id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16857	Crash moving window between screens	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.3-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Current thread 0x00000001f4d70840 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree (total: 57)


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  ""experiments"" : [

  ]
}
}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/mk16/Desktop/220250214.cxs format session

opened ChimeraX session  

> select add #8

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> hide sel atoms

> hide #!1 models

> show #!1 models

> select ::name=""01A""

116 atoms, 122 bonds, 2 residues, 1 model selected  

> select ::name=""8LE""

116 atoms, 124 bonds, 4 residues, 3 models selected  

> select ::name=""BCO""

106 atoms, 110 bonds, 2 residues, 1 model selected  

> select ::name=""COA""

288 atoms, 300 bonds, 6 residues, 4 models selected  

> select add #9

4252 atoms, 4200 bonds, 1 pseudobond, 649 residues, 6 models selected  

> select subtract #9

240 atoms, 250 bonds, 5 residues, 3 models selected  

> select add #3

10981 atoms, 10398 bonds, 14 pseudobonds, 2137 residues, 6 models selected  

> select subtract #3

144 atoms, 150 bonds, 3 residues, 2 models selected  

> select add #2

7549 atoms, 7464 bonds, 4 pseudobonds, 1188 residues, 4 models selected  

> select subtract #2

48 atoms, 50 bonds, 1 residue, 1 model selected  

> select sel : select add #2

9222 atoms, 9064 bonds, 5 pseudobonds, 1423 residues, 11 models selected  

> select subtract #2

1721 atoms, 1650 bonds, 1 pseudobond, 236 residues, 8 models selected  

> select add #3

12302 atoms, 11659 bonds, 15 pseudobonds, 2327 residues, 11 models selected  

> select subtract #3

1465 atoms, 1411 bonds, 1 pseudobond, 193 residues, 7 models selected  

> select add #4

10026 atoms, 9736 bonds, 1 pseudobond, 1679 residues, 7 models selected  

> select subtract #4

1202 atoms, 1157 bonds, 1 pseudobond, 162 residues, 6 models selected  

> select add #5

9517 atoms, 8838 bonds, 5 pseudobonds, 1937 residues, 6 models selected  

> select subtract #5

933 atoms, 906 bonds, 121 residues, 4 models selected  

> select add #6

6269 atoms, 6360 bonds, 805 residues, 4 models selected  

> select subtract #6

716 atoms, 693 bonds, 94 residues, 3 models selected  

> select add #7

5464 atoms, 5559 bonds, 689 residues, 3 models selected  

> select subtract #7

506 atoms, 486 bonds, 69 residues, 2 models selected  

> select add #1

4225 atoms, 4160 bonds, 1 pseudobond, 669 residues, 4 models selected  

> select subtract #1

213 atoms, 210 bonds, 25 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 213 atom styles  

> select clear

> style #8#!1,9 sphere

Changed 12982 atom styles  

> undo

> select #9/A:164,208,239,273

41 atoms, 40 bonds, 4 residues, 1 model selected  

> select #9/A:164,208,239,273

41 atoms, 40 bonds, 4 residues, 1 model selected  

> select add #9

4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected  

> select subtract #9

Nothing selected  

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> select #9/A:164,208,239,273

41 atoms, 40 bonds, 4 residues, 1 model selected  

> color sel byhetero

> select #8/A:311

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

> show sel atoms

> select add #8

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> select subtract #8

Nothing selected  

> hide #!9 models

> hide #8 models

> hide #!1 models

> open /Users/mk16/works/acyl-
> CoA_synthetase/Aquincola_tertiaricarbonis/6he0_Thioesterification_2-HIB-
> AMP_CoA.pdb

6he0_Thioesterification_2-HIB-AMP_CoA.pdb title:  
Crystal structure of 2-hydroxyisobutyryl-coa ligase (HCL) In complex with
2-hib-amp and coa In the thioesterfication state [more info...]  
  
Chain information for 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #10  
---  
Chain | Description | UniProt  
A | 2-hydroxyisobutyryl-coa synthetase | I3VE75_9BURK 1-477  
  
Non-standard residues in 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #10  
---  
8LE —
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-
oxidanyl-phosphoryl]2-methyl-2-oxidanyl-propanoate  
AMP — adenosine monophosphate  
COA — coenzyme A  
  
116 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> rainbow #!10

> style #!10 ball

Changed 4012 atom styles  

> close #10

> show #!1 models

> show #!9 models

> show #8 models

> select
> ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL""

55620 atoms, 56947 bonds, 8 pseudobonds, 7139 residues, 13 models selected  

> hide sel & #8#!1,9 atoms

> select clear

> hide #8 models

> show #8 models

> select add #8

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel wheat

> select #8/A:482-900

1119 atoms, 1144 bonds, 139 residues, 1 model selected  

> rainbow sel

> select add #8

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> select subtract #8

Nothing selected  

> select add #9

4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected  

> color sel wheat

> select #9/A:360-999

902 atoms, 911 bonds, 1 pseudobond, 116 residues, 2 models selected  

> rainbow sel

> select
> ::name=""01A""::name=""8LE""::name=""AMP""::name=""BCO""::name=""CL""::name=""COA""::name=""EDO""::name=""HOH""::name=""MG""::name=""NO3""::name=""PRX""

3619 atoms, 939 bonds, 11 pseudobonds, 2754 residues, 8 models selected  

> color (#!1,9 & sel) byelement

> select clear

> select #9/A:438

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

> show sel atoms

> color sel byhetero

> select add #9

4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected  

> select subtract #9

Nothing selected  

> select #9/A:438,3366

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

> select #9/A:438,366

22 atoms, 20 bonds, 2 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> style sel ball

Changed 22 atom styles  

> undo

> label sel text ""{0.name} {0.number}{0.insertion_code}""

> undo

> show sel atoms

> color sel byhetero

> ~label sel residues

> select add #9

4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected  

> select subtract #9

Nothing selected  

> ui mousemode right distance

> distance #9/A:438@NH2 #9/A:1003@O1A

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A ARG 438 NH2
and COA 1003 O1A (alt loc A): 2.807Å  

> distance #9/A:366@NH2 #9/A:1003@O5A

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A ARG 366 NH2
and COA 1003 O5A (alt loc A): 2.875Å  

> hide #10.1 models

> ui mousemode right ""translate selected models""

> ui mousemode right translate

> select #8/A:

Expected an objects specifier or a keyword  

> select #8/A:555,557,488

31 atoms, 28 bonds, 3 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 31 atom styles  

> color sel byhetero

> select add #8

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> select subtract #8

Nothing selected  

> ui mousemode right distance

> distance #9/A:1003@OAP #8/A:488@NZ

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A COA 1003 OAP
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A LYS 488 NZ: 70.464Å  

> undo

> select subtract #8

Nothing selected  

> ~distance #9/A:1003@OAP #8/A:488@NZ

> distance #8/A:488@NZ #1/A:1003@O1A

Distance between AF-O14975-F1-model_v4_FATP2.pdb #8/A LYS 488 NZ and
6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O1A (alt loc A):
3.679Å  

> distance #8/A:555@NH1 #1/A:1003@O4A

Distance between AF-O14975-F1-model_v4_FATP2.pdb #8/A ARG 555 NH1 and
6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O4A (alt loc A):
7.704Å  

> ui mousemode right translate

> ui mousemode right distance

> distance #1/A:1003@O4A #8/A:557@NH2

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O4A
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A ARG 557 NH2: 10.556Å  

> ui mousemode right translate

> close #10

> select
> ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL""

55620 atoms, 56947 bonds, 8 pseudobonds, 7139 residues, 13 models selected  

> hide sel & #8#!1,9 atoms

> select clear

> select #9/A:190,192,193,216

25 atoms, 23 bonds, 4 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select add #9

4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected  

> select subtract #9

Nothing selected  

> select #9/A:190,192,193,216

25 atoms, 23 bonds, 4 residues, 1 model selected  

> color sel byhetero

> select add #9

4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected  

> select subtract #9

Nothing selected  

> ui mousemode right distance

> distance #9/A:192@OG #9/A:1003@O8A

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A SER 192 OG and
COA 1003 O8A (alt loc A): 2.856Å  

> distance #9/A:216@NE2 #9/A:1003@O8A

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A HIS 216 NE2
and COA 1003 O8A (alt loc A): 2.666Å  

> distance #9/A:1003@O7A #9/A:193@CB

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A COA 1003 O7A
(alt loc A) and ALA 193 CB: 6.160Å  

> select #9/A:190

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

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> distance #9/A:1003@O7A #9/A:190@CA

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A COA 1003 O7A
(alt loc A) and GLY 190 CA (alt loc B): 4.060Å  

> show sel cartoons

> select add #9

4012 atoms, 3950 bonds, 5 pseudobonds, 644 residues, 4 models selected  

> select subtract #9

Nothing selected  

> hide #10.1 models

> ui mousemode right translate

> select #8/A:291,293,318

27 atoms, 25 bonds, 3 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 27 atom styles  

> color sel byhetero

> select add #8

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> select subtract #8

Nothing selected  

> ui mousemode right distance

> distance #1/A:1003@O7A #8/A:291@NZ

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O7A
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A LYS 291 NZ: 5.283Å  

> distance #1/A:1003@O8A #8/A:318@OH

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O8A
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A TYR 318 OH: 7.996Å  

> distance #1/A:1003@O8A #8/A:293@OG

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O8A
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A SER 293 OG: 4.461Å  

> ui mousemode right translate

> close #10

> select
> ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL""

55620 atoms, 56947 bonds, 8 pseudobonds, 7139 residues, 13 models selected  

> hide sel & #8#!1,9 atoms

> select clear

> select #9/A:159,160,210

19 atoms, 17 bonds, 3 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> show sel atoms

> ui mousemode right distance

> distance #9/A:1003@N1A #9/A:160@CG1

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A COA 1003 N1A
(alt loc A) and VAL 160 CG1: 6.394Å  

> distance #9/A:1003@N1A #9/A:159@CB

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A COA 1003 N1A
(alt loc A) and ALA 159 CB: 5.492Å  

> hide #10.1 models

> distance #9/A:210@OG1 #9/A:1003@N1A

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A THR 210 OG1
and COA 1003 N1A (alt loc A): 4.292Å  

> ui mousemode right translate

> select add #9

4012 atoms, 3950 bonds, 4 pseudobonds, 644 residues, 4 models selected  

> select subtract #9

Nothing selected  

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> ui tool show ""Side View""

> select #8/A:264,263,314,292

35 atoms, 33 bonds, 4 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 35 atom styles  

> color sel byhetero

> ui mousemode right distance

> distance #1/A:1003@N1A #8/A:264@CD2

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 N1A
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A LEU 264 CD2: 3.037Å  

> distance #1/A:1003@N1A #8/A:263@OG1

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 N1A
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A THR 263 OG1: 4.946Å  

