:1016
Nothing selected
> select #0:994, sel #1:1016
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
124 atoms, 124 bonds, 14 residues, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> undo
[Repeated 9 time(s)]
> close #5
> hide #!1 models
> show #!1 models
> define axis
Axis 'root #/axis' centered at [144.89054199 152.99878053 127.5712724 ] with
direction [-0.11302511 -0.42209342 0.899479 ], radius 26.8925, and length
139.347
> select #5
1 model selected
> ~select #5
Nothing selected
> show #!2 models
> select #2/E:1010
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/E:1009
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #2/E:1011
18 atoms, 16 bonds, 2 residues, 2 models selected
No items chosen in table
> close #5
> select #1/E:999
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/E:1001
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 6 residues
> select #1/E:998
7 atoms, 6 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
14832 atoms, 15380 bonds, 3 pseudobonds, 1680 residues, 2 models selected
> select up
14834 atoms, 15380 bonds, 3 pseudobonds, 1681 residues, 2 models selected
> select down
14832 atoms, 15380 bonds, 3 pseudobonds, 1680 residues, 2 models selected
> select #1:994, sel #1:1016
16 atoms, 14 bonds, 2 residues, 1 model selected
value: None default: None
> define axis sel name axis
Axis 'mtIC_J781_rsr_V6.pdb #1/axis' centered at [138.21345944 126.58902823
166.74979034] with direction [ 0.46219199 -0.80600302 -0.36978061], radius
1.62632, and length 22.0063
> select #1:994, sel #2:1016
16 atoms, 14 bonds, 2 residues, 2 models selected
value: None default: None
> define axis sel name axis
Axis 'root #/axis' centered at [143.18724721 129.16103936 167.14252142] with
direction [-0.83845783 0.46457166 0.28488883], radius 1.82509, and length
24.2111
> rename #1.2 id #6
> angle #5 #6
Angle between axis #5 and axis #6: 29.851
> measure rotation #1/E:1004-1018 toModel #2/E:1004-1018
Position of mtIC_J781_rsr_V6.pdb #1 relative to mtIC_J792_rsr_V5.pdb #2
coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
Rotation angle is near zero (0 degrees)
> hide #5 models
> close #5-6
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select add #2
14766 atoms, 15306 bonds, 3 pseudobonds, 1679 residues, 4 models selected
> select add #1
29598 atoms, 30686 bonds, 6 pseudobonds, 3359 residues, 9 models selected
> select subtract #2
14839 atoms, 15386 bonds, 3 pseudobonds, 1681 residues, 7 models selected
> select subtract #1
Nothing selected
> hide #!2 models
> hide #!1 models
> select add #1
14839 atoms, 15386 bonds, 3 pseudobonds, 1681 residues, 2 models selected
> show #!1 models
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select
Missing or invalid "atoms" argument: empty atom specifier
> interfaces
38 buried areas: #1/E #2/E 27218, #2/B #1/B 8875, #1/A #2/A 6435, #1/N #2/N
4796, #1/T #2/T 4472, #2/N #2/T 2047, #1/N #1/T 1889, #2/N #1/T 1876, #1/A
#2/T 1854, #1/N #2/T 1694, #2/E #1/T 1473, #1/A #1/N 1386, #1/E #2/A 1371,
#1/A #1/T 1318, #1/E #1/T 1288, #1/A #2/N 1261, #2/E #2/T 1111, #2/A #2/N
1078, #1/E #2/B 988, #2/B #1/N 978, #2/A #1/N 958, #1/E #2/N 944, #2/E #2/B
915, #1/E #1/A 889, #1/E #1/B 879, #2/E #1/B 836, #2/A #2/T 824, #2/E #2/A
817, #1/B #1/N 756, #1/E #1/N 731, #2/B #2/N 719, #1/E #2/T 714, #2/E #2/N
557, #1/B #2/N 554, #2/E #1/N 468, #2/E #1/R 424, #2/A #1/T 386, #1/E #1/R 314
> hide #!1 models
> show #!1 models
> select ~sel & ##selected
Nothing selected
> interfaces #1
9 buried areas: N T 1889, A N 1386, A T 1318, E T 1288, E A 889, E B 879, B N
756, E N 731, E R 314
> lighting soft
> lighting simple
> lighting soft
> lighting gentle
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting gentle
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting gentle
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting gentle
> help help:user/preferences.html#startup
> select add #1
14839 atoms, 15386 bonds, 3 pseudobonds, 1681 residues, 2 models selected
> hide #!1 models
> show #!1 models
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 14771 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select subtract #1
Nothing selected
> show #!2 models
> hide #!1 models
> show #!1 models
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> default_mol_display
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (single color)"
Using preset: Initial Styles / Space-Filling (Single Color)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 29598 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> default_mol_display
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> hide #!1 models
> color_ic #1
> color_ic #2
> show #!1 models
> hide #!2 models
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> hide #!1 models
> hide #!4 models
> show #!1 models
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" interactive
Using preset: Overall Look / Interactive
> set bgColor transparent
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
> set bgColor #ffffff00
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> save D:/IC_Modelling/ChimeraX/IC_PDB_2.cxs includeMaps true
——— End of log from Sun Aug 18 23:50:44 2024 ———
opened ChimeraX session
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!2 models
> volume #3 step 1
> hide #!2 surfaces
> volume #3 level 0.009555
> surface dust #3 size 7.51
> volume #3 style surface
> volume #3 color #74747433
> volume #3 color #ffffff33
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
——— End of log from Tue Aug 20 14:15:31 2024 ———
opened ChimeraX session
> open C:/Users/krh021/Desktop/ChimeraX/6ERP.pdb
6ERP.pdb title:
Structure of the human mitochondrial transcription initiation complex At the
LSP promoter [more info...]
Chain information for 6ERP.pdb #5
---
Chain | Description | UniProt
A | mtrpol | TFAM_HUMAN 43-245
B | mtrpol | RPOM_HUMAN 105-1230
E | template DNA | RPOM_HUMAN 105-1230
N | No description available |
T | No description available |
> open C:/Users/krh021/Desktop/ChimeraX/6erp_map2.mrc
Opened 6erp_map2.mrc as #6, grid size 117,115,117, pixel 1.24,1.23,1.23, shown
at level 0.126, step 1, values float32
> hide #!5 models
> show #!5 models
> color #*/E:122-355 #199999
> color #*/E:356-643 #B2B2B2
> color #*/E:588-605 #FF9999
> color #*/E:605-623 #BF00BF
> color #*/E:643-1230 #00FF7F
> color #*/E:711-790 #FFB233
> color #*/E:954-1044 #FFA5D8
> color #*/T blue
> color #*/R red
> color #*/N cyan
> color #*/A red
> color #*/B #007FFF
> select add #6
2 models selected
> select add #5
13849 atoms, 14342 bonds, 8 pseudobonds, 1582 residues, 4 models selected
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #5,1,0,0,174.51,0,1,0,219.26,0,0,1,234.8,#6,1,0,0,174.51,0,1,0,219.26,0,0,1,234.8
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.74171,0.6707,0.0039138,156.95,-0.52753,0.58696,-0.61416,202.12,-0.41422,0.45347,0.78917,213.17,#6,0.74171,0.6707,0.0039138,156.95,-0.52753,0.58696,-0.61416,202.12,-0.41422,0.45347,0.78917,213.17
> view matrix models
> #5,0.052253,0.76883,-0.63731,125.26,-0.62088,-0.47484,-0.62373,228.73,-0.78216,0.42829,0.45254,198.48,#6,0.052253,0.76883,-0.63731,125.26,-0.62088,-0.47484,-0.62373,228.73,-0.78216,0.42829,0.45254,198.48
> view matrix models
> #5,-0.34086,-0.27379,-0.89936,139.82,0.17669,-0.95826,0.22475,279.48,-0.92336,-0.082302,0.37501,207.92,#6,-0.34086,-0.27379,-0.89936,139.82,0.17669,-0.95826,0.22475,279.48,-0.92336,-0.082302,0.37501,207.92
> view matrix models
> #5,-0.32975,-0.62258,-0.70969,156.98,0.60085,-0.71823,0.35089,279.69,-0.72818,-0.31072,0.61091,224.39,#6,-0.32975,-0.62258,-0.70969,156.98,0.60085,-0.71823,0.35089,279.69,-0.72818,-0.31072,0.61091,224.39
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.32975,-0.62258,-0.70969,100.44,0.60085,-0.71823,0.35089,210.07,-0.72818,-0.31072,0.61091,152.49,#6,-0.32975,-0.62258,-0.70969,100.44,0.60085,-0.71823,0.35089,210.07,-0.72818,-0.31072,0.61091,152.49
> ui mousemode right select
> select subtract #5
2 models selected
> select subtract #6
Nothing selected
> hide #!5 models
> hide #!2 models
> show #!5 models
> hide #!5 atoms
> show #!5 cartoons
> show #!6 models
> volume #6 level 0.007
> volume #6 level 0.04215
> volume #6 level 0.05911
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
——— End of log from Tue Aug 20 14:24:19 2024 ———
opened ChimeraX session
> volume #6 level 0.0753
> volume #6
> volume #6 color white
> transparency #6.1 50
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> mmaker #5 to #2
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 mtIC_J792_rsr_V5.pdb, chain E (#2) with 6ERP.pdb, chain E (#5),
sequence alignment score = 5200.2
RMSD between 882 pruned atom pairs is 1.212 angstroms; (across all 1011 pairs:
1.552)
> ui tool show "Fit in Map"
> fitmap #6 inMap #3
Fit map 6erp_map2.mrc in map J792 using 40915 points
correlation = 0.557, correlation about mean = 0.1467, overlap = 841.9
steps = 396, shift = 37.9, angle = 16.1 degrees
Position of 6erp_map2.mrc (#6) relative to J792 (#3) coordinates:
Matrix rotation and translation
-0.06604760 -0.61996546 -0.78184432 124.70104816
0.67589120 -0.60421348 0.42201560 185.14116274
-0.73403597 -0.50056858 0.45893605 159.57334154
Axis -0.57971541 -0.03004087 0.81426506
Axis point 62.33882725 142.64935529 0.00000000
Rotation angle (degrees) 127.27653094
Shift along axis 52.08207594
> hide #!2 models
> color #6 white models
> show #!2 models
> hide #!5 models
> show #!3 models
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
> show #!6 models
> show #!5 models
> hide #!2 models
> hide #!3 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> show #!5 models
> save test.png width 3000 transparentBackground true
> color zone #6 near #5 distance 7.42
> show #!2 models
> hide #!6 models
> hide #!5 models
> show #!3 models
> color zone #3 near #2 distance 4.51
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!6 models
> hide #!3 models
> hide #!2 models
> graphics silhouettes false
> graphics silhouettes true
> save test.png width 3000 transparentBackground true
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> save test2.png width 3000 transparentBackground true
> surface dust #3 size 7.51
> volume #3 level 0.04473
> volume #3 level 0.02519
> volume #3 level 0.02128
> volume #3 level 0.01737
> show #!6 models
> hide #!3 models
> volume #6 level 0.04405
> surface dust #6 size 12.4
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> show #!5 models
> color zone #6 near #5 distance 7.42
> color zone #6 near #5 distance 73
> color zone #6 near #5 distance 10
> color zone #6 near #5 distance 20
> select ~sel & ##selected
Nothing selected
> color zone #6 near #5 distance 18
> color zone #6 near #5 distance 15
> color zone #6 near #5 distance 12
> 5
Unknown command: 5
> color zone #6 near #5 distance 15
> hide #!5 models
> hide #!6 models
> show #!4 models
> show #!3 models
> hide #!4 models
> show #!2 models
> color zone #3 near #2 distance 4.51
> color zone #3 near #2 distance 10
> color zone #3 near #2 distance 12
> hide #!2 models
> save test2.png width 3000 transparentBackground true
> show #!6 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> transparency #6.1 0
> show #!5 models
> transparency #6.1 50
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!3 models
> hide #!6 models
> hide #!5 models
> show #!2 models
> transparency #2.2-6#3.1 0
> transparency #2.2-6#3.1 50
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> save test2.png width 3000 transparentBackground true
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> windowsize 1000 1000
QWindowsWindow::setGeometry: Unable to set geometry 1580x1198+8+31 (frame:
1596x1237+0+0) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1580x1061+8+31 (frame: 1596x1100+0+0) margins: 8, 31, 8, 8
minimum size: 422x596 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=635)))
> windowsize 1000 1000
QWindowsWindow::setGeometry: Unable to set geometry 1580x1280+0+23 (frame:
1596x1319-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1580x1061+0+23 (frame: 1596x1100-8-8) margins: 8, 31, 8, 8
minimum size: 422x596 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=635)))
> save test2.png width 3000 transparentBackground true
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes width 2
> save test2.png width 3000
> hide #!3 models
> hide #!2 models
> show #!5 models
> show #!6 models
> save test.png width 3000
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> transparency #6.1 0
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> save test3.png width 3000
> show #!3 models
> hide #!6 models
> transparency #3.1 0
> save test4.png width 3000
> view name IC
> view IC
> turn y 90
[Repeated 3 time(s)]
> turn x 90
[Repeated 10 time(s)]
> ui tool show "Map Eraser"
> volume erase #3 center 192.35,160.41,114.44 radius 20.619
> hide #!3 models
> show #!3 models
> show #!2 models
> color zone #3 near #2 distance 4.51
> color zone #3 near #2 distance 12
> view IC
> hide #!3 models
> show #!3 models
> hide #!2 models
> turn x 180
> color zone #3 near #2 distance 10
> color zone #3 near #2 distance 15
> color zone #3 near #2 distance 12
> turn x 180
> hide #!3 models
> show #!2 models
> color #*/E:122-355 #199999
> color #*/E:356-643 #B2B2B2
> color #*/E:588-605 #FF9999
> color #*/E:605-623 #BF00BF
> color #*/E:643-1230 #00FF7F
> color #*/E:711-790 #FFB233
> color #*/E:954-1044 #FFA5D8
