The following bug report has been submitted:
Platform: macOS-13.0-arm64-arm-64bit
ChimeraX Version: 1.5rc202210241843 (2022-10-24 18:43:45 UTC)
Description
I selected a residue /H:167 in the structure PDB 7Z13 and then tried to select residues with Zone but it selects the whole chain. In the Zone window it says "<5,000 angstroms" which might mean it tries to select eveyrthing within 5 thousand A instead of 5. I cannot put a dot "." there, only comma ",". It might be related to the fact that in my language settings I use "," as decimal separator and the program is confused about this.
Log:
UCSF ChimeraX version: 1.5rc202210241843 (2022-10-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/krystian/Desktop/PSF1_human_yeast.cxs
Log from Tue Oct 25 15:49:36 2022 Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.5rc202210241843 (2022-10-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> 2E9X
Unknown command: 2E9X
> fetch 2E9X
Unknown command: fetch 2E9X
> close session
> open 2E9X
Summary of feedback from opening 2E9X fetched from pdb
---
notes | Fetching compressed mmCIF 2e9x from
http://files.rcsb.org/download/2e9x.cif
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif
2e9x title:
The crystal structure of human GINS core complex [more info...]
Chain information for 2e9x #1
---
Chain | Description | UniProt
A E | DNA replication complex GINS protein PSF1 | PSF1_HUMAN
B F | DNA replication complex GINS protein PSF2 | PSF2_HUMAN
C G | GINS complex subunit 3 | Q9BRX5_HUMAN
D H | GINS complex subunit 4 | Q9BRT9_HUMAN
Non-standard residues in 2e9x #1
---
SO4 — sulfate ion
2e9x mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| software_defined_assembly
4| software_defined_assembly
> hide atoms
> show atoms
> show cartoons
> hide atoms
> toolshed show
> ui tool show AlphaFold
> hbonds reveal true
2811 hydrogen bonds found
> hbonds reveal true
2811 hydrogen bonds found
> hbonds reveal false
2811 hydrogen bonds found
> undo
> redo
> ~hbonds
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 2e9x_A SES surface #1.2: minimum, -13.71, mean 0.18,
maximum 13.10
Coulombic values for 2e9x_B SES surface #1.3: minimum, -16.69, mean -1.17,
maximum 13.91
Coulombic values for 2e9x_C SES surface #1.4: minimum, -17.68, mean -2.33,
maximum 11.98
Coulombic values for 2e9x_D SES surface #1.5: minimum, -22.67, mean -3.72,
maximum 16.46
Coulombic values for 2e9x_E SES surface #1.6: minimum, -15.33, mean -0.16,
maximum 13.33
Coulombic values for 2e9x_F SES surface #1.7: minimum, -15.50, mean -1.43,
maximum 10.33
Coulombic values for 2e9x_G SES surface #1.8: minimum, -20.48, mean -2.64,
maximum 8.72
Coulombic values for 2e9x_H SES surface #1.9: minimum, -21.80, mean -3.38,
maximum 11.77
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> show cartoons
> hide atoms
> style stick
Changed 11975 atom styles
> hide surfaces
> show surfaces
> hide surfaces
> show atoms
> hide atoms
> open 7QHS
Summary of feedback from opening 7QHS fetched from pdb
---
notes | Fetching compressed mmCIF 7qhs from
http://files.rcsb.org/download/7qhs.cif
Fetching CCD ATP from http://ligand-expo.rcsb.org/reports/A/ATP/ATP.cif
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
Fetching CCD ADP from http://ligand-expo.rcsb.org/reports/A/ADP/ADP.cif
7qhs title:
S. cerevisiae CMGE nucleating origin DNA melting [more info...]
Chain information for 7qhs #2
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | A0A6A5Q1S9_YEASX
3 | DNA replication licensing factor MCM3 | MCM3_YEAST
4 | DNA replication licensing factor MCM4 | MCM4_YEAST
5 | DNA replication licensing factor MCM5 | A0A6A5PUY8_YEASX
6 | DNA replication licensing factor MCM6 | MCM6_YEAST
7 | DNA replication licensing factor MCM7 | MCM7_YEAST
A | DNA (26-MER) |
B | DNA (26-MER) |
C | DNA replication complex GINS protein PSF3 | PSF3_YEAST
D | DNA replication complex GINS protein SLD5 | SLD5_YEAST
E | Cell division control protein 45 | CDC45_YEAST
F | DNA polymerase epsilon subunit B | DPB2_YEAST
G | DNA polymerase epsilon catalytic subunit A | DPOE_YEAST
H | DNA replication complex GINS protein PSF1 | A0A6A5Q203_YEASX
I | DNA replication complex GINS protein PSF2 | A0A6A5PX40_YEASX
Non-standard residues in 7qhs #2
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> hide surfaces
> hide atoms
> hide cartoons
> show cartoons
> select #2/2
5263 atoms, 5352 bonds, 5 pseudobonds, 662 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/A#2/B
1066 atoms, 1194 bonds, 33 pseudobonds, 52 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/E
4599 atoms, 4685 bonds, 3 pseudobonds, 566 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/G
6115 atoms, 6250 bonds, 11 pseudobonds, 758 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/F
4396 atoms, 4492 bonds, 3 pseudobonds, 551 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/3
4990 atoms, 5077 bonds, 6 pseudobonds, 635 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/4
4878 atoms, 4950 bonds, 7 pseudobonds, 611 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/5
5483 atoms, 5563 bonds, 11 pseudobonds, 693 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/6
5000 atoms, 5080 bonds, 8 pseudobonds, 631 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/7
5214 atoms, 5294 bonds, 9 pseudobonds, 661 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #1/A
1247 atoms, 1216 bonds, 198 residues, 1 model selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/B
1477 atoms, 1454 bonds, 228 residues, 1 model selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/C
1548 atoms, 1524 bonds, 1 pseudobond, 246 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/D