> distance #1/A:1003@N1A #8/A:314@OE1

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 N1A
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A GLU 314 OE1: 9.093Å  

> distance #8/A:292@CD1 #8/A:292@CG

Distance between AF-O14975-F1-model_v4_FATP2.pdb #8/A PHE 292 CD1 and CG:
1.408Å  

> distance #8/A:292@CG #1/A:1003@C2A

Distance between AF-O14975-F1-model_v4_FATP2.pdb #8/A PHE 292 CG and
6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 C2A (alt loc A):
3.120Å  

> select add #8

4958 atoms, 5073 bonds, 1 pseudobond, 620 residues, 2 models selected  

> select subtract #8

Nothing selected  

> ui mousemode right translate

> select
> ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL""

55620 atoms, 56947 bonds, 9 pseudobonds, 7139 residues, 14 models selected  

> hide sel & #8#!1,9 atoms

> close #10

> select clear

> view clip false

> select #8/A:136,267,490

33 atoms, 32 bonds, 3 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 33 atom styles  

> color sel byhetero

> ui mousemode right distance

> distance #8/A:490@OE1 #1/A:1003@O9P

Distance between AF-O14975-F1-model_v4_FATP2.pdb #8/A GLU 490 OE1 and
6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O9P (alt loc A):
2.421Å  

> distance #8/A:267@OH #1/A:1003@O9P

Distance between AF-O14975-F1-model_v4_FATP2.pdb #8/A TYR 267 OH and
6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O9P (alt loc A):
1.918Å  

> distance #1/A:1003@O9P #8/A:136@OH

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O9P
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A TYR 136 OH: 4.522Å  

> hide #10.1 models

> ui mousemode right translate

> select #8/A:136,267,490

33 atoms, 32 bonds, 3 residues, 1 model selected  

> select #9/A:164

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

> show sel atoms

> color sel byhetero

> ui mousemode right distance

> distance #9/A:164@OH #9/A:1003@O9P

Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A TYR 164 OH and
COA 1003 O9P (alt loc A): 4.322Å  

> ui mousemode right translate

> ui tool show ""Side View""

> select add #9

4012 atoms, 3950 bonds, 2 pseudobonds, 644 residues, 4 models selected  

> select subtract #9

Nothing selected  

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> hide #!9 models

> view #8 clip false


===== Log before crash end =====

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

> open /Users/mk16/Desktop/220250214.cxs

Log from Fri Feb 14 11:22:12 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/mk16/works/acyl-
> CoA_synthetase/Aquincola_tertiaricarbonis/6he0_Thioesterification_2-HIB-
> AMP_CoA.pdb

6he0_Thioesterification_2-HIB-AMP_CoA.pdb title:  
Crystal structure of 2-hydroxyisobutyryl-coa ligase (HCL) In complex with
2-hib-amp and coa In the thioesterfication state [more info...]  
  
Chain information for 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1  
---  
Chain | Description | UniProt  
A | 2-hydroxyisobutyryl-coa synthetase | I3VE75_9BURK 1-477  
  
Non-standard residues in 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1  
---  
8LE —
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-
oxidanyl-phosphoryl]2-methyl-2-oxidanyl-propanoate  
AMP — adenosine monophosphate  
COA — coenzyme A  
  
116 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open /Users/mk16/works/acyl-
> CoA_synthetase/Aquincola_tertiaricarbonis/6he2_openConformatin_2-HIB-
> AMP_CoA.pdb

6he2_openConformatin_2-HIB-AMP_CoA.pdb title:  
Crystal structure of an open conformation of 2-hydroxyisobutyryl-coa ligase
(HCL) In complex with 2-hib-amp and coa [more info...]  
  
Chain information for 6he2_openConformatin_2-HIB-AMP_CoA.pdb #2  
---  
Chain | Description | UniProt  
A B | 2-hydroxyisobutyryl-coa synthetase | I3VE75_9BURK 1-477  
  
Non-standard residues in 6he2_openConformatin_2-HIB-AMP_CoA.pdb #2  
---  
8LE —
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-
oxidanyl-phosphoryl]2-methyl-2-oxidanyl-propanoate  
AMP — adenosine monophosphate  
COA — coenzyme A  
  
104 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open /Users/mk16/works/acyl-
> CoA_synthetase/1pg4_AcetylCoASynthetase_Salmonella.pdb

1pg4_AcetylCoASynthetase_Salmonella.pdb title:  
Acetyl coa synthetase, salmonella enterica [more info...]  
  
Chain information for 1pg4_AcetylCoASynthetase_Salmonella.pdb #3  
---  
Chain | Description | UniProt  
A B | acetyl-coa synthetase | ACSA_SALTY 1-652  
  
Non-standard residues in 1pg4_AcetylCoASynthetase_Salmonella.pdb #3  
---  
CL — chloride ion  
COA — coenzyme A  
EDO — 1,2-ethanediol (ethylene glycol)  
MG — magnesium ion  
PRX — adenosine-5'-monophosphate-propyl ester
(adenosine-5'-propylphosphate)  
  

> open /Users/mk16/works/acyl-CoA_synthetase/3eq6_ACSM2A_bCoA_AMP.pdb

3eq6_ACSM2A_bCoA_AMP.pdb title:  
Crystal structure of human acyl-coa synthetase medium-chain family member 2A
(L64P mutation) In A ternary complex with products [more info...]  
  
Chain information for 3eq6_ACSM2A_bCoA_AMP.pdb #4  
---  
Chain | Description | UniProt  
A B | acyl-coenzyme A synthetase ACSM2A | ACS2A_HUMAN 32-577  
  
Non-standard residues in 3eq6_ACSM2A_bCoA_AMP.pdb #4  
---  
AMP — adenosine monophosphate  
BCO — butyryl coenzyme A
(S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3Λ~5~,5Λ~5~-diphosphaheptadecan-17-yl}
butanethioate (non-preferred name))  
  
28 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open /Users/mk16/works/acyl-
> CoA_synthetase/3cw9_Alcaligenes_ChlorobenzoylCoA.pdb

3cw9_Alcaligenes_ChlorobenzoylCoA.pdb title:  
4-chlorobenzoyl-coa ligase/synthetase In the thioester-forming conformation,
bound to 4-chlorophenacyl-coa [more info...]  
  
Chain information for 3cw9_Alcaligenes_ChlorobenzoylCoA.pdb #5  
---  
Chain | Description  
A B | chlorobenzoate COA ligase/synthetase  
  
Non-standard residues in 3cw9_Alcaligenes_ChlorobenzoylCoA.pdb #5  
---  
01A — 4-chlorophenacyl-coenzyme A  
AMP — adenosine monophosphate  
EDO — 1,2-ethanediol (ethylene glycol)  
MG — magnesium ion  
NO3 — nitrate ion  
  

> open /Users/mk16/works/acyl-CoA_synthetase/AF3/acsl4/fold_acsl4_model_0.cif

Chain information for fold_acsl4_model_0.cif #6  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> open /Users/mk16/works/acyl-CoA_synthetase/AF3/fatp2/fold_fatp2_model_0.cif

Chain information for fold_fatp2_model_0.cif #7  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> open /Users/mk16/works/acyl-CoA_synthetase/AF-O14975-F1-model_v4_FATP2.pdb

AF-O14975-F1-model_v4_FATP2.pdb title:  
Alphafold monomer V2.0 prediction for very long-chain acyl-coa synthetase
(O14975) [more info...]  
  
Chain information for AF-O14975-F1-model_v4_FATP2.pdb #8  
---  
Chain | Description | UniProt  
A | very long-chain acyl-coa synthetase | S27A2_HUMAN 1-620  
  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #4,6-7#!1-3,5 to #8

Computing secondary structure  
[Repeated 7 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#4), sequence alignment score = 652.7  
RMSD between 276 pruned atom pairs is 1.237 angstroms; (across all 507 pairs:
3.918)  
  
Matchmaker AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8) with
fold_acsl4_model_0.cif, chain A (#6), sequence alignment score = 523.9  
RMSD between 232 pruned atom pairs is 1.201 angstroms; (across all 551 pairs:
15.586)  
  
Matchmaker AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8) with
fold_fatp2_model_0.cif, chain A (#7), sequence alignment score = 3219.7  
RMSD between 477 pruned atom pairs is 0.494 angstroms; (across all 620 pairs:
11.781)  
  
Matchmaker AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8) with
6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1), sequence alignment
score = 189.9  
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)  
  
Matchmaker AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8) with
6he2_openConformatin_2-HIB-AMP_CoA.pdb, chain A (#2), sequence alignment score
= 201.4  
RMSD between 67 pruned atom pairs is 1.344 angstroms; (across all 395 pairs:
23.598)  
  
Matchmaker AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8) with
1pg4_AcetylCoASynthetase_Salmonella.pdb, chain A (#3), sequence alignment
score = 619.5  
RMSD between 268 pruned atom pairs is 1.196 angstroms; (across all 553 pairs:
6.864)  
  
Matchmaker AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8) with
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb, chain A (#5), sequence alignment score
= 649.4  
RMSD between 270 pruned atom pairs is 1.148 angstroms; (across all 490 pairs:
4.490)  
  

> select #3/B#4/A

9879 atoms, 9439 bonds, 7 pseudobonds, 1851 residues, 4 models selected  

> hide sel atoms

> hide sel cartoons

> select #3/B#4/A#5/B

14202 atoms, 13418 bonds, 8 pseudobonds, 2777 residues, 6 models selected  

> hide sel atoms

> hide sel cartoons

> select #3/B#4/A#5/B#2/B

17814 atoms, 16998 bonds, 10 pseudobonds, 3342 residues, 8 models selected  

> hide sel atoms

> hide sel cartoons

> lighting soft

> graphics silhouettes true

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> ui tool show ""Color Actions""

> color sel wheat

[Repeated 1 time(s)]

> select

55227 atoms, 53936 bonds, 24 pseudobonds, 9249 residues, 16 models selected  

> color sel wheat

> select
> ::name=""01A""::name=""8LE""::name=""AMP""::name=""BCO""::name=""CL""::name=""COA""::name=""EDO""::name=""HOH""::name=""MG""::name=""NO3""::name=""PRX""

3355 atoms, 833 bonds, 11 pseudobonds, 2587 residues, 7 models selected  

> color (#4#!1-3,5 & sel) byelement

> show sel atoms

> undo

> style sel ball

Changed 3355 atom styles  

> style sel sphere

Changed 3355 atom styles  

> style sel ball

Changed 3355 atom styles  

> select ::name=""HOH""

2551 atoms, 2551 residues, 5 models selected  

> hide sel atoms

> select clear

> select ::name=""MG""