> color #*/E:res 1085-1109 #FFDD5E; color #*/T blue; color #*/R red; color
> #*/N cyan; color #*/A red; color #*/B #007FFF
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #*/E:122-355 #199999
> color #*/E:356-643 #B2B2B2
> color #*/E:588-605 #FF9999
> color #*/E:605-623 #BF00BF
> color #*/E:643-1230 #00FF7F
> color #*/E:711-790 #FFB233
> color #*/E:954-1044 #FFA5D8
> color #*/E:1085-1109 #FFDD5E
> color #*/T blue
> color #*/R red
> color #*/N cyan
> color #*/A red
> color #*/B #007FFF
> view name IC
> view IC
> show #!3 models
> hide #!2 models
> color zone #3 near #2 distance 15
> save test5.png width 3000 transparentBackground true
> show #!6 models
> hide #!3 models
> show #!5 models
> color zone #6 near #5 distance 7.42
> color zone #6 near #5 distance 12
> hide #!5 models
> save test6.png width 3000 transparentBackground true
> save test6.png width 1000 height 1000 transparentBackground true
> save test6.png width 1000 height 1000 superSample 1 transparentBackground
> True
Expected a keyword
> save test6.png width 1000 height 1000 superSample 1 transparentBackground
> True
Expected a keyword
> save test6.png width 1000 height 1000 supersample 1 transparentBackground
> true
> save test6.png width 1000 height 1000 pixelSize 0.1 transparentBackground
> true
Cannot specify width or height if pixel_size is given
> save test6.png width 1000 height 1000 pixelSize 1 transparentBackground true
Cannot specify width or height if pixel_size is given
> save test6.png width 3000 transparentBackground true
> save test6.png width 4000 transparentBackground true
> save test6.png width 3000 transparentBackground true
> turn x 180
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> ui tool show "Map Eraser"
> transparency #7#6.1 0
> transparency #7#6.1 50
> show #!5 models
> volume erase #6 center 186.13,162.19,125.58 radius 14.899
> volume erase #6 center 195.58,174.47,110.87 radius 14.899
> volume erase #6 center 195.32,168.11,111.99 radius 14.899
> hide #!6 models
> hide #!5 models
> show #!6 models
> show #!5 models
> transparency #6.1 0
> color zone #6 near #5 distance 7.42
> color zone #6 near #5 distance 12
> view IC
> turn x 180
> color zone #6 near #5 distance 13
> color zone #6 near #5 distance 15
> save test.png width 3000 transparentBackground true
> hide #!5 models
> save test.png width 3000 transparentBackground true
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!3 models
> save test.png width 3000 transparentBackground true
> show #!6 models
> hide #!3 models
> save test2.png width 3000 transparentBackground true
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
> depthcue
Unknown command: depthcue
> lighting soft depthCue false
> lighting soft depthCue true
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!6 models
> lighting soft depthCue true
[Repeated 1 time(s)]
> lighting soft depthCue false
> lighting soft depthCue true
> windowsize 1000 1000
QWindowsWindow::setGeometry: Unable to set geometry 1580x1280+144+42 (frame:
1596x1319+136+11) on QWidgetWindow/"MainWindowClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1580x1061+144+42 (frame:
1596x1100+136+11) margins: 8, 31, 8, 8 minimum size: 422x596
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=635)))
> windowsize 1000 1000
QWindowsWindow::setGeometry: Unable to set geometry 1580x1280+0+23 (frame:
1596x1319-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1580x1061+0+23 (frame: 1596x1100-8-8) margins: 8, 31, 8, 8
minimum size: 422x596 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=635)))
> save test.png width 3000 transparentBackground true
> lighting soft depthCue false
> lighting soft
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> select ~sel & ##selected
Nothing selected
> lighting soft
[Repeated 1 time(s)]
> lighting soft depthCue false
> lighting soft depthCue true
> lighting soft depthCue true shadows true
> lighting soft depthCue true shadows false
> lighting simple
> lighting soft
> lighting soft depthCue true depthCueStart 0.5 depthCueEnd 1.0
> lighting soft depthCue true depthCueStart 0.5 depthCueEnd 0.5
> lighting soft depthCue true depthCueStart 0.5 depthCueEnd 1
> lighting soft depthCue true depthCueStart 0.1 depthCueEnd 1
> lighting soft depthCue true depthCueStart 0.3 depthCueEnd 1
> lighting soft depthCue true depthCueStart 0.2 depthCueEnd 1
> lighting soft depthCue true depthCueStart 0.4 depthCueEnd 1
> lighting soft depthCue true depthCueStart 0.7 depthCueEnd 1
> lighting soft depthCue true depthCueStart 1 depthCueEnd 1
> lighting soft depthCue true depthCueStart 0.5 depthCueEnd 1
> lighting soft depthCue true depthCueStart 0.3 depthCueEnd 1
> lighting soft depthCue true depthCueStart 0.4 depthCueEnd 1
> lighting soft depthCue true depthCueStart 0.4 depthCueEnd 1 depthCueColor
> black
> lighting soft depthCue true depthCueStart 0.2 depthCueEnd 1 depthCueColor
> black
> lighting soft depthCue true depthCueStart 0.5 depthCueEnd 1 depthCueColor
> black
> lighting soft depthCue true depthCueStart 1 depthCueEnd 1 depthCueColor
> black
> lighting soft depthCue true depthCueStart 2 depthCueEnd 1 depthCueColor
> black
> lighting soft depthCue true depthCueStart 1 depthCueEnd 1 depthCueColor
> black
> lighting soft depthCue true depthCueStart 0.4 depthCueEnd 1 depthCueColor
> black
> lighting soft depthCue true depthCueStart 0.4 depthCueEnd 1
> lighting soft depthCue true depthCueStart 0.4 depthCueEnd 1 depthCueColor
> default
Invalid "depthCueColor" argument: Invalid color name or specifier
> lighting soft depthCue true depthCueStart 0.4 depthCueEnd 1 depthCueColor
> white
> save test.png width 3000 transparentBackground true
> lighting soft depthCue true depthCueStart 0.1 depthCueEnd 1 depthCueColor
> white
> view IC
> lighting soft depthCue true depthCueStart 0.4 depthCueEnd 1 depthCueColor
> white
> save test2.png width 3000 transparentBackground true
> turn x 180
> lighting soft
> graphics silhouettes false
> view IC
> turn x 180
> save test3.png width 3000 transparentBackground true
> lighting soft depthCue false
> save test4.png width 3000 transparentBackground true
> lighting soft depthCue true
> lighting soft depthCue true depthCueStart 0.5 depthCueEnd 1 depthCueColor
> white
> lighting flat
> lighting soft
> lighting soft depthCue true depthCueStart 0.5 depthCueEnd 1 depthCueColor
> white
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
[Repeated 1 time(s)]
> lighting full
[Repeated 1 time(s)]
> lighting soft
> lighting soft depthCue true depthCueStart 0.5 depthCueEnd 1 depthCueColor
> white
> save test4.png width 3000 transparentBackground true
> turn x 180
> save test3.png width 3000 transparentBackground true
> show #!5 models
> hide #!3 models
> show #!6 models
> hide #!5 models
> save test2.png width 3000 transparentBackground true
> turn x 180
[Repeated 2 time(s)]
> save test1.png width 3000 transparentBackground true
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
> show #!2 models
> hide #!6 models
> show #!1 models
> hide #!2 models
> hide #!1 surfaces
> show #!2 models
> hide #!1 models
> show #!4 models
> hide #!2 models
> show #!1 models
> color zone #4 near #1 distance 4.51
> volume #4 style surface
> volume #4 level 0.01023
> volume #4 level 0.0174
> color zone #4 near #1 distance 12
> hide #!1 models
> surface dust #4 size 7.51
> volume #4 level 0.02926
> ui tool show "Map Eraser"
> volume erase #4 center 151.68,179.07,105.68 radius 9.4886
> view IC
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> lighting soft depthCue true depthCueStart 0.5 depthCueEnd 1 depthCueColor
> white
> save C:\Users\krh021/Desktop/test1.png width 3000 transparentBackground true
> turn x, 180
Expected an axis vector or a keyword
> turn x 180
> save C:\Users\krh021/Desktop/test1.png width 3000 transparentBackground true
> turn x 180
> save C:\Users\krh021/Desktop/test2.png width 3000 transparentBackground true
> open C:/Users/krh021/Desktop/Images/IC3_J1043_map_locres.mrc
Opened IC3_J1043_map_locres.mrc as #7, grid size 384,384,384, pixel 0.751,
shown at level 6.47, step 2, values float32
> open C:/Users/krh021/Desktop/Images/IC0_J1044_map_locres.mrc
Opened IC0_J1044_map_locres.mrc as #8, grid size 384,384,384, pixel 0.751,
shown at level 6.98, step 2, values float32
> ui tool show "Surface Color"
> hide #!4 models
> hide #!7 models
> hide #!8 models
> show #!3 models
> combine #3
No structures specified
> copy #3
Unknown command: copy #3
> hide #!3 models
> show #!3 models
> volume copy #3
Opened J792 copy as #9, grid size 384,384,384, pixel 0.751, shown at step 1,
values float32
> hide #!9 models
> show #!9 models
> color #9 #aaaaff33 models
> volume copy #4
Opened J781 copy as #10, grid size 384,384,384, pixel 0.751, shown at step 1,
values float32
> transparency #9.1#10.1 0
> hide #!9 models
> volume #10 level 0.07669
> color sample #10.1 map #7 palette #3d0cff:#00ff00:#ff0000
Map values for surface "surface": minimum 0, mean 3.441, maximum 8.018
> color sample #10.1 map #7 palette 2,#3d0cff:3,#00ff00:5,#ff0000
Map values for surface "surface": minimum 0, mean 3.441, maximum 8.018
> color sample #10.1 map #7 palette 2.5,#3d0cff:3.5,#00ff00:4.5,#ff0000
Map values for surface "surface": minimum 0, mean 3.441, maximum 8.018
> color sample #10.1 map #7 palette 2.5,#3d0cff:3,#00ff00:4,#ff0000
Map values for surface "surface": minimum 0, mean 3.441, maximum 8.018
> color sample #10.1 map #7 palette 2.5,#3d0cff:3,#00ff00:5,#ff0000
Map values for surface "surface": minimum 0, mean 3.441, maximum 8.018
> color sample #10.1 map #7 palette 2.5,#3d0cff:3,#00ffff:5,#ff0000
Map values for surface "surface": minimum 0, mean 3.441, maximum 8.018
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
> key #3d0cff:2.5 cyan:3.0 red:5.0 showTool true
> ui mousemode right "color key"
> key #3d0cff:2.5 cyan:3.0 red:5.0 white:
> key #3d0cff:2.5 cyan:3.0 red:5.0 white: white:
> key #3d0cff:2 cyan:3.0 red:5.0 white: white:
> key #3d0cff:2 cyan:3.0 red:4 white: white:
> key #3d0cff:2 cyan:3.0 red:4 white:5 white:
> key #3d0cff:2 cyan:3.0 red:4 white:5 white:6
> key #3d0cff:2 cyan:3.0 red:4 white:5 red:6
> key #3d0cff:2 cyan:3.0 lime:4 white:5 red:6
> key #3d0cff:2 cyan:3.0 lime:4 yellow:5 red:6
> ui mousemode right "map eraser"
> color sample #10.1 map #7 palette
> 2,#3d0cff:3,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000
Map values for surface "surface": minimum 0, mean 3.441, maximum 8.018
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
> show #!3 models
> hide #11 models
> hide #!10 models
> view IC
> turn x 180
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> volume #4 level 0.0174
> surface dust #4 size 7.51
> ui tool show "Map Eraser"
> volume erase #4 center 148.23,187.69,97.159 radius 14.443
> volume erase #4 center 130.43,198.24,105.88 radius 14.443
> show #!3 models
> hide #!4 models
> ui tool show "Side View"
> clip near #1/T
Invalid "near" argument: Expected 'off' or a number
> clip front 5 #3
Expected a keyword
> clip #3
Expected a keyword
> clip #3 front
Expected a keyword
> clip #3 front 0
Expected a keyword
> clip on #3
Expected a keyword
> clip on
Expected a keyword
> clip #3
Expected a keyword
> clip #3 on
Expected a keyword
> clip
> clip off
> clip front 0 #3
Expected a keyword
> clip front 0
> clip front -1
> clip front -3
> clip front -4
> clip front -5
> clip front -4.5
[Repeated 1 time(s)]
> clip off
> clip front -1
> clip off
> clip front -3
> clip off
> clip front -4
> clip off
> clip front -4.5
> surface cap true
[Repeated 1 time(s)]
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> surface cap offset
Missing "offset" keyword's argument
> surface cap false
[Repeated 1 time(s)]
> select ~sel & ##selected
Nothing selected
> clip off
> clip front -5
> clip off
> clip front -6
> clip off
> clip front -9
> clip off
> clip front -12
> clip off
> clip front -15
> clip off
> clip front -14
> surface cap #4 true
Expected true or false or a keyword
> surface cap #4 on
Expected true or false or a keyword
> surface cap #4 true
Expected true or false or a keyword
> surface cap true #4
Expected a keyword
> surface cap true
[Repeated 1 time(s)]
> show #!1 models
> hide #!1 models
> volume #!4 style surface
> volume #!4 hide
> volume show
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!3 models
> hide #!6 models
> transparency #4.1 0
> transparency #4.1 50
> transparency #4.1 0
> transparency #4.1 50
> transparency #4.1 0
> show #!1 models
> color zone #4 near #1 distance 4.51
> clip off
> hide #!1 models
> show #!1 models
> color zone #4 near #1 distance 12
> clip front -14
[Repeated 1 time(s)]
> clip front 10
[Repeated 1 time(s)]
> lighting simple
> hide #!1 models
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes true
> graphics silhouettes false
> clip front 10
> clip off
> clip 10
Expected a keyword
> clip front 10
> clip off
> clip front 1
> clip off
> clip front -5
> clip off
> clip front -10
> clip off
> surface zone #4 nearAtoms #1/N/R/T
> hide #!4 models
> show #!4 models
> volume #4 level 0.1004
> volume #4 level 0.03716
> volume #4 level 0.0174
> volume zone #4 nearAtoms #1/N/R/T range 1.5 minimalBounds true newMap true
Opened J781 zone as #12, grid size 109,96,136, pixel 0.751, shown at step 1,
values float32
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!3 models
> lighting soft
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!3 models
> show #!4 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 2 maps.