1713 atoms, 1655 bonds, 1 pseudobond, 286 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> matchmaker #2 to #1
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 2e9x, chain F (#1) with 7qhs, chain I (#2), sequence alignment
score = 337.6
RMSD between 127 pruned atom pairs is 1.255 angstroms; (across all 159 pairs:
2.471)
> select #1/E
1240 atoms, 1208 bonds, 199 residues, 1 model selected
> color (#!1 & sel) #9437ffff
> color (#!1 & sel) #7a81ffff
> color (#!1 & sel) #0096ffff
> select #2/H
1697 atoms, 1719 bonds, 208 residues, 1 model selected
> color sel #73fdffff
> select #1/F
1503 atoms, 1458 bonds, 250 residues, 1 model selected
> color (#!1 & sel) #ff9300ff
> select #2/I
1581 atoms, 1613 bonds, 1 pseudobond, 189 residues, 2 models selected
> color (#!2 & sel) #ffd479ff
> select #2/C
1398 atoms, 1431 bonds, 2 pseudobonds, 173 residues, 2 models selected
> color (#!2 & sel) #531b93ff
> select #1/G
1534 atoms, 1501 bonds, 1 pseudobond, 250 residues, 2 models selected
> color (#!1 & sel) #d783ffff
> select #1/G
1534 atoms, 1501 bonds, 1 pseudobond, 250 residues, 2 models selected
> select #2/D
1990 atoms, 2032 bonds, 242 residues, 1 model selected
> color sel #008f00ff
> color sel #4f8f00ff
> select #1/H
1713 atoms, 1659 bonds, 1 pseudobond, 282 residues, 2 models selected
> color (#!1 & sel) #d4fb79ff
> select clear
> background color white
Unknown command: background color white
> set background color white
Expected a keyword
> set bgColor white
> lighting soft
> lighting simple
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> lighting full
> select #1/E#2/H
2937 atoms, 2927 bonds, 407 residues, 2 models selected
> save /Users/krystian/Desktop/GINS_human_yeast.cxs
> select #1/F#2/I
3084 atoms, 3071 bonds, 1 pseudobond, 439 residues, 3 models selected
> delete atoms (#!1-2 & sel)
> delete bonds (#!1-2 & sel)
> select #2/C
1398 atoms, 1431 bonds, 2 pseudobonds, 173 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/D
1990 atoms, 2032 bonds, 242 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/G
1534 atoms, 1501 bonds, 1 pseudobond, 250 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/H
1713 atoms, 1659 bonds, 1 pseudobond, 282 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> matchmaker #2 to #1
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 2e9x, chain E (#1) with 7qhs, chain H (#2), sequence alignment
score = 245.9
RMSD between 109 pruned atom pairs is 1.065 angstroms; (across all 142 pairs:
2.411)
> set bgColor gray
> set bgColor white
> set bgColor gray
> volume style surface
No volumes specified
> show surfaces
> hide surfaces
Hide dust shortcut requires a displayed map surface
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
Hide dust shortcut requires a displayed map surface
> select 84.e
Expected an objects specifier or a keyword
> select :84.e
Expected an objects specifier or a keyword
> select :84/E
1251 atoms, 1218 bonds, 200 residues, 2 models selected
> select :84.E
Expected an objects specifier or a keyword
> select :84#1
1251 atoms, 1218 bonds, 200 residues, 2 models selected
> select :84
19 atoms, 17 bonds, 2 residues, 2 models selected
> select #1/E
1240 atoms, 1208 bonds, 199 residues, 1 model selected
> select clear
> save /Users/krystian/Desktop/PSF1_human_yeast.cxs
——— End of log from Tue Oct 25 15:49:36 2022 ———
opened ChimeraX session
> select :84
19 atoms, 17 bonds, 2 residues, 2 models selected
> select :83
20 atoms, 18 bonds, 2 residues, 2 models selected
> select :84
19 atoms, 17 bonds, 2 residues, 2 models selected
> select clear
> select :152
6 atoms, 5 bonds, 1 residue, 1 model selected
> open 2q9q
Summary of feedback from opening 2q9q fetched from pdb
---
note | Fetching compressed mmCIF 2q9q from
http://files.rcsb.org/download/2q9q.cif
2q9q title:
The crystal structure of full length human GINS complex [more info...]
Chain information for 2q9q #3
---
Chain | Description | UniProt
A E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN
B F | GINS complex subunit 4 | Q9BRT9_HUMAN
C G | DNA replication complex GINS protein PSF1 | PSF1_HUMAN
D H | GINS complex subunit 3 | Q9BRX5_HUMAN
2q9q mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> show sel cartoons
> hide sel surfaces
> hide sel atoms
[Repeated 1 time(s)]
> hide sel surfaces
> hide sel cartoons
> show sel cartoons
> select
14820 atoms, 14593 bonds, 4 pseudobonds, 2264 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> hide sel surfaces
> select #3/D#3/H
3072 atoms, 3046 bonds, 2 pseudobonds, 466 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select #3/B#3/F
3374 atoms, 3290 bonds, 2 pseudobonds, 538 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select #1/E
1240 atoms, 1208 bonds, 199 residues, 1 model selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #3/A#3/E
2969 atoms, 2908 bonds, 471 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/G
1233 atoms, 1211 bonds, 190 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/C
1235 atoms, 1211 bonds, 192 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #0096ffff
> matchmaker #2 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 2q9q, chain C (#3) with 7qhs, chain H (#2), sequence alignment
score = 286.7
RMSD between 106 pruned atom pairs is 1.064 angstroms; (across all 142 pairs:
4.078)
> select :152
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/C
1235 atoms, 1211 bonds, 192 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> open 7PFO
Summary of feedback from opening 7PFO fetched from pdb
---
notes | Fetching compressed mmCIF 7pfo from
http://files.rcsb.org/download/7pfo.cif
Fetching CCD ANP from http://ligand-expo.rcsb.org/reports/A/ANP/ANP.cif
7pfo title:
Core human replisome [more info...]