4 atoms, 4 residues, 2 models selected  

> show sel atoms

> undo

> style sel sphere

Changed 4 atom styles  

> select clear

> hide #!2 models

> hide #!3 models

> hide #4 models

> hide #!5 models

> hide #6 models

> hide #7 models

> hide #8 models

> select

55227 atoms, 53936 bonds, 24 pseudobonds, 9249 residues, 16 models selected  

> show #4,6-8#!1-3,5 target m

> color sel byhetero

> select clear

> hide #4,6-8#!2-3,5 target m

> select #1/:367

Expected an objects specifier or a keyword  

> select #1/A:367

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

> select #1/A:367-900

841 atoms, 849 bonds, 1 pseudobond, 109 residues, 2 models selected  

> color sel powder blue

> color sel light blue

> select #2/A:367-900

974 atoms, 829 bonds, 1 pseudobond, 255 residues, 2 models selected  

> show #!2 models

> show #!3 models

> show #4 models

> show #!5 models

> hide #!5 models

> show #6 models

> show #!5 models

> show #7 models

> show #8 models

> select #2/A:367-900

974 atoms, 829 bonds, 1 pseudobond, 255 residues, 2 models selected  

> color sel light blue

> hide #!1 models

> hide #!2 models

> select add #2

7501 atoms, 7414 bonds, 4 pseudobonds, 1187 residues, 3 models selected  

> select subtract #2

Nothing selected  

> select #3/A:524-900

847 atoms, 864 bonds, 1 pseudobond, 114 residues, 2 models selected  

> color sel light blue

> select #4/A:470-900

787 atoms, 805 bonds, 100 residues, 1 model selected  

> select #4/B:470-900

775 atoms, 793 bonds, 100 residues, 1 model selected  

> color sel light blue

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #4 models

> select #5/B:409-900

739 atoms, 750 bonds, 95 residues, 1 model selected  

> select #5/A:409-900

728 atoms, 739 bonds, 95 residues, 1 model selected  

> color sel light blue

> select add #5

8584 atoms, 7932 bonds, 5 pseudobonds, 1816 residues, 2 models selected  

> select subtract #5

Nothing selected  

> hide #!5 models

> select #7/A:580-900

326 atoms, 332 bonds, 41 residues, 1 model selected  

> color sel light blue

> hide #8 models

> hide #6 models

> show #6 models

> show #8 models

> select #6/A:580-900

1052 atoms, 1071 bonds, 132 residues, 1 model selected  

> color sel light blue

> select add #6

5553 atoms, 5667 bonds, 711 residues, 1 model selected  

> select subtract #6

Nothing selected  

> hide #6 models

> select #7/A:489-900

1055 atoms, 1077 bonds, 132 residues, 1 model selected  

> color sel light blue

> select #8/A:489-900

1055 atoms, 1077 bonds, 132 residues, 1 model selected  

> color sel light blue

> select add #8

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> select subtract #8

Nothing selected  

> hide #8 models

> hide #7 models

> show #!1 models

> select #1/A

4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 2 models selected  

> select #1/A:

Expected an objects specifier or a keyword  

> select #1/A:

Expected an objects specifier or a keyword  

> select #1/A:455

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

> select #1/A:455,367

13 atoms, 11 bonds, 2 residues, 1 model selected  

> show #!2 models

> show #!3 models

> show #4 models

> show #!5 models

> show #6 models

> show #8 models

> show #7 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select #1/A:455,367#2/A

3902 atoms, 3845 bonds, 2 pseudobonds, 624 residues, 3 models selected  

> select #1/A:455,367#2/A:455,367

26 atoms, 22 bonds, 4 residues, 2 models selected  

> select #1/A:455,367#2/A:455,367#3/A

5480 atoms, 5133 bonds, 7 pseudobonds, 1117 residues, 5 models selected  

> select #1/A:455,367#2/A:455,367#3/A:609,524#4/A

4531 atoms, 4331 bonds, 836 residues, 4 models selected  

> select #1/A:455,367#2/A:455,367#3/A:609,524#4/B

4363 atoms, 4306 bonds, 693 residues, 4 models selected  

> select #1/A:455,367#2/A:455,367#3/A:609,524#4/B:557,470

46 atoms, 38 bonds, 8 residues, 4 models selected  

> select #1/A:455,367#2/A:455,367#3/A:609,524#4/B:557,470#5/A

4307 atoms, 3991 bonds, 4 pseudobonds, 898 residues, 6 models selected  

> select #1/A:455,367#2/A:455,367#3/A:609,524#4/B:557,470#5/A:492,409

55 atoms, 45 bonds, 10 residues, 5 models selected  

> select
> #1/A:455,367#2/A:455,367#3/A:609,524#4/B:557,470#5/A:492,409#6/A:690,580#7/A:572,489

81 atoms, 67 bonds, 14 residues, 7 models selected  

> select
> #1/A:455,367#2/A:455,367#3/A:609,524#4/B:557,470#5/A:492,409#6/A:690,580#7/A:572,489#8/A:572,489

94 atoms, 78 bonds, 16 residues, 8 models selected  

> show sel atoms

> color sel magenta

> select clear

> hide #4,6-8#!1-3,5 target m

> show #!1 models

> hide #!1 models

> show #!1 models

> select #1/A:159,160,164,186,190,192,193,210,213,216,366,399,424,437,438

121 atoms, 112 bonds, 15 residues, 1 model selected  

> color sel orange

> show sel atoms

> color sel byhetero

> select #1/A:424

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

> hide sel atoms

> color sel wheat

> color sel light blue

> select add #1

4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select #2/A:159,160,164,186,190,192,193,210,213,216,366,399,424,437,438

121 atoms, 112 bonds, 15 residues, 1 model selected  

> show #!2 models

> hide #!1 models

> select #2/A:159,160,164,186,190,192,193,210,213,216,366,399,437,438

110 atoms, 102 bonds, 14 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> color sel orange

> color sel byhetero

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select add #2

7501 atoms, 7414 bonds, 4 pseudobonds, 1187 residues, 3 models selected  

> select subtract #2

Nothing selected  

> select #3/A:159,160,164,186,190,192,193,210,213,216,366,399,437,438

96 atoms, 89 bonds, 14 residues, 1 model selected  

> select add #3

10837 atoms, 10248 bonds, 14 pseudobonds, 2134 residues, 4 models selected  

> select subtract #3

Nothing selected  

> select #3/A:163,191,194,196,164,165,305,306,309,357,335,360,523,584

111 atoms, 103 bonds, 14 residues, 1 model selected  

> color sel byhetero

> color sel orange

> color sel byhetero

> select add #3

10837 atoms, 10248 bonds, 14 pseudobonds, 2134 residues, 4 models selected  

> select subtract #3

Nothing selected  

> show #7 models

> hide #7 models

> show #7 models

> hide #7 models

> show #7 models

> hide #7 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #4 models

> hide #4 models

> show #4 models

> select #4/A:

Expected an objects specifier or a keyword  

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> select #4/B

4328 atoms, 4277 bonds, 687 residues, 1 model selected  

> select #4/B:137,138,139,261,262,265,249,290,311,469,532

84 atoms, 78 bonds, 11 residues, 1 model selected  

> select #4/B:137,138,139,261,262,265,249,290,311,469,532

84 atoms, 78 bonds, 11 residues, 1 model selected  

> show sel atoms

> color sel orange

> color sel byhetero

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> show #!5 models

> show #!3 models

> hide #!3 models

> hide #4 models

> select #5/A:137,138,139,261,262,265,249,290,311,469,532

80 atoms, 76 bonds, 10 residues, 1 model selected  

> select #5/A:85,86,87,203,204,207,230,251,254,408,466

92 atoms, 88 bonds, 11 residues, 1 model selected  

> color sel orange

> show sel atoms

> color sel byhetero

> select add #5

8584 atoms, 7932 bonds, 5 pseudobonds, 1816 residues, 2 models selected  

> color sel byhetero

> select subtract #5

Nothing selected  

> select add #5

8584 atoms, 7932 bonds, 5 pseudobonds, 1816 residues, 2 models selected  

> select subtract #5

Nothing selected  

> hide #!5 models

> show #6 models

> show #!5 models

> hide #!5 models

> show #6 models

> select #6/A:181,182,183,319,320,323,374,377,579,654,662

88 atoms, 83 bonds, 11 residues, 1 model selected  

> show sel atoms

> color sel orange

> color sel byhetero

[Repeated 1 time(s)]

> show sel atoms

> color sel byhetero

> show #7 models

> select add #6

5553 atoms, 5667 bonds, 711 residues, 1 model selected  

> hide #6 models

> select subtract #6

Nothing selected  

> select #7/A:135,136,137,264,265,268,312,315,488,547,550

91 atoms, 86 bonds, 11 residues, 1 model selected  

> show sel atoms

> color sel orange

> color sel byhetero

> show #8 models

> hide #7 models

> select add #7

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> select subtract #7

Nothing selected  

> select add #8

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> select subtract #8

Nothing selected  

> select #8/A:135,136,137,264,265,268,312,315,488,547,550

91 atoms, 86 bonds, 11 residues, 1 model selected  

> show sel atoms

> color sel orange

> color sel byhetero

> select add #8

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> select subtract #8

Nothing selected  

> show #7 models

> hide #8 models

> hide #7 models

> show #!1 models

> hide #!1 models

> show #8 models

> show #4 models

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> hide #8 models

> show #7 models

> hide #7 models

> show #7 models

> hide #7 models

> show #8 models

> select
> ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL""

51872 atoms, 53103 bonds, 7 pseudobonds, 6662 residues, 11 models selected  

> select
> ::name=""01A""::name=""8LE""::name=""AMP""::name=""BCO""::name=""CL""::name=""COA""::name=""EDO""::name=""HOH""::name=""MG""::name=""NO3""::name=""PRX""

3355 atoms, 833 bonds, 11 pseudobonds, 2587 residues, 7 models selected  

> select add #1

7103 atoms, 4677 bonds, 12 pseudobonds, 3064 residues, 9 models selected  

> select subtract #1

3091 atoms, 727 bonds, 11 pseudobonds, 2420 residues, 6 models selected  

> select add #2

10101 atoms, 7929 bonds, 15 pseudobonds, 3310 residues, 8 models selected  

> select subtract #2

2600 atoms, 515 bonds, 11 pseudobonds, 2123 residues, 5 models selected  

> select add #3

12416 atoms, 10592 bonds, 19 pseudobonds, 3395 residues, 7 models selected  

> select subtract #3

1579 atoms, 344 bonds, 5 pseudobonds, 1261 residues, 3 models selected  

> select add #5

9183 atoms, 8092 bonds, 5 pseudobonds, 2267 residues, 3 models selected  

> select subtract #5

599 atoms, 160 bonds, 451 residues, 1 model selected  

> select ~sel & ##selected

8225 atoms, 8419 bonds, 1066 residues, 1 model selected  

> hide sel atoms

> undo

> hide sel cartoons

> hide sel atoms

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> undo

[Repeated 2 time(s)]