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!12 models
> volume show
> volume hide
> show #!4 models
> undo
[Repeated 9 time(s)]
> show #!4 models
> hide #!3 models
> undo
[Repeated 1 time(s)]
> show #!4 models
> hide #!3 models
> surface zone #4 nearAtoms #1
> surface zone #4
Missing required "near_atoms" argument
> volume #!4,12 style surface
> show #4
> hide #!12 models
> volume #4 level 0.1083
> volume #4 level 0.00159
> transparency #4.1 0
> transparency #4.1 50
> transparency #4.1 0
> volume #!4 style surface
[Repeated 1 time(s)]
> volume #!4 region all imageMode "full region"
> volume unzone #!4
> mousemode rightMode "crop volume"
> volume #!4 style surface
> volume #4 level 0.0174
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> volume show
> volume hide
> show #!4 models
> volume #!4 style surface
> transparency #4.1 0
> show #!1 models
> color zone #4 near #1 distance 4.51
> color zone #4 near #1 distance 12
> hide #!1 models
> surface dust #4 size 7.51
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!1 models
> hide #!4 models
> show #!12 models
> color zone #12 near #1 distance 4.51
> hide #!12 models
> show #!12 models
> hide #!1 models
> surface dust #12 size 7.51
> volume zone #4 nearAtoms #1/N/R/T range 2 minimalBounds true newMap true
Opened J781 zone as #13, grid size 110,97,138, pixel 0.751, shown at step 1,
values float32
> close #12-13
> volume zone #4 nearAtoms #1/N/R/T range 3 minimalBounds true newMap true
Opened J781 zone as #12, grid size 113,100,140, pixel 0.751, shown at step 1,
values float32
> show #!2 models
> hide #!2 models
> show #!1 models
> color zone #12 near #1 distance 4.51
> hide #!1 models
> volume #12 level 0.02472
> volume #12 level 0.03571
> volume #12 level 0.05035
> volume #12 level 0.09429
> volume #12 level 0.1163
> volume #12 level 0.1053
> volume #12 level 0.07965
> close #12
> volume zone #4 nearAtoms #1/N/R/T range 2 minimalBounds true newMap true
Opened J781 zone as #12, grid size 110,97,138, pixel 0.751, shown at step 1,
values float32
> show #!1 models
> color zone #12 near #1 distance 4.51
> hide #!1 models
> color zone #12 near #1 distance 12
> color zone #12 near #1 distance 1
> color zone #12 near #1 distance 3
> color zone #12 near #1 distance 2
> color zone #12 near #1 distance 3
> color zone #12 near #1 distance 4
> color zone #12 near #1 distance 5
> color zone #12 near #1 distance 4
> volume #12 level 0.09096
> volume zone #4 nearAtoms #1/N/R/T range 2 newMap true
Opened J781 zone as #13, grid size 384,384,384, pixel 0.751, shown at step 1,
values float32
> hide #!12 models
> show #!1 models
> color zone #13 near #1 distance 4.51
> hide #!1 models
> hide #!13 models
> show #!13 models
> surface dust #13 size 7.51
> close #12
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!13 models
> volume zone #3 nearAtoms #2/N/R/T range 2 newMap true
Opened J792 zone as #12, grid size 384,384,384, pixel 0.751, shown at step 1,
values float32
> color zone #12 near #2 distance 4.51
> hide #!2 models
> surface dust #12 size 7.51
> volume #12 level 0.01012
> volume zone #3 nearAtoms #2/N/R/T range 3 newMap true
Opened J792 zone as #14, grid size 384,384,384, pixel 0.751, shown at step 1,
values float32
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!2 models
> color zone #14 near #2 distance 4.51
> hide #!2 models
> surface dust #14 size 7.51
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!14 models
> show #!14 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> hide #!14 models
> show #!12 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> close #14
> show #!13 models
> hide #!13 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
> show #!3 models
> ui tool show "Surface Zone"
> surface zone #3 nearAtoms #2 distance 4.51
> surface zone #3 nearAtoms #2/N/R/T distance 4.51
> surface zone #3 nearAtoms #2/N/R/T distance 10
> surface zone #3 nearAtoms #2/N/R/T distance 1
> surface zone #3 nearAtoms #2/N/R/T distance 2
> surface zone #3 nearAtoms #2/N/R/T distance 2.5
> surface zone #3 nearAtoms #2/N/R/T distance 3
> surface unzone #3
> hide #!3 models
> show #!3 models
> show #!2 models
> color zone #3 near #2 distance 4.51
> color zone #3 near #2 distance 12
> transparency #2.2-6#3.1 0
> transparency #2.2-6#3.1 50
> transparency #2.2-6#3.1 0
> color zone #3 near #2 distance 12
> clip off
> color zone #3 near #2 distance 14
> surface dust #3 size 7.51
> hide #!3 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!12 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!12 models
> show #!12 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!13 models
> hide #!12 models
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> hide #!4 models
> show #!4 models
> hide #!13 models
> show #!13 models
> hide #!4 models
> show #!4 models
> view name IC2
> turn x 90
[Repeated 3 time(s)]
> turn y 90
[Repeated 11 time(s)]
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!13 models
> turn y 90
[Repeated 3 time(s)]
> turn y 120
[Repeated 5 time(s)]
> show #!3 models
> hide #!4 models
> show #!12 models
> hide #!3 models
> show #!13 models
> hide #!12 models
> show #!2 models
> combine #2
> hide #!2 models
> hide #!13 models
> close #14
> combine #1
> select #14:/N/R/T
Expected an objects specifier or a keyword
> select #14/N/R/T
2108 atoms, 2364 bonds, 103 residues, 1 model selected
> select ~sel & ##selected
12731 atoms, 13022 bonds, 3 pseudobonds, 1578 residues, 2 models selected
> hide sel cartoons
> show sel atoms
> delete sel
> volume zone #4 nearAtoms #14/N/R/T range 2 newMap true
Opened J781 zone as #15, grid size 384,384,384, pixel 0.751, shown at step 1,
values float32
> hide #!14 models
> show #!14 models
> color zone #15 near #14 distance 4.51
> hide #!15 models
> show #!15 models
> hide #!14 models
> close #12
> close #13
> combine #2
> select #16/N/R/T
Nothing selected
> select #12/N/R/T
2040 atoms, 2288 bonds, 100 residues, 1 model selected
> select ~sel & ##selected
12719 atoms, 13012 bonds, 3 pseudobonds, 1578 residues, 2 models selected
> delete sel
> hide #!12 models
> show #!12 models
> hide #!15 models
> volume zone #3 nearAtoms #12/N/R/T range 2 newMap true
Opened J792 zone as #13, grid size 384,384,384, pixel 0.751, shown at step 1,
values float32
> color zone #13 near #12 distance 4.51
> hide #!12 models
> show #!15 models
> hide #!15 models
> surface dust #13 size 7.51
> show #!15 models
> hide #!13 models
> surface dust #15 size 7.51
> show #!13 models
> hide #!13 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!15 models
> surface dust #3 size 7.51
> windowsize 1000 1000
QWindowsWindow::setGeometry: Unable to set geometry 1580x1198+0+23 (frame:
1596x1237-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1580x1061+0+23 (frame: 1596x1100-8-8) margins: 8, 31, 8, 8
minimum size: 422x471 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=510)))
> windowsize 1000 1000
QWindowsWindow::setGeometry: Unable to set geometry 1580x1302+0+23 (frame:
1596x1341-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1580x1061+0+23 (frame: 1596x1100-8-8) margins: 8, 31, 8, 8
minimum size: 422x471 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=510)))
> save C:\Users\krh021/Desktop/test.png width 3000 transparentBackground true
> show #!13 models
> hide #!3 models
> hide #!13 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
> show #!3 models
> copy #3
Unknown command: copy #3
> volume copy #3
Opened J792 copy as #16, grid size 384,384,384, pixel 0.751, shown at step 1,
values float32
> volume copy #4
Opened J781 copy as #17, grid size 384,384,384, pixel 0.751, shown at step 1,
values float32
> hide #!16 models
> hide #!17 models
> show #!16 models
> transparency #16.1 0
> surface dust #16 size 7.51
> volume #10 level 0.0174
> show #!13 models
> hide #!13 models
> clip front 10
> show #!13 models
> hide #!13 models
> clip off
> clip model #16 front 10
Expected true or false or a keyword
> clip model #16 true
> clip front 10
> show #!13 models
> hide #!13 models
> clip #16 front 10
Expected a keyword
> clip front 10 #16
Expected a keyword
> hide #!16 models
> show #!16 models
> show #!13 models
> clip off
> hide #!16 models
> show #!16 models
> clip front 0
> clip model #!12 false
> clip model #!13 false
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!13 models
> show #!16 models
> color #16 light gray
> clip model #!13 false
> clip model #13 false
> show #!13 models
> hide #!16 models
> show #!16 models
> clip front 0
> clip front 2
> clip front 4
> clip front 0
> clip front -2
> clip front -4
> hide #!13 models
> show #!13 models
> hide #!13 models
> clip front -5
> show #!14 models
> hide #!14 models
> show #!13 models
> surface #16
Expected fewer arguments
> surface off #16
Expected fewer arguments
> surface off
Expected fewer arguments
> surface
Expected fewer arguments
> volume #16 color #5555ff
> color #13,16 gray
> hide #!16 models
> undo
[Repeated 3 time(s)]
> hide #!14 models
> show #!13 models
> hide #!16 models
> show #!16 models
> hide #!13 models
> color #16 dark gray
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> clip front -5
> clip front -3
> clip front -6
> clip front 0
> clip front 2
[Repeated 1 time(s)]
> clip front 1
[Repeated 21 time(s)]
> clip front -1
[Repeated 4 time(s)]
> clip front
Missing "front" keyword's argument
> clip front 1
> clip front -1
[Repeated 1 time(s)]
> transparency #16 50
> transparency #16 10
> clip front -1
[Repeated 5 time(s)]
> clip front 1
[Repeated 9 time(s)]
> clip front -1
> transparency #16 180
> transparency #16 60
> transparency #16 50
> transparency #16 40
> transparency #16 60
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
——— End of log from Fri Aug 23 11:39:06 2024 ———
opened ChimeraX session
> hide #!16 models
> show #!16 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!16 models
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> select #12/N:30-50
429 atoms, 482 bonds, 21 residues, 1 model selected
> select #12/N:1-29
606 atoms, 681 bonds, 29 residues, 1 model selected
> select #12/N:1-20
418 atoms, 469 bonds, 20 residues, 1 model selected
> delete sel
> select #12/T:31-50
399 atoms, 446 bonds, 20 residues, 1 model selected
> delete sel
> show #!13 models
> hide #!12 models
> hide #!13 models
> show #!12 models
> volume zone #3 nearAtoms #12/N/R/T range 2 newMap true
Opened J792 zone as #18, grid size 384,384,384, pixel 0.751, shown at step 1,
values float32
> hide #!18 models
> show #!18 models
> clip off #18
Expected fewer arguments
> clip model #18 false
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!18 models
> hide #!12 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> surface dust #13 size 7.51
> surface dust #18 size 7.51
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!12 models
> color zone #18 near #12 distance 4.51
> hide #!12 models
> show #!13 models
> hide #!18 models
> show #!18 models
> hide #!13 models
> close #13
> rename #18 id #13
> show #!16 models
> hide #!13 models
> hide #!16 models
> show #!14 models
> clip model #1-14 false
> show #!15 models
> hide #!14 models
> clip model #1-15 false
> hide #!15 models
> show #!15 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!15 models
> show #!15 models
> hide #!13 models
> show #!14 models
> hide #!15 models
> select #14/T:31-50
399 atoms, 446 bonds, 20 residues, 1 model selected
> delete sel
> select #14/N:1-20
418 atoms, 469 bonds, 20 residues, 1 model selected
> delete sel
> volume zone #4 nearAtoms #14/N/R/T range 2 newMap true
Opened J781 zone as #18, grid size 384,384,384, pixel 0.751, shown at step 1,
values float32
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!14 models
> color zone #18 near #14 distance 4.51
> hide #!14 models
> close #15
> rename #18 id #15
> select ~sel & ##selected
Nothing selected
> clip model #1-15 false
> hide #!15 models
> show #!15 models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!15 models
> show #!15 models
> hide #!17 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!13 models
> show #!16 models
> graphics silhouettes true
> save C:\Users\krh021/Desktop/test2.png width 3000 transparentBackground true
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
> show #!17 models
> hide #!16 models
> hide #!13 models
> surface dust #17 size 7.51
> show #!16 models
> hide #!17 models
> surface dust #16 size 7.51
> show #!17 models
> hide #!16 models
> color #17 gray
> transparency #17 60
> show #!16 models
> hide #!17 models
> show #!17 models
> hide #!16 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!15 models
> save C:\Users\krh021/Desktop/test3.png width 3000 transparentBackground true
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
——— End of log from Fri Aug 23 12:03:12 2024 ———
opened ChimeraX session
> close #11#7-10
> show #!1 models
> hide #!1 models
> hide #!15 models
> hide #!17 models
> show #!12 models
> rename #12 IC0_30_DNA.pdb
> rename #14 IC3_30_DNA.pdb
> show #!14 models
> hide #!14 models
> hide #!12 models
> rename #16 "J792 Clipped"
> rename #17 "J781 Clipped"
> rename #3 J792.mrc
> rename #4 J781.mr
> rename #4 J781.mrc
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
> show #!16 models
> show #!17 models
> hide #!16 models
> hide #!17 models
> show #!17 models
> clip model #17 false
> show #!14 models
> hide #!14 models
> show #!15 models
> save C:\Users\krh021/Desktop/test4.png width 3000 transparentBackground true
> hide #!17 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!13 models
> clip front -1
[Repeated 12 time(s)]
> clip model #16 false
> color #16 #ffffff66 models
> save C:\Users\krh021/Desktop/test4.png width 3000 transparentBackground true
> hide #!16 models
> save C:\Users\krh021/Desktop/test5.png width 3000 transparentBackground true
> hide #!13 models
> show #!17 models
> transparency #17 0
> color #17 gray
> color #17 light gray
> color #17 dark gray
> color #17 dim gray
> color #17 dark gray
> save C:\Users\krh021/Desktop/test7.png width 3000 transparentBackground true
> show #!15 models
> hide #!17 models
> save C:\Users\krh021/Desktop/test8.png width 3000 transparentBackground true
> show #!17 models
> clip model #17 true
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> clip front -1
[Repeated 3 time(s)]
> show #!16 models
> hide #!16 models
> show #!15 models
> transparency #17 50
> transparency #17 70
> transparency #17 80
> save C:\Users\krh021/Desktop/test10.png width 3000 transparentBackground
> true
> hide #!15 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!16 models
> show #!17 models
> hide #!17 models
> clip model #16 true
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!17 models
> show #!16 models
> color #16 dark gray
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
> hide #!16 models
> show #!15 models
> show #!16 models
> hide #!17 models
> show #!17 models
> hide #!16 models
> save C:\Users\krh021/Desktop/test10.png width 3000 transparentBackground
> true
> hide #!15 models
> show #!13 models
> hide #!17 models
> show #!16 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> view name IC2
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!13 models
> show #!16 models
> hide #!15 models
> show #!15 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> hide #!15 models
> show #!16 models
> show #!14 models
> hide #!14 models
> show #!13 models
> select ~sel & ##selected
Nothing selected
> save C:\Users\krh021/Desktop/test11.png width 3000 transparentBackground
> true
> transparency #17 50
> transparency #16 50
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!13 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!16 models
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
> combine #2
> combine #1
> hide #!16 models
> hide #!17 models
> hide #!8 models
> rename #7 IC0_protein_only.pdb
> show #!8 models
> hide #!7 models
> rename #8 IC3_protein_only.pdb
> select #7,8/N/R/T
4148 atoms, 4652 bonds, 203 residues, 2 models selected
> delete sel
> show #!7 models
> hide #!8 models
> volume zone #3 nearAtoms #7 range 2 newMap true
Opened J792.mrc zone as #9, grid size 384,384,384, pixel 0.751, shown at step
1, values float32
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!7 models
> surface dust #13 size 7.51
> surface dust #9 size 7.51
> hide #!13 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!9 models
> show #!9 models
> hide #!16 models
> show #!16 models
> hide #!9 models
> show #!9 models
> hide #!16 models
> volume zone #3 nearAtoms #7 newMap true
Opened J792.mrc zone as #10, grid size 384,384,384, pixel 0.751, shown at step
1, values float32
> hide #!10 models
> show #!10 models
> hide #!9 models
> surface dust #10 size 7.51
> show #!9 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> show #!16 models
> hide #!10 models
> transparency #16 0
> hide #!16 models
> close #9-10
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!7 models
> select #8,7/A
3230 atoms, 3292 bonds, 384 residues, 2 models selected
> delete sel
> select #8,7/E:122-146
436 atoms, 438 bonds, 50 residues, 2 models selected
> delete sel
> show #!8 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> volume zone #3 nearAtoms #7 newMap true
Opened J792.mrc zone as #9, grid size 384,384,384, pixel 0.751, shown at step
1, values float32
> hide #!7 models
> show #!13 models
> transparency #9 50
> hide #!13 models
> hide #!9 models
> show #!8 models
> show #!7 models
> select #7,8/E
16517 atoms, 16904 bonds, 6 pseudobonds, 2074 residues, 4 models selected
> color #7,8/E #B2B2B2
> select add #7
19152 atoms, 19605 bonds, 6 pseudobonds, 2398 residues, 4 models selected
> select add #8
21784 atoms, 22302 bonds, 6 pseudobonds, 2722 residues, 4 models selected
> select subtract #8
10886 atoms, 11146 bonds, 3 pseudobonds, 1361 residues, 2 models selected
> select subtract #7
Nothing selected
> show #!9 models
> hide #!8 models
> color zone #9 near #7 distance 4.51
> hide #!7 models
> transparency #9 50
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> color #9 #b2b2b280 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 2 maps.