Chain information for 7pfo #1
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_HUMAN
3 | DNA replication licensing factor MCM3 | MCM3_HUMAN
4 | DNA replication licensing factor MCM4 | MCM4_HUMAN
5 | DNA replication licensing factor MCM5 | MCM5_HUMAN
6 | DNA replication licensing factor MCM6 | MCM6_HUMAN
7 | DNA replication licensing factor MCM7 | MCM7_HUMAN
A | DNA polymerase epsilon subunit 2 | DPOE2_HUMAN
B | DNA polymerase epsilon catalytic subunit A | DPOE1_HUMAN
C | Cell division control protein 45 homolog,Cell division control protein 45
homolog | CDC45_HUMAN
D | DNA replication complex GINS protein PSF1 | PSF1_HUMAN
E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN
F | DNA replication complex GINS protein PSF3 | PSF3_HUMAN
G | DNA replication complex GINS protein SLD5 | SLD5_HUMAN
H I J | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN
K | Protein timeless homolog | TIM_HUMAN
L | TIMELESS-interacting protein | TIPIN_HUMAN
M | Leading strand DNA |
N | Lagging Strand DNA |
Q | Claspin | CLSPN_HUMAN
Non-standard residues in 7pfo #1
---
ANP — phosphoaminophosphonic acid-adenylate ester
MG — magnesium ion
SO4 — sulfate ion
ZN — zinc ion
> select
69751 atoms, 71186 bonds, 120 pseudobonds, 8642 residues, 5 models selected
> show sel surfaces
> hide sel surfaces
> hide sel atoms
> show sel cartoons
> select #1/C
4347 atoms, 4439 bonds, 1 pseudobond, 534 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/Q
683 atoms, 693 bonds, 2 pseudobonds, 79 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/B
6062 atoms, 6180 bonds, 17 pseudobonds, 760 residues, 3 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/A
4204 atoms, 4314 bonds, 528 residues, 1 model selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/D#2/H
3303 atoms, 3357 bonds, 403 residues, 2 models selected
> select ~sel
51152 atoms, 52203 bonds, 100 pseudobonds, 6338 residues, 4 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #2/H
1697 atoms, 1719 bonds, 208 residues, 1 model selected
> color (#!2 & sel) #011993ff
> color (#!2 & sel) #0096ffff
> color (#!2 & sel) #73fdffff
> select #1/D
1606 atoms, 1638 bonds, 195 residues, 1 model selected
> color (#!1 & sel) #0096ffff
> matchmaker #1 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 7qhs, chain H (#2) with 7pfo, chain D (#1), sequence alignment
score = 334.1
RMSD between 107 pruned atom pairs is 0.909 angstroms; (across all 190 pairs:
3.777)
> select :152
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #2/H:166
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/H:168
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D:152
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/D:153
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/D:151
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/H:166
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/D:152
6 atoms, 5 bonds, 1 residue, 1 model selected
> label (#!1 & sel) attribute name
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> label (#!2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
> select #1/D:152
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!1 & sel) forest green
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!2 & sel) lime
> select clear
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color (#!2 & sel) #73fa79ff
> select :83
20 atoms, 18 bonds, 2 residues, 2 models selected
> select #1/D:83
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #2/H:93
22 atoms, 20 bonds, 2 residues, 3 models selected
> label (#!1-2 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
> select #1/D:83
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) #9437ffff
> select #2/H:93
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!2 & sel) #d783ffff
> color (#!2 & sel) #ff8ad8ff
> select clear
> select #2/H:93
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!2 & sel) #d783ffff
> color (#!2 & sel) #afafafff
[Repeated 1 time(s)]
> color (#!2 & sel) #b1b1b1ff
> color (#!2 & sel) #b5b5b5ff
> color (#!2 & sel) #bcbcbcff
> color (#!2 & sel) #bfbfbfff
> color (#!2 & sel) #c3c3c3ff
> color (#!2 & sel) #c6c6c6ff
> color (#!2 & sel) #c5c5c5ff
[Repeated 1 time(s)]
> color (#!2 & sel) #c4c4c4ff
> color (#!2 & sel) #c3c3c3ff
> color (#!2 & sel) #c2c2c2ff
> color (#!2 & sel) #c0c0c0ff
> color (#!2 & sel) #bfbfbfff
> color (#!2 & sel) #bababaff
> color (#!2 & sel) #b9b9b9ff
> color (#!2 & sel) #b5b5b5ff
> color (#!2 & sel) #b3b3b3ff
[Repeated 1 time(s)]
> color (#!2 & sel) #b2b2b2ff
> color (#!2 & sel) #b0b0b0ff
> color (#!2 & sel) #adadadff
> color (#!2 & sel) #abababff
> color (#!2 & sel) #aaaaaaff
> color (#!2 & sel) #a7a7a7ff
[Repeated 1 time(s)]
> color (#!2 & sel) #d783ffff
> color (#!2 & sel) #e2b5f8ff
[Repeated 1 time(s)]
> color (#!2 & sel) #e1b5f8ff
[Repeated 1 time(s)]
> color (#!2 & sel) #e0b5f8ff
> select #1/D:83
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) #dd91f8ff
> color (#!1 & sel) #dc91f8ff
> color (#!1 & sel) #db91f8ff
> color (#!1 & sel) #d791f8ff
> color (#!1 & sel) #d192f8ff
> color (#!1 & sel) #d092f8ff
> color (#!1 & sel) #cf92f8ff
> color (#!1 & sel) #d093f8ff
> color (#!1 & sel) #d195f8ff
[Repeated 1 time(s)]
> color (#!1 & sel) #d196f8ff
> color (#!1 & sel) #d298f8ff
> color (#!1 & sel) #d399f8ff
> color (#!1 & sel) #d59df8ff
> color (#!1 & sel) #d9a0f8ff
> color (#!1 & sel) #dd9df8ff
> color (#!1 & sel) #d88cf8ff
> color (#!1 & sel) #d683f8ff
> color (#!1 & sel) #d47ff8ff
> color (#!1 & sel) #d27af8ff
> color (#!1 & sel) #cf75f8ff
> color (#!1 & sel) #ce6df8ff
> color (#!1 & sel) #cc64f8ff
> color (#!1 & sel) #cc5ff8ff
> color (#!1 & sel) #cb5bf8ff
> color (#!1 & sel) #cb57f8ff
> color (#!1 & sel) #cb54f8ff
> color (#!1 & sel) #ca4ff8ff
> color (#!1 & sel) #c94af8ff
> color (#!1 & sel) #c848f8ff
> color (#!1 & sel) #c847f8ff
> color (#!1 & sel) #c747f8ff
[Repeated 1 time(s)]
> color (#!1 & sel) #dd58f8ff
> color (#!1 & sel) #dc59f8ff
> color (#!1 & sel) #d95af8ff
> color (#!1 & sel) #d35cf8ff
> color (#!1 & sel) #d25cf8ff
> color (#!1 & sel) #d15cf8ff
> color (#!1 & sel) #ce5df8ff
> color (#!1 & sel) #c55ef8ff
> color (#!1 & sel) #ba5ff8ff
> color (#!1 & sel) #b85ff8ff
> color (#!1 & sel) #b55df8ff
> color (#!1 & sel) #b35df8ff
> color (#!1 & sel) #b05cf8ff
> color (#!1 & sel) #ad5cf8ff
> color (#!1 & sel) #ac5bf8ff
> color (#!1 & sel) #a858f8ff
> color (#!1 & sel) #a455f8ff
> color (#!1 & sel) #a052f8ff
> color (#!1 & sel) #9e50f8ff
> color (#!1 & sel) #9d4ff8ff
> color (#!1 & sel) #9d4ef8ff
> color (#!1 & sel) #9c4df8ff
> color (#!1 & sel) #9b4cf8ff
> color (#!1 & sel) #9a4bf8ff
[Repeated 1 time(s)]
> color (#!1 & sel) #994af8ff
> color (#!1 & sel) #9949f8ff
> color (#!1 & sel) #994af8ff
> color (#!1 & sel) #9a4bf8ff
> color (#!1 & sel) #a551f8ff
> color (#!1 & sel) #a953f8ff
[Repeated 1 time(s)]
> color (#!1 & sel) #aa53f8ff
[Repeated 1 time(s)]
> color (#!1 & sel) #aa54f8ff
> color (#!1 & sel) #a954f8ff
[Repeated 1 time(s)]
> select clear
> select :84
19 atoms, 17 bonds, 2 residues, 2 models selected
> ui tool show "Side View"
> set bgColor white
> select clear
Drag select of 5 residues
> select clear
> select #1/D:83
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right "move planes"
[Repeated 1 time(s)]
> ui tool show "Blast Protein"
[Repeated 1 time(s)]
> blastprotein #2/H database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1
Webservices job id: 9Z39200QRDDK53EE
Alignment identifier is bp1 [1]
Associated 7qhs chain H to #2/H with 0 mismatches
Associated 7pfo chain D to 7PFO_D with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp1 [1]
> set bgColor gray
> set bgColor white
> save /Users/krystian/Desktop/image1.png supersample 3
> save /Users/krystian/Desktop/image2.png supersample 3
> save /Users/krystian/Desktop/image3.png supersample 3
> save /Users/krystian/Desktop/image4.png supersample 3
> save /Users/krystian/Desktop/PSF1_human_yeast_2.cxs
> close session
> open 7PFO
7pfo title:
Core human replisome [more info...]
Chain information for 7pfo #1
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_HUMAN
3 | DNA replication licensing factor MCM3 | MCM3_HUMAN
4 | DNA replication licensing factor MCM4 | MCM4_HUMAN
5 | DNA replication licensing factor MCM5 | MCM5_HUMAN
6 | DNA replication licensing factor MCM6 | MCM6_HUMAN
7 | DNA replication licensing factor MCM7 | MCM7_HUMAN
A | DNA polymerase epsilon subunit 2 | DPOE2_HUMAN
B | DNA polymerase epsilon catalytic subunit A | DPOE1_HUMAN
C | Cell division control protein 45 homolog,Cell division control protein 45
homolog | CDC45_HUMAN
D | DNA replication complex GINS protein PSF1 | PSF1_HUMAN
E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN
F | DNA replication complex GINS protein PSF3 | PSF3_HUMAN
G | DNA replication complex GINS protein SLD5 | SLD5_HUMAN
H I J | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN
K | Protein timeless homolog | TIM_HUMAN
L | TIMELESS-interacting protein | TIPIN_HUMAN
M | Leading strand DNA |
N | Lagging Strand DNA |
Q | Claspin | CLSPN_HUMAN
Non-standard residues in 7pfo #1
---
ANP — phosphoaminophosphonic acid-adenylate ester
MG — magnesium ion
SO4 — sulfate ion
ZN — zinc ion
> hide surfaces
> show cartoons
> hide atoms
> set bgColor white
> select /Q
683 atoms, 693 bonds, 2 pseudobonds, 79 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /N
438 atoms, 488 bonds, 22 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /M
662 atoms, 738 bonds, 1 pseudobond, 32 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /K
5215 atoms, 5317 bonds, 2 pseudobonds, 636 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> delete atoms
> delete bonds
> open 7PFO
7pfo title:
Core human replisome [more info...]
Chain information for 7pfo #1
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_HUMAN
3 | DNA replication licensing factor MCM3 | MCM3_HUMAN
4 | DNA replication licensing factor MCM4 | MCM4_HUMAN
5 | DNA replication licensing factor MCM5 | MCM5_HUMAN
6 | DNA replication licensing factor MCM6 | MCM6_HUMAN
7 | DNA replication licensing factor MCM7 | MCM7_HUMAN
A | DNA polymerase epsilon subunit 2 | DPOE2_HUMAN
B | DNA polymerase epsilon catalytic subunit A | DPOE1_HUMAN
C | Cell division control protein 45 homolog,Cell division control protein 45
homolog | CDC45_HUMAN
D | DNA replication complex GINS protein PSF1 | PSF1_HUMAN
E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN
F | DNA replication complex GINS protein PSF3 | PSF3_HUMAN
G | DNA replication complex GINS protein SLD5 | SLD5_HUMAN
H I J | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN
K | Protein timeless homolog | TIM_HUMAN
L | TIMELESS-interacting protein | TIPIN_HUMAN
M | Leading strand DNA |
N | Lagging Strand DNA |
Q | Claspin | CLSPN_HUMAN
Non-standard residues in 7pfo #1
---
ANP — phosphoaminophosphonic acid-adenylate ester
MG — magnesium ion
SO4 — sulfate ion
ZN — zinc ion
> open 7PFO
7pfo title:
Core human replisome [more info...]
Chain information for 7pfo #2
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_HUMAN
3 | DNA replication licensing factor MCM3 | MCM3_HUMAN
4 | DNA replication licensing factor MCM4 | MCM4_HUMAN
5 | DNA replication licensing factor MCM5 | MCM5_HUMAN
6 | DNA replication licensing factor MCM6 | MCM6_HUMAN
7 | DNA replication licensing factor MCM7 | MCM7_HUMAN
A | DNA polymerase epsilon subunit 2 | DPOE2_HUMAN
B | DNA polymerase epsilon catalytic subunit A | DPOE1_HUMAN
C | Cell division control protein 45 homolog,Cell division control protein 45
homolog | CDC45_HUMAN
D | DNA replication complex GINS protein PSF1 | PSF1_HUMAN
E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN
F | DNA replication complex GINS protein PSF3 | PSF3_HUMAN
G | DNA replication complex GINS protein SLD5 | SLD5_HUMAN
H I J | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN
K | Protein timeless homolog | TIM_HUMAN
L | TIMELESS-interacting protein | TIPIN_HUMAN
M | Leading strand DNA |
N | Lagging Strand DNA |
Q | Claspin | CLSPN_HUMAN
Non-standard residues in 7pfo #2
---
ANP — phosphoaminophosphonic acid-adenylate ester
MG — magnesium ion
SO4 — sulfate ion
ZN — zinc ion
> hide atoms
> show cartoons
> close session
> open 7PFO
7pfo title:
Core human replisome [more info...]
Chain information for 7pfo #1
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_HUMAN
3 | DNA replication licensing factor MCM3 | MCM3_HUMAN
4 | DNA replication licensing factor MCM4 | MCM4_HUMAN
5 | DNA replication licensing factor MCM5 | MCM5_HUMAN
6 | DNA replication licensing factor MCM6 | MCM6_HUMAN
7 | DNA replication licensing factor MCM7 | MCM7_HUMAN
A | DNA polymerase epsilon subunit 2 | DPOE2_HUMAN
B | DNA polymerase epsilon catalytic subunit A | DPOE1_HUMAN
C | Cell division control protein 45 homolog,Cell division control protein 45
homolog | CDC45_HUMAN
D | DNA replication complex GINS protein PSF1 | PSF1_HUMAN
E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN
F | DNA replication complex GINS protein PSF3 | PSF3_HUMAN
G | DNA replication complex GINS protein SLD5 | SLD5_HUMAN
H I J | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN
K | Protein timeless homolog | TIM_HUMAN
L | TIMELESS-interacting protein | TIPIN_HUMAN
M | Leading strand DNA |
N | Lagging Strand DNA |
Q | Claspin | CLSPN_HUMAN
Non-standard residues in 7pfo #1
---
ANP — phosphoaminophosphonic acid-adenylate ester
MG — magnesium ion
SO4 — sulfate ion
ZN — zinc ion
> select /N
438 atoms, 488 bonds, 22 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide atoms
> show cartoons
> set bgColor white
> select /C
4347 atoms, 4439 bonds, 1 pseudobond, 534 residues, 2 models selected
> select /Q
683 atoms, 693 bonds, 2 pseudobonds, 79 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /M
662 atoms, 738 bonds, 1 pseudobond, 32 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /H/I/J
9507 atoms, 9732 bonds, 1203 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /K
5215 atoms, 5317 bonds, 2 pseudobonds, 636 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select /L
735 atoms, 750 bonds, 87 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /D
1606 atoms, 1638 bonds, 195 residues, 1 model selected
> select :83.D
Expected an objects specifier or a keyword
> select :83/D
1686 atoms, 1711 bonds, 204 residues, 1 model selected
> select clear
> select :83/D
1686 atoms, 1711 bonds, 204 residues, 1 model selected
> select :83
91 atoms, 83 bonds, 10 residues, 1 model selected
> select /D:83
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select /D:83
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> select /D:22
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /D:23
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add /D:22
12 atoms, 11 bonds, 2 residues, 1 model selected
> select add /D:24
23 atoms, 22 bonds, 3 residues, 1 model selected
> style sel stick
Changed 23 atom styles
> show sel atoms
> select /D:107
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add /D:106
13 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> show sel cartoons
> style sel stick
Changed 13 atom styles
> style sel ball
Changed 13 atom styles
> style sel stick
Changed 13 atom styles
> select /D:83
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel red
> color sel orange
> select clear
> select /D:83
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /D:106
8 atoms, 8 bonds, 1 residue, 1 model selected
> select add /D:23
13 atoms, 12 bonds, 2 residues, 1 model selected
> select add /D:24
24 atoms, 23 bonds, 3 residues, 1 model selected
> select add /D:22
31 atoms, 30 bonds, 4 residues, 1 model selected
> color sel byhetero
> select /D:83
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byhetero
> select /5:394
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select /D:83
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show "Change Chain IDs"
> ui tool show "Build Structure"
> select /D:22
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add /D:24
18 atoms, 18 bonds, 2 residues, 1 model selected
> select add /D:83
29 atoms, 28 bonds, 3 residues, 1 model selected
> select add /D:107
34 atoms, 32 bonds, 4 residues, 1 model selected
> select add /D:106
42 atoms, 39 bonds, 5 residues, 1 model selected
> select ~sel
50772 atoms, 51701 bonds, 65 pseudobonds, 6370 residues, 3 models selected
> show sel surfaces
> hide sel surfaces
> select clear
> select /D:83
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /D:152
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> color (#!1 & sel) byhetero
> color (#!1 & sel) lime
> color (#!1 & sel) byhetero
> ui tool show Matchmaker
> ui mousemode right "pick blobs"
[Repeated 1 time(s)]
> select clear
> open 7z13
Summary of feedback from opening 7z13 fetched from pdb
---
note | Fetching compressed mmCIF 7z13 from
http://files.rcsb.org/download/7z13.cif
7z13 title:
S. cerevisiae CMGE dimer nucleating origin DNA melting [more info...]
Chain information for 7z13 #2
---
Chain | Description | UniProt
2 a | DNA replication licensing factor MCM2 | A0A6A5Q1S9_YEASX
3 b | DNA replication licensing factor MCM3 | MCM3_YEAST
4 c | DNA replication licensing factor MCM4 | MCM4_YEAST
5 d | DNA helicase | A0A6A5PUY8_YEASX
6 e | DNA replication licensing factor MCM6 | MCM6_YEAST
7 f | DNA replication licensing factor MCM7 | A0A6A5Q4N0_YEASX
A | DNA (53-MER) |
B | DNA (53-MER) |
C J | DNA replication complex GINS protein PSF3 | PSF3_YEAST
D K | DNA replication complex GINS protein SLD5 | SLD5_YEAST
E L | Cell division control protein 45 | CDC45_YEAST
F M | DNA polymerase epsilon subunit B | DPB2_YEAST
H O | DNA replication complex GINS protein PSF1 | A0A6A5Q203_YEASX
I P | DNA replication complex GINS protein PSF2 | A0A6A5PX40_YEASX
N Q | DNA polymerase epsilon catalytic subunit A | DPOE_YEAST
Non-standard residues in 7z13 #2
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> select #2/L
4599 atoms, 4685 bonds, 3 pseudobonds, 566 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/A#2/B
2173 atoms, 2436 bonds, 71 pseudobonds, 106 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #1/2
5613 atoms, 5717 bonds, 9 pseudobonds, 706 residues, 3 models selected
> select #2/2
5263 atoms, 5352 bonds, 5 pseudobonds, 662 residues, 3 models selected
> select #2/a
5263 atoms, 5352 bonds, 5 pseudobonds, 662 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/b
4990 atoms, 5077 bonds, 6 pseudobonds, 635 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/c
4878 atoms, 4950 bonds, 7 pseudobonds, 611 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/e
5000 atoms, 5080 bonds, 8 pseudobonds, 631 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/f
5214 atoms, 5294 bonds, 9 pseudobonds, 661 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/O
1697 atoms, 1719 bonds, 208 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/P
1581 atoms, 1613 bonds, 1 pseudobond, 189 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/J
1398 atoms, 1431 bonds, 2 pseudobonds, 173 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/K
1990 atoms, 2032 bonds, 242 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/M
4396 atoms, 4492 bonds, 3 pseudobonds, 551 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/Q
6115 atoms, 6250 bonds, 11 pseudobonds, 758 residues, 3 models selected
> select #2/N
6115 atoms, 6250 bonds, 11 pseudobonds, 758 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/d
5483 atoms, 5563 bonds, 11 pseudobonds, 693 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> hide atoms
> show cartoons
> ui tool show Matchmaker
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5-rc2022.10.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.5-rc2022.10.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File
"/Applications/ChimeraX-1.5-rc2022.10.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File
"/Applications/ChimeraX-1.5-rc2022.10.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
> matchmaker #!2 to #1
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 7pfo, chain B (#1) with 7z13, chain Q (#2), sequence alignment
score = 3162.8
RMSD between 142 pruned atom pairs is 1.199 angstroms; (across all 612 pairs:
22.863)
> select #1/2#2/2
10876 atoms, 11069 bonds, 14 pseudobonds, 1368 residues, 6 models selected
> select #1/D#2/H
3303 atoms, 3357 bonds, 403 residues, 2 models selected
> select #2/E
4599 atoms, 4685 bonds, 3 pseudobonds, 566 residues, 2 models selected
> ui tool show Matchmaker
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.5-rc2022.10.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.5-rc2022.10.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())
File
"/Applications/ChimeraX-1.5-rc2022.10.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
AttributeError: 'NoneType' object has no attribute 'setChecked'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'setChecked'
File
"/Applications/ChimeraX-1.5-rc2022.10.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value
self.__button_group.button(self.values.index(value)).setChecked(True)
See log for complete Python traceback.
> select #1/D#2/H
3303 atoms, 3357 bonds, 403 residues, 2 models selected
> select #1/D#2/H
3303 atoms, 3357 bonds, 403 residues, 2 models selected
> select ~sel
100115 atoms, 101930 bonds, 131 pseudobonds, 12552 residues, 20 models
selected
> hide (#!1-2 & sel) target a
> cartoon hide (#!1-2 & sel)
> select /D:84
16 atoms, 14 bonds, 2 residues, 2 models selected
> select /H:84
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/F#2/C
2944 atoms, 3011 bonds, 3 pseudobonds, 367 residues, 4 models selected
> show sel cartoons
> select /H:84
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select /H:164
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /H:161-164
34 atoms, 34 bonds, 4 residues, 1 model selected
> ui dockable false "Side View"
> ui dockable true "Side View"
> show sel surfaces
> hide sel surfaces
> style sel sphere
Changed 34 atom styles
> show sel atoms
> style sel ball
Changed 34 atom styles
> style sel stick
Changed 34 atom styles
> 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
> nucleotides sel ladder
> nucleotides sel tube/slab shape box
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel sphere
Changed 34 atom styles
> style sel stick
Changed 34 atom styles
> hide sel atoms
> select #2/F
4396 atoms, 4492 bonds, 3 pseudobonds, 551 residues, 2 models selected
> select #2/F
4396 atoms, 4492 bonds, 3 pseudobonds, 551 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> select #2/E
4599 atoms, 4685 bonds, 3 pseudobonds, 566 residues, 2 models selected
> show sel cartoons
> select /H:161-164
34 atoms, 34 bonds, 4 residues, 1 model selected
> select #1/C
4347 atoms, 4439 bonds, 1 pseudobond, 534 residues, 2 models selected
> show sel cartoons
> select #2/F
4396 atoms, 4492 bonds, 3 pseudobonds, 551 residues, 2 models selected
> show sel cartoons
> select /H:161-164
34 atoms, 34 bonds, 4 residues, 1 model selected
> show sel atoms
> select #1/D:152
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/H:166
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/D:152
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select clear
> select /H:161-164
34 atoms, 34 bonds, 4 residues, 1 model selected
> select #1/D:152
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/D:153
14 atoms, 12 bonds, 2 residues, 2 models selected
> select add #1/D:154
23 atoms, 20 bonds, 3 residues, 2 models selected
> select add #1/D:171
32 atoms, 28 bonds, 4 residues, 2 models selected
> style sel stick
Changed 32 atom styles
> show sel atoms
> select add #1/D:155
40 atoms, 35 bonds, 5 residues, 2 models selected
> select subtract #1/D:155
32 atoms, 28 bonds, 4 residues, 2 models selected
> select add #1/D:156
44 atoms, 40 bonds, 5 residues, 2 models selected
> select add #1/D:155
52 atoms, 47 bonds, 6 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 52 atom styles
> style sel sphere
Changed 52 atom styles
> style sel stick
Changed 52 atom styles
> select #1/D#2/H
3303 atoms, 3357 bonds, 403 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
[Repeated 1 time(s)]Coulombic values for 7pfo_D SES surface #1.13: minimum,
-16.05, mean -0.36, maximum 13.70
Coulombic values for 7z13_H SES surface #2.4: minimum, -18.77, mean -2.09,
maximum 13.14
To also show corresponding color key, enter the above coulombic command and
add key true
> select /H:161-164
34 atoms, 34 bonds, 4 residues, 1 model selected
> select /H:152
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> mlp sel
Map values for surface "7z13_H SES surface": minimum -29.07, mean -3.46,
maximum 24.75
To also show corresponding color key, enter the above mlp command and add key
true
> select #1/D#2/H
3303 atoms, 3357 bonds, 403 residues, 2 models selected
> mlp sel
Map values for surface "7pfo_D SES surface": minimum -25.17, mean -3.532,
maximum 22.99
Map values for surface "7z13_H SES surface": minimum -29.07, mean -3.46,
maximum 24.75
To also show corresponding color key, enter the above mlp command and add key
true
> select /H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> surface style #!2.4 mesh
> surface style #2 dot
> surface style #2 mesh
> transparency (#!2 & sel) 50
> hide sel surfaces
> show sel surfaces
> surface hidePatches (#!2 & sel)
> select #1/D#2/H
3303 atoms, 3357 bonds, 403 residues, 2 models selected
> surface style #2#!1.13 mesh
> surface style #2#1.13 dot
> surface style #2#1.13 mesh
> transparency (#!1-2 & sel) 50
> show sel cartoons
> select /H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /H:161-164
34 atoms, 34 bonds, 4 residues, 1 model selected
> select #1/D#2/H
3303 atoms, 3357 bonds, 403 residues, 2 models selected
> surface style #2#1.13 solid
> transparency (#!1-2 & sel) 30
> transparency (#!1-2 & sel) 70
> transparency (#!1-2 & sel) 60
> select /H:161-164
34 atoms, 34 bonds, 4 residues, 1 model selected
> select #1/E#2/I
3012 atoms, 3075 bonds, 1 pseudobond, 365 residues, 3 models selected
> show sel cartoons
> select /H:161-164
34 atoms, 34 bonds, 4 residues, 1 model selected
> select /H:164
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/D
1606 atoms, 1638 bonds, 195 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> select #1/E
1431 atoms, 1462 bonds, 176 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> select #1/C
4347 atoms, 4439 bonds, 1 pseudobond, 534 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select #1/A
4204 atoms, 4314 bonds, 528 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> select /H:164
8 atoms, 7 bonds, 1 residue, 1 model selected
> coulombic sel
Coulombic values for 7z13_H SES surface #2.4: minimum, -18.77, mean -2.09,
maximum 13.14
To also show corresponding color key, enter the above coulombic command and
add key true
> select /H:207
9 atoms, 8 bonds, 1 residue, 1 model selected
> coulombic sel
Coulombic values for 7z13_H SES surface #2.4: minimum, -18.77, mean -2.09,
maximum 13.14
To also show corresponding color key, enter the above coulombic command and
add key true
> select /H:207,164
17 atoms, 15 bonds, 2 residues, 1 model selected
> select /H:207,164,/E:50
Expected an objects specifier or a keyword
> select /H:207,164
17 atoms, 15 bonds, 2 residues, 1 model selected
> /E:50
Unknown command: /E:50
> select /H:207,164,/E:50
Expected an objects specifier or a keyword
> select /E:50
17 atoms, 15 bonds, 2 residues, 2 models selected
> select /H:207,164,
Expected an objects specifier or a keyword
> select /H:207,164
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/E:50
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /H:207,164
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #2/E:50
26 atoms, 23 bonds, 3 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 7z13_E SES surface #2.5: minimum, -21.23, mean -2.59,
maximum 15.49
Coulombic values for 7z13_H SES surface #2.4: minimum, -18.77, mean -2.09,
maximum 13.14
To also show corresponding color key, enter the above coulombic command and
add key true
> transparency (#!2 & sel) 50
> show sel atoms
> style sel stick
Changed 26 atom styles
> style sel sphere
Changed 26 atom styles
> style sel ball
Changed 26 atom styles
> style sel stick
Changed 26 atom styles
> style sel ball
Changed 26 atom styles
> select /F
5942 atoms, 6072 bonds, 4 pseudobonds, 745 residues, 4 models selected
> hide (#!1-2 & sel) target a
> hide sel cartoons