> hide #8 models

> style sel ball

Changed 8225 atom styles  

> undo

> color sel byhetero

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> lighting soft

> show (#4 & sidechain) target ab

> undo

> show #4 cartoons

> undo

[Repeated 4 time(s)]

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> hide #8 models

> show #8 models

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> color sel cornflower blue

> color sel byhetero

> color sel byelement

> undo

> select subtract #4

Nothing selected  

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> select
> ::name=""01A""::name=""8LE""::name=""AMP""::name=""BCO""::name=""CL""::name=""COA""::name=""EDO""::name=""HOH""::name=""MG""::name=""NO3""::name=""PRX""

3355 atoms, 833 bonds, 11 pseudobonds, 2587 residues, 7 models selected  

> color (#4 & sel) byelement

> select clear

> select C1

Nothing selected  

> hide (#4,8 & (protein|nucleic)) target a

> cartoon hide #4,8

> show (#4,8 & backbone) target ab

> undo

[Repeated 2 time(s)]

> hide #4 models

> show #4 models

> hide #4,8 atoms

> undo

> select
> ::name=""01A""::name=""8LE""::name=""AMP""::name=""BCO""::name=""CL""::name=""COA""::name=""EDO""::name=""HOH""::name=""MG""::name=""NO3""::name=""PRX""

3355 atoms, 833 bonds, 11 pseudobonds, 2587 residues, 7 models selected  

> select ~sel & ##selected

36403 atoms, 37290 bonds, 13 pseudobonds, 4711 residues, 9 models selected  

> hide sel & #4 atoms

> color sel & #4 byhetero

> select clear

> color #4,8 byhetero

[Repeated 1 time(s)]

> select sel :< 7

Nothing selected  

> select ::name=""BCO""

106 atoms, 110 bonds, 2 residues, 1 model selected  

> select sel :< 7

4242 atoms, 4092 bonds, 4 pseudobonds, 606 residues, 9 models selected  

> select sel :< 5

15531 atoms, 15168 bonds, 4 pseudobonds, 2317 residues, 9 models selected  

> undo

[Repeated 1 time(s)]

> select sel :< 5

2572 atoms, 2451 bonds, 2 pseudobonds, 344 residues, 9 models selected  

> show sel & #4,8 atoms

> undo

> select add #4

10756 atoms, 10420 bonds, 2 pseudobonds, 1783 residues, 9 models selected  

> select subtract #4

1932 atoms, 1841 bonds, 2 pseudobonds, 266 residues, 8 models selected  

> select add #1

5620 atoms, 5485 bonds, 3 pseudobonds, 864 residues, 10 models selected  

> select subtract #1

1608 atoms, 1535 bonds, 2 pseudobonds, 220 residues, 7 models selected  

> select add #2

8790 atoms, 8636 bonds, 6 pseudobonds, 1371 residues, 9 models selected  

> select subtract #2

1289 atoms, 1222 bonds, 2 pseudobonds, 184 residues, 6 models selected  

> select add #3

11838 atoms, 11202 bonds, 16 pseudobonds, 2274 residues, 9 models selected  

> select subtract #3

1001 atoms, 954 bonds, 2 pseudobonds, 140 residues, 5 models selected  

> select add #5

9284 atoms, 8614 bonds, 5 pseudobonds, 1903 residues, 5 models selected  

> select subtract #5

700 atoms, 682 bonds, 87 residues, 3 models selected  

> select add #6

6001 atoms, 6101 bonds, 765 residues, 3 models selected  

> select subtract #6

448 atoms, 434 bonds, 54 residues, 2 models selected  

> select add #7

5189 atoms, 5297 bonds, 647 residues, 2 models selected  

> select subtract #7

231 atoms, 224 bonds, 27 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select add #8

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> select subtract #8

Nothing selected  

> color #4,8 byhetero

> graphics silhouettes false

> lighting flat

> lighting soft

> lighting full

> lighting simple

> lighting soft

[Repeated 3 time(s)]

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> hide #4 models

> show #4 models

> select ::name=""COA""

240 atoms, 250 bonds, 5 residues, 3 models selected  

> select ::name=""BCO""

106 atoms, 110 bonds, 2 residues, 1 model selected  

> select ~sel & ##selected

8718 atoms, 8469 bonds, 1515 residues, 1 model selected  

> show sel cartoons

> ui mousemode right ""move picked models""

> view matrix models
> #4,-0.62545,-0.2296,0.74572,19.831,0.65333,-0.67662,0.33964,94.363,0.42658,0.69962,0.5732,26.168

> undo

> ui mousemode right ""translate selected atoms""

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> select #4/A

4496 atoms, 4302 bonds, 830 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #4/B

4328 atoms, 4277 bonds, 687 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel wheat

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> undo

[Repeated 9 time(s)]

> select #4/B

4328 atoms, 4277 bonds, 687 residues, 1 model selected  

> select ::name=""BCO""

106 atoms, 110 bonds, 2 residues, 1 model selected  

> select ~sel & ##selected

8718 atoms, 8469 bonds, 1515 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> color sel byhetero

> ui mousemode right ""move picked models""

> view matrix models #8,1,0,0,-5.6333,0,1,0,-3.5595,0,0,1,0.25735

> undo

> ui mousemode right translate

> open /Users/mk16/works/acyl-CoA_synthetase/3eq6_ACSM2A_bCoA_AMP.pdb

3eq6_ACSM2A_bCoA_AMP.pdb title:  
Crystal structure of human acyl-coa synthetase medium-chain family member 2A
(L64P mutation) In A ternary complex with products [more info...]  
  
Chain information for 3eq6_ACSM2A_bCoA_AMP.pdb #9  
---  
Chain | Description | UniProt  
A B | acyl-coenzyme A synthetase ACSM2A | ACS2A_HUMAN 32-577  
  
Non-standard residues in 3eq6_ACSM2A_bCoA_AMP.pdb #9  
---  
AMP — adenosine monophosphate  
BCO — butyryl coenzyme A
(S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3Λ~5~,5Λ~5~-diphosphaheptadecan-17-yl}
butanethioate (non-preferred name))  
  
28 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show Matchmaker

> matchmaker #4,6-9#!2-3,5 to #1

Computing secondary structure  
[Repeated 8 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#4), sequence alignment score = 290.3  
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_acsl4_model_0.cif, chain A (#6), sequence alignment score = 181.7  
RMSD between 80 pruned atom pairs is 1.286 angstroms; (across all 430 pairs:
23.367)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_fatp2_model_0.cif, chain A (#7), sequence alignment score = 179.1  
RMSD between 56 pruned atom pairs is 1.119 angstroms; (across all 410 pairs:
23.522)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8), sequence alignment score =
189.9  
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#9), sequence alignment score = 290.3  
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
6he2_openConformatin_2-HIB-AMP_CoA.pdb, chain A (#2), sequence alignment score
= 2511  
RMSD between 355 pruned atom pairs is 0.323 angstroms; (across all 456 pairs:
14.640)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
1pg4_AcetylCoASynthetase_Salmonella.pdb, chain A (#3), sequence alignment
score = 279.5  
RMSD between 81 pruned atom pairs is 1.236 angstroms; (across all 444 pairs:
18.441)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb, chain B (#5), sequence alignment score
= 323.5  
RMSD between 64 pruned atom pairs is 1.175 angstroms; (across all 400 pairs:
15.376)  
  

> ui mousemode right ""translate selected models""

> view matrix models
> #4,-0.63144,-0.10227,0.76865,-11.141,0.61652,-0.66743,0.41766,18.391,0.47031,0.73761,0.48449,-79.835

> undo

[Repeated 2 time(s)]

> select #4/B

4328 atoms, 4277 bonds, 687 residues, 1 model selected  

> hide sel atoms

> select #9/A

4496 atoms, 4302 bonds, 830 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> hide sel cartoons

> view matrix models
> #9,-0.63144,-0.10227,0.76865,31.62,0.61652,-0.66743,0.41766,84.912,0.47031,0.73761,0.48449,-23.225

> undo

> view matrix models
> #9,-0.63144,-0.10227,0.76865,32.675,0.61652,-0.66743,0.41766,90.596,0.47031,0.73761,0.48449,-17.236

> undo

> ui mousemode right ""move picked models""

> view matrix models
> #9,-0.63144,-0.10227,0.76865,15.223,0.61652,-0.66743,0.41766,93.645,0.47031,0.73761,0.48449,41.798

> view matrix models
> #9,-0.63144,-0.10227,0.76865,10.46,0.61652,-0.66743,0.41766,101.22,0.47031,0.73761,0.48449,70.451

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> select add #4

13320 atoms, 12881 bonds, 2347 residues, 2 models selected  

> show sel cartoons

> undo

> select subtract #4

4496 atoms, 4302 bonds, 830 residues, 1 model selected  

> select add #4

13320 atoms, 12881 bonds, 2347 residues, 2 models selected  

> select subtract #4

4496 atoms, 4302 bonds, 830 residues, 1 model selected  

> select add #9

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #9

Nothing selected  

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> show sel cartoons

> undo

[Repeated 1 time(s)]

> ui tool show Matchmaker

> matchmaker #4,6-9#!2-3,5 to #1

Computing secondary structure  
[Repeated 8 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#4), sequence alignment score = 290.3  
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_acsl4_model_0.cif, chain A (#6), sequence alignment score = 181.7  
RMSD between 80 pruned atom pairs is 1.286 angstroms; (across all 430 pairs:
23.367)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_fatp2_model_0.cif, chain A (#7), sequence alignment score = 179.1  
RMSD between 56 pruned atom pairs is 1.119 angstroms; (across all 410 pairs:
23.522)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8), sequence alignment score =
189.9  
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#9), sequence alignment score = 290.3  
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
6he2_openConformatin_2-HIB-AMP_CoA.pdb, chain A (#2), sequence alignment score
= 2511  
RMSD between 355 pruned atom pairs is 0.323 angstroms; (across all 456 pairs:
14.640)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
1pg4_AcetylCoASynthetase_Salmonella.pdb, chain A (#3), sequence alignment
score = 279.5  
RMSD between 81 pruned atom pairs is 1.236 angstroms; (across all 444 pairs:
18.441)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb, chain B (#5), sequence alignment score
= 323.5  
RMSD between 64 pruned atom pairs is 1.175 angstroms; (across all 400 pairs:
15.376)  
  

> view matrix models
> #9,-0.63144,-0.10227,0.76865,4.7933,0.61652,-0.66743,0.41766,97.428,0.47031,0.73761,0.48449,56.96

> hide #4 models

> show #4 models

> hide #4 models

> undo

[Repeated 2 time(s)]

> show #4,8-9 cartoons

> undo

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select ::name=""BCO""

212 atoms, 220 bonds, 4 residues, 2 models selected  

> show sel atoms

[Repeated 1 time(s)]