> hide #!13 models
> show #!7 models
> color zone #9 near #7 distance 4.51
> hide #!7 models
> transparency #9 50
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!9 models
> show #!9 models
> transparency #9 50
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!9 models
> show #!9 models
> show #!12 models
> hide #!12 models
> show #!13 models
> save C:\Users\krh021/Desktop/test12.png width 3000 transparentBackground
> true
> hide #!9 models
> show #!9 models
> hide #!13 models
> color #9 dark gray
> color #9 #b2b2b180 models
> color #9 #b2b2b380 models
> color #9 #b2b2b280 models
> color #9 #b2b2b380 models
> color #9 #aaff0080 models
> color #9 #aaaaff80 models
> color #9 #b2b2b280 models
> show #!8 models
> hide #!8 models
> show #!13 models
> transparency #9 60
> transparency #9 70
> save C:\Users\krh021/Desktop/test12.png width 3000 transparentBackground
> true
> transparency #9 60
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes width 2
> graphics silhouettes width 3
> graphics silhouettes width 1
> graphics silhouettes width 2
> graphics silhouettes width 3
> save C:\Users\krh021/Desktop/test12.png width 3000 transparentBackground
> true
> hide #!9 models
> hide #!13 models
> show #!7 models
> hide #!7 models
> show #!8 models
> volume zone #4 nearAtoms #8 newMap true
Opened J781.mrc zone as #10, grid size 384,384,384, pixel 0.751, shown at step
1, values float32
> hide #!8 models
> color #10 #b2b2b2ff models
> show #!15 models
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
> clip front -1
> clip front 1
[Repeated 13 time(s)]
> clip front -1
[Repeated 3 time(s)]
> surface dust #15 size 7.51
> surface dust #10 size 7.51
> save C:\Users\krh021/Desktop/test13.png width 3000 transparentBackground
> true
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!15 models
> show #!3 models
> save C:\Users\krh021/Desktop/ic0_map1.png width 3000 transparentBackground
> true
> show #!4 models
> hide #!3 models
> save C:\Users\krh021/Desktop/ic3_map1.png width 3000 transparentBackground
> true
> windowsize 1000 1000
QWindowsWindow::setGeometry: Unable to set geometry 1579x1198+0+23 (frame:
1595x1237-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1579x1061+0+23 (frame: 1595x1100-8-8) margins: 8, 31, 8, 8
minimum size: 422x402 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=441)))
> windowsize 1000 1000
QWindowsWindow::setGeometry: Unable to set geometry 1579x1265+0+23 (frame:
1595x1304-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1579x1061+0+23 (frame: 1595x1100-8-8) margins: 8, 31, 8, 8
minimum size: 422x402 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=441)))
> windowsize 1000 1000
QWindowsWindow::setGeometry: Unable to set geometry 1579x1265+0+23 (frame:
1595x1304-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1579x1061+0+23 (frame: 1595x1100-8-8) margins: 8, 31, 8, 8
minimum size: 422x402 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=441)))
> windowsize 1000 1000
QWindowsWindow::setGeometry: Unable to set geometry 1579x1265+1+31 (frame:
1595x1304-7+0) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1579x1061+1+31 (frame: 1595x1100-7+0) margins: 8, 31, 8, 8
minimum size: 422x402 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=441)))
> save C:\Users\krh021/Desktop/ic3_map1.png width 3000 transparentBackground
> true
> graphics silhouettes false
> save C:\Users\krh021/Desktop/ic3_map2.png width 3000 transparentBackground
> true
> hide #!4 models
> show #!10 models
> show #!15 models
> save C:\Users\krh021/Desktop/ic3_map3.png width 3000 transparentBackground
> true
> hide #!10 models
> show #!17 models
> transparency #17 0
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> surface dust #17 size 7.51
> surface dust #15 size 7.51
> hide #!17 models
> hide #!15 models
> show #!7 models
> hide #!7 models
> show #!8 models
> close #8
> combine #2
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!8 models
> rename #8 IC0_protein_only.pdb
> close #7
> rename #8 id #7
> combine #1
> hide #!7 models
> select #7,8/N:21-50
1234 atoms, 1388 bonds, 60 residues, 2 models selected
> delete sel
> select #7,8/T:1-29
1170 atoms, 1306 bonds, 58 residues, 2 models selected
> delete sel
> show #!7 models
> hide #!8 models
> volume zone #4 nearAtoms #8 newMap true
Opened J781.mrc zone as #11, grid size 384,384,384, pixel 0.751, shown at step
1, values float32
> hide #!7 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> close #11
> select #7,8/R
68 atoms, 76 bonds, 3 residues, 1 model selected
> delete sel
> volume zone #4 nearAtoms #8 newMap true
Opened J781.mrc zone as #11, grid size 384,384,384, pixel 0.751, shown at step
1, values float32
> surface dust #11 size 7.51
> color #11 #bb22bbff models
> color #11 #b2b2b2ff models
> show #!15 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> save C:\Users\krh021/Desktop/ic3_map3.png width 3000 transparentBackground
> true
> surface dust #15 size 7.51
> surface dust #11 size 7.51
> hide #!11 models
> show #!11 models
> hide #!15 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!11 models
> show #!11 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> surface dust #17 size 7.51
> surface dust #11 size 7.51
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!11 models
> show #!11 models
> hide #!17 models
> color #17 #bb22bbff models
> color #17 #b2b2b2ff models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!11 models
> show #!15 models
> show #!11 models
> hide #!17 models
> hide #!15 models
> hide #!11 models
> show #!11 models
> show #!15 models
> graphics silhouettes true
> save C:\Users\krh021/Desktop/ic3_map3.png width 3000 transparentBackground
> true
> transparency #11 50
> save C:\Users\krh021/Desktop/ic3_map3.png width 3000 transparentBackground
> true
> transparency #11 30
> transparency #11 20
> transparency #11 10
> transparency #11 20
> save C:\Users\krh021/Desktop/ic3_map3.png width 3000 transparentBackground
> true
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> close #9
> show #!10 models
> undo
[Repeated 2 time(s)]
> show #!10 models
> close #10
> show #!11 models
> transparency #11 0
> hide #!11 models
> show #!7 models
> hide #!15 models
> rename #8 IC3_protein_only.pdb
> volume zone #3 nearAtoms #7 newMap true
Opened J792.mrc zone as #9, grid size 384,384,384, pixel 0.751, shown at step
1, values float32
> color #9 #b2b2b2ff models
> surface dust #9 size 7.51
> hide #!7 models
> show #!16 models
> hide #!16 models
> show #!13 models
> save C:\Users\krh021/Desktop/ic0_map3.png width 3000 transparentBackground
> true
> center
Unknown command: center
> save C:\Users\krh021/Desktop/ic0_map3.png width 3000 transparentBackground
> true
> hide #!9 models
> hide #!13 models
> show #!11 models
> show #!15 models
> save C:\Users\krh021/Desktop/ic3_map3.png width 3000 transparentBackground
> true
> hide #!15 models
> hide #!11 models
> show #!3 models
> windowsize 1000 1000
QWindowsWindow::setGeometry: Unable to set geometry 1579x1265+1+31 (frame:
1595x1304-7+0) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1579x1061+1+31 (frame: 1595x1100-7+0) margins: 8, 31, 8, 8
minimum size: 422x402 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=441)))
> windowsize 1000 1000
QWindowsWindow::setGeometry: Unable to set geometry 1579x1265+1+31 (frame:
1595x1304-7+0) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1579x1061+1+31 (frame: 1595x1100-7+0) margins: 8, 31, 8, 8
minimum size: 422x402 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=441)))
> windowsize 800 800
QWindowsWindow::setGeometry: Unable to set geometry 1379x1065+0+23 (frame:
1395x1104-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1379x1061+0+23 (frame: 1395x1100-8-8) margins: 8, 31, 8, 8
minimum size: 422x402 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=441)))
> save C:\Users\krh021/Desktop/ic0_map3.png width 3000 transparentBackground
> true
> show #!4 models
> hide #!3 models
> save C:\Users\krh021/Desktop/ic3_map3.png width 3000 transparentBackground
> true
> surface dust #4 size 7.51
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!9 models
> show #!15 models
> save C:\Users\krh021/Desktop/ic3_map4.png width 3000 transparentBackground
> true
> hide #!9 models
> show #!11 models
> save C:\Users\krh021/Desktop/ic3_map4.png width 3000 transparentBackground
> true
> show #!13 models
> hide #!15 models
> hide #!11 models
> show #!9 models
> save C:\Users\krh021/Desktop/ic0_map4.png width 3000 transparentBackground
> true
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
> hide #!9 models
> hide #!13 models
> show #!3 models
> turn x 180
[Repeated 1 time(s)]
> turn x 120
[Repeated 2 time(s)]
> turn y 180
> save C:\Users\krh021/Desktop/ic0_map5.png width 3000 transparentBackground
> true
> hide #!3 models
> show #!13 models
> hide #!13 models
> turn y 180
> show #!13 models
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> show #!9 models
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
> hide #!13 models
> hide #!9 models
> show #!17 models
> show #!11 models
> hide #!11 models
> show #!15 models
> clip model #17 false
> hide #!17 models
> show #!17 models
> transparency #17 50
> save C:\Users\krh021/Desktop/ic3_map5.png width 3000 transparentBackground
> true
> hide #!15 models
> show #!2 models
> hide #!2 models
> show #!1 models
> color zone #17 near #1 distance 4.51
> hide #!1 models
> transparency #17 50
> color zone #17 near #1 distance 12
> transparency #17 50
> show #!15 models
> hide #!15 models
> show #!15 models
> transparency #17 580
> transparency #17 80
> transparency #17 90
> save C:\Users\krh021/Desktop/ic3_map5.png width 3000 transparentBackground
> true
> transparency #17 70
> save C:\Users\krh021/Desktop/ic3_map5.png width 3000 transparentBackground
> true
> clip model #17 true
> save C:\Users\krh021/Desktop/ic3_map5.png width 3000 transparentBackground
> true
> transparency #17 50
> save C:\Users\krh021/Desktop/ic3_map5.png width 3000 transparentBackground
> true
> clip model #17 true front -1
Expected a keyword
> clip front 1
[Repeated 10 time(s)]
> hide #!1 models
> show #!15 models
> clip front -1
[Repeated 22 time(s)]
> clip front 1
[Repeated 5 time(s)]
> hide #!15 models
> show #!1 models
> hide #!1 models
> show #!1 models
> color zone #17 near #1 distance 4.51
> hide #!1 models
> transparency #17 50
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> save C:\Users\krh021/Desktop/ic3_map5.png width 3000 transparentBackground
> true
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> clip model #17 false
> hide #!15 models
> show #!1 models
> color zone #17 near #1 distance 4.51
> hide #!1 models
> color zone #17 near #1 distance 12
> save C:\Users\krh021/Desktop/1.png width 3000 transparentBackground true
> show #!15 models
> hide #!17 models
> save C:\Users\krh021/Desktop/2.png width 3000 transparentBackground true
> show #!17 models
> hide #!15 models
> show #!15 models
> transparency #17 50
> transparency #17 570
> transparency #17 70
> transparency #17 80
> save C:\Users\krh021/Desktop/ic3_map5.png width 3000 transparentBackground
> true
> show #!16 models
> hide #!17 models
> hide #!15 models
> show #!13 models
> clip model #16 false
> hide #!16 models
> show #!16 models
> hide #!13 models
> show #!2 models
> color zone #16 near #2 distance 4.51
> color zone #16 near #2 distance 12
> hide #!2 models
> transparency #16 80
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> hide #!16 models
> show #!16 models
> clip model #16 false
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!13 models
> hide #!13 models
> show #!13 models
> transparency #16 80
> save C:\Users\krh021/Desktop/ic0_map6.png width 3000 transparentBackground
> true
> hide #!16 models
> hide #!13 models
> show #!2 models
> hide #!2 models
> show #!3 models
> turn y 180
> save C:\Users\krh021/Desktop/ic0_map5.png width 3000 transparentBackground
> true
> windowsize 800 800
QWindowsWindow::setGeometry: Unable to set geometry 1379x1065+463+82 (frame:
1395x1104+455+51) on QWidgetWindow/"MainWindowClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1379x1061+463+82 (frame:
1395x1100+455+51) margins: 8, 31, 8, 8 minimum size: 422x402
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=441)))
> windowsize 800 800
QWindowsWindow::setGeometry: Unable to set geometry 1379x1065+0+23 (frame:
1395x1104-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1379x1061+0+23 (frame: 1395x1100-8-8) margins: 8, 31, 8, 8
minimum size: 422x402 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=441)))
> windowsize 800 800
QWindowsWindow::setGeometry: Unable to set geometry 1238x1065+0+23 (frame:
1254x1104-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1238x1061+0+23 (frame: 1254x1100-8-8) margins: 8, 31, 8, 8
minimum size: 422x402 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=441)))
> windowsize 800 800
QWindowsWindow::setGeometry: Unable to set geometry 1238x1065+0+23 (frame:
1254x1104-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1238x1061+0+23 (frame: 1254x1100-8-8) margins: 8, 31, 8, 8
minimum size: 422x402 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=438, y=441)))
> windowsize 800 800
> turn y 180
[Repeated 1 time(s)]
> save C:\Users\krh021/Desktop/ic0_map5.png width 3000 transparentBackground
> true
> turn y 180
> save C:\Users\krh021/Desktop/ic0_map3.png width 3000 transparentBackground
> true
> hide #!3 models
> show #!4 models
> save C:\Users\krh021/Desktop/ic3_map3.png width 3000 transparentBackground
> true
> turn y 180
> save C:\Users\krh021/Desktop/ic3_map5.png width 3000 transparentBackground
> true
> turn y 180
> hide #!4 models
> show #!13 models
> show #!16 models
> hide #!16 models
> show #!16 models
> transparency #16 80
> save C:\Users\krh021/Desktop/ic0_map6.png width 3000 transparentBackground
> true
> hide #!13 models
> hide #!16 models
> show #!17 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!15 models
> save C:\Users\krh021/Desktop/ic3_map6.png width 3000 transparentBackground
> true
> hide #!17 models
> show #!11 models
> clip 1
Expected a keyword
> clip front 1
[Repeated 5 time(s)]
> clip front -1
[Repeated 2 time(s)]
> surface dust #15 size 7.51
> surface dust #11 size 7.51
> clip front -1
> clip front 1
[Repeated 1 time(s)]
> save C:\Users\krh021/Desktop/ic3_map4.png width 3000 transparentBackground
> true
> hide #!15 models
> show #!13 models
> hide #!11 models
> show #!9 models
> clip front 1
[Repeated 1 time(s)]
> clip front -1
> clip front 1
> save C:\Users\krh021/Desktop/ic0_map4.png width 3000 transparentBackground
> true
> save C:/Users/krh021/Desktop/ChimeraX/IC_PDB.cxs includeMaps true
——— End of log from Fri Aug 23 15:56:25 2024 ———
opened ChimeraX session
> show #!2 models
> hide #!9 models
> hide #!2 models
> hide #!13 models
> show #!1 models
> save C:\Users\krh021/Desktop/test4.png width 3000 transparentBackground true
> cartoon style #1 modeHelix tube sides 20
> nucleotides #!1 ladder
> save C:\Users\krh021/Desktop/test4.png width 3000 transparentBackground true
> lighting flat
> lighting soft
> lighting simple
> lighting soft
> lighting full
[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
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> save C:\Users\krh021/Desktop/test4.png width 3000 transparentBackground true
> graphics silhouettes width 4
> save C:\Users\krh021/Desktop/test4.png width 3000 transparentBackground true
> dssp
> view IC
> view IC2
> save C:\Users\krh021/Desktop/test4.png width 3000 transparentBackground true
> graphics silhouettes width 6
> save C:\Users\krh021/Desktop/test4.png width 3000 transparentBackground true
> alias cylinders cartoon style protein modeh tube rad 2 sides 24
> alias cylinders cartoon style protein modeh tube rad 4 sides 24
> cylinders
> alias cylinders cartoon style protein modeh tube rad 2 sides 24
> cylinders
> cartoon style coil thickness 0.25
> cartoon style coil thickness 1
> cartoon style coil thickness 0.5
> save C:\Users\krh021/Desktop/test4.png width 3000 transparentBackground true
> cartoon style coil thickness 0.75
> save C:\Users\krh021/Desktop/test4.png width 3000 transparentBackground true
> lighting flat
> 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 shadows true
> lighting shadows false
> lighting flat
> graphics silhouettes width 8
> save C:\Users\krh021/Desktop/test4.png width 3000 transparentBackground true
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> save C:\Users\krh021/Desktop/test3.png width 3000 transparentBackground true
> hide #!2 models
> show #!3 models
> lighting soft
> lighting full
> graphics silhouettes false
> graphics silhouettes true
> hide #!3 models
> show #!2 models
> lighting flat
> nucleotides #!2 ladder
> save C:\Users\krh021/Desktop/test3.png width 3000 transparentBackground true
> save C:/Users/krh021/Desktop/ChimeraX/IC3/IC3_PDB.cxs includeMaps true
——— End of log from Tue Sep 10 16:34:01 2024 ———
opened ChimeraX session
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> graphics silhouettes false
> lighting soft
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> windowsize 800 800
> view name 2D
> save C:\Users\krh021/Desktop/test.png width 3000 transparentBackground true
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> save C:\Users\krh021/Desktop/test2.png width 3000 transparentBackground true
[Repeated 1 time(s)]
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> save C:/Users/krh021/Desktop/ChimeraX/IC3/IC3_PDB.cxs includeMaps true
——— End of log from Wed Sep 11 17:48:32 2024 ———
opened ChimeraX session
> close #1,4-9,11-17
> save C:/Users/krh021/Desktop/ChimeraX/IC_Models_Maps.cxs includeMaps true
> show #!2 models
> hide #!2 models
> show #!2 models
> open pymol_view.py
executed pymol_view.py
> open pymol_view.py
FYI: command is replacing existing command: "pymolview"
executed pymol_view.py
> pymolview 0.5338886380195618, 0.19662711024284363, 0.8223745822906494,
> 0.1919989138841629, 0.9189900159835815, -0.34437406063079834,
> -0.8234677910804749, 0.34175243973731995, 0.452885240316391, 0.0, 0.0,
> -177.17364501953125, -27.024879455566406, 14.224754333496094,
> -6.485495567321777, 139.68505859375, 214.6622314453125, -20.0
> pymolview -0.254299551, -0.347804695, 0.902413368,\
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pymol_view.py", line 12, in pymol_view
view = [float(p) for p in parameters.split(',')]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pymol_view.py", line 12, in <listcomp>
view = [float(p) for p in parameters.split(',')]
^^^^^^^^
ValueError: could not convert string to float: '\\\'
ValueError: could not convert string to float: '\\\'
File "pymol_view.py", line 12, in
view = [float(p) for p in parameters.split(',')]
^^^^^^^^
See log for complete Python traceback.
> pymolview -0.254299551, -0.347804695, 0.902413368,
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pymol_view.py", line 12, in pymol_view
view = [float(p) for p in parameters.split(',')]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pymol_view.py", line 12, in <listcomp>
view = [float(p) for p in parameters.split(',')]
^^^^^^^^
ValueError: could not convert string to float: ''
ValueError: could not convert string to float: ''
File "pymol_view.py", line 12, in
view = [float(p) for p in parameters.split(',')]
^^^^^^^^
See log for complete Python traceback.
> pymolview -0.254299551, -0.347804695, 0.902413368, -0.433934182,
> -0.792852163, -0.427871048, 0.864304245, -0.500397503, 0.050697379,
> 0.000675187, 0.004853413, -369.187286377, 138.818176270, 139.298034668,
> 142.332214355, -3933.625000000, 4671.653808594, 20.000000000
[Repeated 1 time(s)]
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> open C:/Users/krh021/Desktop/IC2024/final_models/IC0_J792_V5.pdb
> C:/Users/krh021/Desktop/IC2024/final_models/IC3_J1131_V9.pdb
Summary of feedback from opening
C:/Users/krh021/Desktop/IC2024/final_models/IC3_J1131_V9.pdb
---
warning | End residue of secondary structure not found: HELIX 43 43 PRO E 549 GLU E 555 1 7
Chain information for IC0_J792_V5.pdb #1
---
Chain | Description
A | No description available
B | No description available
E | No description available
N | No description available
T | No description available
Chain information for IC3_J1131_V9.pdb #4
---
Chain | Description
A | No description available
B | No description available
E | No description available
N | No description available
R | No description available
T | No description available
> hide #!3 models
> hide #!4 models
> ~clip
> hide #!2 models
> hide #!1 models
> show #!2 models
> color #*/E:1-218 #199999
> color #*/E:219-355 #199999
> color #*/E:356-710 #B2B2B2
> color #*/E:588-604 #BF00BF
> color #*/E:605-624 #BF00BF
> color #*/E:711-790 #FFB233
> color #*/E:791-1230 #00FF7F
> color #*/E:954-1044 #FFA5D8
> color #*/E:1079-1111 #FFDD5E
> color #*/T blue
> color #*/R red
> color #*/N cyan
> color #*/A #B12121
> color #*/B #007FFF
> show #!1 models
> hide #!2 models
> hide #!1 atoms
> show #!1 cartoons
> show #!4 models
> show #!1,4 cartoons
> hide #!1,4 atoms
> hide #!4 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> mcopy #2 toAtoms #4 settings c
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!2 models
> hide #!4 models
> mcopy #2 toAtoms #1 settings a
> hide #!2 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
> hide #!2 models
> ribbon style nucleic xsect round width 0.5 thick 0.5
> hide #!1 models
> show #!2 models
> save C:/Users/krh021/Desktop/ChimeraX/IC_Models_Maps.cxs includeMaps true
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> lighting flat
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> view list
Named views: 2D, IC, IC2
> view name, all
Expected an objects specifier or a view name or a keyword
> view name all
> view 2D
> view IC
> view IC2
> save C:\Users\krh021/Desktop/test.png
> view all
> view IC2
> view all
> pymolview -0.254299551, -0.347804695, 0.902413368, -0.433934182,
> -0.792852163, -0.427871048, 0.864304245, -0.500397503, 0.050697379,
> 0.000675187, 0.004853413, -369.187286377, 138.818176270, 139.298034668,
> 142.332214355, -3933.625000000, 4671.653808594, 20.000000000
> lighting soft
> windowsize 800 800
> view name all
> view IC2
> view name all
> view name IC2
> pymolview -0.254299551, -0.347804695, 0.902413368, -0.433934182,
> -0.792852163, -0.427871048, 0.864304245, -0.500397503, 0.050697379,
> 0.000675187, 0.004853413, -369.187286377, 138.818176270, 139.298034668,
> 142.332214355, -3933.625000000, 4671.653808594, 20.000000000
> view name all
> view all
> view name all
> view IC2
> view all
> view name all
> lighting flat
> lighting flat depthCue false
> show #!1 models
> hide #!2 models
> ~clip
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> save C:\Users\krh021/Desktop/test.png width 3000 transparentBackground true
> cartoon style coil thickness 0.25
> show #!2 models
> hide #!1 models
> undo
[Repeated 1 time(s)]
> show #!2 models
> hide #!2 models
> undo
[Repeated 2 time(s)]
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!1 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
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!4 models
> hide #!1 models
> mcopy #2 toAtoms #4 settings a
> show #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> show #!1 models
> select #*/N/T
6120 atoms, 6864 bonds, 300 residues, 3 models selected
> show sel atoms
> nucleotides sel ladder
> hide #!4 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> select add #2
18839 atoms, 19876 bonds, 3 pseudobonds, 1878 residues, 6 models selected
> select add #1
31558 atoms, 32888 bonds, 6 pseudobonds, 3456 residues, 10 models selected
> select add #4
44353 atoms, 45983 bonds, 9 pseudobonds, 5037 residues, 11 models selected
> select subtract #2
29594 atoms, 30683 bonds, 6 pseudobonds, 3359 residues, 9 models selected
> select subtract #1
14835 atoms, 15383 bonds, 3 pseudobonds, 1681 residues, 2 models selected
> select subtract #4
Nothing selected
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!4 models
> show #!2 models
> hide #!4 models
> cartoon style coil thickness 0.25
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> select ~sel & ##selected
Nothing selected
> cartoon style coil thickness 0.5
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> show #!4 models
> hide #!2 models
> hide #!4 models
> show #!2 models
> hide #!1 models
> cartoon style coil thickness 0.6
> show #!1 models
> hide #!2 models
> dssp
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> close #2
> rename #3 id #2
> rename #4 id #3
> save C:/Users/krh021/Desktop/ChimeraX/IC_Models_Maps.cxs includeMaps true
> save C:\Users\krh021/Desktop/test.png width 3000 transparentBackground true
> save C:\Users\krh021/Desktop/test.png width 3000
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes width 3
> graphics silhouettes width 6
[Repeated 1 time(s)]
> save C:\Users\krh021/Desktop/test.png width 3000 transparentBackground true
> show #!3 models
> hide #!1 models
> save C:\Users\krh021/Desktop/test2.png width 3000
> save C:\Users\krh021/Desktop/test2.png width 3000 transparentBackground true
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> open C:/Users/krh021/Desktop/IC2024/final_maps/DeepEM_highRes_J1131.mrc
Opened DeepEM_highRes_J1131.mrc as #4, grid size 384,384,384, pixel 0.751,
shown at level 0.00298, step 2, values float32
> hide #!4 models
> volume #4 level 0.0174
> volume #4 step 1
> surface dust #4 size 7.51
> show #!3 models
> hide #!4 models
> rename #4 IC3_map.mrc
> rename #2 IC0_map.mrc
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!2 models
> show #!1 models
> color zone #2 near #1 distance 4.51
> color zone #2 near #1 distance 12
> show #!3 models
> show #!4 models
> hide #!2 models
> hide #!1 models
> color zone #4 near #3 distance 4.51
[Repeated 1 time(s)]
> color zone #4 near #3 distance 12
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> lighting soft
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> show #!4 models
> hide #!2 models
> lighting soft
> view all
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> ui tool show "Map Eraser"
> volume erase #4 center 194.9,159.38,112.99 radius 20.655
Opened IC3_map.mrc copy as #6, grid size 384,384,384, pixel 0.751, shown at
step 1, values float32
> show #!4 models
> hide #!6 models
> hide #!4 models
> show #!6 models
> surface dust #6 size 7.51
> color zone #6 near #3 distance 12
> close #4
> rename #6 IC3_map.mrc
> rename #6 id #4
> view all
> view IC2
> ~clip
> view name IC2
> view IC2
> view IC1
Expected an objects specifier or a view name or a keyword
> view IC
> ~clip
> view name IC
> view IC2
> view all
> view list
Named views: 2D, IC, IC2, all
> view all delete
Expected an integer >= 1 or a keyword
> view delete all
> view list
No named views.
> view name IC2
> turn x 180
[Repeated 1 time(s)]
> turn y 180
[Repeated 1 time(s)]
> turn x 90
[Repeated 3 time(s)]
> turn x 180
[Repeated 1 time(s)]
> turn x 150
[Repeated 1 time(s)]
> view IC2
> turn x 160
> turn y 160
> turn z 180
[Repeated 1 time(s)]
> turn z 90
[Repeated 3 time(s)]
> turn x 180
> view name IC
> pymolview -0.254299551, -0.347804695, 0.902413368, -0.433934182,
> -0.792852163, -0.427871048, 0.864304245, -0.500397503, 0.050697379,
> 0.000675187, 0.004853413, -369.187286377, 138.818176270, 139.298034668,
> 142.332214355, -3933.625000000, 4671.653808594, 20.000000000
> windowsize 800 800
> view name IC3
> show #!1 models
> hide #!4 models
> show #!2 models
> hide #!1 models
> view name IC
> view name IC3
> view IC2
> turn x 180
> view IC2
> turn x 180
> turn y 2
> turn y -2
> turn z 50
> turn z -50
[Repeated 1 time(s)]
> view name IC1
> view list
Named views: IC, IC1, IC2, IC3
> view delete IC
> view list
Named views: IC1, IC2, IC3
> view IC3
> save C:/Users/krh021/Desktop/ChimeraX/IC_Models_Maps.cxs includeMaps true
[Repeated 1 time(s)]
> windowsize 800 800
> depthcue off
Unknown command: depthcue off
> lighting depthCue false
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> show #!3 models
> color zone #4 near #3 distance 4.51
> color zone #4 near #3 distance 15
> hide #!3 models
> volume #4 level 0.08924
> volume #4 level 0.1252
> volume #4 level 0.0174
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!4 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> save C:\Users\krh021/Desktop/test2.png width 3000 transparentBackground true
> show #!4 models
> hide #!2 models
> save C:\Users\krh021/Desktop/test2.png width 3000 transparentBackground true
> show #!1 models
> hide #!4 models
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> save C:\Users\krh021/Desktop/test2.png width 3000 transparentBackground true
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> save C:\Users\krh021/Desktop/test2.png width 3000 transparentBackground true
> save C:/Users/krh021/Desktop/ChimeraX/IC_Models_Maps.cxs includeMaps true
——— End of log from Fri Sep 27 15:53:32 2024 ———
opened ChimeraX session
> open C:/Users/krh021/Desktop/IC2024/final_maps/DeepEM_highRes_J340.mrc
Opened DeepEM_highRes_J340.mrc as #5, grid size 384,384,384, pixel 0.73, shown
at level 0.000487, step 2, values float32
> volume #5 step 1
> volume #5 level 0.0174
> open C:/Users/krh021/Desktop/IC2024/final_maps/DeepEM_highRes_J58.mrc
Opened DeepEM_highRes_J58.mrc as #6, grid size 384,384,384, pixel 0.73, shown
at level 0.000506, step 2, values float32
> volume #6 step 1
> volume #6 level 0.0174
> surface dust #5 size 7.3
> surface dust #6 size 7.3
> open C:/Users/krh021/Desktop/IC2024/final_models/EC8_J340_V9.pdb
Summary of feedback from opening
C:/Users/krh021/Desktop/IC2024/final_models/EC8_J340_V9.pdb
---
warning | End residue of secondary structure not found: HELIX 17 17 PRO E 549 GLU E 555 1 7
Chain information for EC8_J340_V9.pdb #7
---
Chain | Description
E | No description available
N | No description available
R | No description available
T | No description available
> open C:/Users/krh021/Desktop/IC2024/final_models/EC13_J58_V7.pdb
Summary of feedback from opening
C:/Users/krh021/Desktop/IC2024/final_models/EC13_J58_V7.pdb
---
warning | End residue of secondary structure not found: HELIX 18 18 PRO E 549 GLU E 555 1 7
Chain information for EC13_J58_V7.pdb #8
---
Chain | Description
E | No description available
N | No description available
R | No description available
T | No description available
> hide #!6 models
> hide #!5 models
> mmaker #7 to #3
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 IC3_J1131_V9.pdb, chain E (#3) with EC8_J340_V9.pdb, chain E (#7),
sequence alignment score = 4714.8
RMSD between 686 pruned atom pairs is 1.100 angstroms; (across all 963 pairs:
2.492)
> mmaker #8 to #3
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 IC3_J1131_V9.pdb, chain E (#3) with EC13_J58_V7.pdb, chain E (#8),
sequence alignment score = 4734.1
RMSD between 795 pruned atom pairs is 1.208 angstroms; (across all 969 pairs:
2.216)
> hide #!3 models
> cartoon style #7-8 modeHelix tube sides 20
> dssp
> cartoon style coil thickness 0.6
> color #*/E:1-218 #199999
> color #*/E:219-355 #199999
> color #*/E:356-710 #B2B2B2
> color #*/E:588-604 #BF00BF
> color #*/E:605-624 #BF00BF
> color #*/E:711-790 #FFB233
> color #*/E:791-1230 #00FF7F
> color #*/E:954-1044 #FFA5D8
> color #*/E:1079-1111 #FFDD5E
> color #*/T blue
> color #*/R red
> color #*/N cyan
> color #*/A #B12121
> color #*/B #007FFF
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!7 models
> hide #!8 models
> show #!3 models
> hide #!3 models
> show #!8 models
> show #!7 models
> select #7.8/N/R/T
Nothing selected
> select #7,8/N/R/T
1700 atoms, 1896 bonds, 1 pseudobond, 81 residues, 3 models selected
> show sel atoms
> nucleotides sel ladder
> select clear
> select #7/R:9
31 atoms, 33 bonds, 1 residue, 1 model selected
> color sel yellow
> hide #!7 models
> select #8/R:14
29 atoms, 30 bonds, 1 residue, 1 model selected
> color sel yellow
> hide #!8 models
> show #!8 models
> show #!7 models
> show #!6 models
> hide #!6 models
> save C:/Users/krh021/Desktop/ChimeraX/EC8_EC13_Models_Maps.cxs includeMaps
> true
> ui tool show "Fit in Map"
> fitmap #5 inMap #4
Fit map DeepEM_highRes_J340.mrc in map IC3_map.mrc using 191505 points
correlation = 0.6529, correlation about mean = 0.4212, overlap = 1.277e+04
steps = 324, shift = 14.7, angle = 15.8 degrees
Position of DeepEM_highRes_J340.mrc (#5) relative to IC3_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99543110 -0.09498877 0.00969802 19.58140973
0.08935815 0.96255524 0.25593461 -36.73748394
-0.03364580 -0.25389868 0.96664545 57.41517225
Axis -0.93742092 0.07969546 0.33895524
Axis point 0.00000000 205.82884149 173.08888752
Rotation angle (degrees) 15.77938510
Shift along axis -1.82266021
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> hide #!5 models
> show #!5 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> fitmap #5 inMap #2
Fit map DeepEM_highRes_J340.mrc in map IC0_map.mrc using 191505 points
correlation = 0.6768, correlation about mean = 0.4547, overlap = 1.336e+04
steps = 88, shift = 1.69, angle = 4.35 degrees
Position of DeepEM_highRes_J340.mrc (#5) relative to IC0_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.98677623 -0.16196321 -0.00637133 31.85751254
0.15701410 0.94538676 0.28564041 -49.10579119
-0.04023987 -0.28286356 0.95831569 64.69299366
Axis -0.87092878 0.05188545 0.48866242
Axis point 0.00000000 195.54853425 209.54246055
Rotation angle (degrees) 19.04908101
Shift along axis 1.31953401
> fitmap #6 inMap #2
Fit map DeepEM_highRes_J58.mrc in map IC0_map.mrc using 194375 points
correlation = 0.276, correlation about mean = 0.03212, overlap = 3434
steps = 132, shift = 2.27, angle = 8 degrees
Position of DeepEM_highRes_J58.mrc (#6) relative to IC0_map.mrc (#2)
coordinates:
Matrix rotation and translation
0.99488083 0.09223932 -0.04127997 -5.67922596
-0.09577863 0.99094541 -0.09409384 29.33677253
0.03222705 0.09756589 0.99470715 -19.02093621
Axis 0.68851769 -0.26406635 -0.67543494
Axis point 0.00000000 202.75111541 295.61195479
Rotation angle (degrees) 8.00056506
Shift along axis 1.19030287
> fitmap #6 inMap #5
Fit map DeepEM_highRes_J58.mrc in map DeepEM_highRes_J340.mrc using 194375
points
correlation = 0.2666, correlation about mean = 0.04597, overlap = 2678
steps = 176, shift = 14.1, angle = 5.85 degrees
Position of DeepEM_highRes_J58.mrc (#6) relative to DeepEM_highRes_J340.mrc
(#5) coordinates:
Matrix rotation and translation
0.94188046 0.31330617 -0.12124541 -18.83101623
-0.33483521 0.84613633 -0.41465490 134.39576255
-0.02732379 0.43115258 0.90186521 -46.33824261
Axis 0.79068190 -0.08780027 -0.60589870
Axis point 0.00000000 165.39588010 263.03588776
Rotation angle (degrees) 32.33438492
Shift along axis 1.38695254
> select add #6
29 atoms, 30 bonds, 1 residue, 3 models selected
> select add #8
8744 atoms, 9039 bonds, 3 pseudobonds, 1023 residues, 4 models selected
> select subtract #8
2 models selected
> select subtract #6
Nothing selected
> select add #6
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.40076,0.9006,0.16826,-46.962,0.23338,0.077245,-0.96931,232.24,-0.88596,0.42773,-0.17922,254
> view matrix models
> #6,0.70647,0.55942,-0.43353,38.26,0.071417,-0.66578,-0.74273,316.4,-0.70413,0.49375,-0.5103,267.04
> view matrix models
> #6,-0.011409,-0.85559,-0.51752,333.76,-0.9549,-0.14425,0.25953,256.51,-0.29671,0.49714,-0.81536,250.93
> view matrix models
> #6,-0.95733,-0.25441,0.13712,302.54,-0.023417,0.54116,0.84059,-51.144,-0.28806,0.80151,-0.52402,169.13
> fitmap #6 inMap #5
Fit map DeepEM_highRes_J58.mrc in map DeepEM_highRes_J340.mrc using 194375
points
correlation = 0.8091, correlation about mean = 0.6633, overlap = 1.574e+04
steps = 460, shift = 14, angle = 32.2 degrees
Position of DeepEM_highRes_J58.mrc (#6) relative to DeepEM_highRes_J340.mrc
(#5) coordinates:
Matrix rotation and translation
-0.79803397 -0.59682182 0.08333973 323.68812245
-0.22848543 0.42764448 0.87459397 -5.53642490
-0.55761654 0.67891378 -0.47763991 200.57748958
Axis -0.25588679 0.83816478 0.48166560
Axis point 184.25528743 0.00000000 63.22898338
Rotation angle (degrees) 157.52024563
Shift along axis 9.14332510
> select subtract #6
Nothing selected
> view IC3
> show #!8 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> rename #6 EC13_map.mrc
> rename #5 EC8_map.mrc
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!5 models
> color zone #6 near #8 distance 4.38
> color zone #6 near #8 distance 12
> color zone #6 near #8 distance 15
> color zone #6 near #8 distance 20
> hide #!8 models
> hide #!6 models
> show #!7 models
> show #!5 models
> color zone #5 near #7 distance 4.38
> color zone #5 near #7 distance 20
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!5 models
> show #!5 models
> show #!7 models
> hide #!7 models
> hide #!5 models
> show #!7 models
> show #!3 models
> hide #!3 models
> 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 #!1 models
> hide #!1 models
> close #1-4
> rename #7 id #1
> rename #5 id #2
> rename #6 id #4
> rename #8 id #3
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!4 models
> show #!4 models
> ui tool show "Map Eraser"
> lighting soft
> graphics silhouettes false
> volume erase #4 center 169.83,122.21,118.51 radius 7.0435
Opened EC13_map.mrc copy as #6, grid size 384,384,384, pixel 0.73, shown at
step 1, values float32
> volume erase #6 center 170.46,116.02,112.5 radius 7.0118
> hide #!3 models
> hide #!6 models
> show #!2 models
> volume erase #2 center 146.08,128.71,124.75 radius 7.012
Opened EC8_map.mrc copy as #7, grid size 384,384,384, pixel 0.73, shown at
step 1, values float32
> show #!6 models
> close #5
> surface dust #6 size 7.3
> surface dust #7 size 7.3
> hide #!7 models
> close #5
> show #!4 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> close #4
> rename #6 id #4
> close #2
> rename #7 id #2
> rename #2 EC8_map.mrc
> rename #4 EC13_map.mrc
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> color zone #4 near #3 distance 4.38
> color zone #4 near #3 distance 20
> hide #!4 models
> hide #!3 models
> show #!2 models
> show #!1 models
> close #5
> color zone #2 near #1 distance 4.38
> color zone #2 near #1 distance 20
> view IC3
> hide #!1 models
> save C:/Users/krh021/Desktop/ChimeraX/EC8_EC13_Models_Maps.cxs includeMaps
> true
> save C:\Users\krh021/Desktop/test2.png width 3000 transparentBackground true
> view IC3
> show #!4 models
> hide #!2 models
> view IC3
> save C:\Users\krh021/Desktop/test2.png width 3000 transparentBackground true
> close #5
> save C:\Users\krh021/Desktop/test2.png width 3000 transparentBackground true
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!1 models
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> save C:\Users\krh021/Desktop/test2.png width 3000 transparentBackground true
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!2 models
> hide #!4 models
> show #!1 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> save C:\Users\krh021/Desktop/test2.png width 3000 transparentBackground true
> show #!1 models
> select #*/R
436 atoms, 487 bonds, 19 residues, 2 models selected
> show sel cartoons
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> select clear
> save C:\Users\krh021/Desktop/test2.png width 3000 transparentBackground true
> show #!3 models
> hide #!1 models
> save C:\Users\krh021/Desktop/test2.png width 3000 transparentBackground true
> save C:/Users/krh021/Desktop/ChimeraX/EC8_EC13_Models_Maps.cxs includeMaps
> true
——— End of log from Fri Sep 27 16:57:34 2024 ———
opened ChimeraX session
> lighting soft
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> color #*/E:1-218 #199999
> color #*/E:219-355 #199999
> color #*/E:356-710 #B2B2B2
> color #*/E:588-604 #FF9999
> color #*/E:605-624 #BF00BF
> color #*/E:711-790 #FFB233
> color #*/E:791-1230 #00FF7F
> color #*/E:954-1044 #FFA5D8
> color #*/E:1079-1111 #FFDD5E
> color #*/T blue
> color #*/R red
> color #*/N cyan
> color #*/A #B12121
> color #*/B #007FFF
> color #*/R:ATP yellow
> color #*/R:CTP yellow
> color #*:MG purple
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> view
> open C:/Users/krh021/Desktop/IC2024/final_models/IC0_J792_V5.pdb
Summary of feedback from opening
C:/Users/krh021/Desktop/IC2024/final_models/IC0_J792_V5.pdb
---
warnings | End residue of secondary structure not found: HELIX 1 1 SER A 55 GLN A 70 1 16
Start residue of secondary structure not found: HELIX 2 2 THR A 76 GLU A 89 1
14
Start residue of secondary structure not found: HELIX 3 3 ASP A 92 GLN A 119 1
28
Start residue of secondary structure not found: HELIX 4 4 PRO A 122 LEU A 150
1 29
Start residue of secondary structure not found: HELIX 5 5 ALA A 160 ARG A 168
1 9
Start residue of secondary structure not found: HELIX 6 6 PRO A 177 ASN A 190
1 14
1 messages similar to the above omitted
Chain information for IC0_J792_V5.pdb #5
---
Chain | Description
A | No description available
B | No description available
E | No description available
N | No description available
T | No description available
> view
> hide #!5 models
> show #!5 models
> view
> hide #!5 models
> view
> show #!5 models
> hide #!3 models
> hide #!1 models
> hide #!5 atoms
> show #!5 cartoons
> select #5/N/R/T
2040 atoms, 2288 bonds, 100 residues, 1 model selected
> show sel atoms
> nucleotides sel ladder
> select add #5
14759 atoms, 15300 bonds, 3 pseudobonds, 1678 residues, 2 models selected
> select subtract #5
Nothing selected
> dssp
> hide #!5 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> hide #!5 models
> show #!3 models
> view name IC5
> show #!5 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!4 models
> cartoon style protein modeHelix tube radius 1.5 sides 24
> cartoon style nucleic xsection oval width 1.2 thickness 1.2
> hide #!5 models
> hide #!4 models
> hide #!2 models
> select #*:MG
2 atoms, 2 residues, 2 models selected
> size atomRadius +.5
Changed 32004 atom radii
> select add #3
8745 atoms, 9039 bonds, 3 pseudobonds, 1024 residues, 3 models selected
> select subtract #3
1 atom, 1 residue, 1 model selected
> select add #1
8501 atoms, 8771 bonds, 3 pseudobonds, 1008 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #1
8501 atoms, 8771 bonds, 3 pseudobonds, 1008 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!3 models
> save C:\Users\krh021/Desktop/7.png width 3000 transparentBackground true
> hide #!1 models
> show #!2 models
> lighting soft
> alias soft lighting soft depthCue off
> soft
> lighting soft
> select ~sel & ##selected
Nothing selected
> lighting soft depthCue false
> graphics silhouettes false
> save C:\Users\krh021/Desktop/8.png width 3000 transparentBackground true
> turn y 180
> save C:\Users\krh021/Desktop/9.png width 3000 transparentBackground true
> turn y 180
> save C:/Users/krh021/Desktop/ChimeraX/EC8_EC13_Models_Maps.cxs includeMaps
> true
——— End of log from Mon Oct 14 15:36:43 2024 ———
opened ChimeraX session
> show #!1 models
> hide #!2 models
> soft
> graphics silhouettes true
> graphics silhouettes width 2
> save C:\Users\krh021/Desktop/icec8.png width 3000
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> show #!3 models
> color zone #4 near #3 distance 4.38
> color zone #4 near #3 distance 12
> surface dust #4 size 7.3
> hide #!3 models
> graphics silhouettes false
> save C:\Users\krh021/Desktop/icec13_map1.png width 3000
> save C:\Users\krh021/Desktop/icec13_map1.png width 3000
> transparentBackground true
> turn y 180
> save C:\Users\krh021/Desktop/icec13_map2.png width 3000
> transparentBackground true
> turn y 180
> hide #!4 models
> show #!3 models
> graphics silhouettes true
> save C:\Users\krh021/Desktop/icec13.png width 3000
> hide #!3 models
> show #!1 models
> select #1/E
7742 atoms, 7926 bonds, 3 pseudobonds, 971 residues, 2 models selected
> hide sel atoms
> select add #1
8501 atoms, 8771 bonds, 3 pseudobonds, 1008 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!3 models
> hide #!1 models
> select #3/E
7801 atoms, 7988 bonds, 2 pseudobonds, 977 residues, 2 models selected
> hide sel atoms
> select add #3
8744 atoms, 9039 bonds, 3 pseudobonds, 1023 residues, 2 models selected
> select subtract #3
Nothing selected
> save C:\Users\krh021/Desktop/icec13.png width 3000
> graphics silhouettes width 2
> hide #!3 models
> show #!1 models
> save C:\Users\krh021/Desktop/icec8.png width 3000
> view list
Named views: IC1, IC2, IC3, IC5
> view IC5
> save C:/Users/krh021/Desktop/ChimeraX/EC8_EC13_Models_Maps.cxs includeMaps
> true
——— End of log from Tue Oct 15 12:06:28 2024 ———
opened ChimeraX session
> show #!2 models
> hide #!1 models
> show #!1 models
> color zone #2 near #1 distance 4.38
> color zone #2 near #1 distance 12
> color zone #2 near #1 distance 10
> hide #!1 models
> color zone #2 near #1 distance 8
> 10
Unknown command: 10
> save C:\Users\kherb/Desktop/1.png width 3000 transparentBackground true
> view list
Named views: IC1, IC2, IC3, IC5
> view IC1
> view IC2
> view IC3
> view IC5
> turn y 180
> save C:\Users\kherb/Desktop/2.png width 3000 transparentBackground true
> show #!3 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!2 models
> save C:/Users/kherb/Desktop/ChimeraX/EC13/EC8_EC13_Models_Maps.cxs
> includeMaps true
——— End of log from Sun Nov 17 21:45:19 2024 ———
opened ChimeraX session
> open "D:/Temiakov Lab/KH Cryo-EM/IC_modeling/IC2024/final_models/TEFM-
> EC9_J113_v6.pdb"
Chain information for TEFM-EC9_J113_v6.pdb #6
---
Chain | Description
A | No description available
B | No description available
E | No description available
N | No description available
R | No description available
T | No description available
> open "D:/Temiakov Lab/KH Cryo-
> EM/IC_modeling/IC2024/final_maps/DeepEM_tight_J113.mrc"
Opened DeepEM_tight_J113.mrc as #7, grid size 320,320,320, pixel 0.73, shown
at level 0.00511, step 1, values float32
> hide #!2 models
> hide #!6 models
> show #!1 models
> mcopy #1 on #6 settings all
Expected a keyword
> mcopy #1 toAtoms #6 settings all
> hide #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> undo
[Repeated 8 time(s)]
> hide #!7 models
> hide #!2 models
> close #6
> open "D:/Temiakov Lab/KH Cryo-EM/IC_modeling/IC2024/final_models/TEFM-
> EC9_J113_v6.pdb"
Chain information for TEFM-EC9_J113_v6.pdb #6
---
Chain | Description
A | No description available
B | No description available
E | No description available
N | No description available
R | No description available
T | No description available
> show #!7 models
> color #*/E:122-355 #199999
> color #*/E:356-643 #B2B2B2
> color #*/E:588-605 #FF9999
> color #*/E:605-623 #BF00BF
> color #*/E:643-1230 #00FF7F
> color #*/E:711-790 #FFB233
> color #*/E:954-1044 #FFA5D8
> color #*/T blue
> color #*/R red
> color #*/N cyan
> color #*/A/B #B24C66
> color #*/R:ATP yellow
> color #*/R:CTP yellow
> color #*:MG purple
> color #*:APC yellow
> hide #!6 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!6 models
> hide #!6 atoms
> show #!6 cartoons
> cartoon style protein modeHelix tube radius 1.5 sides 24
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> close #5
> show #!6 models
> hide #!6 models
> show #!1 models
> cartoon style nucleic xsection oval width 1.2 thickness 1.2
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> size atomRadius +.5
Changed 29321 atom radii
> select #6/N/R/T
1461 atoms, 1637 bonds, 70 residues, 1 model selected
> show sel atoms
> nucleotides sel tube/slab shape box
> nucleotides sel ladder
> select clear
> select #6/MG
Nothing selected
> select #6:MG
1 atom, 1 residue, 1 model selected
> show sel atoms
> size atomRadius +.5 ## for MG
Expected a keyword
> size atomRadius +.5
Changed 29321 atom radii
> show #!1 models
> hide #!6 models
> show #!6 models
> cartoon style coil thickness 0.6
> graphics silhouettes width 6
> hide #!6 models
> hide #!1 models
> show #!7 models
> hide #!7 models
> show #!4 models