> show sel cartoons
> select #1/A
4204 atoms, 4314 bonds, 528 residues, 1 model selected
> select #1/F
1546 atoms, 1580 bonds, 1 pseudobond, 194 residues, 2 models selected
> hide sel cartoons
> select #2/F:19
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/H:176
14 atoms, 13 bonds, 2 residues, 1 model selected
> ui tool show Distances
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #2/H:176
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/H:176
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/H:176
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/F:34
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #2/H:174
17 atoms, 15 bonds, 2 residues, 1 model selected
> style sel stick
Changed 17 atom styles
> style sel stick
Changed 17 atom styles
> show sel atoms
> select clear
> select #2/H:176
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #2/H:175
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #2/H:174
24 atoms, 21 bonds, 3 residues, 2 models selected
> select add #2/H:173
33 atoms, 29 bonds, 4 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 33 atom styles
> select #2/F:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #2/F:31
14 atoms, 12 bonds, 2 residues, 1 model selected
> select add #2/F:26
20 atoms, 17 bonds, 3 residues, 1 model selected
> style sel stick
Changed 20 atom styles
> show sel atoms
> select #2/H:173@CA
1 atom, 1 residue, 1 model selected
> select #2/H:174
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/H:173
17 atoms, 15 bonds, 2 residues, 2 models selected
> select add #2/H:175
26 atoms, 23 bonds, 3 residues, 2 models selected
> select add #2/F:35
32 atoms, 28 bonds, 4 residues, 2 models selected
> select add #2/F:34
41 atoms, 36 bonds, 5 residues, 2 models selected
> select add #2/F:33
49 atoms, 43 bonds, 6 residues, 2 models selected
> select add #2/F:32
55 atoms, 48 bonds, 7 residues, 2 models selected
> select add #2/F:31
63 atoms, 55 bonds, 8 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> hbonds sel reveal true
10 hydrogen bonds found
> select /H:207,164
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/E:50@CE
1 atom, 1 residue, 1 model selected
> select /H:207,164
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #2/E:50@CE
18 atoms, 15 bonds, 3 residues, 2 models selected
> hbonds sel reveal true
1 hydrogen bonds found
> hide sel surfaces
[Repeated 2 time(s)]
> hide sel cartoons
> show sel cartoons
> select add #2/E:50@CG
19 atoms, 15 bonds, 3 residues, 3 models selected
> hide sel surfaces
> select subtract #2/E:50
17 atoms, 15 bonds, 2 residues, 3 models selected
> select add #2/E:50
26 atoms, 23 bonds, 3 residues, 2 models selected
> hide sel surfaces
> hbonds sel reveal true
3 hydrogen bonds found
> select /H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> mlp sel
Map values for surface "7z13_H SES surface": minimum -29.07, mean -3.46,
maximum 24.75
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Coulombic values for 7z13_H SES surface #2.4: minimum, -18.77, mean -2.09,
maximum 13.14
To also show corresponding color key, enter the above coulombic command and
add key true
> ui tool show "Show Sequence Viewer"
> sequence chain #2/H
Alignment identifier is 2/H
> select #2/H:162-167,173-176,179-182,188-192,205-206
181 atoms, 180 bonds, 21 residues, 1 model selected
> select #2/H:165
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/H:165-171
55 atoms, 54 bonds, 7 residues, 1 model selected
> select #2/H:172
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/H:172-173
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/H:108-109
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #2/H:108-111
30 atoms, 29 bonds, 4 residues, 1 model selected
> select #2/H:160
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/H:160-161
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/H:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/H:155
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/H:161
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/H:161
7 atoms, 6 bonds, 1 residue, 1 model selected
> select sel @< 5
1740 atoms, 69 bonds, 220 residues, 2 models selected
> select #2/H:162
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/H:162
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/H:161
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/H:161
7 atoms, 6 bonds, 1 residue, 1 model selected
> select sel @< 5
1740 atoms, 69 bonds, 220 residues, 2 models selected
> select #2/H:156
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/H:156
7 atoms, 6 bonds, 1 residue, 1 model selected
> select sel @< 3
1710 atoms, 26 bonds, 211 residues, 2 models selected
> select sel @< 3
3614 atoms, 3371 bonds, 1 pseudobond, 496 residues, 3 models selected
> select sel @< 3
30572 atoms, 4185 bonds, 1 pseudobond, 3830 residues, 3 models selected
> select sel @< 3
39108 atoms, 39333 bonds, 17 pseudobonds, 5175 residues, 7 models selected
> select sel @< 3
61563 atoms, 42144 bonds, 19 pseudobonds, 7843 residues, 7 models selected
> select #2/H:156
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/H:156-157
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/H:156
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/H:156
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #2/H:156-157
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/H:156
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> select sel @< 3
1715 atoms, 27 bonds, 213 residues, 2 models selected
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> select sel @< 5
1752 atoms, 95 bonds, 1 pseudobond, 221 residues, 3 models selected
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> select sel :< 5
1804 atoms, 224 bonds, 1 pseudobond, 221 residues, 3 models selected
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> select sel :< 0
1697 atoms, 6 bonds, 208 residues, 1 model selected
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/H:167
7 atoms, 6 bonds, 1 residue, 1 model selected
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGN63ZE/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 8419.41.10
OS Loader Version: 8419.41.10
Software:
System Software Overview:
System Version: macOS 13.0 (22A380)
Kernel Version: Darwin 22.1.0
Time since boot: 1 day, 21 hours, 43 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.0.8
Babel: 2.10.3
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.4
ChimeraX-AtomicLibrary: 8.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5rc202210241843
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.2
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.3
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.1.1
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 5.0.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 4.11.2
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.3
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
prompt-toolkit: 3.0.31
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.5
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.2.1
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.5.1
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.12
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.10.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Reported by Krystian