> show sel cartoons

[Repeated 1 time(s)]

> select add #4

8930 atoms, 8689 bonds, 1519 residues, 2 models selected  

> select subtract #4

106 atoms, 110 bonds, 2 residues, 1 model selected  

> select add #9

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #9

Nothing selected  

> select add #9

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #9

Nothing selected  

> select add #9

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #9

Nothing selected  

> select
> ::name=""01A""::name=""8LE""::name=""AMP""::name=""BCO""::name=""CL""::name=""COA""::name=""EDO""::name=""HOH""::name=""MG""::name=""NO3""::name=""PRX""

3954 atoms, 993 bonds, 11 pseudobonds, 3038 residues, 8 models selected  

> color (#4,9 & sel) byelement

> style sel & #4,9 ball

Changed 1198 atom styles  

> select #9/A

4496 atoms, 4302 bonds, 830 residues, 1 model selected  

> hide sel atoms

> select add #9

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #9

Nothing selected  

> select add #3

10837 atoms, 10248 bonds, 14 pseudobonds, 2134 residues, 4 models selected  

> select add #4

19661 atoms, 18827 bonds, 14 pseudobonds, 3651 residues, 5 models selected  

> select subtract #3

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> select ::name=""BCO""

212 atoms, 220 bonds, 4 residues, 2 models selected  

> select add #9

8930 atoms, 8689 bonds, 1519 residues, 2 models selected  

> select subtract #9

106 atoms, 110 bonds, 2 residues, 1 model selected  

> show sel atoms

[Repeated 6 time(s)]

> ui tool show Matchmaker

> matchmaker #4,6-9#!2-3,5 to #1

Computing secondary structure  
[Repeated 8 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#4), sequence alignment score = 290.3  
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_acsl4_model_0.cif, chain A (#6), sequence alignment score = 181.7  
RMSD between 80 pruned atom pairs is 1.286 angstroms; (across all 430 pairs:
23.367)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_fatp2_model_0.cif, chain A (#7), sequence alignment score = 179.1  
RMSD between 56 pruned atom pairs is 1.119 angstroms; (across all 410 pairs:
23.522)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8), sequence alignment score =
189.9  
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#9), sequence alignment score = 290.3  
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
6he2_openConformatin_2-HIB-AMP_CoA.pdb, chain A (#2), sequence alignment score
= 2511  
RMSD between 355 pruned atom pairs is 0.323 angstroms; (across all 456 pairs:
14.640)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
1pg4_AcetylCoASynthetase_Salmonella.pdb, chain A (#3), sequence alignment
score = 279.5  
RMSD between 81 pruned atom pairs is 1.236 angstroms; (across all 444 pairs:
18.441)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb, chain B (#5), sequence alignment score
= 323.5  
RMSD between 64 pruned atom pairs is 1.175 angstroms; (across all 400 pairs:
15.376)  
  

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> close #4

> view matrix models
> #8,1,-1.0888e-15,6.5046e-16,-11.075,1.0888e-15,1,-5.4026e-16,-8.7467,-6.5046e-16,5.4026e-16,1,-65.524

> undo

[Repeated 1 time(s)]Undo failed, probably because structures have been
modified.  

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> select
> ::name=""01A""::name=""8LE""::name=""AMP""::name=""BCO""::name=""CL""::name=""COA""::name=""EDO""::name=""HOH""::name=""MG""::name=""NO3""::name=""PRX""

3355 atoms, 833 bonds, 11 pseudobonds, 2587 residues, 7 models selected  

> select ~sel & ##selected

36403 atoms, 37290 bonds, 13 pseudobonds, 4711 residues, 9 models selected  

> select add #9

37002 atoms, 37450 bonds, 13 pseudobonds, 5162 residues, 9 models selected  

> select subtract #9

28178 atoms, 28871 bonds, 13 pseudobonds, 3645 residues, 8 models selected  

> select add #9

37002 atoms, 37450 bonds, 13 pseudobonds, 5162 residues, 9 models selected  

> select subtract #9

28178 atoms, 28871 bonds, 13 pseudobonds, 3645 residues, 8 models selected  

> select ::name=""BCO""

106 atoms, 110 bonds, 2 residues, 1 model selected  

> select add #9

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #9

Nothing selected  

> color wheat

> undo

> select add #9

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> color sel wheat

> hide #8 models

> rename #9 id #4

> view matrix models
> #4,-0.63144,-0.10227,0.76865,17.743,0.61652,-0.66743,0.41766,86.782,0.47031,0.73761,0.48449,2.3275

> select #4/A

4496 atoms, 4302 bonds, 830 residues, 1 model selected  

> select #4/B

4328 atoms, 4277 bonds, 687 residues, 1 model selected  

> select #4/B:470-900

775 atoms, 793 bonds, 100 residues, 1 model selected  

> color sel light blue

> select
> ::name=""01A""::name=""8LE""::name=""AMP""::name=""BCO""::name=""CL""::name=""COA""::name=""EDO""::name=""HOH""::name=""MG""::name=""NO3""::name=""PRX""

3355 atoms, 833 bonds, 11 pseudobonds, 2587 residues, 7 models selected  

> color (#4 & sel) byelement

> select ::name=""HOH""

2551 atoms, 2551 residues, 5 models selected  

> hide sel & #4 atoms

> color sel & #4 byhetero

[Repeated 1 time(s)]

> select clear

> color #4 byhetero

> view matrix models
> #4,-0.63144,-0.10227,0.76865,5.0026,0.61652,-0.66743,0.41766,100.71,0.47031,0.73761,0.48449,69.138

> show #!3 models

> hide #!3 models

> show #!3 models

> view matrix models
> #4,-0.63144,-0.10227,0.76865,-2.3827,0.61652,-0.66743,0.41766,95.152,0.47031,0.73761,0.48449,63.671

> hide #!3 models

> show #8 models

> open /Users/mk16/works/acyl-CoA_synthetase/AF-O14975-F1-model_v4_FATP2.pdb

AF-O14975-F1-model_v4_FATP2.pdb title:  
Alphafold monomer V2.0 prediction for very long-chain acyl-coa synthetase
(O14975) [more info...]  
  
Chain information for AF-O14975-F1-model_v4_FATP2.pdb #9  
---  
Chain | Description | UniProt  
A | very long-chain acyl-coa synthetase | S27A2_HUMAN 1-620  
  
Computing secondary structure  

> select ::name=""BCO""

106 atoms, 110 bonds, 2 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #4,6-9#!2-3,5 to #1

Computing secondary structure  
[Repeated 8 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#4), sequence alignment score = 290.3  
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_acsl4_model_0.cif, chain A (#6), sequence alignment score = 181.7  
RMSD between 80 pruned atom pairs is 1.286 angstroms; (across all 430 pairs:
23.367)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_fatp2_model_0.cif, chain A (#7), sequence alignment score = 179.1  
RMSD between 56 pruned atom pairs is 1.119 angstroms; (across all 410 pairs:
23.522)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8), sequence alignment score =
189.9  
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#9), sequence alignment score =
189.9  
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
6he2_openConformatin_2-HIB-AMP_CoA.pdb, chain A (#2), sequence alignment score
= 2511  
RMSD between 355 pruned atom pairs is 0.323 angstroms; (across all 456 pairs:
14.640)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
1pg4_AcetylCoASynthetase_Salmonella.pdb, chain A (#3), sequence alignment
score = 279.5  
RMSD between 81 pruned atom pairs is 1.236 angstroms; (across all 444 pairs:
18.441)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb, chain B (#5), sequence alignment score
= 323.5  
RMSD between 64 pruned atom pairs is 1.175 angstroms; (across all 400 pairs:
15.376)  
  

> view matrix models
> #4,-0.63144,-0.10227,0.76865,-2.948,0.61652,-0.66743,0.41766,99.232,0.47031,0.73761,0.48449,61.83

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> select add #9

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> select subtract #9

Nothing selected  

> select add #9

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> select ::name=""BCO""

106 atoms, 110 bonds, 2 residues, 1 model selected  

> close #9

> open /Users/mk16/works/acyl-CoA_synthetase/3eq6_ACSM2A_bCoA_AMP.pdb

3eq6_ACSM2A_bCoA_AMP.pdb title:  
Crystal structure of human acyl-coa synthetase medium-chain family member 2A
(L64P mutation) In A ternary complex with products [more info...]  
  
Chain information for 3eq6_ACSM2A_bCoA_AMP.pdb #9  
---  
Chain | Description | UniProt  
A B | acyl-coenzyme A synthetase ACSM2A | ACS2A_HUMAN 32-577  
  
Non-standard residues in 3eq6_ACSM2A_bCoA_AMP.pdb #9  
---  
AMP — adenosine monophosphate  
BCO — butyryl coenzyme A
(S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3Λ~5~,5Λ~5~-diphosphaheptadecan-17-yl}
butanethioate (non-preferred name))  
  
28 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show Matchmaker

> matchmaker #4,6-9#!2-3,5 to #1

Computing secondary structure  
[Repeated 8 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#4), sequence alignment score = 290.3  
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_acsl4_model_0.cif, chain A (#6), sequence alignment score = 181.7  
RMSD between 80 pruned atom pairs is 1.286 angstroms; (across all 430 pairs:
23.367)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_fatp2_model_0.cif, chain A (#7), sequence alignment score = 179.1  
RMSD between 56 pruned atom pairs is 1.119 angstroms; (across all 410 pairs:
23.522)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8), sequence alignment score =
189.9  
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#9), sequence alignment score = 290.3  
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
6he2_openConformatin_2-HIB-AMP_CoA.pdb, chain A (#2), sequence alignment score
= 2511  
RMSD between 355 pruned atom pairs is 0.323 angstroms; (across all 456 pairs:
14.640)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
1pg4_AcetylCoASynthetase_Salmonella.pdb, chain A (#3), sequence alignment
score = 279.5  
RMSD between 81 pruned atom pairs is 1.236 angstroms; (across all 444 pairs:
18.441)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb, chain B (#5), sequence alignment score
= 323.5  
RMSD between 64 pruned atom pairs is 1.175 angstroms; (across all 400 pairs:
15.376)  
  

> view matrix models
> #8,1,-1.0792e-15,6.9772e-16,-26.958,1.0792e-15,1,-5.1093e-16,23.071,-6.9772e-16,5.1093e-16,1,82.515