> graphics silhouettes false
> graphics silhouettes true
> view list
Named views: IC1, IC2, IC3, IC5
> view IC1
> view IC2
> view IC3
> view IC5
> hide #!4 models
> show #!4 models
> graphics silhouettes false
> save C:\Users\kherb/Desktop/EC13.png width 3000
> windowsize 800 800
> show #!6 models
> hide #!4 models
> graphics silhouettes true
> dssp
Computing secondary structure
> view name EC9
> select clear
> view name EC9
> save C:\Users\kherb/Desktop/EC9.png width 3000
> size atomRadius -.5
Changed 29321 atom radii
> save C:\Users\kherb/Desktop/EC9.png width 3000
> save C:\Users\kherb/Desktop/EC9.png width 3000 transparentBackground true
> graphics silhouettes width 3
> save C:\Users\kherb/Desktop/EC9.png width 3000 transparentBackground true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> graphics silhouettes width 2
> lighting gentle intensity 0.2
> save C:\Users\kherb/Desktop/EC9.png width 3000 transparentBackground true
> lighting gentle intensity 0.1
> graphics silhouettes width 3
> save C:\Users\kherb/Desktop/EC9.png width 3000 transparentBackground true
> lighting gentle intensity 0
> save C:\Users\kherb/Desktop/EC9.png width 3000 transparentBackground true
> save C:\Users\kherb/Desktop/EC9.png width 3000
> windowsize 800 800
> view name EC9
> hide #!6 models
> show #!7 models
> show #!6 models
> volume #7 level 0.02476
> volume #7 level 0.005107
> volume #7 level 0.00611
> volume #7 level 0.00711
> volume #7 level 0.00811
> surface dust #7 size 7.3
> color zone #7 near #6 distance 4.38
> color zone #7 near #6 distance 15
> hide #!6 models
> volume #7 level 0.0111
> volume #7 level 0.012
> graphics silhouettes false
> save C:\Users\kherb/Desktop/EC9_map1.png width 3000
> turn x 180
[Repeated 1 time(s)]
> turn y 180
> lighting soft
> save C:\Users\kherb/Desktop/EC9_map2.png width 3000
> turn y 180
> save C:\Users\kherb/Desktop/EC9_map1.png width 3000
> close #1-2
> rename #3 id #1
> rename #4 id #2
> rename #6 id #3
> rename #7 id #4
> save "D:/Temiakov Lab/KH Cryo-
> EM/IC_modeling/ChimeraX/EC9-TEFM/EC9TEFM_Models_Maps.cxs"
> hide #!4 models
> show #!3 models
> graphics silhouettes true
> lighting soft
> save C:\Users\kherb/Desktop/EC9.png width 3000
> lighting soft depthCue false
> graphics silhouettes width 2
> save C:\Users\kherb/Desktop/EC9.png width 3000
> show #!1 models
> hide #!1 models
> save C:\Users\kherb/Desktop/EC92.png width 3000
[Repeated 1 time(s)]
> save "D:/Temiakov Lab/KH Cryo-
> EM/IC_modeling/ChimeraX/EC9-TEFM/EC9TEFM_Models_Maps.cxs"
——— End of log from Thu Dec 26 20:14:27 2024 ———
> view name session-start
opened ChimeraX session
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> view list
Named views: EC9, IC1, IC2, IC3, IC5, session-start
> view EC9
> view IC1
> view IC2
> view name C3_1
> view remove IC2
Expected an objects specifier or a view name or a keyword
> view delete IC2
> view list
Named views: C3_1, EC9, IC1, IC3, IC5, session-start
> view IC1
> view name C3_2
> view delete IC1
> view IC3
> view name C3_3
> view delete IC3
> view list
Named views: C3_1, C3_2, C3_3, EC9, IC5, session-start
> view session-start
> view delete session-start
> view IC5
> view name C3_4
> view delete IC5
> ls
Unknown command: ls
> view list
Named views: C3_1, C3_2, C3_3, C3_4, EC9
> open /data/C3Modeling/models/C3_J42_model_V6.pdb
Chain information for C3_J42_model_V6.pdb #4
---
Chain | Description
A | No description available
B | No description available
E | No description available
> hide #!1 models
Alignment identifier is 1/E
Alignment identifier is 1/N
Alignment identifier is 1/T
Alignment identifier is 1/R
Alignment identifier is 3/A
Alignment identifier is 3/B
Alignment identifier is 3/E
Alignment identifier is 3/N
Alignment identifier is 3/T
Alignment identifier is 3/R
Alignment identifier is 4/A
Alignment identifier is 4/B
Alignment identifier is 4/E
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> close #3
> save /data/C3Modeling/ChimeraX/C3_Models_Maps.cxs includeMaps true
> olor #*/A:1-105 #007FFF;
Unknown command: olor #*/A:1-105 #007FFF;
> color #*/A:106-206 #FF007F
> color #*/A:207-329 #FF33CC
> color #*/A:330-430 #7F7F7F
> color #*/A:431-536 #3FFFBF
> color #*/A:537-577 #FFA5D8
> color #*/A:578-650 #FCD1A5
> color #*/B:651-726 #FF0000
> color #*/B:727-803 #FFA5D8
> color #*/B:804-910 #7FFFFF
> color #*/B:911-963 #4C4CFF
> color #*/B:1269-1333 #4C4CFF
> color #*/B:964-1268 #00FF7F
> color #*/B:1334-1476 #FFDD5E
> color #*/B:1477-1641 #B12121
> select #4/E
110 atoms, 114 bonds, 14 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> color sel byhetero
> style sel stick
Changed 110 atom styles
> style sel sphere
Changed 110 atom styles
> style sel ball
Changed 110 atom styles
> color sel gray
> color sel white
> color sel byhetero
> select clear
> select #4/E
110 atoms, 114 bonds, 14 residues, 1 model selected
> color sel bychain
> select clear
> color #!4 bychain
> select #4/E
110 atoms, 114 bonds, 14 residues, 1 model selected
> color sel white
> color sel byhetero
> select clear
> open /data/C3Modeling/maps/J94_EMReady.mrc
Opened J94_EMReady.mrc as #3, grid size 360,360,360, pixel 0.887, shown at
level 0.121, step 2, values float32
> volume #3 step 1
> volume #3 level 1.301
> volume #3 level 2.7
> surface dust #3 size 8.87
> color zone #3 near #4 distance 5.32
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> select #4/A
4950 atoms, 5049 bonds, 2 pseudobonds, 635 residues, 2 models selected
> color (#!4 & sel) orange
> color (#!4 & sel) light sea green
> color (#!4 & sel) cyan
> color (#!4 & sel) light sea green
> select #4/B
7800 atoms, 7963 bonds, 2 pseudobonds, 973 residues, 2 models selected
> hide #!4 models
> show #!4 models
> select clear
> save /home/exx/Desktop/test.png width 3000 transparentBackground true
> volume zone #3 nearAtoms #4/E range 1.5 minimalBounds true newMap true
Opened J94_EMReady.mrc zone as #5, grid size 24,24,25, pixel 0.887, shown at
step 1, values float32
> volume zone #3 nearAtoms #4/E range 5 minimalBounds true newMap true
Opened J94_EMReady.mrc zone as #6, grid size 32,32,33, pixel 0.887, shown at
step 1, values float32
> close #6
> volume #2 style mesh
> volume #2 style surface
> volume #5 style mesh
> view name c3
> close #5
> volume zone #3 nearAtoms #4/E range 2 minimalBounds true newMap true
Opened J94_EMReady.mrc zone as #5, grid size 25,26,27, pixel 0.887, shown at
step 1, values float32
> volume #5 style mesh
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!5 models
> hide #!4 models
> volume #3 level 4.482
> show #!4 models
> hide #!3 models
> open /data/C3Modeling/models/CP40.pdb
Summary of feedback from opening /data/C3Modeling/models/CP40.pdb
---
warnings | CONECT record for nonexistent atom: 3962
Start residue of secondary structure not found: HELIX 1 1 PRO A 263 SER A 265
1 3
Start residue of secondary structure not found: HELIX 2 2 ARG A 282 VAL A 289
1 8
Start residue of secondary structure not found: HELIX 3 3 ALA A 294 LEU A 297
1 4
Start residue of secondary structure not found: HELIX 4 4 GLU A 411 GLU A 413
1 3
Start residue of secondary structure not found: HELIX 5 5 VAL A 427 ASN A 429
1 3
102 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (537 )
Cannot find LINK/SSBOND residue CYS (605 )
Cannot find LINK/SSBOND residue CYS (851 )
Cannot find LINK/SSBOND residue CYS (1079 )
Cannot find LINK/SSBOND residue CYS (1336 )
14 messages similar to the above omitted
PDB SEQRES record for chain C is incomplete. Ignoring input sequence records
as basis for sequence.
CP40.pdb title:
C3B In complex with CP40 [more info...]
Chain information for CP40.pdb #6
---
Chain | Description
C | compstatin CP40
Non-standard residues in CP40.pdb #6
---
DTY — D-tyrosine
EXL — 1-methyl-L-tryptophan ((2S)-2-azanyl-3-(1-methylindol-3-yl)propanoic
acid)
IML — N-methyl-isoleucine
NH2 — amino group
SAR — sarcosine
Computing secondary structure
> mmaker #6 to #4/E
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 C3_J42_model_V6.pdb, chain E (#4) with CP40.pdb, chain C (#6),
sequence alignment score = 59
RMSD between 11 pruned atom pairs is 1.066 angstroms; (across all 13 pairs:
1.408)
> select #6/C
130 atoms, 132 bonds, 19 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #4/E
110 atoms, 114 bonds, 14 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel cartoons
> save /data/C3Modeling/ChimeraX/C3_Models_Maps.cxs includeMaps true
> view list
Named views: C3_1, C3_2, C3_3, C3_4, EC9, c3
> select ~sel & ##selected
12839 atoms, 13109 bonds, 4 pseudobonds, 1615 residues, 2 models selected
> view c3
> hide #6 models
> hide #!4 models
> show #!4 models
> select add #4
12949 atoms, 13223 bonds, 4 pseudobonds, 1629 residues, 2 models selected
> select subtract #4
Nothing selected
> open /data/C3Modeling/models/C3_J42_model_V8.pdb
Chain information for C3_J42_model_V8.pdb #7
---
Chain | Description
A | No description available
B | No description available
E | No description available
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!7 models
> show #!7 models
> show #!4 models
> hide #!7 models
> show #!7 models
> hide #!4 models
> color #!7 bychain
> select #7/A
4950 atoms, 5049 bonds, 2 pseudobonds, 635 residues, 2 models selected
> color (#!7 & sel) light sea green
> hide #!7 models
> show #!4 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> close #4
> show #!7 models
> select #7/E
110 atoms, 115 bonds, 14 residues, 1 model selected
> color sel white
> hide #!7 models
> show #!7 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!7 models
> show #!5 models
> hide #!5 models
> show #!3 models
> show #!7 models
> color zone #3 near sel & #7 distance 5.32
> hide #!7 models
> show #!7 models
> hide #!3 models
> show #!3 models
> color zone #3 near sel & #7 distance 5.32
> color zone #3 near #7 distance 5.32
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!7 models
> volume #3 level 2.935
> volume #3 level 3.132
> surface dust #3 size 8.87
> graphics silhouettes true
> lighting soft
> windowsize 1000 1000
> camera ortho
> windowsize 1000 1000
> select clear
> save /home/exx/Desktop/test.png width 3000 transparentBackground true
> show #!7 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> save /home/exx/Desktop/test2.png width 3000 transparentBackground true
> show #!2 models
> hide #!2 models
> close #2
> close #1
> rename #7 id #1
> rename #6 id #2
> rename #5 id #4
> color #4 #77767bff models
> show #!4 models
> hide #!4 models
> show #!4 models
> color #4 #dc8addff models
> color #4 #ffbe6fff models
> color #4 #8ff0a4ff models
> color #4 #33d17aff models
> color #4 #1c71d8ff models
> select #1/E
110 atoms, 115 bonds, 14 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 110 atom styles
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> style sel ball
Changed 110 atom styles
> style sel stick
Changed 110 atom styles
> color sel byhetero
> select clear
> ui tool show "Side View"
> select #1/A
4950 atoms, 5049 bonds, 2 pseudobonds, 635 residues, 2 models selected
> select #1/A/B
12750 atoms, 13014 bonds, 4 pseudobonds, 1608 residues, 2 models selected
> hide sel cartoons
> select #1/A/B/C/D
12839 atoms, 13110 bonds, 4 pseudobonds, 1615 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> volume surfaceSmoothing true
> volume squareMesh true
> volume meshLighting true
> volume smoothLines true
> volume dimTransparency true
> volume meshLighting false
> volume meshLighting true
> select #1/E
110 atoms, 115 bonds, 14 residues, 1 model selected
> volume #4 color white
> volume #4 color #77767b
> select clear
> save /home/exx/Desktop/test.png width 3000 transparentBackground true
> size stickRadius 0.25
Changed 13357 bond radii
> volume subdivideSurface true
> save /home/exx/Desktop/test.png width 3000 transparentBackground true
> volume #4 color #deddda
> volume #4 color #c0bfbc
> save /home/exx/Desktop/test.png width 3000 transparentBackground true
> volume subdivideSurface false
> size stickRadius 0.1
Changed 13357 bond radii
> size stickRadius 0.15
Changed 13357 bond radii
> size atomRadius 0.4
Changed 13079 atom radii
> save /home/exx/Desktop/test.png width 3000 transparentBackground true
> view name apl2
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> select #1/A/B/C/D
12839 atoms, 13110 bonds, 4 pseudobonds, 1615 residues, 2 models selected
> show sel cartoons
> select add #1
12949 atoms, 13225 bonds, 4 pseudobonds, 1629 residues, 2 models selected
> select subtract #1
Nothing selected
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!1 models
> show #!1 models
> view apl2
> select #1/E
110 atoms, 115 bonds, 14 residues, 1 model selected
> hide sel atoms
> select #2/c
130 atoms, 132 bonds, 19 residues, 1 model selected
> color sel orange
[Repeated 1 time(s)]
> color sel orange red
> color sel red
> color sel yellow
> select clear
> save /home/exx/Desktop/apl2-cp40_overlay1.png width 3000
> transparentBackground true
> select #2/c
130 atoms, 132 bonds, 19 residues, 1 model selected
> color sel orange
> save /home/exx/Desktop/apl2-cp40_overlay1.png width 3000
> transparentBackground true
> select clear
> save /home/exx/Desktop/apl2-cp40_overlay1.png width 3000
> transparentBackground true
> save /data/C3Modeling/ChimeraX/C3_Models_Maps.cxs includeMaps true
> color #1-2 light sea green
> undo
> select #1/B
7800 atoms, 7964 bonds, 2 pseudobonds, 973 residues, 2 models selected
> select #1/A
4950 atoms, 5049 bonds, 2 pseudobonds, 635 residues, 2 models selected
> select #1/B
7800 atoms, 7964 bonds, 2 pseudobonds, 973 residues, 2 models selected
> ui tool show "Color Actions"
> color sel salmon
> hide #!1 models
> show #!1 models
> select add #1
12949 atoms, 13225 bonds, 4 pseudobonds, 1629 residues, 2 models selected
> select subtract #1
Nothing selected
> undo
[Repeated 4 time(s)]
> redo
> select #1/A
4950 atoms, 5049 bonds, 2 pseudobonds, 635 residues, 2 models selected
> select add #1
12949 atoms, 13225 bonds, 4 pseudobonds, 1629 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #1
12949 atoms, 13225 bonds, 4 pseudobonds, 1629 residues, 2 models selected
> color (#!1 & sel) light sea green
> undo
> select #1/C/D
89 atoms, 94 bonds, 7 residues, 1 model selected
> show sel atoms
> select add #1
12949 atoms, 13225 bonds, 4 pseudobonds, 1629 residues, 2 models selected
> select subtract #1
Nothing selected
> select #1/C
28 atoms, 29 bonds, 2 residues, 1 model selected
> infocolor
Unknown command: infocolor
> info color
Expected a models specifier or a keyword
> info color #1/C
Expected a models specifier or a keyword
> info color #1/C
Expected a models specifier or a keyword
> info atomcolor #1/C
#1/C:1@C1 color #8fbc8f
#1/C:1@C2 color #8fbc8f
#1/C:1@C3 color #8fbc8f
#1/C:1@C4 color #8fbc8f
#1/C:1@C5 color #8fbc8f
#1/C:1@C6 color #8fbc8f
#1/C:1@C7 color #8fbc8f
#1/C:1@C8 color #8fbc8f
#1/C:1@N2 color #8fbc8f
#1/C:1@O3 color #8fbc8f
#1/C:1@O4 color #8fbc8f
#1/C:1@O5 color #8fbc8f
#1/C:1@O6 color #8fbc8f
#1/C:1@O7 color #8fbc8f
#1/C:2@C1 color #8fbc8f
#1/C:2@C2 color #8fbc8f
#1/C:2@C3 color #8fbc8f
#1/C:2@C4 color #8fbc8f
#1/C:2@C5 color #8fbc8f
#1/C:2@C6 color #8fbc8f
#1/C:2@C7 color #8fbc8f
#1/C:2@C8 color #8fbc8f
#1/C:2@N2 color #8fbc8f
#1/C:2@O3 color #8fbc8f
#1/C:2@O4 color #8fbc8f
#1/C:2@O5 color #8fbc8f
#1/C:2@O6 color #8fbc8f
#1/C:2@O7 color #8fbc8f
> select ~sel & ##selected
12921 atoms, 13196 bonds, 4 pseudobonds, 1627 residues, 2 models selected
> info atomcolor #1/D
#1/D:1@C1 color #deb887
#1/D:1@C2 color #deb887
#1/D:1@C3 color #deb887
#1/D:1@C4 color #deb887
#1/D:1@C5 color #deb887
#1/D:1@C6 color #deb887
#1/D:1@C7 color #deb887
#1/D:1@C8 color #deb887
#1/D:1@N2 color #deb887
#1/D:1@O3 color #deb887
#1/D:1@O4 color #deb887
#1/D:1@O5 color #deb887
#1/D:1@O6 color #deb887
#1/D:1@O7 color #deb887
#1/D:2@C1 color #deb887
#1/D:2@C2 color #deb887
#1/D:2@C3 color #deb887
#1/D:2@C4 color #deb887
#1/D:2@C5 color #deb887
#1/D:2@C6 color #deb887
#1/D:2@C7 color #deb887
#1/D:2@C8 color #deb887
#1/D:2@N2 color #deb887
#1/D:2@O3 color #deb887
#1/D:2@O4 color #deb887
#1/D:2@O5 color #deb887
#1/D:2@O6 color #deb887
#1/D:2@O7 color #deb887
#1/D:3@C1 color #deb887
#1/D:3@C2 color #deb887
#1/D:3@C3 color #deb887
#1/D:3@C4 color #deb887
#1/D:3@C5 color #deb887
#1/D:3@C6 color #deb887
#1/D:3@O2 color #deb887
#1/D:3@O3 color #deb887
#1/D:3@O4 color #deb887
#1/D:3@O5 color #deb887
#1/D:3@O6 color #deb887
#1/D:4@C1 color #deb887
#1/D:4@C2 color #deb887
#1/D:4@C3 color #deb887
#1/D:4@C4 color #deb887
#1/D:4@C5 color #deb887
#1/D:4@C6 color #deb887
#1/D:4@O2 color #deb887
#1/D:4@O3 color #deb887
#1/D:4@O4 color #deb887
#1/D:4@O5 color #deb887
#1/D:4@O6 color #deb887
#1/D:5@C1 color #deb887
#1/D:5@C2 color #deb887
#1/D:5@C3 color #deb887
#1/D:5@C4 color #deb887
#1/D:5@C5 color #deb887
#1/D:5@C6 color #deb887
#1/D:5@O2 color #deb887
#1/D:5@O3 color #deb887
#1/D:5@O4 color #deb887
#1/D:5@O5 color #deb887
#1/D:5@O6 color #deb887
> open /data/CS-c3-inhibitors/J120/J120_map_locres.mrc
Opened J120_map_locres.mrc as #5, grid size 360,360,360, pixel 0.887, shown at
level 6.43, step 2, values float32
> ui tool show "Surface Color"
> open /data/CS-c3-inhibitors/J94/J94_EMReady.mrc
Opened J94_EMReady.mrc as #6, grid size 360,360,360, pixel 0.887, shown at
level 0.121, step 2, values float32
> rename #6 J94_EMReady_localres.mrc
> key red-white-blue :0.0 :0.5 :1.0 showTool true
> ui mousemode right "color key"
> close #6
> close #7
> close #5
> select clear
> save /data/C3Modeling/ChimeraX/C3_Models_Maps.cxs includeMaps true
——— End of log from Thu Jul 31 11:23:53 2025 ———
> view name session-start
opened ChimeraX session
> open /data/C3Modeling/maps/J119_EMReady.mrc
Opened J119_EMReady.mrc as #5, grid size 360,360,360, pixel 0.887, shown at
level 1.75, step 2, values float32
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> open /data/C3Modeling/models/C3Dimer_J41_model_V2.pdb
Chain information for C3Dimer_J41_model_V2.pdb #6
---
Chain | Description
A F | No description available
B G | No description available
C H | No description available
> hide #!5 models
> hide atoms
> show cartoons
Computing secondary structure
> undo
[Repeated 1 time(s)]
> hide #!1 models
> hide #2 models
> rename #5 id #7
ID must be one or more integers separated by '.' characters
> rename #6 id #5
> rename #7 id #6
> select #5/A
4950 atoms, 5048 bonds, 2 pseudobonds, 635 residues, 2 models selected
> color (#!5 & sel) light sea green
> select #5/A/E
5011 atoms, 5112 bonds, 2 pseudobonds, 640 residues, 2 models selected
> select #5/A/F
9900 atoms, 10096 bonds, 4 pseudobonds, 1270 residues, 2 models selected
> color (#!5 & sel) light sea green
> select #5/B/G
15600 atoms, 15904 bonds, 4 pseudobonds, 1946 residues, 2 models selected
> ui tool show "Color Actions"
> color sel salmon
> select #5/C
110 atoms, 113 bonds, 14 residues, 1 model selected
> select #5/C/H
220 atoms, 226 bonds, 28 residues, 1 model selected
> color sel white
> select #5/D/H
138 atoms, 142 bonds, 16 residues, 1 model selected
> select #5/D/I
56 atoms, 58 bonds, 4 residues, 1 model selected
> select #5/D/I, color sel #8fbc8f;
Expected a keyword
> select #5/D/I
56 atoms, 58 bonds, 4 residues, 1 model selected
> color sel #8fbc8f
> select #5/E/J
122 atoms, 128 bonds, 10 residues, 1 model selected
> color sel #deb887
> select #5
25898 atoms, 26412 bonds, 8 pseudobonds, 3258 residues, 2 models selected
> select #5
25898 atoms, 26412 bonds, 8 pseudobonds, 3258 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select subtract #5
Nothing selected
> turn x 180
[Repeated 1 time(s)]
> turn x 90
> turn x -90
> view name dimer
> select #5/C/H
220 atoms, 226 bonds, 28 residues, 1 model selected
> color sel magenta
> select add #5
25898 atoms, 26412 bonds, 8 pseudobonds, 3258 residues, 2 models selected
> select subtract #5
Nothing selected
> select #5/C/H
220 atoms, 226 bonds, 28 residues, 1 model selected
> color sel hot pink
> ui tool show "Color Actions"
> color sel deep pink
> color sel hot pink
> color sel orchid
> select add #5
25898 atoms, 26412 bonds, 8 pseudobonds, 3258 residues, 2 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> show #!5 models
> windowsize 1000 1000
[Repeated 1 time(s)]
> view name dimer
> save /home/exx/Desktop/c3-apl2_dimer_model.png width 3000
> transparentBackground true
> show #!6 models
> hide #!5 models
> show #!5 models
> color zone #6 near #5 distance 5.32
> hide #!5 models
> volume #6 step 1
> volume #6 level 2.99
> save /home/exx/Desktop/c3-apl2_dimer_map.png width 3000
> transparentBackground true
> save /data/C3Modeling/ChimeraX/C3_Models_Maps.cxs includeMaps true
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!1 models
> show #2 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #2 models
> select #1/C
28 atoms, 29 bonds, 2 residues, 1 model selected
> select #1/E
110 atoms, 115 bonds, 14 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orchid
> color sel medium orchid
> color sel orchid
> select add #1
12949 atoms, 13225 bonds, 4 pseudobonds, 1629 residues, 2 models selected
> select subtract #1
Nothing selected
> view c3
> select #1/E
110 atoms, 115 bonds, 14 residues, 1 model selected
> show sel atoms
> select clear
> save /home/exx/Desktop/C3-APL2_model2.png width 3000 transparentBackground
> true
> show #!3 models
> hide #!1 models
> show #!1 models
> color zone #3 near #1 distance 5.32
> hide #!3 models
> show #!3 models
> hide #!1 models
> save /home/exx/Desktop/C3-APL2_map2.png width 3000 transparentBackground
> true
> view apl2
> hide #!3 models
> show #!4 models
> select #1/E
110 atoms, 115 bonds, 14 residues, 1 model selected
> show #!1 models
> color sel byhetero
> select !#1/E
Expected an objects specifier or a keyword
> sel! #1/E
Unknown command: sel! #1/E
> sel~ #1/E
Unknown command: sel~ #1/E
> select ~! #1/E
Expected an objects specifier or a keyword
> select ~!1/E
Expected an objects specifier or a keyword
> select #1/E
110 atoms, 115 bonds, 14 residues, 1 model selected
> select ~sel & ##selected
12839 atoms, 13110 bonds, 4 pseudobonds, 1615 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> color #4 white models
> save /home/exx/Desktop/APL2_density2.png width 3000 transparentBackground
> true
> view list
Named views: C3_1, C3_2, C3_3, C3_4, EC9, apl2, c3, dimer, session-start
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #2 models
> hide #!1 models
> show #!1 models
> select #1
12949 atoms, 13225 bonds, 4 pseudobonds, 1629 residues, 2 models selected
> show sel atoms
> hide sel atoms
> show sel cartoons
> select clear
> color #2 white
> save /home/exx/Desktop/apl2-cp40_overlay2.png width 3000
> transparentBackground true
> save /data/C3Modeling/ChimeraX/C3_Models_Maps.cxs includeMaps true
> view c3
> view name c3
> hide #2 models
> hide #!1 models
> open /data/C3Modeling/maps/J58_002_volume_map.mrc
Opened J58_002_volume_map.mrc as #7, grid size 360,360,360, pixel 0.887, shown
at level 0.0301, step 2, values float32
> volume #7 step 1
> volume #7 level 0.02732
> volume #7 color #99c1f1
> open /data/C3Modeling/maps/J59_002_volume_map.mrc
Opened J59_002_volume_map.mrc as #8, grid size 360,360,360, pixel 0.887, shown
at level 0.0378, step 2, values float32
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> save /home/exx/Desktop/C3-APL2_trimer_map1.png width 3000
> transparentBackground true
> turn y 180
[Repeated 3 time(s)]
> turn y 90
[Repeated 3 time(s)]
> turn x 90
> save /home/exx/Desktop/C3-APL2_trimer_map2.png width 3000
> transparentBackground true
> show #!8 models
> hide #!7 models
> turn x 90
[Repeated 2 time(s)]
> volume #8 step 1
> volume #8 level 0.02267
> turn x 90
[Repeated 3 time(s)]
> turn x 180
> center
Unknown command: center
> turn x 90
[Repeated 3 time(s)]
> save /home/exx/Desktop/C3-APL2_trimer_map3.png width 3000
> transparentBackground true
> turn x 180
[Repeated 1 time(s)]
> turn x 90
> save /home/exx/Desktop/C3-APL2_trimer_map4.png width 3000
> transparentBackground true
> hide #!8 models
> show #!1 models
> view c3
> save /data/C3Modeling/ChimeraX/C3_Models_Maps.cxs includeMaps true
——— End of log from Thu Jul 31 12:08:46 2025 ———
> view name session-start
opened ChimeraX session
> open /data/C3Modeling/models/C3_J42_model_V12.pdb
Chain information for C3_J42_model_V12.pdb #9
---
Chain | Description
A | No description available
B | No description available
E | No description available
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #2 models
> hide #2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> dssp
> hide #!1 models
> select #9/E
113 atoms, 118 bonds, 14 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 113 atom styles
> hide sel cartoons
> show #!1 models
> select #1/E
110 atoms, 115 bonds, 14 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!9 models
> ui tool show Distances
> select add #5/C:13
117 atoms, 121 bonds, 15 residues, 2 models selected
> select add #5/H:13
124 atoms, 127 bonds, 16 residues, 2 models selected
Exactly two atoms must be selected!
> select clear
> select #5/C:13
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:13
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #5/C:13
14 atoms, 12 bonds, 2 residues, 1 model selected
> select subtract #5/C:13
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/C:13
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/C:13
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select add #5/C:13
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #5/H:13
14 atoms, 12 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> color sel byhetero
> select subtract #5/C:13
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/C:13
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/C:13
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/H:13@OG1
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select #5/H:13
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #5/H:13@CG2
1 atom, 1 residue, 1 model selected
> select #5/C:13
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/C:13
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/C:13@CG2
1 atom, 1 residue, 1 model selected
> select add #5/H:13@CG2
2 atoms, 2 residues, 1 model selected
> distance #5/C:13@CG2 #5/H:13@CG2
Distance between C3Dimer_J41_model_V2.pdb #5/C THR 13 CG2 and /H THR 13 CG2:
86.973Å
> distance style color #c01c28
[Repeated 2 time(s)]
> distance style color #e01b24
[Repeated 2 time(s)]
> distance style color #f66151
[Repeated 2 time(s)]
> distance style color #ed333b
[Repeated 2 time(s)]
> distance style color #77767b
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> distance style dashes 8
[Repeated 2 time(s)]
> distance style dashes 7
[Repeated 2 time(s)]
> distance style dashes 6
[Repeated 2 time(s)]
> distance style dashes 5
[Repeated 2 time(s)]
> distance style dashes 4
[Repeated 2 time(s)]
> distance style dashes 0
[Repeated 2 time(s)]
> distance style dashes 20
[Repeated 2 time(s)]
> distance style dashes 50
[Repeated 2 time(s)]
> distance style radius 1
[Repeated 2 time(s)]
> distance style radius 0.01
[Repeated 3 time(s)]
> distance style radius 0.2
[Repeated 2 time(s)]
> distance style radius 0.05
[Repeated 2 time(s)]
> distance style radius 0.08
[Repeated 2 time(s)]
> distance style symbol false
[Repeated 2 time(s)]
> distance style symbol true
[Repeated 2 time(s)]
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> distance style radius 0.02
[Repeated 2 time(s)]
> distance style dashes 1
[Repeated 2 time(s)]
> distance style dashes 2
[Repeated 2 time(s)]
> ui mousemode right "resize markers"
> ui mousemode right "tape measure"
Drag select of 4 atoms, 16 residues, 3 bonds, 1 pseudobonds
> ui mousemode right "tape measure"
[Repeated 1 time(s)]
> ui mousemode right "rotate slab"
> ui mousemode right "tape measure"
> select subtract #5/C:12
125 atoms, 4 bonds, 1 pseudobond, 15 residues, 2 models selected
> select clear
> ui mousemode right "tape measure"
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/bundle.py", line 68, in run_provider
from chmerax.segmentations.actions import run_toolbar_button
ModuleNotFoundError: No module named 'chmerax'
ModuleNotFoundError: No module named 'chmerax'
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-
packages/chimerax/segmentations/bundle.py", line 68, in run_provider
from chmerax.segmentations.actions import run_toolbar_button
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 570.153.02
OpenGL renderer: NVIDIA RTX 4500 Ada Generation/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:0
Manufacturer: ASUS
Model: System Product Name
OS: Rocky Linux 9.6
Architecture: 64bit ELF
Virtual Machine: none
CPU: 72 Intel(R) Xeon(R) w9-3475X
Cache Size: 84480 KB
Memory:
total used free shared buff/cache available
Mem: 250Gi 35Gi 2.2Gi 5.0Gi 221Gi 214Gi
Swap: 9Gi 601Mi 9.4Gi
Graphics:
05:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 52)
Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]
Kernel modules: ast
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Use a daily build. This will be fixed when our windows signing key allows us to release a 1.10.2