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> hide #9 models

> show #9 models

> hide #9 models

> ui tool show Matchmaker

> matchmaker #4,6-9#!2-3,5 to #1

Computing secondary structure  
[Repeated 8 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#4), sequence alignment score = 290.3  
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_acsl4_model_0.cif, chain A (#6), sequence alignment score = 181.7  
RMSD between 80 pruned atom pairs is 1.286 angstroms; (across all 430 pairs:
23.367)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_fatp2_model_0.cif, chain A (#7), sequence alignment score = 179.1  
RMSD between 56 pruned atom pairs is 1.119 angstroms; (across all 410 pairs:
23.522)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8), sequence alignment score =
189.9  
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#9), sequence alignment score = 290.3  
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
6he2_openConformatin_2-HIB-AMP_CoA.pdb, chain A (#2), sequence alignment score
= 2511  
RMSD between 355 pruned atom pairs is 0.323 angstroms; (across all 456 pairs:
14.640)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
1pg4_AcetylCoASynthetase_Salmonella.pdb, chain A (#3), sequence alignment
score = 279.5  
RMSD between 81 pruned atom pairs is 1.236 angstroms; (across all 444 pairs:
18.441)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb, chain B (#5), sequence alignment score
= 323.5  
RMSD between 64 pruned atom pairs is 1.175 angstroms; (across all 400 pairs:
15.376)  
  

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> view matrix models
> #4,-0.63144,-0.10227,0.76865,2.611,0.61652,-0.66743,0.41766,93.529,0.47031,0.73761,0.48449,59.378

> select subtract #4

Nothing selected  

> select add #4

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #4

Nothing selected  

> show #9 models

> hide #9 models

> show #9 models

> select ::name=""BCO""

212 atoms, 220 bonds, 4 residues, 2 models selected  

> select ~sel & ##selected

17436 atoms, 16938 bonds, 3030 residues, 2 models selected  

> select add #4

17542 atoms, 17048 bonds, 3032 residues, 2 models selected  

> select subtract #4

8718 atoms, 8469 bonds, 1515 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #9/A

4496 atoms, 4302 bonds, 830 residues, 1 model selected  

> hide sel atoms

> select add #9

8824 atoms, 8579 bonds, 1517 residues, 1 model selected  

> select subtract #9

Nothing selected  

> select
> ::name=""01A""::name=""8LE""::name=""AMP""::name=""BCO""::name=""CL""::name=""COA""::name=""EDO""::name=""HOH""::name=""MG""::name=""NO3""::name=""PRX""

3954 atoms, 993 bonds, 11 pseudobonds, 3038 residues, 8 models selected  

> color (#4,9 & sel) byelement

> style sel & #4,9 ball

Changed 1198 atom styles  

> select clear

> view matrix models
> #4,-0.63144,-0.10227,0.76865,-12.792,0.61652,-0.66743,0.41766,80.371,0.47031,0.73761,0.48449,44.336

> view matrix models
> #4,-0.63144,-0.10227,0.76865,-8.8339,0.61652,-0.66743,0.41766,79.275,0.47031,0.73761,0.48449,38.312

> select ::name=""LYS""

3571 atoms, 3187 bonds, 417 residues, 9 models selected  

> view matrix models
> #8,1,-9.0489e-16,6.1096e-16,-4.9505,9.0489e-16,1,-4.8312e-16,-8.8155,-6.1096e-16,4.8312e-16,1,14.889

> undo

> select clear

> color #4,8-9 byhetero

> hide #4 models

> hide #8 models

> hide #9 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!3 models

> show #!5 models

> hide #!3 models

> hide #!5 models

> show #9 models

> show #8 models

> ui mousemode right translate

> hide #8 models

> show #8 models

> show #!3 models

> show #4 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #8 models

> hide #9 models

> show #8 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 #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!1 models

> select ::name=""COA""

240 atoms, 250 bonds, 5 residues, 3 models selected  

> select add #2

7645 atoms, 7564 bonds, 4 pseudobonds, 1190 residues, 5 models selected  

> select subtract #2

144 atoms, 150 bonds, 3 residues, 2 models selected  

> select add #3

10885 atoms, 10298 bonds, 14 pseudobonds, 2135 residues, 5 models selected  

> select subtract #3

48 atoms, 50 bonds, 1 residue, 1 model selected  

> select ~sel & ##selected

3964 atoms, 3900 bonds, 1 pseudobond, 643 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> undo

[Repeated 1 time(s)]

> hide #4 models

> show #4 models

> hide #4 models

> show #9 models

> hide #8 models

> hide #9 models

> show #8 models

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> select add #1

4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected  

> select subtract #1

Nothing selected  

> hide #!1 models

> hide #8 models

> show #8 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #!5 models

> select #5/A

4261 atoms, 3953 bonds, 4 pseudobonds, 890 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select #5/B

4323 atoms, 3979 bonds, 1 pseudobond, 926 residues, 2 models selected  

> show sel atoms

> show sel cartoons

> undo

[Repeated 1 time(s)]

> show sel cartoons

> select #5/B:409-900

739 atoms, 750 bonds, 95 residues, 1 model selected  

> color sel light blue

[Repeated 1 time(s)]

> select add #5

8584 atoms, 7932 bonds, 5 pseudobonds, 1816 residues, 2 models selected  

> select subtract #5

Nothing selected  

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #8 models

> hide #!5 models

> show #!5 models

> select
> ::name=""01A""::name=""8LE""::name=""AMP""::name=""BCO""::name=""CL""::name=""COA""::name=""EDO""::name=""HOH""::name=""MG""::name=""NO3""::name=""PRX""

3954 atoms, 993 bonds, 11 pseudobonds, 3038 residues, 8 models selected  

> select add #1

7702 atoms, 4837 bonds, 12 pseudobonds, 3515 residues, 10 models selected  

> select add #2

14712 atoms, 12039 bonds, 16 pseudobonds, 4405 residues, 12 models selected  

> select subtract #1

10700 atoms, 8089 bonds, 15 pseudobonds, 3761 residues, 9 models selected  

> select subtract #2

3199 atoms, 675 bonds, 11 pseudobonds, 2574 residues, 6 models selected  

> select add #2

10700 atoms, 8089 bonds, 15 pseudobonds, 3761 residues, 9 models selected  

> select add #3

20516 atoms, 18166 bonds, 23 pseudobonds, 5033 residues, 11 models selected  

> select subtract #3

9679 atoms, 7918 bonds, 9 pseudobonds, 2899 residues, 7 models selected  

> select subtract #2

2178 atoms, 504 bonds, 5 pseudobonds, 1712 residues, 4 models selected  

> select add #2

9679 atoms, 7918 bonds, 9 pseudobonds, 2899 residues, 7 models selected  

> select subtract #2

2178 atoms, 504 bonds, 5 pseudobonds, 1712 residues, 4 models selected  

> select add #4

10403 atoms, 8923 bonds, 5 pseudobonds, 2778 residues, 4 models selected  

> select subtract #4

1579 atoms, 344 bonds, 5 pseudobonds, 1261 residues, 3 models selected  

> select add #9

9804 atoms, 8763 bonds, 5 pseudobonds, 2327 residues, 3 models selected  

> select subtract #9

980 atoms, 184 bonds, 5 pseudobonds, 810 residues, 2 models selected  

> show sel atoms

> select ::name=""HOH""

2998 atoms, 2998 residues, 6 models selected  

> hide sel & #!5 atoms

> select #5/A

4261 atoms, 3953 bonds, 4 pseudobonds, 890 residues, 2 models selected  

> hide sel atoms

> select add #5

8584 atoms, 7932 bonds, 5 pseudobonds, 1816 residues, 2 models selected  

> select subtract #5

Nothing selected  

> show #8 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #8 models

> show #!5 models

> select ::name=""COA""

240 atoms, 250 bonds, 5 residues, 3 models selected  

> select ::name=""8LE""

87 atoms, 93 bonds, 3 residues, 2 models selected  

> select ::name=""PRX""

52 atoms, 56 bonds, 2 residues, 1 model selected  

> select ::name=""01A""

116 atoms, 122 bonds, 2 residues, 1 model selected  

> select sel :< 5

2861 atoms, 2743 bonds, 5 pseudobonds, 398 residues, 9 models selected  

> show sel & #!5 atoms

> select ::name=""HOH""

2998 atoms, 2998 residues, 6 models selected  

> hide sel & #!5 atoms

> color sel & #!5 byhetero

[Repeated 1 time(s)]

> select clear

> color #!5 byhetero

> hide #!5 models

> show #!5 models

> show #7 models

> hide #7 models

> show #8 models

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> hide #8 models

> show #7 models

> hide #7 models

> show #6 models

> hide #6 models

> show #6 models

> hide #6 models

> show #7 models

> hide #7 models

> show #6 models

> hide #6 models

> show #6 models

> hide #6 models

> show #8 models

> select ::name=""01A""

116 atoms, 122 bonds, 2 residues, 1 model selected  

> select ~sel & ##selected

8468 atoms, 7810 bonds, 5 pseudobonds, 1814 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select add #5

8584 atoms, 7932 bonds, 5 pseudobonds, 1816 residues, 2 models selected  

> select subtract #5

Nothing selected  

> undo

[Repeated 3 time(s)]

> select add #5

8584 atoms, 7932 bonds, 5 pseudobonds, 1816 residues, 2 models selected  

> select subtract #5

Nothing selected  

> hide #!5 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #!5 models

> hide #!5 models

> show #9 models

> hide #8 models

> show #8 models

> show #!1 models

> hide #8 models

> hide #9 models

> hide #!1 models

> show #!1 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 #8 models

> hide #8 models

> show #!2 models

> hide #!1 models

> select
> ::name=""01A""::name=""8LE""::name=""AMP""::name=""BCO""::name=""CL""::name=""COA""::name=""EDO""::name=""HOH""::name=""MG""::name=""NO3""::name=""PRX""

3954 atoms, 993 bonds, 11 pseudobonds, 3038 residues, 8 models selected  

> color (#!2 & sel) byelement

> select clear

> show #!1 models

> hide #!2 models

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/A #2/A #2/B

Alignment identifier is 1  

> select #1/A:158 #2/A-B:158

15 atoms, 12 bonds, 3 residues, 2 models selected  

> select #1/A:158-159 #2/A-B:158-159

30 atoms, 27 bonds, 6 residues, 2 models selected  
2-Hydroxyisobutyryl-Coa Synthetase [ID: 1] region 3 chains [169-170] RMSD:
0.246  
  

> select add #2

7511 atoms, 7423 bonds, 4 pseudobonds, 1189 residues, 4 models selected  

> select subtract #2

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select add #1

4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected  

> select subtract #1

Nothing selected  

> hide #!1 models

> show #!1 models

> show #8 models

> select #8/A:

Expected an objects specifier or a keyword  

> select #8/A:269

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

> select #1/A:159 #2/A-B:159

15 atoms, 12 bonds, 3 residues, 2 models selected  

> select #1/A:159 #2/A-B:159

15 atoms, 12 bonds, 3 residues, 2 models selected  
2-Hydroxyisobutyryl-Coa Synthetase [ID: 1] region 3 chains [170] RMSD: 0.235  
  

> select #8/A:269#1/A:159

11 atoms, 9 bonds, 2 residues, 2 models selected  

> select #8/A:323#1/A:159

12 atoms, 11 bonds, 2 residues, 2 models selected  

> select #8/A:268#1/A:159

15 atoms, 14 bonds, 2 residues, 2 models selected  

> select #8/A:124

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

> select #8/A:111

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

> open /Users/mk16/works/acyl-CoA_synthetase/acyl-
> CoA_synthetase_homolog/mustang/2-HIBA_FATP2/results.afasta

Summary of feedback from opening /Users/mk16/works/acyl-CoA_synthetase/acyl-
CoA_synthetase_homolog/mustang/2-HIBA_FATP2/results.afasta  
---  
notes | Alignment identifier is results.afasta  
Associated 6he0_Thioesterification_2-HIB-AMP_CoA.pdb chain A to
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb with 18 mismatches  
Associated 6he2_openConformatin_2-HIB-AMP_CoA.pdb chain A to
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb with 18 mismatches  
Associated 6he2_openConformatin_2-HIB-AMP_CoA.pdb chain B to
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb with 18 mismatches  
Associated fold_fatp2_model_0.cif chain A to AF-O14975-F1-model_v4_FATP2.pdb
with 0 mismatches  
Associated AF-O14975-F1-model_v4_FATP2.pdb chain A to
AF-O14975-F1-model_v4_FATP2.pdb with 0 mismatches  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment results.afasta  
  
Opened 2 sequences from results.afasta  

> select #1/A:24-25 #2/A-B:24-25

54 atoms, 57 bonds, 6 residues, 2 models selected  

> select #1/A:24-29 #2/A-B:24-29

168 atoms, 171 bonds, 18 residues, 2 models selected  
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [41-46] RMSD: 0.157  
  

> select #7/A:20 #8/A:20

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #7/A:20 #8/A:20

16 atoms, 14 bonds, 2 residues, 2 models selected  
Results.afasta [ID: results.afasta] region AF-O14975-F1-model_v4_FATP2.pdb
[45] RMSD: 2.166  
  

> select #1/A:27 #2/A-B:27

33 atoms, 30 bonds, 3 residues, 2 models selected  

> select #1/A:27-28 #2/A-B:27-28

60 atoms, 57 bonds, 6 residues, 2 models selected  
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [44-45] RMSD: 0.083  
  

> select #1/A:-1 #2/A-B:-1

18 atoms, 15 bonds, 3 residues, 2 models selected  

> select #1/A:-1-12 #2/A-B:-1-12

363 atoms, 375 bonds, 42 residues, 2 models selected  
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [1-14] RMSD: 0.157  
  

> select #1/A:46 #2/A-B:46

21 atoms, 18 bonds, 3 residues, 2 models selected  

> select #1/A:46 #2/A-B:46 #7/A:43 #8/A:43

35 atoms, 30 bonds, 5 residues, 4 models selected  
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-
AMP_CoA.pdb..AF-O14975-F1-model_v4_FATP2.pdb [68] RMSD: 11.142  
  

> select #1/A:104 #2/A-B:104

18 atoms, 15 bonds, 3 residues, 2 models selected  

> select #1/A:104 #2/A-B:104

18 atoms, 15 bonds, 3 residues, 2 models selected  
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [126] RMSD: 0.289  
  

> select clear

[Repeated 1 time(s)]

> select #1/A:133 #2/A-B:133

42 atoms, 45 bonds, 3 residues, 2 models selected  

> select #1/A:133 #2/A-B:133

42 atoms, 45 bonds, 3 residues, 2 models selected  
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [160] RMSD: 0.119  
  

> select #1/A:304-305 #2/A-B:304-305

66 atoms, 63 bonds, 6 residues, 2 models selected  

> select #1/A:304-306 #2/A-B:304-306

87 atoms, 84 bonds, 9 residues, 2 models selected  
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [508-510] RMSD: 0.269  
  

> select #1/A:227 #2/A-B:227

24 atoms, 21 bonds, 3 residues, 2 models selected  

> select #1/A:227-233 #2/A-B:227-233

171 atoms, 174 bonds, 21 residues, 2 models selected  
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [411-417] RMSD: 0.413  
  

> sequence header results.afasta consensus show

Showing consensus header (""seq_consensus"" residue attribute) for alignment
results.afasta  

> undo

> sequence refseq results.afasta:extracted_6he0_Thioesterification_2-HIBA-
> AMP_CoA.pdb

> select #1/A:154 #2/A:154 #2/B:154 #7/A:105 #8/A:105

40 atoms, 35 bonds, 5 residues, 4 models selected  

> select #1/A:155 #2/A:155 #2/B:155 #7/A:106 #8/A:106

33 atoms, 28 bonds, 5 residues, 4 models selected  

> select #1/A:158 #2/A-B:158

15 atoms, 12 bonds, 3 residues, 2 models selected  

> select #1/A:158 #2/A-B:158

15 atoms, 12 bonds, 3 residues, 2 models selected  
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [186] RMSD: 0.256  
  

> select #1/A:159-160 #2/A-B:159-160

36 atoms, 33 bonds, 6 residues, 2 models selected  

> select #1/A:159 #2/A-B:159

15 atoms, 12 bonds, 3 residues, 2 models selected  

> select #1/A:159 #2/A-B:159

15 atoms, 12 bonds, 3 residues, 2 models selected  
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [187] RMSD: 0.235  
  

> select #1/A:159 #2/A-B:159

15 atoms, 12 bonds, 3 residues, 2 models selected  

> select #1/A:159 #2/A-B:159 #7/A:110 #8/A:110

31 atoms, 26 bonds, 5 residues, 4 models selected  
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-
AMP_CoA.pdb..AF-O14975-F1-model_v4_FATP2.pdb [187] RMSD: 12.926  
  

> select #1/A:159 #2/A-B:159

15 atoms, 12 bonds, 3 residues, 2 models selected  

> select #1/A:159 #2/A-B:159 #7/A:110 #8/A:110

31 atoms, 26 bonds, 5 residues, 4 models selected  
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-
AMP_CoA.pdb..AF-O14975-F1-model_v4_FATP2.pdb [187] RMSD: 12.926  
  

> select clear

> ui tool show ""Show Sequence Viewer""

> sequence chain #7/A #8/A

Alignment identifier is 2  

> select #7/A:264 #8/A:264

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #7/A:264 #8/A:264

16 atoms, 14 bonds, 2 residues, 2 models selected  
. [ID: 2] region 2 chains [264] RMSD: 1.127  
  

> select #1/A:159 #2/A-B:159

15 atoms, 12 bonds, 3 residues, 2 models selected  

> open /Users/mk16/works/acyl-CoA_synthetase/acyl-
> CoA_synthetase_homolog/mustang/2-HIBA_FATP2/results.pdb

Summary of feedback from opening /Users/mk16/works/acyl-CoA_synthetase/acyl-
CoA_synthetase_homolog/mustang/2-HIBA_FATP2/results.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Produced by MUSTANG v3.2.4  
  
Ignored bad PDB record found on line 2  
REMARK Authors: A S Konagurthu, J C Whisstock, P J Stuckey, and A M Lesk  
  
Ignored bad PDB record found on line 4  
REMARK Structures: extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb
AF-O14975-F1-model_v4_FATP2.pdb  
  
Ignored bad PDB record found on line 6  
REMARK All structures were superposed on the coordinate frame of:
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
3759 messages similar to the above omitted  
Ignored bad PDB record found on line 8733  
  
Chain information for results.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
  
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> hide #!1 models

> select add #1

4022 atoms, 3958 bonds, 1 pseudobond, 646 residues, 4 models selected  

> select subtract #1

10 atoms, 8 bonds, 2 residues, 1 model selected  

> select add #2

7501 atoms, 7414 bonds, 4 pseudobonds, 1187 residues, 3 models selected  

> select subtract #2

Nothing selected  

> hide #8 models

> select add #10

8706 atoms, 8917 bonds, 1 pseudobond, 1097 residues, 2 models selected  

> rainbow sel

> select subtract #10

Nothing selected  

> select add #10

8706 atoms, 8917 bonds, 1 pseudobond, 1097 residues, 2 models selected  

> close #10

> ui tool show Matchmaker

> matchmaker #8 to #1 showAlignment true

Computing secondary structure  
[Repeated 1 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8), sequence alignment score =
189.9  
Alignment identifier is 3  
Showing conservation header (""seq_conservation"" residue attribute) for
alignment 3  
Hiding conservation header for alignment 3  
Chains used in RMSD evaluation for alignment 3: 6he0_Thioesterification_2-HIB-
AMP_CoA.pdb #1/A, AF-O14975-F1-model_v4_FATP2.pdb #8/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 3  
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)  
  

> show #8 models

> show #!1 models

> sequence refseq ""3:6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A""

> select #1/A:159

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

> select #1/A:159

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

> select #8/A:264

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

> select #8/A:264

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

> save /Users/mk16/works/acyl-CoA_synthetase/acyl-
> CoA_synthetase_homolog/2-HIBA_FATP2_matchmaker.aln.fa format fasta alignment
> 3

> select #1/A:173

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

> select #1/A:173-174

9 atoms, 8 bonds, 2 residues, 1 model selected  

> select #1/A:181

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

> select #1/A:181

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

> select #1/A:186

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

> select #1/A:186

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

> select #8/A:292

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

> select #1/A:186 #8/A:292

16 atoms, 15 bonds, 2 residues, 2 models selected  
MatchMaker Alignment [ID: 3] region 6he0_Thioesterification_2-HIB-AMP_CoA.pdb,
chain A..AF-O14975-F1-model_v4_FATP2.pdb, chain A [318] RMSD: 3.521  
  

> select #1/A:165-166

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select #1/A:165-169

36 atoms, 37 bonds, 5 residues, 1 model selected  

> select #1/A:199-202 #8/A:299-302

64 atoms, 62 bonds, 8 residues, 2 models selected  

> select #1/A:199-203 #8/A:299-304

94 atoms, 93 bonds, 11 residues, 2 models selected  
MatchMaker Alignment [ID: 3] region 6he0_Thioesterification_2-HIB-AMP_CoA.pdb,
chain A..AF-O14975-F1-model_v4_FATP2.pdb, chain A [331-336] RMSD: 5.198  
  

> select #1/A:197

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

> select #1/A:197-201 #8/A:297-301

93 atoms, 96 bonds, 10 residues, 2 models selected  
MatchMaker Alignment [ID: 3] region 6he0_Thioesterification_2-HIB-AMP_CoA.pdb,
chain A..AF-O14975-F1-model_v4_FATP2.pdb, chain A [329-333] RMSD: 5.871  
  

> select #1/A:196-197

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #1/A:196-200

46 atoms, 47 bonds, 5 residues, 1 model selected  

> select #1/A:152

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

> select #1/A:152

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

> select #1/A:166

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

> select #1/A:166

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

> select #1/A:190

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

> select #1/A:190

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

> select #8/A:296

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

> select #1/A:190 #8/A:296

13 atoms, 11 bonds, 2 residues, 2 models selected  
MatchMaker Alignment [ID: 3] region 6he0_Thioesterification_2-HIB-AMP_CoA.pdb,
chain A..AF-O14975-F1-model_v4_FATP2.pdb, chain A [322] RMSD: 8.166  
  

> select #1/A:190

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

> select #1/A:190 #8/A:296

13 atoms, 11 bonds, 2 residues, 2 models selected  
MatchMaker Alignment [ID: 3] region 6he0_Thioesterification_2-HIB-AMP_CoA.pdb,
chain A..AF-O14975-F1-model_v4_FATP2.pdb, chain A [322] RMSD: 8.166  
  

> show sel atoms

> undo

> select add #1

4021 atoms, 3958 bonds, 1 pseudobond, 645 residues, 4 models selected  

> select subtract #1

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

> hide #!1 models

> select add #8

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> select subtract #8

Nothing selected  

> show #!1 models

> select ::name=""01A""

116 atoms, 122 bonds, 2 residues, 1 model selected  

> select ::name=""COA""

240 atoms, 250 bonds, 5 residues, 3 models selected  

> select ~sel & ##selected

22110 atoms, 21362 bonds, 19 pseudobonds, 3960 residues, 7 models selected  

> hide sel & #!1 atoms

> hide sel & #!1 cartoons

> select add #1

22158 atoms, 21412 bonds, 19 pseudobonds, 3961 residues, 8 models selected  

> select subtract #1

18146 atoms, 17462 bonds, 18 pseudobonds, 3317 residues, 5 models selected  

> select add #2

18242 atoms, 17562 bonds, 18 pseudobonds, 3319 residues, 6 models selected  

> select subtract #2

10741 atoms, 10148 bonds, 14 pseudobonds, 2132 residues, 3 models selected  

> select add #3

10837 atoms, 10248 bonds, 14 pseudobonds, 2134 residues, 4 models selected  

> select subtract #3

Nothing selected  

> hide #!1 models

> show #!1 models

> close #9

> open /Users/mk16/works/acyl-
> CoA_synthetase/Aquincola_tertiaricarbonis/6he0_Thioesterification_2-HIB-
> AMP_CoA.pdb

6he0_Thioesterification_2-HIB-AMP_CoA.pdb title:  
Crystal structure of 2-hydroxyisobutyryl-coa ligase (HCL) In complex with
2-hib-amp and coa In the thioesterfication state [more info...]  
  
Chain information for 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9  
---  
Chain | Description | UniProt  
A | 2-hydroxyisobutyryl-coa synthetase | I3VE75_9BURK 1-477  
  
Non-standard residues in 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9  
---  
8LE —
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-
oxidanyl-phosphoryl]2-methyl-2-oxidanyl-propanoate  
AMP — adenosine monophosphate  
COA — coenzyme A  
  
116 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> ui tool show Matchmaker

> matchmaker #4,6-8#!2-3,5,9 to #1 showAlignment true

Computing secondary structure  
[Repeated 8 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#4), sequence alignment score = 290.3  
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_acsl4_model_0.cif, chain A (#6), sequence alignment score = 181.7  
RMSD between 80 pruned atom pairs is 1.286 angstroms; (across all 430 pairs:
23.367)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_fatp2_model_0.cif, chain A (#7), sequence alignment score = 179.1  
RMSD between 56 pruned atom pairs is 1.119 angstroms; (across all 410 pairs:
23.522)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8), sequence alignment score =
189.9  
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
6he2_openConformatin_2-HIB-AMP_CoA.pdb, chain A (#2), sequence alignment score
= 2511  
RMSD between 355 pruned atom pairs is 0.323 angstroms; (across all 456 pairs:
14.640)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
1pg4_AcetylCoASynthetase_Salmonella.pdb, chain A (#3), sequence alignment
score = 279.5  
RMSD between 81 pruned atom pairs is 1.236 angstroms; (across all 444 pairs:
18.441)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb, chain B (#5), sequence alignment score
= 323.5  
RMSD between 64 pruned atom pairs is 1.175 angstroms; (across all 400 pairs:
15.376)  
  
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#9), sequence alignment
score = 2593.8  
RMSD between 477 pruned atom pairs is 0.000 angstroms; (across all 477 pairs:
0.000)  
  

> ui mousemode right ""move picked models""

> view matrix models
> #9,0.78064,-0.60853,-0.14245,-13.659,0.51267,0.75386,-0.41094,-55.023,0.35745,0.24776,0.90047,-84.152

> select add #9

4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected  

> color (#!9 & sel) light gray

> select
> ::name=""01A""::name=""8LE""::name=""AMP""::name=""BCO""::name=""CL""::name=""COA""::name=""EDO""::name=""HOH""::name=""MG""::name=""NO3""::name=""PRX""

3619 atoms, 939 bonds, 11 pseudobonds, 2754 residues, 8 models selected  

> color (#!1,9 & sel) byelement

> style sel & #!1,9 ball

Changed 528 atom styles  

> select ::name=""HOH""

2715 atoms, 2715 residues, 6 models selected  

> hide sel & #!1,9 atoms

> select clear

> color #8#!1,9 byhetero

> select #8/A:111

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

> select #8/A:111

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

> select #8/A:111

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

> select #9/A

4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 2 models selected  

> select #9/A:159,160,164,186,190,192,193,210,213,216,366,399,437,438

110 atoms, 102 bonds, 14 residues, 1 model selected  

> color sel forest green

> color sel byhetero

> select add #9

4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected  

> select subtract #9

Nothing selected  

> select #9/A:360-900

902 atoms, 911 bonds, 1 pseudobond, 116 residues, 2 models selected  

> rainbow sel

> select #9/A:159,160,164,186,190,192,193,210,213,216,366,399,437,438

110 atoms, 102 bonds, 14 residues, 1 model selected  

> color sel forest green

> color sel byhetero

> select add #9

4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected  

> select subtract #9

Nothing selected  

> select #8/A:482-900

1119 atoms, 1144 bonds, 139 residues, 1 model selected  

> rainbow sel

> color sel byhetero

> select add #8

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> select subtract #8

Nothing selected  

> view matrix models
> #8,1,-1.1256e-15,6.5835e-16,0.24975,1.1256e-15,1,-5.5169e-16,-1.821,-6.5835e-16,5.5169e-16,1,-0.7586

> undo

> ui mousemode right select

Drag select of 1 bonds, 1 atoms  
Drag select of 1 atoms  
Drag select of 2 residues  

> select clear

[Repeated 1 time(s)]Drag select of 1 atoms  

> select sel :< 5

415 atoms, 415 bonds, 35 residues, 8 models selected  

> show sel & #8#!1 atoms

> undo

> select add #8

5356 atoms, 5471 bonds, 653 residues, 8 models selected  

> select subtract #8

398 atoms, 398 bonds, 33 residues, 7 models selected  

> undo

[Repeated 1 time(s)]

> select add #1

4361 atoms, 4300 bonds, 1 pseudobond, 674 residues, 10 models selected  

> select subtract #1

349 atoms, 350 bonds, 30 residues, 7 models selected  

> select add #2

7768 atoms, 7683 bonds, 4 pseudobonds, 1209 residues, 9 models selected  

> select subtract #2

267 atoms, 269 bonds, 22 residues, 6 models selected  

> select add #3

11070 atoms, 10484 bonds, 14 pseudobonds, 2152 residues, 9 models selected  

> select subtract #3

233 atoms, 236 bonds, 18 residues, 5 models selected  

> select add #4

8973 atoms, 8728 bonds, 1530 residues, 5 models selected  

> select subtract #4

149 atoms, 149 bonds, 13 residues, 4 models selected  

> select add #5

8644 atoms, 7990 bonds, 5 pseudobonds, 1823 residues, 5 models selected  

> select subtract #5

60 atoms, 58 bonds, 7 residues, 3 models selected  

> select add #6

5581 atoms, 5695 bonds, 714 residues, 3 models selected  

> select subtract #6

28 atoms, 28 bonds, 3 residues, 2 models selected  

> select add #7

4975 atoms, 5090 bonds, 622 residues, 2 models selected  

> select subtract #7

17 atoms, 17 bonds, 2 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select add #8

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> select subtract #8

Nothing selected  

> select clear

> ui mousemode right translate

> ui tool show Matchmaker

> select #8/A

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> show sel atoms

> select clear

> select #9/A:

Expected an objects specifier or a keyword  

> select #9/A

4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 2 models selected  

> select #9/A:190,192,193,216

25 atoms, 23 bonds, 4 residues, 1 model selected  

> color sel byhetero

> select #9/A:159

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

> select #9/A:159,160,210

19 atoms, 17 bonds, 3 residues, 1 model selected  

> show sel atoms

> hide #!1 models

> hide #8 models

> show #8 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> show #!1 models

> hide #!9 models

> select add #9

4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected  

> select subtract #9

Nothing selected  

> select add #8

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 4958 atom styles  

> style sel ball

Changed 4958 atom styles  

> undo

[Repeated 1 time(s)]

> select subtract #8

Nothing selected  

> select add #8

4958 atoms, 5073 bonds, 620 residues, 1 model selected  

> select add #1

8970 atoms, 9023 bonds, 1 pseudobond, 1264 residues, 4 models selected  

> select clear

> open /Users/mk16/Desktop/2pv7_model.cif

Summary of feedback from opening /Users/mk16/Desktop/2pv7_model.cif  
---  
note | Fetching CCD COA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/COA/COA.cif  
  
Chain information for 2pv7_model.cif #10  
---  
Chain | Description  
A B | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'C')  

Computing secondary structure  

> open /Users/mk16/Desktop/2pv7_model.cif

Chain information for 2pv7_model.cif #11  
---  
Chain | Description  
A B | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'C')  

Computing secondary structure  

> close #11

> hide #8 models

> hide #!1 models

> close #10

> show #!1 models

> show #8 models

> show #!9 models

> save /Users/mk16/Desktop/220250214.cxs

——— End of log from Fri Feb 14 11:22:12 2025 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,6
      Model Number: MRX43J/A
      Chip: Apple M3 Pro
      Total Number of Cores: 12 (6 performance and 6 efficiency)
      Memory: 18 GB
      System Firmware Version: 11881.81.2
      OS Loader Version: 11881.81.2

Software:

    System Software Overview:

      System Version: macOS 15.3 (24D60)
      Kernel Version: Darwin 24.3.0
      Time since boot: 9日 6時間 36分

Graphics/Displays:

    Apple M3 Pro:

      Chipset Model: Apple M3 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 18
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        Studio Display:
          Display Type: Retina LCD
          Resolution: 5120 x 2880 Retina
          Display Serial Number: KCR2L4HL0M
          Display Firmware Version: Version 17.0 (Build 21A329)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX