![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Last modified 6 months ago
#17437 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001fb080840 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix (total: 61)
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{
"uptime" : 220000,
"procRole" : "Background",
"version" : 2,
"userID" : 1195785599,
"deployVersion" : 210,
"modelCode" : "Mac14,5",
"coalitionID" : 3340,
"osVersion" : {
"train" : "macOS 15.3.2",
"build" : "24D81",
"releaseType" : "User"
},
"captureTime" : "2025-04-15 18:00:50.6769 -0400",
"codeSigningMonitor" : 1,
"incident" : "A17AB552-C016-46D3-B3CB-1304B1800468",
"pid" : 84570,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-15 08:57:28.0211 -0400",
"procStartAbsTime" : 4766988439682,
"procExitAbsTime" : 5402549828780,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"0EC3B9EC-4136-540D-AC90-521AA6712099","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "AAE09EAA-E991-08DE-E25C-56BCD904E286",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "0ECD1CCF-EF3D-4D11-9891-619770104F9D",
"wakeTime" : 22917,
"sleepWakeUUID" : "969E71C4-1BB1-479F-9349-3B8CFDCCC13D",
"sip" : "enabled",
"vmRegionInfo" : "0xa38e3fd69f8 is not in any region. Bytes after previous region: 10758423144953 Bytes before following region: 94313656784392\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00008a38e3fd69f8","rawCodes":[1,151976947837432],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00008a38e3fd69f8 -> 0x00000a38e3fd69f8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":84570},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0xa38e3fd69f8 is not in any region. Bytes after previous region: 10758423144953 Bytes before following region: 94313656784392\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"arch" : "arm64e",
"base" : 6734106624,
"size" : 581628,
"uuid" : "bbab286c-2e51-3d64-9ae3-a4102935fe32",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
}
],
"sharedCache" : {
"base" : 6730563584,
"size" : 4865835008,
"uuid" : "5700d77a-6190-36e0-884d-fee6d586d62f"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=18.4G written=9959K(0%) resident=9959K(0%) swapped_out=0K(0%) unallocated=18.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 1232K 58 \nColorSync 736K 38 \nCoreAnimation 4416K 214 \nCoreGraphics 48K 3 \nCoreImage 128K 4 \nCoreServices 624K 2 \nCoreUI image data 5552K 43 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 17.5G 300 \nMALLOC guard page 288K 18 \nMALLOC_LARGE (reserved) 122.0M 1 reserved VM address space (unallocated)\nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 752K 47 \nStack 160.2M 48 \nStack Guard 56.0M 1 \nVM_ALLOCATE 328.1M 332 \nVM_ALLOCATE (reserved) 256.0M 3 reserved VM address space (unallocated)\n__AUTH 5288K 672 \n__AUTH_CONST 70.9M 920 \n__CTF 824 1 \n__DATA 33.5M 1068 \n__DATA_CONST 34.2M 1083 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 638.0M 157 \n__OBJC_RW 2374K 1 \n__TEXT 1.3G 1103 \n__TPRO_CONST 272K 2 \ndyld private memory 32K 1 \nmapped file 580.0M 95 \nowned unmapped memory 100.6M 1 \npage table in kernel 9959K 1 \nshared memory 3184K 23 \n=========== ======= ======= \nTOTAL 21.1G 6597 \nTOTAL, minus reserved VM space 20.7G 6597 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "f911532e1b8949a51df4d8aa97dafc9c5b5adf57",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "658361a603dc58766bab2d2a",
"factorPackIds" : {
"SIRI_TTS_DEVICE_TRAINING" : "6736733a26c1270f5a9ef53d"
},
"deploymentId" : 240000045
},
{
"rolloutId" : "648cada15dbc71671bb3aa1b",
"factorPackIds" : {
"SIRI_EXPERIENCE_CAM" : "65a81173096f6a1f1ba46525"
},
"deploymentId" : 240000116
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/dout2/Downloads/OAT1_ligand_density.cxs
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.0151, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00516, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0108, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0128, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0683, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at level 0.0118, step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00686, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Opened rOAT1-AKG_OF.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
level 0.0122, step 1, values float32
Opened rOAT1-AKG_OOC.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
level 0.0102, step 1, values float32
Opened rOAT1-R466A.mrc as #46, grid size 480,480,480, pixel 0.553, shown at
level 0.0115, step 1, values float32
Opened rOAT1-Apo.mrc as #48, grid size 240,240,240, pixel 0.553, shown at step
1, values float32
Log from Sat Apr 12 21:31:41 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/dout2/Downloads/OAT1_ligand_density.cxs
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.0151, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00516, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0108, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0128, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0683, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at level 0.0118, step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00686, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Opened rOAT1-AKG_OF.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
level 0.0122, step 1, values float32
Opened rOAT1-AKG_OOC.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
level 0.0102, step 1, values float32
Opened postprocess_rescaled.mrc as #46, grid size 480,480,480, pixel 0.553,
shown at level 0.0115, step 1, values float32
Log from Thu Apr 10 15:43:35 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/dout2/Downloads/OAT1_ligand_density.cxs format session
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.0151, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0116, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00383, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0141, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0546, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at level 0.0118, step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Log from Thu Apr 10 14:06:06 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/dout2/Downloads/OAT1_ligand_density.cxs
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.0151, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0116, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00383, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0141, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0546, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at level 0.0118, step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Log from Tue Mar 11 12:00:09 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/dout2/Downloads/OAT1_ligand_density.cxs
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.0151, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0116, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00383, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0141, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0546, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Log from Mon Feb 10 17:46:10 2025UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
Opened relion_locres_filtered.mrc as #3, grid size 320,320,320, pixel 0.83,
shown at level 0.00928, step 1, values float32
Log from Wed Dec 11 13:28:04 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> format session
Opened relion_locres_filtered.mrc as #3, grid size 320,320,320, pixel 0.83,
shown at level 0.00928, step 1, values float32
Log from Tue Dec 10 11:33:02 2024 Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
> hOCT1-VB1_3_real_space_refined_002.pdb"
Chain information for hOCT1-VB1_3_real_space_refined_002.pdb #1
---
Chain | Description
A | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 1650, resource id:
35652789, major code: 40 (TranslateCoords), minor code: 0
> select ::name="VIB"
18 atoms, 19 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> save
> "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
> hOCT1-noVB1.pdb" relModel #1
QXcbConnection: XCB error: 3 (BadWindow), sequence: 7992, resource id:
35652794, major code: 40 (TranslateCoords), minor code: 0
> close session
> open
> "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
> hOCT1-noVB1.pdb"
Chain information for hOCT1-noVB1.pdb #1
---
Chain | Description
A | No description available
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt
Summary of feedback from opening
/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1
Ignored bad PDB record found on line 2
REMARK SMILES IDX 15 1 14 2 10 3 9 4 8 5 7 6 11 7 12 8 13 9 6 11 5 12 4 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 16 14 3 15 18 16 2 17 1 18 17 19
Ignored bad PDB record found on line 4
REMARK H PARENT 13 10 17 20 17 21
Ignored bad PDB record found on line 5
REMARK Flexibility Score: inf
15 messages similar to the above omitted
Opened ligand.pdbqt containing 1 structures (21 atoms, 22 bonds)
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt
Summary of feedback from opening
/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1
Ignored bad PDB record found on line 2
REMARK SMILES IDX 15 1 14 2 10 3 9 4 8 5 7 6 11 7 12 8 13 9 6 11 5 12 4 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 16 14 3 15 18 16 2 17 1 18 17 19
Ignored bad PDB record found on line 4
REMARK H PARENT 13 10 17 20 17 21
Ignored bad PDB record found on line 5
REMARK Flexibility Score: inf
15 messages similar to the above omitted
Opened ligand.pdbqt containing 1 structures (21 atoms, 22 bonds)
QXcbConnection: XCB error: 3 (BadWindow), sequence: 6676, resource id:
35652851, major code: 40 (TranslateCoords), minor code: 0
> hide #3 models
> show #3 models
> hide #3 models
> close #2-3
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/vina_dock.pdbqt
Summary of feedback from opening
/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/vina_dock.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.139 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -8.396
Ignored bad PDB record found on line 4
REMARK INTER: -7.934
Ignored bad PDB record found on line 5
REMARK INTRA: -0.463
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.463
495 messages similar to the above omitted
Opened vina_dock.pdbqt containing 20 structures (420 atoms, 440 bonds)
> viewdockx #2.1-20
> set bgColor white
> select #2.9/?:1@@serial_number=16
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 22 bonds, 1 residue, 1 model selected
> view sel
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job320/note.txt
Unrecognized file suffix '.txt'
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job320/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #3, grid size 320,320,320, pixel 0.83,
shown at level 0.00146, step 2, values float32
> color #3 #b2b2b296 models
> volume #3 step 1
> ui tool show "Side View"
> volume #3 level 0.01472
> select add #1
3482 atoms, 3578 bonds, 1 pseudobond, 448 residues, 3 models selected
> show sel atoms
JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
properties of undefined (reading 'id')
> hide #2.1-20 models
> show #2.1 models
> select clear
> volume #3 level 0.01037
> show #2.2 models
> show #2.3 models
> hide #2.2 models
> hide #2.1 models
> volume #3 level 0.009064
> volume #3 level 0.009281
> hide #2.3 models
> show #2.4 models
> hide #2.4 models
> show #2.5 models
> close #1
> open
> "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
> hOCT1-noVB1.pdb"
Chain information for hOCT1-noVB1.pdb #1
---
Chain | Description
A | No description available
> select add #1
3461 atoms, 3556 bonds, 1 pseudobond, 447 residues, 2 models selected
> show sel atoms
> select clear
> hide #2.5 models
> show #2.6 models
> hide #2.6 models
> show #2.7 models
> hide #2.7 models
> show #2.8 models
> hide #2.8 models
> show #2.9 models
> hide #2.9 models
> show #2.10 models
> hide #2.10 models
> show #2.10 models
> hide #2.10 models
> show #2.11 models
> hide #2.11 models
> show #2.12 models
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> includeMaps true
> lighting soft
> lighting simple
> color #3 #b2b2b264 models
> hide #2.12 models
> show #2.13 models
> hide #2.13 models
> show #2.14 models
> hide #2.14 models
> show #2.15 models
> hide #2.15 models
> show #2.15 models
> hide #2.15 models
> show #2.16 models
> hide #2.16 models
> show #2.17 models
> hide #2.17 models
> show #2.18 models
> hide #2.18 models
> show #2.19 models
> hide #2.19 models
> show #2.20 models
> hide #2.20 models
> show #2.19 models
> hide #2.19 models
> show #2.20 models
> hide #2.20 models
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.3 models
> hide #2.3 models
> show #2.3 models
> hide #2.3 models
> show #2.4 models
> hide #2.4 models
> show #2.5 models
> hide #2.5 models
> show #2.6 models
> hide #2.6 models
> show #2.7 models
> hide #2.7 models
> show #2.7 models
> hide #2.7 models
> show #2.8 models
> hide #2.8 models
> show #2.9 models
> hide #2.9 models
> show #2.10 models
> select down
Nothing selected
> hide #2.10 models
> show #2.10 models
> hide #2.10 models
> show #2.11 models
> hide #2.11 models
> show #2.12 models
> hide #2.12 models
> show #2.13 models
> hide #2.13 models
> show #2.14 models
> hide #2.14 models
> show #2.15 models
> hide #2.15 models
> show #2.15 models
> hide #2.15 models
> show #2.15 models
> hide #2.15 models
> show #2.16 models
> hide #2.16 models
> show #2.16 models
> hide #2.16 models
> show #2.17 models
> hide #2.17 models
> show #2.17 models
> hide #2.17 models
> show #2.18 models
> hide #2.18 models
> show #2.19 models
> hide #2.19 models
> show #2.20 models
> volume #3 level 0.01124
> hide #2.20 models
> show #2.20 models
> hide #2.20 models
> show #2.20 models
> hide #2.20 models
> show #2.19 models
> hide #2.19 models
> show #2.18 models
> hide #2.18 models
> show #2.19 models
> hide #2.19 models
> show #2.18 models
> volume #3 level 0.008629
> hide #2.18 models
> show #2.18 models
> hide #2.18 models
> show #2.17 models
> hide #2.17 models
> show #2.16 models
> hide #2.16 models
> show #2.15 models
> hide #2.15 models
> show #2.14 models
> hide #2.14 models
> show #2.13 models
> hide #2.13 models
> show #2.12 models
> hide #2.12 models
> show #2.11 models
> hide #2.11 models
> show #2.10 models
> hide #2.10 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.3 models
> hide #2.3 models
> show #2.4 models
> hide #2.4 models
> show #2.5 models
> hide #2.5 models
> show #2.6 models
> hide #2.6 models
> show #2.7 models
> hide #2.7 models
> show #2.8 models
> hide #2.8 models
> show #2.9 models
> hide #2.9 models
> show #2.9 models
> hide #2.9 models
> show #2.9 models
> hide #2.9 models
> show #2.10 models
> hide #2.10 models
> show #2.11 models
> hide #2.11 models
> show #2.12 models
> hide #2.12 models
> show #2.13 models
> hide #2.13 models
> show #2.12 models
> hide #2.12 models
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.3 models
> hide #2.3 models
> show #2.4 models
> hide #2.4 models
> show #2.5 models
> hide #2.5 models
> show #2.6 models
> hide #2.6 models
> show #2.7 models
> hide #2.7 models
> show #2.8 models
> hide #2.8 models
> show #2.8 models
> hide #2.8 models
> show #2.9 models
> hide #2.9 models
> show #2.10 models
> hide #2.10 models
> show #2.11 models
> hide #2.11 models
> show #2.12 models
> hide #2.12 models
> show #2.1 models
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 35492, resource id:
35652978, major code: 40 (TranslateCoords), minor code: 0
> volume #3 level 0.009281
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.3 models
> hide #2.3 models
> show #2.4 models
> show #2.5 models
> hide #2.4 models
> hide #2.5 models
> show #2.18 models
> hide #2.18 models
> show #2.18 models
> hide #2.18 models
> show #2.17 models
> hide #2.17 models
> show #2.16 models
> hide #2.16 models
> show #2.15 models
> hide #2.15 models
> show #2.14 models
> hide #2.14 models
> show #2.13 models
> hide #2.13 models
> show #2.12 models
> hide #2.12 models
> show #2.12 models
> hide #2.12 models
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 32670, resource id:
35652988, major code: 40 (TranslateCoords), minor code: 0
——— End of log from Tue Dec 10 11:33:02 2024 ———
opened ChimeraX session
JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined
JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 7404, resource id:
35653140, major code: 40 (TranslateCoords), minor code: 0
QXcbConnection: XCB error: 3 (BadWindow), sequence: 7416, resource id:
35653135, major code: 40 (TranslateCoords), minor code: 0
> show #2.11 models
> hide #2.11 models
> show #2.12 models
> hide #2.12 models
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 60442, resource id:
35653379, major code: 40 (TranslateCoords), minor code: 0
——— End of log from Wed Dec 11 13:28:04 2024 ———
opened ChimeraX session
JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined
JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined
> show #2.11 models
> show #2.12 models
> hide #2.11 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_7/hOCT1VB1007.pdb
Chain information for hOCT1VB1007.pdb #4
---
Chain | Description
A | No description available
> open
> "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_8/
> hOCT1-VB_Dock2_real_space_refined_008.pdb"
Chain information for hOCT1-VB_Dock2_real_space_refined_008.pdb #5
---
Chain | Description
A | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 17659, resource id:
35653657, major code: 40 (TranslateCoords), minor code: 0
> close session
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/P3_J149_fsc_iteration_010_after_fsc_mask_auto_tightening.pdf
QXcbConnection: XCB error: 3 (BadWindow), sequence: 50929, resource id:
35654568, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/cryosparc_P3_J154__localfilter_240.mrc
Opened cryosparc_P3_J154__localfilter_240.mrc as #1, grid size 240,240,240,
pixel 0.553, shown at level 0.207, step 1, values float32
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/cryosparc_P3_J154__localfilter_240_VB1.mrc
Opened cryosparc_P3_J154__localfilter_240_VB1.mrc as #2, grid size
240,240,240, pixel 0.553, shown at level 0.000117, step 1, values float32
> volume #2 level 0.3318
Drag select of 2 cryosparc_P3_J154__localfilter_240_VB1.mrc
> view orient
> select clear
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_RSF_014_VB1.pdb
Summary of feedback from opening
/home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_RSF_014_VB1.pdb
---
warnings | Cannot find LINK/SSBOND residue CYS (50 )
Cannot find LINK/SSBOND residue CYS (62 )
Cannot find LINK/SSBOND residue CYS (89 )
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/RealSpaceRefine_6/mOCT1-VB1-coot-11_real_space_refined_006.pdb
Chain information for mOCT1-VB1-coot-11_real_space_refined_006.pdb #4
---
Chain | Description
A | No description available
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_real_space_refined_014.pdb
Chain information for mOCT1-VB1_real_space_refined_014.pdb #5
---
Chain | Description
A | No description available
> close #3#4
> volume #2 color #ffffb296
> volume #2 color #ffffb2c8
> volume #2 level 0.4304
> volume #2 level 0.3677
> select /A:601@C15
1 atom, 1 residue, 1 model selected
> select up
18 atoms, 19 bonds, 1 residue, 1 model selected
> view sel
> select clear
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-ABC_Model/mOCT1-ABC_real_space_refined_009.pdb
Chain information for mOCT1-ABC_real_space_refined_009.pdb #3
---
Chain | Description
A | No description available
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-ABC_20220411_cryoSPARC/J142_2.25A_clip-240/cryosparc_P3_J150__localfilter_240.mrc
Opened cryosparc_P3_J150__localfilter_240.mrc as #4, grid size 240,240,240,
pixel 0.553, shown at level 0.229, step 1, values float32
> volume #4 level 0.7041
> hide #!2 models
> hide #!3 models
> hide #!5 models
> show #!3 models
> select ::name="ABC"
42 atoms, 48 bonds, 2 residues, 1 model selected
> view sel
> volume #4 level 0.5273
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!3 models
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 57982, resource id:
35654641, major code: 40 (TranslateCoords), minor code: 0
> hide #!1 models
> rename #1 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
> rename #2 mOCT1-VB1_cryosparc_P3_J154__localfilter_240_VB1.mrc
> rename #4 mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc
> show #!3 models
> select clear
> hide #!4 models
> select ::name="ABC"
42 atoms, 48 bonds, 2 residues, 1 model selected
> select add #3
3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected
> color (#!3 & sel) white
> select clear
> select ::name="ABC"
42 atoms, 48 bonds, 2 residues, 1 model selected
> color sel red
> show #!4 models
> ui tool show "Color Zone"
> color zone #4 near #3 distance 3.32
> volume splitbyzone #4
Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 0 as #6.1, grid size
240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32
Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 1 as #6.2, grid size
240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32
Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 2 as #6.3, grid size
240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32
> hide #!3 models
> select add #3
3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected
> select subtract #3
Nothing selected
> hide #!6.1 models
> hide #!6.3 models
> show #!6.3 models
> hide #!6.2 models
> close #6.1-2
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 18121, resource id:
35654647, major code: 40 (TranslateCoords), minor code: 0
> show #!3 models
> color #3 #fffffbff
> color #3 #ddddaaff
> color #3 #dda0deff
> color #3 plum
> select add #3
3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected
> color (#!3 & sel) byhetero
> color #6.3 #ddddaaff models
> color #6.3 plum models
> color #6.3 #ffffb2ff models
Drag select of 6.3 mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 2 , 5
atoms, 5 residues, 5 bonds
> select clear
> color #6.3 #ffffb2c8 models
> select ::name="ABC"
42 atoms, 48 bonds, 2 residues, 1 model selected
> view sel
> select #3/A:234
11 atoms, 10 bonds, 1 residue, 1 model selected
> color #6.3 #ffffb296 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!6 models
> hide #!6.3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!3 models
> hide #!3 models
> select #5/A:36
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!5 models
> hide #!2 models
> show #!1 models
> view
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 5156, resource id:
35654673, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-3TC_20240411/job207/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #7, grid size 320,320,320, pixel 0.83,
shown at level 0.00144, step 2, values float32
> volume #7 level 0.01204
> select add #7
12 atoms, 12 bonds, 1 residue, 3 models selected
> select add #5
3526 atoms, 3584 bonds, 1 pseudobond, 489 residues, 4 models selected
> select subtract #5
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,-67.025,0,1,0,-62.171,0,0,1,-62.016
> view matrix models #7,1,0,0,-65.422,0,1,0,-60.829,0,0,1,-69.057
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.44906,0.62428,0.63923,-47.882,-0.83076,-0.55508,-0.041522,263.31,0.32891,-0.5497,0.76789,-6.0495
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.44906,0.62428,0.63923,-43.112,-0.83076,-0.55508,-0.041522,259.52,0.32891,-0.5497,0.76789,-3.3226
> view matrix models
> #7,-0.44906,0.62428,0.63923,-46.691,-0.83076,-0.55508,-0.041522,257.64,0.32891,-0.5497,0.76789,-5.4256
> view matrix models
> #7,-0.44906,0.62428,0.63923,-43.086,-0.83076,-0.55508,-0.041522,254.57,0.32891,-0.5497,0.76789,-5.2175
> ui tool show "Fit in Map"
> fitmap #7 inMap #1
Fit map relion_locres_filtered.mrc in map
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 3812 points
correlation = 0.2373, correlation about mean = 0.07089, overlap = 11.07
steps = 116, shift = 1.21, angle = 8.84 degrees
Position of relion_locres_filtered.mrc (#7) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
-0.36461695 0.73265397 0.57469351 -59.14787422
-0.87490183 -0.48082660 0.05790126 236.29988230
0.31874951 -0.48168862 0.81631784 -18.80617873
Axis -0.31464704 0.14924672 -0.93740208
Axis point 41.71559551 127.71968026 0.00000000
Rotation angle (degrees) 120.96824033
Shift along axis 71.50663710
> rename #7 mOCT1-3TC
> select clear
[Repeated 1 time(s)]
> rename #7 mOCT1-3TC.mrc
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-3TC_Model/RealSpaceRefine_6/mOCT1-3TC-
> coot-14_real_space_refined_006.pdb
Chain information for mOCT1-3TC-coot-14_real_space_refined_006.pdb #8
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #!8 to #5
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 mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1-3TC-
coot-14_real_space_refined_006.pdb, chain A (#8), sequence alignment score =
2352.2
RMSD between 450 pruned atom pairs is 0.409 angstroms; (across all 450 pairs:
0.409)
> hide #!1 models
> hide #!7 models
> show #!1 models
> hide #!8 models
> show #!7 models
> select add #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.49719,-0.57211,-0.6523,173.98,0.80196,0.58997,0.093813,-133.23,0.33116,-0.56976,0.75214,0.34956
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.49719,-0.57211,-0.6523,164.87,0.80196,0.58997,0.093813,-137.47,0.33116,-0.56976,0.75214,-2.3096
> fitmap #7 inMap #1
Fit map mOCT1-3TC.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 3812 points
correlation = 0.9181, correlation about mean = 0.7496, overlap = 65.08
steps = 160, shift = 6.4, angle = 20.1 degrees
Position of mOCT1-3TC.mrc (#7) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
0.27009123 -0.75134279 -0.60210857 210.67160095
0.83888334 0.49056205 -0.23584655 -78.20606144
0.47257322 -0.44139877 0.76278546 -39.17036140
Axis -0.10648785 -0.55674686 0.82382842
Axis point 169.78551241 113.86943556 0.00000000
Rotation angle (degrees) 74.82789173
Shift along axis -11.16264322
> fitmap #8 inMap #7
Fit molecule mOCT1-3TC-coot-14_real_space_refined_006.pdb (#8) to map
mOCT1-3TC.mrc (#7) using 7048 atoms
average map value = 0.01706, steps = 60
shifted from previous position = 0.0823
rotated from previous position = 0.357 degrees
atoms outside contour = 4146, contour level = 0.012041
Position of mOCT1-3TC-coot-14_real_space_refined_006.pdb (#8) relative to
mOCT1-3TC.mrc (#7) coordinates:
Matrix rotation and translation
0.99999991 -0.00005602 -0.00043067 0.07339565
0.00005621 0.99999991 0.00043709 -0.06044298
0.00043064 -0.00043712 0.99999982 0.02180230
Axis -0.70938425 -0.69891365 0.09106970
Axis point 0.00000000 51.44490735 150.82453668
Rotation angle (degrees) 0.03530433
Shift along axis -0.00783577
> show #!8 models
> hide #!8 models
> select subtract #7
Nothing selected
> hide #!1 models
> show #!8 models
> select ::name="3TC"
26 atoms, 27 bonds, 1 residue, 1 model selected
> select add #8
7048 atoms, 7109 bonds, 1 pseudobond, 486 residues, 2 models selected
> color (#!8 & sel) white
> select ::name="3TC"
26 atoms, 27 bonds, 1 residue, 1 model selected
> color sel red
> view sel
> volume #7 step 1
> color zone #7 near #8 distance 4.98
> volume splitbyzone #7
Opened mOCT1-3TC.mrc 0 as #9.1, grid size 320,320,320, pixel 0.83, shown at
level 0.012, step 1, values float32
Opened mOCT1-3TC.mrc 1 as #9.2, grid size 320,320,320, pixel 0.83, shown at
level 0.012, step 1, values float32
Opened mOCT1-3TC.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.012, step 1, values float32
> close #9.2
> close #9.1
> color #9.3 white models
> color #9.3 #ffffb2ff models
> color #9.3 #ffffb296 models
> select #8/A:447
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #8
7048 atoms, 7109 bonds, 1 pseudobond, 486 residues, 2 models selected
> color #8 #bb22ffff
> color #8 #b2fffbff
> color #8 #b2ffb2ff
> color (#!8 & sel) byhetero
> select clear
[Repeated 1 time(s)]
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
> hide #!9.3 models
> hide #!9 models
> hide #!8 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-AZT_20240413/job307/relion_locres_filtered_flipz.mrc
Opened relion_locres_filtered_flipz.mrc as #10, grid size 320,320,320, pixel
0.83, shown at level 0.00125, step 2, values float32
> show #!1 models
> view
> volume #1 level 0.3063
> volume #10 step 1
> volume #10 level 0.01019
> rename #10 mOCT1-AZT.mrc
> select add #10
2 models selected
> view matrix models #10,1,0,0,-48.383,0,1,0,-77.671,0,0,1,-67.093
> view matrix models #10,1,0,0,-54.836,0,1,0,-59.483,0,0,1,-63.826
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.55307,0.83192,0.044939,-108.96,-0.78881,0.54024,-0.29312,148.24,-0.26813,0.12666,0.95502,-37.718
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.55307,0.83192,0.044939,-120.39,-0.78881,0.54024,-0.29312,136.85,-0.26813,0.12666,0.95502,-39.969
> view matrix models
> #10,0.55307,0.83192,0.044939,-121.53,-0.78881,0.54024,-0.29312,137.41,-0.26813,0.12666,0.95502,-39.609
> fitmap #10 inMap #1
Fit map mOCT1-AZT.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 33175 points
correlation = 0.9169, correlation about mean = 0.7611, overlap = 495.2
steps = 172, shift = 3.01, angle = 24.4 degrees
Position of mOCT1-AZT.mrc (#10) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
0.17958596 0.98366820 0.01207312 -89.49221412
-0.89232990 0.16805236 -0.41893408 218.60375344
-0.41412105 0.06446147 0.90793639 -7.62218964
Axis 0.24369569 0.21485858 -0.94575272
Axis point 81.50821029 166.97786454 0.00000000
Rotation angle (degrees) 82.65824965
Shift along axis 32.36873253
> view
> view orient
> ui tool show "Side View"
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-AZT_Model/RealSpaceRefine_4/mOCT1-AZT_14_real_space_refined_004.pdb
Chain information for mOCT1-AZT_14_real_space_refined_004.pdb #11
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #!11 to #5
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 mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with
mOCT1-AZT_14_real_space_refined_004.pdb, chain A (#11), sequence alignment
score = 2367.3
RMSD between 449 pruned atom pairs is 0.415 angstroms; (across all 449 pairs:
0.415)
> fitmap #11 inMap #10
Fit molecule mOCT1-AZT_14_real_space_refined_004.pdb (#11) to map
mOCT1-AZT.mrc (#10) using 7017 atoms
average map value = 0.01592, steps = 48
shifted from previous position = 0.0651
rotated from previous position = 0.278 degrees
atoms outside contour = 3029, contour level = 0.010186
Position of mOCT1-AZT_14_real_space_refined_004.pdb (#11) relative to
mOCT1-AZT.mrc (#10) coordinates:
Matrix rotation and translation
-0.89530533 -0.39092164 -0.21356179 331.89133766
0.43778783 -0.68362766 -0.58394781 243.21431714
0.08228108 -0.61630634 0.78319622 99.39179726
Axis -0.03674901 -0.33598352 0.94115067
Axis point 137.92729950 180.24940846 0.00000000
Rotation angle (degrees) 153.87927506
Shift along axis -0.37002346
> hide #!1 models
> select ::name="AZZ"
19 atoms, 20 bonds, 1 residue, 1 model selected
> hide #!10 models
> select add #11
7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected
> select subtract #11
Nothing selected
> select add #11
7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected
> color (#!11 & sel) white
> color #11 #aaaaffff
> color (#!11 & sel) white
> select ::name="AZZ"
19 atoms, 20 bonds, 1 residue, 1 model selected
> color sel red
> color zone #10 near #11 distance 4.98
> show #!10 models
> volume splitbyzone #10
Opened mOCT1-AZT.mrc 0 as #12.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0102, step 1, values float32
Opened mOCT1-AZT.mrc 1 as #12.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0102, step 1, values float32
Opened mOCT1-AZT.mrc 2 as #12.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0102, step 1, values float32
> close #12.2
> close #12.1
> color #12.3 #ff0000fe models
> color #12.3 #ff000096 models
> color #12.3 #ffffff96 models
> color #12.3 #ffffb296 models
> color #11 #aaffffff
> color #11 #aaaaffff
> select add #11
7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected
> color (#!11 & sel) byhetero
> select clear
> show #!3 models
> hide #!3 models
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
> hide #!12.3 models
> hide #!12 models
> hide #!11 models
> show #!1 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-MTF_20240702/job350/postprocess.mrc
Opened postprocess.mrc as #13, grid size 320,320,320, pixel 0.83, shown at
level 0.00595, step 2, values float32
> volume #13 step 1
> volume #13 level 0.02012
> select add #13
2 models selected
> view matrix models #13,1,0,0,-56.643,0,1,0,-72.238,0,0,1,-68.565
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.02465,-0.61986,0.78433,49.618,-0.43145,0.70114,0.56768,-50.105,-0.9018,-0.35239,-0.25015,252.26
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.02465,-0.61986,0.78433,42.91,-0.43145,0.70114,0.56768,-47.812,-0.9018,-0.35239,-0.25015,260.75
> view matrix models
> #13,0.02465,-0.61986,0.78433,45.137,-0.43145,0.70114,0.56768,-48.218,-0.9018,-0.35239,-0.25015,267.86
> rename #13 mOCT1-MTF.mrc
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-MTF_20240603/RealSpaceRefine_3/mOCT1_MTF-
> coot-9_real_space_refined_003.pdb
Chain information for mOCT1_MTF-coot-9_real_space_refined_003.pdb #14
---
Chain | Description
A | No description available
> fitmap #13 inMap #1
Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 17817 points
correlation = 0.2983, correlation about mean = 0.07385, overlap = 82.29
steps = 200, shift = 2.4, angle = 7.61 degrees
Position of mOCT1-MTF.mrc (#13) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
-0.05771312 -0.64461025 0.76232987 59.74942259
-0.34050237 0.73052504 0.59193860 -66.21901607
-0.93847075 -0.22541250 -0.26165220 256.68697920
Axis -0.42762978 0.88984156 0.15910615
Axis point 123.33045199 0.00000000 117.21732044
Rotation angle (degrees) 107.12276965
Shift along axis -43.63458901
> select subtract #13
Nothing selected
> select add #13
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.50114,0.40107,-0.76681,42.081,-0.045209,-0.87277,-0.48604,255.79,-0.86419,0.27824,-0.41924,198.29
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.50114,0.40107,-0.76681,41.903,-0.045209,-0.87277,-0.48604,247.49,-0.86419,0.27824,-0.41924,198.18
> view matrix models
> #13,0.50114,0.40107,-0.76681,53.046,-0.045209,-0.87277,-0.48604,251.12,-0.86419,0.27824,-0.41924,198.38
> fitmap #13 inMap #1
Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 17817 points
correlation = 0.2273, correlation about mean = 0.06656, overlap = 59.06
steps = 120, shift = 2.59, angle = 4.72 degrees
Position of mOCT1-MTF.mrc (#13) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
0.43566959 0.38627366 -0.81300964 69.55864121
-0.07375796 -0.88487887 -0.45994473 251.91510217
-0.89707959 0.26034986 -0.35702406 194.41028021
Axis 0.83873143 0.09789343 -0.53567385
Axis point 0.00000000 97.27212052 153.57991582
Rotation angle (degrees) 154.57081238
Shift along axis -21.13865268
> view matrix models
> #13,0.43567,0.38627,-0.81301,67.4,-0.073758,-0.88488,-0.45994,259.27,-0.89708,0.26035,-0.35702,197.15
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.3307,0.47313,-0.81657,68.962,0.20831,-0.88051,-0.42581,219.2,-0.92046,-0.029281,-0.38974,244.12
> view matrix models
> #13,0.3796,0.48184,-0.78977,58.246,0.18592,-0.87598,-0.44507,223.83,-0.90628,0.022112,-0.42211,239.42
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.3796,0.48184,-0.78977,53.846,0.18592,-0.87598,-0.44507,217.81,-0.90628,0.022112,-0.42211,235.11
> fitmap #13 inMap #1
Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 17817 points
correlation = 0.2652, correlation about mean = 0.06679, overlap = 73.72
steps = 92, shift = 1.81, angle = 5.01 degrees
Position of mOCT1-MTF.mrc (#13) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
0.31415893 0.53789144 -0.78228958 53.81386032
0.19698588 -0.84300825 -0.50053338 220.95415625
-0.92870918 0.00314703 -0.37079559 234.49017112
Axis 0.80514260 0.23405449 -0.54494394
Axis point 0.00000000 81.07236056 158.23174632
Rotation angle (degrees) 161.77257653
Shift along axis -32.74085292
> view matrix models
> #13,0.31416,0.53789,-0.78229,60.198,0.19699,-0.84301,-0.50053,217.39,-0.92871,0.003147,-0.3708,234.22
> fitmap #13 inMap #1
Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 17817 points
correlation = 0.2449, correlation about mean = 0.05515, overlap = 65.5
steps = 80, shift = 1.45, angle = 5.73 degrees
Position of mOCT1-MTF.mrc (#13) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
0.28419679 0.60053681 -0.74738728 50.81854511
0.27816291 -0.79764719 -0.53514891 205.19579930
-0.91752798 -0.05580782 -0.39373584 245.12613641
Axis 0.79598780 0.28253351 -0.53533003
Axis point 0.00000000 71.54715698 160.41463451
Rotation angle (degrees) 162.47642045
Shift along axis -32.79775064
> view matrix models
> #13,0.2842,0.60054,-0.74739,49.177,0.27816,-0.79765,-0.53515,206.5,-0.91753,-0.055808,-0.39374,243.99
> fitmap #13 inMap #1
Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 17817 points
correlation = 0.3559, correlation about mean = 0.151, overlap = 107.2
steps = 88, shift = 2.33, angle = 2.34 degrees
Position of mOCT1-MTF.mrc (#13) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
0.29378487 0.57675594 -0.76226180 52.65591556
0.29516509 -0.81321822 -0.50155130 203.18767751
-0.90915787 -0.07764488 -0.40914943 245.95334709
Axis 0.80029578 0.27732609 -0.53161726
Axis point 0.00000000 73.19686532 158.33534093
Rotation angle (degrees) 164.64234082
Shift along axis -32.26349399
> view matrix models
> #13,0.29378,0.57676,-0.76226,50.19,0.29517,-0.81322,-0.50155,203.5,-0.90916,-0.077645,-0.40915,251.78
> fitmap #13 inMap #1
Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 17817 points
correlation = 0.9033, correlation about mean = 0.6277, overlap = 419.6
steps = 52, shift = 1.52, angle = 1.92 degrees
Position of mOCT1-MTF.mrc (#13) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
0.29574252 0.60146473 -0.74214321 45.38180479
0.29484975 -0.79643687 -0.52796964 204.44935424
-0.90862533 -0.06267767 -0.41288198 249.74597785
Axis 0.80005949 0.28626242 -0.52721784
Axis point 0.00000000 72.71544700 159.79227740
Rotation angle (degrees) 163.09499009
Shift along axis -36.83622428
> ui tool show Matchmaker
> matchmaker #!14 to #5
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 mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1_MTF-
coot-9_real_space_refined_003.pdb, chain A (#14), sequence alignment score =
2355.8
RMSD between 450 pruned atom pairs is 0.377 angstroms; (across all 450 pairs:
0.377)
> select add #14
7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 4 models selected
> select subtract #13
7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected
> hide #!1 models
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 5891, resource id:
35654810, major code: 40 (TranslateCoords), minor code: 0
> color #14 #95cacdff
> select ::name="MF8"
22 atoms, 21 bonds, 1 residue, 1 model selected
> select add #14
7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected
> select subtract #14
Nothing selected
> select add #14
7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected
> color (#!14 & sel) white
> select ::name="MF8"
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel red
> color zone #10 near #11 distance 4.98
> color zone #13 near #14 distance 4.98
> hide #!14 models
> show #!14 models
> volume #13 level 0.0238
> volume #13 level 0.02122
> volume #13 level 0.01423
> volume splitbyzone #13
Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0142, step 1, values float32
Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0142, step 1, values float32
Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0142, step 1, values float32
> close #15.1
> close #15.2
> volume #15.3 level 0.009273
> volume #15.3 level 0.01703
> close #15#15.3
> select add #14
7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected
> show #!13 models
> color zone #13 near #14 distance 4.88
> color zone #13 near #14 distance 4.78
> color zone #13 near #14 distance 4.68
> color zone #13 near #14 distance 4.58
> color zone #13 near #14 distance 4.48
> color zone #13 near #14 distance 4.38
> color zone #13 near #14 distance 4.28
> color zone #13 near #14 distance 4.18
> color zone #13 near #14 distance 4.08
> color zone #13 near #14 distance 3.98
> color zone #13 near #14 distance 3.88
> color zone #13 near #14 distance 3.78
> color zone #13 near #14 distance 3.68
> color zone #13 near #14 distance 3.58
> color zone #13 near #14 distance 3.48
> color zone #13 near #14 distance 3.38
[Repeated 1 time(s)]
> volume splitbyzone #13
Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0142, step 1, values float32
Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0142, step 1, values float32
Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0142, step 1, values float32
> close #15.1-2
> volume #15.3 level 0.009634
> color zone #13 near #14 distance 3.28
> color zone #13 near #14 distance 3.18
> color zone #13 near #14 distance 3.08
> close #15#15.3
> show #!13 models
> select add #13
7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 4 models selected
> select subtract #13
7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected
> color zone #13 near #14 distance 2.98
> color zone #13 near #14 distance 2.88
> color zone #13 near #14 distance 2.78
> color zone #13 near #14 distance 2.68
> color zone #13 near #14 distance 2.58
> color zone #13 near #14 distance 2.48
> volume #13 level 0.01681
> fitmap #14 inMap #13
Fit molecule mOCT1_MTF-coot-9_real_space_refined_003.pdb (#14) to map
mOCT1-MTF.mrc (#13) using 7044 atoms
average map value = 0.01572, steps = 48
shifted from previous position = 0.0765
rotated from previous position = 0.266 degrees
atoms outside contour = 4386, contour level = 0.016807
Position of mOCT1_MTF-coot-9_real_space_refined_003.pdb (#14) relative to
mOCT1-MTF.mrc (#13) coordinates:
Matrix rotation and translation
0.99946408 0.01781074 -0.02746495 0.87693504
-0.01720783 0.99960910 0.02203450 -1.16466203
0.02784666 -0.02155008 0.99937988 -1.14535630
Axis -0.55418255 -0.70329295 -0.44526478
Axis point 28.72708736 -0.00000000 48.38067452
Rotation angle (degrees) 2.25364092
Shift along axis 0.84310332
> color zone #13 near #14 distance 2.48
[Repeated 1 time(s)]
> color single #13
> color zone #13 near #14 distance 2.48
> color zone #13 near #14 distance 2.38
> color zone #13 near #14 distance 2.28
> color zone #13 near #14 distance 2.18
> color zone #13 near #14 distance 2.08
> color zone #13 near #14 distance 1.98
> color zone #13 near #14 distance 1.88
> color zone #13 near #14 distance 1.78
> color zone #13 near #14 distance 1.68
> color zone #13 near #14 distance 1.58
> color zone #13 near #14 distance 1.48
> color zone #13 near #14 distance 1.38
> color zone #13 near #14 distance 1.48
> color zone #13 near #14 distance 1.58
> color zone #13 near #14 distance 1.68
> color zone #13 near #14 distance 1.78
> color zone #13 near #14 distance 1.88
> color zone #13 near #14 distance 1.98
> volume #13 level 0.01957
> color zone #13 near #14 distance 1.98
> volume splitbyzone #13
Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0196, step 1, values float32
Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0196, step 1, values float32
Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0196, step 1, values float32
> close #15.1-2
> color #15.3 yellow models
> color #15.3 white models
> color #15.3 #ffffb2ff models
> color #15.3 #ffffb296 models
> volume #15.3 level 0.01524
> volume #15.3 level 0.0119
> select subtract #14
Nothing selected
> select add #14
7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected
> color #14 #55dd44ff
> color #14 #5d42cdff
> color #14 #5858cdff
> color #14 #7d76cdff
> color #14 #9d7bcdff
> color #14 #cd75baff
> color #14 #9381cdff
> color (#!14 & sel) byhetero
> select clear
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
> hide #!15.3 models
> hide #!15 models
> hide #!14 models
> show #!1 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job321/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #16, grid size 320,320,320, pixel 0.83,
shown at level 0.00147, step 2, values float32
> volume #13 level 0.01846
> volume #16 step 1
> volume #16 level 0.01137
> select add #16
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.91726,-0.046522,0.39555,-35.801,-0.13266,0.90075,0.41357,-25.02,-0.37554,-0.43183,0.82006,127.4
> view matrix models
> #16,0.97308,0.0084656,-0.23031,32.94,-0.035652,0.99283,-0.11414,20.659,0.2277,0.11927,0.9664,-40.203
> view matrix models
> #16,0.95291,-0.013325,0.30296,-32.366,-0.094841,0.93583,0.33946,-24.554,-0.28805,-0.35221,0.89049,96.605
> view matrix models
> #16,0.68405,0.72927,0.015283,-53.826,0.65561,-0.6055,-0.45117,179.02,-0.31977,0.31864,-0.89231,251.74
> view matrix models
> #16,-0.14871,0.82898,-0.53915,114.85,0.43367,-0.43531,-0.78894,230.9,-0.88872,-0.35114,-0.29476,331.38
> view matrix models
> #16,-0.59154,0.6904,-0.41646,173.56,0.69281,0.17103,-0.70054,108.52,-0.41243,-0.70292,-0.57948,352.16
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.59154,0.6904,-0.41646,98.473,0.69281,0.17103,-0.70054,82.195,-0.41243,-0.70292,-0.57948,295.09
> view matrix models
> #16,-0.59154,0.6904,-0.41646,115.7,0.69281,0.17103,-0.70054,51.467,-0.41243,-0.70292,-0.57948,297.87
> view matrix models
> #16,-0.59154,0.6904,-0.41646,109.24,0.69281,0.17103,-0.70054,49.803,-0.41243,-0.70292,-0.57948,297.08
> view matrix models
> #16,-0.59154,0.6904,-0.41646,112.5,0.69281,0.17103,-0.70054,41.909,-0.41243,-0.70292,-0.57948,292.69
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.52634,0.62911,-0.57201,132.47,0.46428,-0.35094,-0.81319,152.81,-0.71233,-0.69359,-0.10737,267.76
> view matrix models
> #16,-0.56071,0.74447,-0.36245,94.475,0.40226,-0.13769,-0.90511,145.91,-0.72373,-0.6533,-0.22227,279.35
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.56071,0.74447,-0.36245,91.988,0.40226,-0.13769,-0.90511,152.84,-0.72373,-0.6533,-0.22227,276.37
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.69312,0.68147,-0.23491,100.24,0.41746,0.11382,-0.90154,118.42,-0.58764,-0.72294,-0.36338,286.3
> rename #16 hOCT1-VB1.mrc
> fitmap #16 inMap #1
Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 29501 points
correlation = 0.336, correlation about mean = 0.1558, overlap = 114.4
steps = 148, shift = 3.34, angle = 5.64 degrees
Position of hOCT1-VB1.mrc (#16) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
-0.66774800 0.66848229 -0.32748134 111.59775010
0.47076725 0.03845367 -0.88141903 115.78397104
-0.57662015 -0.74273329 -0.34037693 282.67572866
Axis 0.39969377 0.71802066 -0.56981683
Axis point 39.62225841 0.00000000 179.67701786
Rotation angle (degrees) 170.00920250
Shift along axis -33.33317846
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.66775,0.66848,-0.32748,111.72,0.47077,0.038454,-0.88142,115.95,-0.57662,-0.74273,-0.34038,288.9
> fitmap #16 inMap #1
Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 29501 points
correlation = 0.7772, correlation about mean = 0.5328, overlap = 352.7
steps = 60, shift = 1.34, angle = 1.92 degrees
Position of hOCT1-VB1.mrc (#16) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
-0.68896253 0.65809895 -0.30370448 111.90845021
0.45027206 0.06027049 -0.89085495 116.65862228
-0.56796628 -0.75051532 -0.33784768 287.44343290
Axis 0.38522072 0.72537689 -0.57046767
Axis point 41.86637964 0.00000000 181.62562393
Rotation angle (degrees) 169.50470225
Shift along axis -36.24626372
> view matrix models
> #16,-0.68896,0.6581,-0.3037,110.15,0.45027,0.06027,-0.89085,119.19,-0.56797,-0.75052,-0.33785,287.46
> fitmap #16 inMap #1
Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 29501 points
correlation = 0.7772, correlation about mean = 0.5327, overlap = 352.7
steps = 72, shift = 3.09, angle = 0.0182 degrees
Position of hOCT1-VB1.mrc (#16) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
-0.68902052 0.65795875 -0.30387662 111.96278841
0.45022908 0.06002731 -0.89089309 116.69902951
-0.56793001 -0.75065771 -0.33759222 287.41226501
Axis 0.38519550 0.72529614 -0.57058737
Axis point 41.87016659 0.00000000 181.64241189
Rotation angle (degrees) 169.51189271
Shift along axis -36.22489055
> fitmap #16 inMap #1
Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 29501 points
correlation = 0.7772, correlation about mean = 0.5328, overlap = 352.7
steps = 36, shift = 0.00448, angle = 0.00722 degrees
Position of hOCT1-VB1.mrc (#16) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
-0.68898476 0.65802671 -0.30381055 111.93916561
0.45024501 0.06010903 -0.89087953 116.68451889
-0.56796077 -0.75059160 -0.33768744 287.42460080
Axis 0.38521270 0.72532270 -0.57054198
Axis point 41.86758112 0.00000000 181.63640339
Rotation angle (degrees) 169.50839167
Shift along axis -36.23348002
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_10/hOCT1-VB_Dock2_real_space_refined_010.pdb
Chain information for hOCT1-VB_Dock2_real_space_refined_010.pdb #17
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #!17 to #5
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 mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with
hOCT1-VB_Dock2_real_space_refined_010.pdb, chain A (#17), sequence alignment
score = 1980
RMSD between 416 pruned atom pairs is 0.792 angstroms; (across all 446 pairs:
1.346)
> fitmap #17 inMap #16
Fit molecule hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) to map
hOCT1-VB1.mrc (#16) using 3479 atoms
average map value = 0.02025, steps = 64
shifted from previous position = 0.153
rotated from previous position = 0.521 degrees
atoms outside contour = 1063, contour level = 0.011373
Position of hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) relative to
hOCT1-VB1.mrc (#16) coordinates:
Matrix rotation and translation
0.99999651 0.00186028 0.00187897 -0.40239474
-0.00185675 0.99999652 -0.00187607 0.55801929
-0.00188246 0.00187257 0.99999648 0.09469763
Axis 0.57831092 0.58028383 -0.57343453
Axis point 61.09212114 0.00000000 225.59585813
Rotation angle (degrees) 0.18569746
Shift along axis 0.03679741
> fitmap #17 inMap #16
Fit molecule hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) to map
hOCT1-VB1.mrc (#16) using 3479 atoms
average map value = 0.02025, steps = 28
shifted from previous position = 0.0153
rotated from previous position = 0.0146 degrees
atoms outside contour = 1064, contour level = 0.011373
Position of hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) relative to
hOCT1-VB1.mrc (#16) coordinates:
Matrix rotation and translation
0.99999599 0.00211002 0.00188874 -0.43726655
-0.00210638 0.99999592 -0.00192887 0.59237860
-0.00189280 0.00192488 0.99999636 0.07510223
Axis 0.56254941 0.55200867 -0.61548727
Axis point 271.69369003 217.02489508 0.00000000
Rotation angle (degrees) 0.19625280
Shift along axis 0.03478962
> hide #!1 models
> select add #17
3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected
> select subtract #16
3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected
> color (#!17 & sel) white
> select clear
> select ::name="VIB"
18 atoms, 19 bonds, 1 residue, 1 model selected
> color sel red
> color zone #16 near #17 distance 4.98
> color zone #16 near #17 distance 4.88
> color zone #16 near #17 distance 4.78
> color zone #16 near #17 distance 4.68
> color zone #16 near #17 distance 4.58
> color zone #16 near #17 distance 4.48
> color zone #16 near #17 distance 4.38
> color zone #16 near #17 distance 4.28
> color zone #16 near #17 distance 4.18
> color zone #16 near #17 distance 4.08
> color zone #16 near #17 distance 3.98
> color zone #16 near #17 distance 3.88
> color zone #16 near #17 distance 3.78
> color zone #16 near #17 distance 3.68
> color zone #16 near #17 distance 3.58
> color zone #16 near #17 distance 3.48
> color zone #16 near #17 distance 3.38
> color zone #16 near #17 distance 3.28
> color sel white
> select ::name="VIB"
18 atoms, 19 bonds, 1 residue, 1 model selected
> color sel red
> select add #16
18 atoms, 19 bonds, 1 residue, 3 models selected
> select add #17
3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected
> select subtract #17
2 models selected
> color #16.1 white
> color zone #16 near #17 distance 3.28
> color zone #16 near #17 distance 3.18
> color zone #16 near #17 distance 3.08
> color zone #16 near #17 distance 2.98
> color zone #16 near #17 distance 2.88
> color zone #16 near #17 distance 2.98
> color zone #16 near #17 distance 3.08
> color zone #16 near #17 distance 3.18
> color zone #16 near #17 distance 3.28
> color zone #16 near #17 distance 3.38
[Repeated 1 time(s)]
> volume splitbyzone #16
Opened hOCT1-VB1.mrc 0 as #18.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0114, step 1, values float32
Opened hOCT1-VB1.mrc 1 as #18.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0114, step 1, values float32
Opened hOCT1-VB1.mrc 2 as #18.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0114, step 1, values float32
> close #18.1-2
> color #18.3 yellow models
> color #18.3 white models
> color #18.3 #ffffb2ff models
> color #18.3 #ffffb296 models
> select add #17
3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected
> select subtract #16
3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected
> color #17 #6622bbff
> color #17 #62be40ff
> color (#!17 & sel) byhetero
Drag select of 1 atoms, 1 bonds
> volume #18.3 level 0.006511
> volume #18.3 level 0.01112
> close #18#18.3
> select add #17
3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected
> color (#!17 & sel) white
> select ::name="VIB"
18 atoms, 19 bonds, 1 residue, 1 model selected
> color sel red
> show #!16 models
> color zone #16 near #17 distance 3.28
> color zone #16 near #17 distance 3.18
> color zone #16 near #17 distance 3.08
> color zone #16 near #17 distance 2.98
> color zone #16 near #17 distance 2.88
> color zone #16 near #17 distance 2.78
> color zone #16 near #17 distance 2.68
> color zone #16 near #17 distance 2.58
> color zone #16 near #17 distance 2.48
> color zone #16 near #17 distance 2.38
> color zone #16 near #17 distance 2.28
> color zone #16 near #17 distance 2.18
> color zone #16 near #17 distance 2.08
> color zone #16 near #17 distance 1.98
> color zone #16 near #17 distance 1.88
> color zone #16 near #17 distance 1.78
> color zone #16 near #17 distance 1.68
> color zone #16 near #17 distance 1.78
> color zone #16 near #17 distance 1.88
> color zone #16 near #17 distance 1.98
> color zone #16 near #17 distance 2.08
> volume splitbyzone #16
Opened hOCT1-VB1.mrc 0 as #18.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0114, step 1, values float32
Opened hOCT1-VB1.mrc 1 as #18.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0114, step 1, values float32
Opened hOCT1-VB1.mrc 2 as #18.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0114, step 1, values float32
> close #18.1-2
> color #18.3 white models
> color #18.3 #ffffb2ff models
> select add #18.3
18 atoms, 19 bonds, 1 residue, 3 models selected
> color #18.3 #ffffb296 models
> select subtract #18.3
18 atoms, 19 bonds, 1 residue, 1 model selected
> select add #17
3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected
> select subtract #17
Nothing selected
> select add #17
3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected
> color #17 #6622bbff
> color #17 #62be40ff
> color (#!17 & sel) byhetero
> view
> hide #!18.3 models
> hide #!18 models
> hide #!17 models
> select subtract #17
Nothing selected
> show #!1 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241004Krios_hOCT1-AZT/job154/postprocess_masked.mrc
Opened postprocess_masked.mrc as #19, grid size 320,320,320, pixel 0.83, shown
at level 2.83e-06, step 2, values float32
> volume #19 step 1
> volume #19 level 0.0131
> select add #19
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #19,-0.93986,0.28611,-0.18654,253.04,-0.10485,-0.76147,-0.63967,340.05,-0.32506,-0.58164,0.74567,158.04
> ui mousemode right "translate selected models"
> view matrix models
> #19,-0.93986,0.28611,-0.18654,175.89,-0.10485,-0.76147,-0.63967,293,-0.32506,-0.58164,0.74567,91.801
> view matrix models
> #19,-0.93986,0.28611,-0.18654,185.27,-0.10485,-0.76147,-0.63967,269.77,-0.32506,-0.58164,0.74567,91.027
> view matrix models
> #19,-0.93986,0.28611,-0.18654,178.6,-0.10485,-0.76147,-0.63967,268.3,-0.32506,-0.58164,0.74567,89.593
> rename #19 hOCT1-AZT.mrc
> fitmap #19 inMap #16
Fit map hOCT1-AZT.mrc in map hOCT1-VB1.mrc using 23475 points
correlation = 0.9652, correlation about mean = 0.8232, overlap = 14.07
steps = 112, shift = 2.59, angle = 19.3 degrees
Position of hOCT1-AZT.mrc (#19) relative to hOCT1-VB1.mrc (#16) coordinates:
Matrix rotation and translation
0.86934918 -0.02079803 -0.49376051 87.20318527
-0.45396874 0.36123943 -0.81450504 253.58267245
0.19530587 0.93224113 0.30460154 -57.13169181
Axis 0.90642923 -0.35757337 -0.22478286
Axis point 0.00000000 185.25380563 166.58335969
Rotation angle (degrees) 74.47879004
Shift along axis 1.21133072
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241004Krios_hOCT1-AZT/RealSpaceRefine_6/hOCT1_AZT-
> coot-2_real_space_refined_006.pdb
Chain information for hOCT1_AZT-coot-2_real_space_refined_006.pdb #20
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #!20 to #5
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 mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with hOCT1_AZT-
coot-2_real_space_refined_006.pdb, chain A (#20), sequence alignment score =
1978
RMSD between 414 pruned atom pairs is 0.849 angstroms; (across all 446 pairs:
1.482)
> hide #!1 models
> color #19 white models
> select add #20
3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 4 models selected
> color #20 white
> hide #!19 models
> select subtract #19
3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> color sel red
> color zone #19 near #20 distance 4.98
> show #!19 models
> select add #19
19 atoms, 20 bonds, 1 residue, 3 models selected
> select subtract #19
19 atoms, 20 bonds, 1 residue, 1 model selected
> color zone #19 near #20 distance 4.88
> color zone #19 near #20 distance 4.78
> color zone #19 near #20 distance 4.68
> color zone #19 near #20 distance 4.58
> color zone #19 near #20 distance 4.48
> color zone #19 near #20 distance 4.38
> color zone #19 near #20 distance 4.28
> color zone #19 near #20 distance 4.18
> color zone #19 near #20 distance 4.08
> color zone #19 near #20 distance 3.98
> color zone #19 near #20 distance 3.88
> color zone #19 near #20 distance 3.78
> color zone #19 near #20 distance 3.68
> color zone #19 near #20 distance 3.58
> color zone #19 near #20 distance 3.48
> volume #19 level 0.01039
> color zone #19 near #20 distance 3.38
> color zone #19 near #20 distance 3.28
> color zone #19 near #20 distance 3.18
> color zone #19 near #20 distance 3.08
> color zone #19 near #20 distance 2.98
> color zone #19 near #20 distance 2.88
> color zone #19 near #20 distance 2.78
> color zone #19 near #20 distance 2.68
> color zone #19 near #20 distance 2.58
> color zone #19 near #20 distance 2.48
> color zone #19 near #20 distance 2.38
> color zone #19 near #20 distance 2.28
> color zone #19 near #20 distance 2.18
> color zone #19 near #20 distance 2.08
> color zone #19 near #20 distance 1.98
> color zone #19 near #20 distance 1.88
> color zone #19 near #20 distance 1.78
> color zone #19 near #20 distance 1.88
> color zone #19 near #20 distance 1.98
> color zone #19 near #20 distance 2.08
[Repeated 1 time(s)]
> volume splitbyzone #19
Opened hOCT1-AZT.mrc 0 as #21.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
Opened hOCT1-AZT.mrc 1 as #21.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
Opened hOCT1-AZT.mrc 2 as #21.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
> close #21.1-2
> select add #20
3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected
> select subtract #20
Nothing selected
> select add #20
3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected
> color #20 #773333ff
> color #20 #733551ff
> color (#!20 & sel) byhetero
> select clear
> color #21.3 #ff000096 models
> color #21.3 #ffffff96 models
> color #21.3 #ffffb296 models
> volume #21.3 level 0.008896
> hide #!21.3 models
> hide #!21 models
> hide #!20 models
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 59019, resource id:
35654939, major code: 40 (TranslateCoords), minor code: 0
> show #!3 models
> show #!6.3 models
> select ::name="ABC"
42 atoms, 48 bonds, 2 residues, 1 model selected
> view sel
> select clear
> hide #!6.3 models
> hide #!6 models
> hide #!3 models
> show #!2 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> show #!8 models
> show #!9.3 models
> hide #!9.3 models
> hide #!9 models
> hide #!8 models
> show #!11 models
> show #!12.3 models
> hide #!12.3 models
> hide #!12 models
> hide #!11 models
> show #!14 models
> show #!15 models
> hide #!15 models
> show #!15.3 models
> hide #!14 models
> hide #!15 models
> hide #!15.3 models
> show #!17 models
> show #!18.3 models
> hide #!18.3 models
> hide #!18 models
> hide #!17 models
> show #!20 models
> show #!21.3 models
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1_structures_ligand_density.cxs
> includeMaps true
[Repeated 1 time(s)]
> close session
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/0-coot-
> history.scm
Unrecognized file suffix '.scm'
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.cif
Summary of feedback from opening
/home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 187
Missing entity information. Treating each chain as a separate entity.
Bad residue range for struct_conf "3" near line 98
Bad residue range for struct_conf "4" near line 99
Bad residue range for struct_conf "5" near line 100
Bad residue range for struct_conf "6" near line 101
Bad residue range for struct_conf "7" near line 102
15 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "2 1" near line 183
Invalid sheet range for struct_sheet_range "3 1" near line 184
Invalid sheet range for struct_sheet_range "4 1" near line 186
Missing or incomplete sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' near line 4361
Chain information for rOAT1-AZT_coot-4_real_space_refined_002.cif #1
---
Chain | Description
A | No description available
> close session
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.pdb
Chain information for rOAT1-AZT_coot-4_real_space_refined_002.pdb #1
---
Chain | Description
A | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 10568, resource id:
35655077, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/inward_j156_2.7A/postprocess.mrc
Opened postprocess.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.00421, step 2, values float32
> rename #2 rOAT1-AZT.mrc
> volume #2 step 1
> volume #2 level 0.01415
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> select add #1
3905 atoms, 3986 bonds, 515 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.81264,-0.025153,-0.58222,300.85,0.24435,0.8923,-0.37961,31.685,0.52906,-0.45075,-0.71897,210.07
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.81264,-0.025153,-0.58222,320.11,0.24435,0.8923,-0.37961,31.387,0.52906,-0.45075,-0.71897,214.5
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.62181,-0.74054,-0.25487,347.35,-0.028985,0.34697,-0.93743,205.98,0.78263,-0.57551,-0.23722,138.33
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.62181,-0.74054,-0.25487,344.94,-0.028985,0.34697,-0.93743,211.72,0.78263,-0.57551,-0.23722,135.34
> view matrix models
> #1,-0.62181,-0.74054,-0.25487,347.37,-0.028985,0.34697,-0.93743,211.37,0.78263,-0.57551,-0.23722,136.41
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule rOAT1-AZT_coot-4_real_space_refined_002.pdb (#1) to map
rOAT1-AZT.mrc (#2) using 3905 atoms
average map value = 0.01965, steps = 108
shifted from previous position = 2.32
rotated from previous position = 12.8 degrees
atoms outside contour = 1436, contour level = 0.014154
Position of rOAT1-AZT_coot-4_real_space_refined_002.pdb (#1) relative to
rOAT1-AZT.mrc (#2) coordinates:
Matrix rotation and translation
-0.62427498 -0.78041245 -0.03517318 323.27181278
-0.15760640 0.16991691 -0.97277359 257.26632447
0.76514114 -0.60173470 -0.22907287 142.60270901
Axis 0.34360458 -0.74113973 0.57675627
Axis point 193.37147122 0.00000000 235.15956508
Rotation angle (degrees) 147.32171525
Shift along axis 2.65438788
> select subtract #1
Nothing selected
> select add #1
3905 atoms, 3986 bonds, 515 residues, 1 model selected
> color sel white
> select ::name="AZZ"
19 atoms, 20 bonds, 1 residue, 1 model selected
> color sel red
> ui tool show "Color Zone"
> color zone #2 near #1 distance 4.98
> volume #2 level 0.0105
> color zone #2 near #1 distance 4.88
> color zone #2 near #1 distance 4.78
> color zone #2 near #1 distance 4.68
> color zone #2 near #1 distance 4.58
> color zone #2 near #1 distance 4.48
> color zone #2 near #1 distance 4.38
> color zone #2 near #1 distance 4.28
> color zone #2 near #1 distance 4.18
> color zone #2 near #1 distance 4.08
> color zone #2 near #1 distance 3.98
> color zone #2 near #1 distance 3.88
> color zone #2 near #1 distance 3.78
> color zone #2 near #1 distance 3.68
> color zone #2 near #1 distance 3.58
> color zone #2 near #1 distance 3.48
> color zone #2 near #1 distance 3.38
> color zone #2 near #1 distance 3.28
> color zone #2 near #1 distance 3.18
> color zone #2 near #1 distance 3.08
> color zone #2 near #1 distance 2.98
> color zone #2 near #1 distance 2.88
> color zone #2 near #1 distance 2.78
> color zone #2 near #1 distance 2.68
> color zone #2 near #1 distance 2.58
> color zone #2 near #1 distance 2.48
> color zone #2 near #1 distance 2.38
> color zone #2 near #1 distance 2.28
> color zone #2 near #1 distance 2.18
> color zone #2 near #1 distance 2.08
> color zone #2 near #1 distance 1.98
> color zone #2 near #1 distance 1.88
> color zone #2 near #1 distance 1.78
> volume #2 level 0.008069
> volume splitbyzone #2
Opened rOAT1-AZT.mrc 0 as #3.1, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT.mrc 1 as #3.2, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
> close #3.1-2
> color #3.3 white models
> color #3.3 #ffffb2ff models
> select add #1
3905 atoms, 3986 bonds, 515 residues, 1 model selected
> color #1 #dd22bbff
> color #1 tan
> color sel byhetero
> color #3.3 #ffffb296 models
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 355, resource id:
35655128, major code: 40 (TranslateCoords), minor code: 0
QXcbConnection: XCB error: 3 (BadWindow), sequence: 366, resource id:
35655123, major code: 40 (TranslateCoords), minor code: 0
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 14345, resource id:
35655133, major code: 40 (TranslateCoords), minor code: 0
> rename #1 rOAT1-AZT_IF.pdb
> rename #2 rOAT1-AZT_IF.mrc
> rename #3 "rOAT1-AZT_IF.mrc split"
> rename #3.3 "rOAT1-AZT_IF.mrc 2"
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 23455, resource id:
35655148, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/run_class001.mrc
Opened run_class001.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.00134, step 2, values float32
> close #4
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/postprocess.mrc
Opened postprocess.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.00459, step 2, values float32
> volume #4 step 1
> volume #4 level 0.01366
> rename #4 rOAT1-AZT_OF.mrc
> open
> /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PBD_LMNG_combined_20230419_20230217_OF/rOAT1-PBD_OF-
> coot-7_real_space_refined_008.pdb
Chain information for rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb #5
---
Chain | Description
A | No description available
> select subtract #1
Nothing selected
> select add #5
3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected
> hide #!3 models
> hide #!3.3 models
> hide #1 models
> view matrix models #5,1,0,0,68.569,0,1,0,64.41,0,0,1,67.632
> view matrix models #5,1,0,0,67.083,0,1,0,66.14,0,0,1,66.95
> fitmap #5 inMap #4
Fit molecule rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb (#5) to map
rOAT1-AZT_OF.mrc (#4) using 3792 atoms
average map value = 0.01938, steps = 84
shifted from previous position = 0.803
rotated from previous position = 4.35 degrees
atoms outside contour = 1323, contour level = 0.013659
Position of rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb (#5) relative to
rOAT1-AZT_OF.mrc (#4) coordinates:
Matrix rotation and translation
0.99822969 -0.04531644 -0.03852150 72.45731875
0.04345449 0.99790785 -0.04787105 67.21065914
0.04061025 0.04611237 0.99811044 61.32293455
Axis 0.62004547 -0.52206316 0.58565662
Axis point 0.00000000 -669.59173064 1932.22009801
Rotation angle (degrees) 4.34647273
Shift along axis 45.75280586
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/rOAT1-AZT_OF.pdb
> models #5 relModel #4
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/inward_j156_2.7A/rOAT1-AZT_IF.pdb
> models #1
> close #5
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/postprocess.mrc
Opened rOAT1-AZT_OF.mrc as #5, grid size 320,320,320, pixel 0.83, shown at
level 0.00459, step 2, values float32
> close #5
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/rOAT1-AZT_OF-
> coot-0_real_space_refined_003.pdb
Chain information for rOAT1-AZT_OF-coot-0_real_space_refined_003.pdb #5
---
Chain | Description
A | No description available
> select add #4
2 models selected
> select subtract #4
Nothing selected
> select add #5
3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected
> select clear
> select add #5
3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected
> color #5 white
> color #4 white models
> color #2 white models
> select #5/A:601@O4
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> color sel red
> color zone #4 near #5 distance 4.98
> color zone #4 near #5 distance 4.88
> color zone #4 near #5 distance 4.78
> color zone #4 near #5 distance 4.68
> color zone #4 near #5 distance 4.58
> color zone #4 near #5 distance 4.48
> color zone #4 near #5 distance 4.38
> color zone #4 near #5 distance 4.28
> color zone #4 near #5 distance 4.18
> color zone #4 near #5 distance 4.08
> color zone #4 near #5 distance 3.98
> color zone #4 near #5 distance 3.88
> color zone #4 near #5 distance 3.78
> color zone #4 near #5 distance 3.68
> color zone #4 near #5 distance 3.58
> color zone #4 near #5 distance 3.48
> color zone #4 near #5 distance 3.38
> color zone #4 near #5 distance 3.28
> color zone #4 near #5 distance 3.18
> color zone #4 near #5 distance 3.08
> color zone #4 near #5 distance 2.98
> color zone #4 near #5 distance 2.88
> color zone #4 near #5 distance 2.78
> color zone #4 near #5 distance 2.68
> color zone #4 near #5 distance 2.58
> color zone #4 near #5 distance 2.48
> color zone #4 near #5 distance 2.38
> color zone #4 near #5 distance 2.28
> color zone #4 near #5 distance 2.18
> color zone #4 near #5 distance 2.08
> color zone #4 near #5 distance 1.98
> color zone #4 near #5 distance 1.88
> color zone #4 near #5 distance 1.78
> color zone #4 near #5 distance 1.68
> color zone #4 near #5 distance 1.58
> color zone #4 near #5 distance 1.48
> color zone #4 near #5 distance 1.58
> color zone #4 near #5 distance 1.68
> color zone #4 near #5 distance 1.78
> color zone #4 near #5 distance 1.88
> volume splitbyzone #4
Opened rOAT1-AZT_OF.mrc 0 as #6.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 1 as #6.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
> close #6.1-2
> volume #6.3 level 0.0116
> select add #5
3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected
> select subtract #5
Nothing selected
> color #6.3 yellow models
> color #6.3 white models
> color #6.3 #ffffb2ff models
> select add #5
3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected
> color #5 #ffaa88ff
> color #5 salmon
> color (#!5 & sel) byhetero
> color #6.3 #ffffb296 models
> select clear
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> show #!2 models
> hide #!5 models
> hide #!6 models
> hide #!6.3 models
> volume #2 level 0.01456
> color #2 #a5a5a5ff models
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/inward_j261_2.6A/postprocess.mrc
Opened postprocess.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.00408, step 2, values float32
> rename #7 rOAT1-PBD_IF.mrc
> volume #2 level 0.01983
> volume #2 level 0.0151
> hide #!7 models
> volume #7 level 0.01185
> volume #7 step 1
> volume #7 level 0.01094
> hide #!2 models
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/inward_j261_2.6A/rOAT1-PBD-
> coot-6.pdb
Chain information for rOAT1-PBD-coot-6.pdb #8
---
Chain | Description
A | No description available
> select add #8
3912 atoms, 3985 bonds, 522 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,55.004,0,1,0,73.737,0,0,1,58.702
> view matrix models #8,1,0,0,66.378,0,1,0,64.897,0,0,1,63.973
> fitmap #8 inMap #7
Fit molecule rOAT1-PBD-coot-6.pdb (#8) to map rOAT1-PBD_IF.mrc (#7) using 3912
atoms
average map value = 0.02737, steps = 56
shifted from previous position = 2.6
rotated from previous position = 0.396 degrees
atoms outside contour = 571, contour level = 0.010939
Position of rOAT1-PBD-coot-6.pdb (#8) relative to rOAT1-PBD_IF.mrc (#7)
coordinates:
Matrix rotation and translation
0.99998387 0.00531886 -0.00199304 66.36205660
-0.00532668 0.99997806 -0.00393867 67.06308709
0.00197205 0.00394922 0.99999026 65.65327743
Axis 0.57034742 -0.28670293 -0.76974363
Axis point 10937.66555565 -15865.74627304 0.00000000
Rotation angle (degrees) 0.39620277
Shift along axis -31.91394767
> rename #8 rOAT1-PBD_IF.pdb
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 51376, resource id:
35655645, major code: 40 (TranslateCoords), minor code: 0
QXcbConnection: XCB error: 3 (BadWindow), sequence: 51388, resource id:
35655640, major code: 40 (TranslateCoords), minor code: 0
> color #8 white
> hide #!7 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 19 bonds, 1 residue, 1 model selected
> color sel red
> show #!7 models
> color zone #7 near #8 distance 4.98
> color zone #7 near #8 distance 4.88
> color zone #7 near #8 distance 4.78
> color zone #7 near #8 distance 4.68
> color zone #7 near #8 distance 4.58
> color zone #7 near #8 distance 4.48
> color zone #7 near #8 distance 4.38
> color zone #7 near #8 distance 4.28
> color zone #7 near #8 distance 4.18
> color zone #7 near #8 distance 4.08
> color zone #7 near #8 distance 3.98
> color zone #7 near #8 distance 3.88
> color zone #7 near #8 distance 3.78
> color zone #7 near #8 distance 3.68
> volume #7 level 0.02515
> volume #7 level 0.01677
> volume #7 level 0.0124
> volume #7 level 0.01476
> color zone #7 near #8 distance 3.58
> color zone #7 near #8 distance 3.48
> color zone #7 near #8 distance 3.38
> color zone #7 near #8 distance 3.28
> color zone #7 near #8 distance 3.18
> color zone #7 near #8 distance 3.08
> color zone #7 near #8 distance 2.98
> color zone #7 near #8 distance 2.88
> color zone #7 near #8 distance 2.78
> color zone #7 near #8 distance 2.68
> color zone #7 near #8 distance 2.58
> color zone #7 near #8 distance 2.48
> color zone #7 near #8 distance 2.38
> color zone #7 near #8 distance 2.28
> volume #7 level 0.01112
> color zone #7 near #8 distance 2.18
> color zone #7 near #8 distance 2.08
> color zone #7 near #8 distance 1.98
> color zone #7 near #8 distance 1.88
> color zone #7 near #8 distance 1.98
> color zone #7 near #8 distance 2.08
> volume splitbyzone #7
Opened rOAT1-PBD_IF.mrc 0 as #9.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 1 as #9.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
> close #9.1-2
> color #9.3 #ff000096 models
> color #9.3 #ffff0096 models
> color #9.3 #ffffff96 models
> color #9.3 #ffffb296 models
> select add #8
3912 atoms, 3985 bonds, 522 residues, 1 model selected
> color #8 #ffffddff
> color #8 gold
> select clear
> select add #8
3912 atoms, 3985 bonds, 522 residues, 1 model selected
> color sel byhetero
> select clear
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 19133, resource id:
35655670, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/outward_j272_3.0A/postprocess.mrc
Opened postprocess.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00409, step 2, values float32
QXcbConnection: XCB error: 3 (BadWindow), sequence: 23804, resource id:
35655680, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/outward_j272_3.0A/rOAT1-PBD_OF-
> coot-0.pdb
Chain information for rOAT1-PBD_OF-coot-0.pdb #11
---
Chain | Description
A | No description available
> hide #!9 models
> hide #8 models
> rename #10 rOAT1-PBD_OF
> rename #10 rOAT1-PBD_OF.mrc
> show #!2 models
> volume #10 level 0.004712
> volume #10 step 1
> volume #10 level 0.01128
> hide #!2 models
> select add #11
3872 atoms, 3966 bonds, 500 residues, 1 model selected
> view matrix models #11,1,0,0,65.11,0,1,0,69.986,0,0,1,61.035
> view matrix models #11,1,0,0,68.61,0,1,0,68.058,0,0,1,65.073
> view matrix models #11,1,0,0,67.516,0,1,0,68.105,0,0,1,67.386
> fitmap #11 inMap #10
Fit molecule rOAT1-PBD_OF-coot-0.pdb (#11) to map rOAT1-PBD_OF.mrc (#10) using
3872 atoms
average map value = 0.01531, steps = 56
shifted from previous position = 2.42
rotated from previous position = 0.764 degrees
atoms outside contour = 1505, contour level = 0.011277
Position of rOAT1-PBD_OF-coot-0.pdb (#11) relative to rOAT1-PBD_OF.mrc (#10)
coordinates:
Matrix rotation and translation
0.99995211 0.00939248 0.00274947 65.65298070
-0.00936721 0.99991506 -0.00906240 67.47749964
-0.00283436 0.00903621 0.99995516 65.83404461
Axis 0.67891074 0.20945939 -0.70370943
Axis point 6981.74049553 -6059.62250131 0.00000000
Rotation angle (degrees) 0.76372650
Shift along axis 12.37827175
> show sel atoms
> hide #!10 models
> show #!10 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-PBD_LMNG_combined_20230419_20230217_OF/rOAT1-PBD_OF-
> coot-7_real_space_refined_008.pdb
Chain information for rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb #12
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #!12 to #11
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 rOAT1-PBD_OF-coot-0.pdb, chain A (#11) with rOAT1-PBD_OF-
coot-7_real_space_refined_008.pdb, chain A (#12), sequence alignment score =
2423.1
RMSD between 470 pruned atom pairs is 0.696 angstroms; (across all 485 pairs:
1.080)
> hide #11 models
> select subtract #11
Nothing selected
> show #11 models
> hide #!12 models
> hide #!10 models
> show #!12 models
> close #11
> color #12 #bb4455ff
> color #12 #b4503bff
QXcbConnection: XCB error: 3 (BadWindow), sequence: 15705, resource id:
35655708, major code: 40 (TranslateCoords), minor code: 0
> show #!10 models
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 19760, resource id:
35655718, major code: 40 (TranslateCoords), minor code: 0
QXcbConnection: XCB error: 3 (BadWindow), sequence: 19772, resource id:
35655713, major code: 40 (TranslateCoords), minor code: 0
> color #10 #ffb2ff96 models
> volume #10 level 0.009218
> volume #10 level 0.008059
> color #10 #ffb2ffff models
> select add #12
3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected
> hide #!10 models
> color #12 white
> select clear
> select #12/B:601@C11
1 atom, 1 residue, 1 model selected
> select up
37 atoms, 37 bonds, 1 residue, 1 model selected
> color sel red
> color #10 white models
> select add #10
37 atoms, 37 bonds, 1 residue, 3 models selected
> select subtract #10
37 atoms, 37 bonds, 1 residue, 1 model selected
> show #!10 models
> color zone #10 near #12 distance 2
> color zone #10 near #12 distance 1.9
> color zone #10 near #12 distance 1.8
> color zone #10 near #12 distance 1.7
> color zone #10 near #12 distance 1.8
> color zone #10 near #12 distance 1.9
> color zone #10 near #12 distance 2
[Repeated 1 time(s)]
> volume splitbyzone #10
Opened rOAT1-PBD_OF.mrc 0 as #11.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 1 as #11.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
> volume splitbyzone #10
Opened rOAT1-PBD_OF.mrc 0 as #13.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 1 as #13.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
> close #11.1-2
> hide #!12 models
> hide #!11.3 models
> hide #!11 models
> select add #12
3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected
> select subtract #12
Nothing selected
> close #13.1-2
> show #!12 models
> color #11.3 white models
> color #11.3 #ffffb2ff models
> color #13.3 white models
> color #13.3 #ffffb2ff models
> select add #12
3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected
> color #12 #bb4455ff
> color #12 #b4503bff
> color (#!12 & sel) byhetero
> select #12/A:440
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #12
3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected
> select subtract #12
Nothing selected
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> hide #!13 models
> hide #!13.3 models
> hide #!12 models
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/inward_j152_2.7A/postprocess.mrc
Opened postprocess.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00408, step 2, values float32
QXcbConnection: XCB error: 3 (BadWindow), sequence: 27239, resource id:
35655778, major code: 40 (TranslateCoords), minor code: 0
> show #!2 models
> hide #!2 models
> rename #14 rOAT1-TFV_IF.mrc
> show #1 models
> hide #!14 models
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF.pdb
> models #1 relModel #14
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_5/rOAT1-TFV_IF-
> coot-2_real_space_refined_005.pdb
Chain information for rOAT1-TFV_IF-coot-2_real_space_refined_005.pdb #15
---
Chain | Description
A | No description available
> hide #1 models
> show #!14 models
> color #15 white
> color #14 white models
> select ::name="TFV"
31 atoms, 32 bonds, 1 residue, 1 model selected
> color sel red
> color zone #14 near #15 distance 4.68
> color zone #14 near #15 distance 4.58
> color zone #14 near #15 distance 4.48
> color zone #14 near #15 distance 4.38
> color zone #14 near #15 distance 4.28
> color zone #14 near #15 distance 4.18
> color zone #14 near #15 distance 4.08
> color zone #14 near #15 distance 3.98
> color zone #14 near #15 distance 3.88
> color zone #14 near #15 distance 3.78
> color zone #14 near #15 distance 3.68
> color zone #14 near #15 distance 3.58
> color zone #14 near #15 distance 3.48
> color zone #14 near #15 distance 3.38
> color zone #14 near #15 distance 3.28
> color zone #14 near #15 distance 3.18
> color zone #14 near #15 distance 3.08
> color zone #14 near #15 distance 2.98
> color zone #14 near #15 distance 2.88
> color zone #14 near #15 distance 2.78
> color zone #14 near #15 distance 2.68
> volume #14 level 0.007613
> color zone #14 near #15 distance 2.78
> color zone #14 near #15 distance 2.88
> color zone #14 near #15 distance 2.98
> color zone #14 near #15 distance 2.88
> color zone #14 near #15 distance 2.78
> color zone #14 near #15 distance 2.68
> color zone #14 near #15 distance 2.58
> color zone #14 near #15 distance 2.48
> color zone #14 near #15 distance 2.38
> volume #14 level 0.005915
> volume #14 level 0.005632
> volume splitbyzone #14
Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
> close #16.1-2
> color zone #14 near #15 distance 2.09
> close #16#16.3
> show #!14 models
> color zone #14 near #15 distance 1.99
> color zone #14 near #15 distance 2.09
> color zone #14 near #15 distance 2.19
> color zone #14 near #15 distance 2.29
> color zone #14 near #15 distance 2.39
> color zone #14 near #15 distance 2.29
> volume splitbyzone #14
Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
> close #16.1-2
> select add #15
3917 atoms, 3998 bonds, 515 residues, 1 model selected
> color #16.3 #ff5500ff models
> color #16.3 #aa0000ff models
> color #16.3 #ff5500ff models
> color #16.3 #ff557fff models
> color #15 #ff557fff
> color #16.3 white models
> color #16.3 #ffffb2ff models
> color #16.3 #ffffb296 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF-
> coot-3.pdb
Chain information for rOAT1-TFV_IF-coot-3.pdb #17
---
Chain | Description
A | No description available
> close #17#16#16.3
> close #15
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF-
> coot-3.pdb
Chain information for rOAT1-TFV_IF-coot-3.pdb #15
---
Chain | Description
A | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 28850, resource id:
35656402, major code: 40 (TranslateCoords), minor code: 0
> show #!14 models
> select add #15
3917 atoms, 3998 bonds, 515 residues, 1 model selected
> select subtract #15
Nothing selected
> select add #15
3917 atoms, 3998 bonds, 515 residues, 1 model selected
> color #15 white
> color zone #14 near #15 distance 2.29
> select ::name="TFV"
31 atoms, 32 bonds, 1 residue, 1 model selected
> color sel red
> color zone #14 near #15 distance 2.29
> color zone #14 near #15 distance 2.19
> color zone #14 near #15 distance 2.09
> color zone #14 near #15 distance 1.99
> color zone #14 near #15 distance 1.89
> color zone #14 near #15 distance 1.79
> color zone #14 near #15 distance 1.69
> color zone #14 near #15 distance 1.59
> color zone #14 near #15 distance 1.49
> color zone #14 near #15 distance 1.39
> color zone #14 near #15 distance 1.29
> color zone #14 near #15 distance 1.19
> color zone #14 near #15 distance 1.09
> color zone #14 near #15 distance 1.19
> color zone #14 near #15 distance 1.29
> color zone #14 near #15 distance 1.39
> color zone #14 near #15 distance 1.49
> color zone #14 near #15 distance 1.59
> color zone #14 near #15 distance 1.69
> color zone #14 near #15 distance 1.79
> color zone #14 near #15 distance 1.89
> color zone #14 near #15 distance 1.99
> color zone #14 near #15 distance 2.09
[Repeated 1 time(s)]
> volume splitbyzone #14
Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
> close #16.1-2
> color #16.3 white models
> color #16.3 #ffffb2ff models
> color #16.3 #ffffb296 models
> color #15 #ff5500ff
> color #15 #ff557fff
> select add #15
3917 atoms, 3998 bonds, 515 residues, 1 model selected
> color sel byhetero
> select clear
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/postprocess.mrc
Opened postprocess.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.00401, step 2, values float32
> rename #17 rOAT1-TVF_OF.mrc
> hide #15 models
> hide #!16 models
> show #8 models
> hide #8 models
> show #!11.3 models
> hide #!11 models
> hide #!11.3 models
> show #!12 models
> volume #17 step 1
> volume #17 level 0.01305
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF.pdb
> models #12 relModel #17
> hide #!16.3 models
> hide #!12 models
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF.pdb
Chain information for rOAT1-TFV_OF.pdb #18
---
Chain | Description
A | No description available
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> close #18
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_7/rOAT1-TFV_OF-
> coot-1_real_space_refined_007.pdb
Chain information for rOAT1-TFV_OF-coot-1_real_space_refined_007.pdb #18
---
Chain | Description
A | No description available
> select add #18
3786 atoms, 3876 bonds, 5 pseudobonds, 486 residues, 2 models selected
> color #18 white
> color #17 white models
> select #18/A:601@H131
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 32 bonds, 1 residue, 1 model selected
> color sel red
> volume #17 level 0.011
> color zone #17 near #18 distance 4.98
> color zone #17 near #18 distance 4.88
> color zone #17 near #18 distance 4.78
> color zone #17 near #18 distance 4.68
> color zone #17 near #18 distance 4.58
> color zone #17 near #18 distance 4.48
> color zone #17 near #18 distance 4.38
> color zone #17 near #18 distance 4.28
> color zone #17 near #18 distance 4.18
> color zone #17 near #18 distance 4.08
> color zone #17 near #18 distance 3.98
> color zone #17 near #18 distance 3.88
> color zone #17 near #18 distance 3.78
> color zone #17 near #18 distance 3.68
> color zone #17 near #18 distance 3.58
> color zone #17 near #18 distance 3.48
> color zone #17 near #18 distance 3.38
> color zone #17 near #18 distance 3.28
> color zone #17 near #18 distance 3.18
> color zone #17 near #18 distance 3.08
> color zone #17 near #18 distance 2.98
> volume splitbyzone #17
Opened rOAT1-TVF_OF.mrc 0 as #19.1, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 1 as #19.2, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
> close #19.1-2
> color #19.3 white models
> color #19.3 #ffffb2ff models
> select add #18
3786 atoms, 3876 bonds, 5 pseudobonds, 486 residues, 2 models selected
> color #18 #337744ff
> color #18 #374c02ff
> color (#!18 & sel) byhetero
> select clear
> color #19.3 #ffffb296 models
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/inward_j112_2.6A/postprocess.mrc
Opened postprocess.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.00494, step 2, values float32
> volume #20 step 1
> hide #!19 models
> hide #!18 models
> rename #20 rOAT1-AAI_IF.mrc
> volume #20 level 0.0194
QXcbConnection: XCB error: 3 (BadWindow), sequence: 35473, resource id:
35656688, major code: 40 (TranslateCoords), minor code: 0
> show #!2 models
> hide #!2 models
> show #1 models
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/IF/rOAT1-AAI_IF.pdb
> models #1 relModel #20
> hide #1 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/IF/rOAT1-AAI_IF.pdb
Chain information for rOAT1-AAI_IF.pdb #21
---
Chain | Description
A | No description available
> close #21
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_1/rOAT1-AAI_IF_real_space_refined_001.pdb
Chain information for rOAT1-AAI_IF_real_space_refined_001.pdb #21
---
Chain | Description
A | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 12758, resource id:
35656914, major code: 40 (TranslateCoords), minor code: 0
> close #21
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_3/rOAT1-AAI_IF-
> coot-1_real_space_refined_003_initial.geo
Unrecognized file suffix '.geo'
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_3/rOAT1-AAI_IF-
> coot-1_real_space_refined_003.pdb
Chain information for rOAT1-AAI_IF-coot-1_real_space_refined_003.pdb #21
---
Chain | Description
A | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 49188, resource id:
35657106, major code: 40 (TranslateCoords), minor code: 0
> select add #21
3956 atoms, 4042 bonds, 516 residues, 1 model selected
> color #21 white
> color #20 white models
> select clear
> select #21/A:602@O24
1 atom, 1 residue, 1 model selected
> select up
35 atoms, 38 bonds, 1 residue, 1 model selected
> select #21/A:601@O20
1 atom, 1 residue, 1 model selected
> select add #21/A:602@C23
2 atoms, 2 residues, 1 model selected
> select up
70 atoms, 76 bonds, 2 residues, 1 model selected
> color sel red
> color zone #20 near #21 distance 4.98
> color zone #20 near #21 distance 4.88
> color zone #20 near #21 distance 4.78
> color zone #20 near #21 distance 4.68
> color zone #20 near #21 distance 4.58
> color zone #20 near #21 distance 4.48
> color zone #20 near #21 distance 4.38
> color zone #20 near #21 distance 4.28
> color zone #20 near #21 distance 4.18
> color zone #20 near #21 distance 4.08
> color zone #20 near #21 distance 3.98
> color zone #20 near #21 distance 3.88
> color zone #20 near #21 distance 3.78
> color zone #20 near #21 distance 3.68
> color zone #20 near #21 distance 3.58
> color zone #20 near #21 distance 3.48
> color zone #20 near #21 distance 3.38
> color zone #20 near #21 distance 3.28
> color zone #20 near #21 distance 3.18
> color zone #20 near #21 distance 3.08
> color zone #20 near #21 distance 2.98
> color zone #20 near #21 distance 2.88
> volume splitbyzone #20
Opened rOAT1-AAI_IF.mrc 0 as #22.1, grid size 320,320,320, pixel 0.83, shown
at level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 1 as #22.2, grid size 320,320,320, pixel 0.83, shown
at level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0194, step 1, values float32
> close #22.1-2
> color #22.3 yellow models
> color #22.3 white models
> color #22.3 #ffffb2ff models
> color #22.3 #ffffb296 models
> select add #21
3956 atoms, 4042 bonds, 516 residues, 1 model selected
> color #21 #668855ff
> color #21 #685d73ff
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 7603, resource id:
35657141, major code: 40 (TranslateCoords), minor code: 0
QXcbConnection: XCB error: 3 (BadWindow), sequence: 7615, resource id:
35657136, major code: 40 (TranslateCoords), minor code: 0
> hide #!22.3 models
> hide #!22 models
> hide #21 models
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/outward_j122_2.5A/postprocess.mrc
Opened postprocess.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.00494, step 2, values float32
> volume #23 level 0.01307
> volume #23 step 1
> volume #23 level 0.01684
> show #1 models
> hide #1 models
> show #!5 models
> rename #23 rOAT1-AAI_OF.mrc
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/outward_j122_2.5A/rOAT1-AAI_OF.pdb
> models #5 relModel #23
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_4/rOAT1-AAI_OF-
> coot-1_real_space_refined_004.pdb
Chain information for rOAT1-AAI_OF-coot-1_real_space_refined_004.pdb #24
---
Chain | Description
A | No description available
> color #23 white models
> color #24 white
> hide #!5 models
> select add #24/A:601@O24
1 atom, 1 residue, 1 model selected
> select add #24/A:230@OH
2 atoms, 2 residues, 1 model selected
> select clear
> select add #24/A:601@O24
1 atom, 1 residue, 1 model selected
> select up
35 atoms, 38 bonds, 1 residue, 1 model selected
> color sel red
> color zone #23 near #24 distance 4.98
> volume splitbyzone #23
Opened rOAT1-AAI_OF.mrc 0 as #25.1, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 1 as #25.2, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
> close #25.1-2
> select add #24
3790 atoms, 3882 bonds, 5 pseudobonds, 486 residues, 2 models selected
> select subtract #24
Nothing selected
> color #25.3 white models
> color #25.3 #ffffb2ff models
> select add #24
3790 atoms, 3882 bonds, 5 pseudobonds, 486 residues, 2 models selected
> color #24 #1177ccff
> color #24 #17c127ff
> color (#!24 & sel) byhetero
> select #24/A:438@CE2
1 atom, 1 residue, 1 model selected
Drag select of 1 atoms, 1 bonds
> select clear
> color #25.3 #ffffb296 models
> select clear
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> open
> /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/rOAT1-PAH-
> coot-7_real_space_refined_007.pdb
Chain information for rOAT1-PAH-coot-7_real_space_refined_007.pdb #26
---
Chain | Description
A | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 7338, resource id:
35657291, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/cryosparc_P4_J89__localfilter_160.mrc
Opened cryosparc_P4_J89__localfilter_160.mrc as #27, grid size 160,160,160,
pixel 0.83, shown at level 0.134, step 1, values float32
> hide #!24 models
> hide #!25.3 models
> hide #!25 models
> view
> show #!2 models
> select add #26
3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected
> select add #27
3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 4 models selected
> view matrix models
> #26,1,0,0,55.434,0,1,0,82.728,0,0,1,62.865,#27,1,0,0,55.434,0,1,0,82.728,0,0,1,62.865
> view matrix models
> #26,1,0,0,67.067,0,1,0,66.938,0,0,1,64.563,#27,1,0,0,67.067,0,1,0,66.938,0,0,1,64.563
> rename #27 rOAT1-PAH
> rename #27 rOAT1-PAH.mrc
> view
> fitmap #26 inMap #27
Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
rOAT1-PAH.mrc (#27) using 3865 atoms
average map value = 0.3441, steps = 44
shifted from previous position = 0.0131
rotated from previous position = 0.0158 degrees
atoms outside contour = 699, contour level = 0.13428
Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
rOAT1-PAH.mrc (#27) coordinates:
Matrix rotation and translation
0.99999996 -0.00021122 0.00016567 0.00535685
0.00021123 0.99999998 -0.00006568 0.00053709
-0.00016566 0.00006571 0.99999998 -0.00148379
Axis 0.23771757 0.59945172 0.76429575
Axis point -1.23064203 24.84299856 0.00000000
Rotation angle (degrees) 0.01583428
Shift along axis 0.00046132
> hide #!2 models
> color #27 white models
> color #26 white
> hide #!26 models
> select subtract #27
3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected
> select subtract #26
Nothing selected
> hide #!27 models
> show #!26 models
> select #26/B:601@C07
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 23 bonds, 1 residue, 1 model selected
> color sel red
> show #!27 models
> color zone #27 near #26 distance 4.98
> color zone #27 near #26 distance 4.88
> color zone #27 near #26 distance 4.78
> color zone #27 near #26 distance 4.68
> color zone #27 near #26 distance 4.58
> color zone #27 near #26 distance 4.48
> color zone #27 near #26 distance 4.38
> color zone #27 near #26 distance 4.28
> color zone #27 near #26 distance 4.18
> color zone #27 near #26 distance 4.08
> color zone #27 near #26 distance 3.98
> color zone #27 near #26 distance 3.88
> color zone #27 near #26 distance 3.78
> color zone #27 near #26 distance 3.68
> color zone #27 near #26 distance 3.58
> color zone #27 near #26 distance 3.48
> color zone #27 near #26 distance 3.38
> color zone #27 near #26 distance 3.28
> color zone #27 near #26 distance 3.18
> color zone #27 near #26 distance 3.08
> color zone #27 near #26 distance 2.98
> color zone #27 near #26 distance 2.88
> color zone #27 near #26 distance 2.78
> color zone #27 near #26 distance 2.68
> color zone #27 near #26 distance 2.58
> color zone #27 near #26 distance 2.48
> color zone #27 near #26 distance 2.38
> color zone #27 near #26 distance 2.28
> volume #27 level 0.1207
> color zone #27 near #26 distance 2.18
> color zone #27 near #26 distance 2.08
> hide #!27 models
> show #!27 models
> fitmap #26 inMap #27
Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
rOAT1-PAH.mrc (#27) using 3865 atoms
average map value = 0.3441, steps = 44
shifted from previous position = 0.00509
rotated from previous position = 0.0145 degrees
atoms outside contour = 605, contour level = 0.12073
Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
rOAT1-PAH.mrc (#27) coordinates:
Matrix rotation and translation
1.00000000 -0.00003177 0.00004592 0.00408484
0.00003177 1.00000000 0.00006809 -0.00110606
-0.00004592 -0.00006809 1.00000000 0.00040828
Axis -0.77323345 0.52146975 0.36080373
Axis point 0.00000000 25.00840435 -11.23310139
Rotation angle (degrees) 0.00504562
Shift along axis -0.00358800
> fitmap #26 inMap #27
Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
rOAT1-PAH.mrc (#27) using 3865 atoms
average map value = 0.3441, steps = 40
shifted from previous position = 0.0153
rotated from previous position = 0.0197 degrees
atoms outside contour = 607, contour level = 0.12073
Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
rOAT1-PAH.mrc (#27) coordinates:
Matrix rotation and translation
0.99999998 -0.00017402 -0.00004728 0.01145050
0.00017401 0.99999996 -0.00023139 -0.00012574
0.00004732 0.00023138 0.99999997 -0.01696563
Axis 0.78875519 -0.16123857 0.59318410
Axis point 0.00000000 70.72803400 -1.26127659
Rotation angle (degrees) 0.01680827
Shift along axis -0.00101183
> volume splitbyzone #27
Opened rOAT1-PAH.mrc 0 as #28.1, grid size 160,160,160, pixel 0.83, shown at
level 0.121, step 1, values float32
Opened rOAT1-PAH.mrc 1 as #28.2, grid size 160,160,160, pixel 0.83, shown at
level 0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.121, step 1, values float32
> close #28.1-2
> volume #28.3 level 0.05463
> color #28.3 white models
> color #28.3 #ffffb2ff models
> color #28.3 #ffffb296 models
> select add #26
3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected
> color #26 #bf3434ff
> select subtract #26
Nothing selected
> hide #!26 models
> hide #!28 models
> hide #!28.3 models
> show #!28 models
> show #!28.3 models
> hide #!28 models
> show #!28 models
> show #!26 models
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 59852, resource id:
35657337, major code: 40 (TranslateCoords), minor code: 0
> hide #!26 models
> hide #!28 models
> hide #!28.3 models
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20220525_rOAT1-FBP/inward_j46_2.8A/postprocess.mrc
Opened postprocess.mrc as #29, grid size 320,320,320, pixel 0.83, shown at
level 0.0068, step 2, values float32
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-FBP_model/rOAT1-FBP_Model04_RSR_004.pdb
Chain information for rOAT1-FBP_Model04_RSR_004.pdb #30
---
Chain | Description
A | No description available
> show #!2 models
> volume #29 step 1
> volume #29 level 0.01695
> select add #30
4327 atoms, 4393 bonds, 591 residues, 1 model selected
> view matrix models #30,1,0,0,75.395,0,1,0,59.328,0,0,1,65.467
> view matrix models #30,1,0,0,69.37,0,1,0,69.752,0,0,1,66.8
> view matrix models #30,1,0,0,64.899,0,1,0,72.303,0,0,1,66.211
> view matrix models #30,1,0,0,67.675,0,1,0,68.154,0,0,1,64.823
> rename #29 rOAT1-FBP.mrc
> fitmap #30 inMap #29
Fit molecule rOAT1-FBP_Model04_RSR_004.pdb (#30) to map rOAT1-FBP.mrc (#29)
using 4327 atoms
average map value = 0.02366, steps = 64
shifted from previous position = 2.15
rotated from previous position = 1.57 degrees
atoms outside contour = 1497, contour level = 0.016951
Position of rOAT1-FBP_Model04_RSR_004.pdb (#30) relative to rOAT1-FBP.mrc
(#29) coordinates:
Matrix rotation and translation
0.99965949 -0.01809184 -0.01880406 69.16631575
0.01825291 0.99979787 0.00842953 64.90387685
0.01864775 -0.00876989 0.99978765 65.39100171
Axis -0.31300664 -0.68157330 0.66142625
Axis point -4271.01743380 0.00000000 3378.83285764
Rotation angle (degrees) 1.57437238
Shift along axis -22.63494048
> fitmap #29 inMap #28.3
Fit map rOAT1-FBP.mrc in map rOAT1-PAH.mrc 2 using 25401 points
correlation = 0.04397, correlation about mean = 0.03331, overlap = 0.1449
steps = 2000, shift = 8.88, angle = 34.9 degrees
Position of rOAT1-FBP.mrc (#29) relative to rOAT1-PAH.mrc 2 (#28.3)
coordinates:
Matrix rotation and translation
0.83021101 -0.04922054 -0.55527201 36.70411652
0.13130357 0.98533433 0.10897540 -101.23145590
0.54176475 -0.16338178 0.82449824 -98.97434819
Axis -0.23793623 -0.95839145 0.15770918
Axis point 214.13564799 0.00000000 31.76591481
Rotation angle (degrees) 34.91302477
Shift along axis 72.67695975
> fitmap #29 inMap #28.3
Fit map rOAT1-FBP.mrc in map rOAT1-PAH.mrc 2 using 25401 points
correlation = 0.06352, correlation about mean = 0.0448, overlap = 0.3215
steps = 1976, shift = 9.79, angle = 47.5 degrees
Position of rOAT1-FBP.mrc (#29) relative to rOAT1-PAH.mrc 2 (#28.3)
coordinates:
Matrix rotation and translation
0.44591506 0.03168285 -0.89451437 128.47676238
-0.42572042 0.88660402 -0.18081879 31.25418163
0.78735118 0.46144286 0.40883812 -156.17744024
Axis 0.34576253 -0.90543486 -0.24624374
Axis point 186.53313716 0.00000000 6.98625710
Rotation angle (degrees) 68.24252592
Shift along axis 54.58154231
> fitmap #29 inMap #2
Fit map rOAT1-FBP.mrc in map rOAT1-AZT_IF.mrc using 25401 points
correlation = 0.2561, correlation about mean = 0.04268, overlap = 2.051
steps = 232, shift = 3.32, angle = 8.56 degrees
Position of rOAT1-FBP.mrc (#29) relative to rOAT1-AZT_IF.mrc (#2) coordinates:
Matrix rotation and translation
0.54964589 -0.00012465 -0.83539774 175.75622877
-0.44507129 0.84621907 -0.29295875 119.06565669
0.70696602 0.53283512 0.46506536 -99.09845418
Axis 0.45744920 -0.85439368 -0.24647856
Axis point 210.95352936 0.00000000 94.96801349
Rotation angle (degrees) 64.50291620
Shift along axis 3.09624573
> select add #29
4327 atoms, 4393 bonds, 591 residues, 3 models selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!27 models
> view matrix models
> #29,0.54965,-0.00012465,-0.8354,176.85,-0.44507,0.84622,-0.29296,120.37,0.70697,0.53284,0.46507,-99.177,#30,0.99966,-0.018092,-0.018804,70.259,0.018253,0.9998,0.0084295,66.206,0.018648,-0.0087699,0.99979,65.312
> select subtract #30
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.93603,-0.13155,0.32642,-36.684,0.29946,0.78494,-0.54239,70.054,-0.18487,0.60545,0.77412,-40.4
> view matrix models
> #29,0.99097,-0.1328,0.018694,4.0787,0.13411,0.98118,-0.13891,3.4116,0.00010362,0.14016,0.99013,-37.407
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.99097,-0.1328,0.018694,17.811,0.13411,0.98118,-0.13891,8.06,0.00010362,0.14016,0.99013,-17.751
> view matrix models
> #29,0.99097,-0.1328,0.018694,18.852,0.13411,0.98118,-0.13891,3.5023,0.00010362,0.14016,0.99013,-19.331
> fitmap #29 inMap #2
Fit map rOAT1-FBP.mrc in map rOAT1-AZT_IF.mrc using 25401 points
correlation = 0.937, correlation about mean = 0.7119, overlap = 14.98
steps = 260, shift = 2.93, angle = 16.7 degrees
Position of rOAT1-FBP.mrc (#29) relative to rOAT1-AZT_IF.mrc (#2) coordinates:
Matrix rotation and translation
0.99338416 0.10541244 -0.04556454 -5.89234048
-0.10461957 0.99432199 0.01945563 14.33237930
0.04735669 -0.01455997 0.99877192 -4.89753719
Axis -0.14650897 -0.40022199 -0.90463113
Axis point 131.78683646 64.78395429 0.00000000
Rotation angle (degrees) 6.66633138
Shift along axis -0.44238796
> fitmap #30 inMap #29
Fit molecule rOAT1-FBP_Model04_RSR_004.pdb (#30) to map rOAT1-FBP.mrc (#29)
using 4327 atoms
average map value = 0.02366, steps = 84
shifted from previous position = 1.18
rotated from previous position = 6.66 degrees
atoms outside contour = 1496, contour level = 0.016951
Position of rOAT1-FBP_Model04_RSR_004.pdb (#30) relative to rOAT1-FBP.mrc
(#29) coordinates:
Matrix rotation and translation
0.99966027 -0.01808767 -0.01876641 69.16021058
0.01824668 0.99979876 0.00833662 64.90031908
0.01861185 -0.00867622 0.99978914 65.39198117
Axis -0.31026139 -0.68166338 0.66262576
Axis point -4271.35731029 0.00000000 3392.84555643
Rotation angle (degrees) 1.57107230
Shift along axis -22.36750269
> select subtract #29
Nothing selected
> hide #!27 models
> color #29 white models
> color #30 white
> select ::name="FBP"
18 atoms, 19 bonds, 1 residue, 1 model selected
> color sel red
> color zone #29 near #30 distance 4.98
> volume #29 level 0.01043
> volume splitbyzone #29
Opened rOAT1-FBP.mrc 0 as #31.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 1 as #31.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
> close #31.1-2
> volume #31.3 level 0.002491
> volume #31.3 level 0.005476
> close #31#31.3
> show #!29 models
> color zone #29 near #30 distance 2
[Repeated 1 time(s)]
> volume splitbyzone #29
Opened rOAT1-FBP.mrc 0 as #31.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 1 as #31.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
> close #31.1-2
> volume #31.3 level 0.003802
> color #31.3 white models
> color #31.3 #ffffb2ff models
> color #31.3 #ffffb20f models
> color #31.3 #ffffb296 models
> select add #30
4327 atoms, 4393 bonds, 591 residues, 1 model selected
> color #30 #889944ff
> color #30 #894a08ff
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> hide #!31.3 models
> hide #!31 models
> select subtract #30
Nothing selected
> hide #30 models
> show #!2 models
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20220609_rOAT1-CFM/inward_j194_2.7A/postprocess.mrc
Opened postprocess.mrc as #32, grid size 320,320,320, pixel 0.83, shown at
level 0.00396, step 2, values float32
QXcbConnection: XCB error: 3 (BadWindow), sequence: 4668, resource id:
35657387, major code: 40 (TranslateCoords), minor code: 0
> volume #32 step 1
> volume #32 level 0.01186
> rename #32 rOAT1-CFM.mrc
> fitmap #31.3 inMap #32
Fit map rOAT1-FBP.mrc 2 in map rOAT1-CFM.mrc using 186 points
correlation = 0.7788, correlation about mean = 0.1794, overlap = 0.008643
steps = 80, shift = 1.06, angle = 39.7 degrees
Position of rOAT1-FBP.mrc 2 (#31.3) relative to rOAT1-CFM.mrc (#32)
coordinates:
Matrix rotation and translation
0.74404465 0.65679786 0.12253212 -67.09990326
-0.66239846 0.70118044 0.26376935 89.56606533
0.08732602 -0.27742126 0.95677145 29.93219993
Axis -0.37942983 0.02468307 -0.92489121
Axis point 75.79903236 131.70903838 0.00000000
Rotation angle (degrees) 45.49284979
Shift along axis -0.01355792
> fitmap #31.3 inMap #2
Fit map rOAT1-FBP.mrc 2 in map rOAT1-AZT_IF.mrc using 186 points
correlation = 0.8514, correlation about mean = 0.3895, overlap = 0.01295
steps = 76, shift = 0.987, angle = 35 degrees
Position of rOAT1-FBP.mrc 2 (#31.3) relative to rOAT1-AZT_IF.mrc (#2)
coordinates:
Matrix rotation and translation
0.98357109 0.17790518 -0.03062105 -15.98050765
-0.17592201 0.98266732 0.05844983 19.75924781
0.04048883 -0.05210265 0.99782061 1.12732183
Axis -0.29288928 -0.18839308 -0.93740275
Axis point 102.41456930 99.44616144 0.00000000
Rotation angle (degrees) 10.87852675
Shift along axis -0.09874061
> fitmap #32 inMap #2
Fit map rOAT1-CFM.mrc in map rOAT1-AZT_IF.mrc using 30016 points
correlation = 0.9542, correlation about mean = 0.7898, overlap = 13.57
steps = 72, shift = 2.43, angle = 7.06 degrees
Position of rOAT1-CFM.mrc (#32) relative to rOAT1-AZT_IF.mrc (#2) coordinates:
Matrix rotation and translation
0.99240829 0.11776796 -0.03544703 -8.88787383
-0.11778889 0.99303752 0.00150464 18.44106769
0.03537743 0.00268205 0.99937042 -5.69387210
Axis 0.00478670 -0.28793162 -0.95763901
Axis point 151.76616064 85.25679566 0.00000000
Rotation angle (degrees) 7.06459913
Shift along axis 0.10036409
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM_IF.pdb
> models #30 relModel #32
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM_IF.pdb
Chain information for rOAT1-CFM_IF.pdb #33
---
Chain | Description
A | No description available
> color #33 #ffff7fff
> color #33 #55aaffff
> select add #33
4327 atoms, 4393 bonds, 591 residues, 1 model selected
> view matrix models #33,1,0,0,-3.2206,0,1,0,10.827,0,0,1,-3.1224
> view matrix models #33,1,0,0,-4.4307,0,1,0,11.668,0,0,1,-3.5924
> view matrix models #33,1,0,0,-4.3326,0,1,0,9.3726,0,0,1,-2.8036
> fitmap #33 inMap #32
Fit molecule rOAT1-CFM_IF.pdb (#33) to map rOAT1-CFM.mrc (#32) using 4327
atoms
average map value = 0.0191, steps = 80
shifted from previous position = 1.1
rotated from previous position = 7.12 degrees
atoms outside contour = 1362, contour level = 0.01186
Position of rOAT1-CFM_IF.pdb (#33) relative to rOAT1-CFM.mrc (#32)
coordinates:
Matrix rotation and translation
0.99999299 -0.00023005 -0.00373680 -4.70643521
0.00021365 0.99999035 -0.00438786 8.58155234
0.00373777 0.00438703 0.99998339 -3.97966882
Axis 0.76069466 -0.64796926 0.03846397
Axis point 0.00000000 827.85989235 581.48051316
Rotation angle (degrees) 0.33046593
Shift along axis -9.29381608
> save /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM.pdb
> models #33 relModel #32
QXcbConnection: XCB error: 3 (BadWindow), sequence: 60371, resource id:
35657459, major code: 40 (TranslateCoords), minor code: 0
> hide #33 models
> hide #!32 models
> select subtract #33
Nothing selected
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!2 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_7/rOAT1-TFV-
> Cl_OF-coot-2.pdb
Chain information for rOAT1-TFV-Cl_OF-coot-2.pdb #34
---
Chain | Description
A | No description available
> select ::name="CL"
1 atom, 1 residue, 1 model selected
> hide #!17 models
> show sel atoms
> show #!17 models
> style sel stick
Changed 1 atom style
> color zone #17 near #34 distance 2.98
> select add #34
3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected
> color #34 white
> color zone #17 near #34 distance 2.98
> select ::name="CL"
1 atom, 1 residue, 1 model selected
> color sel red
> color zone #17 near #34 distance 2.98
> volume splitbyzone #17
Opened rOAT1-TVF_OF.mrc 0 as #35.1, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 1 as #35.2, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
> rename #35 "rOAT1-TVF-Cl_OF.mrc split"
> close #35.1-2
> rename #35.3 "rOAT1-TVF-Cl_OF.mrc 2"
> hide #!35.3 models
> select #34/B:1@CL
1 atom, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel interModel false ignoreHiddenModels true select true
6 contacts
> ui tool show Contacts
> contacts sel intraRes true ignoreHiddenModels true select true
15 contacts
> show sel atoms
> color #34 yellow
> show sel atoms
> close #36
> select add #34
3787 atoms, 3876 bonds, 11 pseudobonds, 487 residues, 3 models selected
> color #34 white
> hide sel atoms
> select ::name="CL"
1 atom, 1 residue, 1 model selected
> show sel atoms
> hide #35.3.1 models
> show #35.3.1 models
> close #34.2
> hide #!35.3 models
> hide #35.3.1 models
> hide #!35 models
> hide #34.1 models
> select #34/B:1@CL
1 atom, 1 residue, 1 model selected
> select #34/A:216
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #34/A:511
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #34: 219
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #34: 273
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #34/A:4
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #34/A:511
15 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> select add #34/A:512
23 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> select #34/B:1@CL
1 atom, 1 residue, 1 model selected
> color sel lime
> color #35.3.1 white
> color #35.3.1 #ffffb2ff
> color #35.3.1 #ffffb296
> select #34/B:1@CL
1 atom, 1 residue, 1 model selected
> select add #34
3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected
> color #34 #374c02ff
> select #34/B:1@CL
1 atom, 1 residue, 1 model selected
> color sel lime
> select add #34
3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected
> color (#!34 & sel) byhetero
> select #34/A:2
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select #34/A:3
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #34/A:215
18 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> select #34/B:1@CL
1 atom, 1 residue, 1 model selected
> show #35.3.1 models
> view sel
> hide #35.3.1 models
> hide #!35.3 models
> hide #!35 models
> hide #!34 models
> select add #34
3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected
> select subtract #34
Nothing selected
> show #1 models
> view
> hide #1 models
> show #21 models
> select add #21/A:602@C12
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
44 atoms, 46 bonds, 2 residues, 1 model selected
> select clear
> select #21/A:602@O14
1 atom, 1 residue, 1 model selected
> select add #21/A:601@C04
2 atoms, 2 residues, 1 model selected
> select up
70 atoms, 76 bonds, 2 residues, 1 model selected
> view sel
> show #!22.3 models
> hide #!22.3 models
> hide #!22 models
> hide #21 models
> select add #21
3956 atoms, 4042 bonds, 516 residues, 1 model selected
> select subtract #21
Nothing selected
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 40781, resource id:
35657669, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/postprocess.mrc
Opened postprocess.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00418, step 2, values float32
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1_AF-Q4U2R8-F1-model_v4.pdb
hOAT1_AF-Q4U2R8-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for solute carrier family 22 member 6
(Q4U2R8) [more info...]
Chain information for hOAT1_AF-Q4U2R8-F1-model_v4.pdb #37
---
Chain | Description | UniProt
A | solute carrier family 22 member 6 | S22A6_HUMAN 1-563
> rename #36 hOAT1-TFV.mrc
> volume #36 step 1
> volume #36 level 0.008515
> rename #37 hOAT1-TFV_IF.pdb
> view
> show #!2 models
> hide #!2 models
> ui tool show Matchmaker
> matchmaker #37 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rOAT1-AZT_IF.pdb, chain A (#1) with hOAT1-TFV_IF.pdb, chain A
(#37), sequence alignment score = 2359.6
RMSD between 490 pruned atom pairs is 0.806 angstroms; (across all 500 pairs:
0.862)
> matchmaker #37 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rOAT1-AZT_IF.pdb, chain A (#1) with hOAT1-TFV_IF.pdb, chain A
(#37), sequence alignment score = 2359.6
RMSD between 490 pruned atom pairs is 0.806 angstroms; (across all 500 pairs:
0.862)
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1-TVF_IF.pdb
> models #37 relModel #36
> rename #36 hOAT1-TFV_IF.mrc
> hide #37 models
> hide #!36 models
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1_AF-Q4U2R8-F1-model_v4.pdb
hOAT1_AF-Q4U2R8-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for solute carrier family 22 member 6
(Q4U2R8) [more info...]
Chain information for hOAT1_AF-Q4U2R8-F1-model_v4.pdb #38
---
Chain | Description | UniProt
A | solute carrier family 22 member 6 | S22A6_HUMAN 1-563
> close #38
> close #37
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/RealSpaceRefine_2/hOAT1-TVF_IF-
> coot-1_real_space_refined_002.pdb
Chain information for hOAT1-TVF_IF-coot-1_real_space_refined_002.pdb #37
---
Chain | Description
A | No description available
> show #!36 models
> color #36 white models
> color #37 white
> hide #!36 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select #37/A:601@C08
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 32 bonds, 1 residue, 1 model selected
> color sel red
> show #!36 models
> color zone #36 near #37 distance 4.98
> color zone #36 near #37 distance 2
[Repeated 1 time(s)]
> color zone #36 near #37 distance 1.9
> color zone #36 near #37 distance 1.8
> color zone #36 near #37 distance 1.7
> volume splitbyzone #36
Opened hOAT1-TFV_IF.mrc 0 as #38.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 1 as #38.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32
> close #38.1-2
> color #38.3 white models
> color #38.3 #ffffb2ff models
> color #38.3 #ffffb296 models
> color #37 #aaff7fff
> select add #37
4375 atoms, 4481 bonds, 564 residues, 1 model selected
> color sel byhetero
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 48690, resource id:
35657985, major code: 40 (TranslateCoords), minor code: 0
> hide #!38.3 models
> hide #!38 models
> select subtract #37
Nothing selected
> show #!34 models
Drag select of 25 atoms, 383 residues, 24 bonds
> select up
2906 atoms, 2958 bonds, 383 residues, 2 models selected
> select clear
> select add #37/A:326
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> hide #!34 models
> select add #37
4375 atoms, 4481 bonds, 564 residues, 1 model selected
> select subtract #37
Nothing selected
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
> models #37 relModel #36
QXcbConnection: XCB error: 3 (BadWindow), sequence: 16970, resource id:
35658005, major code: 40 (TranslateCoords), minor code: 0
QXcbConnection: XCB error: 3 (BadWindow), sequence: 16981, resource id:
35657995, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/outward_j68_3.1A/postprocess.mrc
Opened postprocess.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.00436, step 2, values float32
QXcbConnection: XCB error: 3 (BadWindow), sequence: 18302, resource id:
35658010, major code: 40 (TranslateCoords), minor code: 0
> rename #39 hOAT1-TFV_OF.mrc
> volume #39 step 1
> volume #39 level 0.01031
> hide #!39 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
Chain information for hOAT1-TFV_OF.pdb #40
---
Chain | Description
A | No description available
> hide #37 models
> select #40: 320-600
1850 atoms, 1888 bonds, 244 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #40 & sel to #18
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 rOAT1-TFV_OF-coot-1_real_space_refined_007.pdb, chain A (#18) with
hOAT1-TFV_OF.pdb, chain A (#40), sequence alignment score = 866.1
RMSD between 164 pruned atom pairs is 0.748 angstroms; (across all 200 pairs:
7.198)
> matchmaker #40 to #15
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 rOAT1-TFV_IF-coot-3.pdb, chain A (#15) with hOAT1-TFV_OF.pdb, chain
A (#40), sequence alignment score = 2368.6
RMSD between 493 pruned atom pairs is 0.665 angstroms; (across all 500 pairs:
0.719)
> show #!18 models
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> view matrix models
> #40,0.99727,-0.025813,-0.069217,13.221,0.025375,0.99965,-0.0072002,-1.7643,0.069379,0.0054242,0.99758,-8.8122
> undo
> ui mousemode right "move picked models"
> view matrix models #18,1,0,0,0.019269,0,1,0,-0.04277,0,0,1,0.28987
> undo
> ui mousemode right pivot
> ui tool show Matchmaker
> matchmaker #40 & sel to #5 & sel
No 'to' model specified
> select clear
> hide #!18 models
> show #!18 models
> select #18,40: 320-600
3274 atoms, 3340 bonds, 2 pseudobonds, 433 residues, 3 models selected
> ui tool show Matchmaker
> matchmaker #40 & sel to #5 & sel
No 'to' model specified
> matchmaker #40 & sel to #5 & sel
No 'to' model specified
> matchmaker #40 & sel to #5 & sel
No 'to' model specified
> ui mousemode right "translate selected atoms"
> select #40: 320-600
1850 atoms, 1888 bonds, 244 residues, 1 model selected
> hide #!18 models
> show #!18 models
> hide #40 models
> hide #!18 models
> show #40 models
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
> models #40 relModel #39
QXcbConnection: XCB error: 3 (BadWindow), sequence: 34583, resource id:
35658147, major code: 40 (TranslateCoords), minor code: 0
> fitmap #40 inMap #39
Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
atoms
average map value = 0.007219, steps = 88
shifted from previous position = 0.909
rotated from previous position = 8.49 degrees
atoms outside contour = 2887, contour level = 0.010308
Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
coordinates:
Matrix rotation and translation
0.99019825 -0.07829950 -0.11565728 27.38037598
0.07892080 0.99688057 0.00079533 -10.70816731
0.11523422 -0.00991530 0.99328886 -13.08861468
Axis -0.03831490 -0.82596303 0.56242070
Axis point 128.86145300 0.00000000 225.96021530
Rotation angle (degrees) 8.03460025
Shift along axis 0.43416611
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
> models #40 relModel #39
> undo
> select clear
> show #!39 models
> fitmap #40 inMap #39
Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
atoms
average map value = 0.007218, steps = 28
shifted from previous position = 0.0175
rotated from previous position = 0.016 degrees
atoms outside contour = 2888, contour level = 0.010308
Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
coordinates:
Matrix rotation and translation
0.99020256 -0.07845145 -0.11551732 27.36683659
0.07909202 0.99686685 0.00096497 -10.76110579
0.11507968 -0.01009202 0.99330500 -13.04322773
Axis -0.03956067 -0.82505023 0.56367284
Axis point 128.67057833 0.00000000 226.14572082
Rotation angle (degrees) 8.03322105
Shift along axis 0.44368911
> fitmap #40 inMap #39
Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
atoms
average map value = 0.007219, steps = 44
shifted from previous position = 0.00455
rotated from previous position = 0.00258 degrees
atoms outside contour = 2889, contour level = 0.010308
Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
coordinates:
Matrix rotation and translation
0.99020340 -0.07846932 -0.11549800 27.37049731
0.07911379 0.99686509 0.00099928 -10.76639922
0.11505751 -0.01012698 0.99330721 -13.03687370
Axis -0.03980982 -0.82492871 0.56383314
Axis point 128.62890621 0.00000000 226.21984207
Rotation angle (degrees) 8.03295687
Shift along axis 0.44127588
> select add #40
4375 atoms, 4481 bonds, 564 residues, 1 model selected
> fitmap #40 inMap #39
Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
atoms
average map value = 0.007219, steps = 60
shifted from previous position = 2.24
rotated from previous position = 0.00666 degrees
atoms outside contour = 2889, contour level = 0.010308
Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
coordinates:
Matrix rotation and translation
0.99020164 -0.07840067 -0.11555975 25.97288245
0.07903810 0.99687116 0.00093711 -9.32824593
0.11512471 -0.01006155 0.99330009 -12.03377088
Axis -0.03935047 -0.82533103 0.56327634
Axis point 116.53468443 0.00000000 214.84157931
Rotation angle (degrees) 8.03353574
Shift along axis -0.10149276
> show #!17 models
> fitmap #39 inMap #19.3
Fit map hOAT1-TFV_OF.mrc in map rOAT1-TVF_OF.mrc 2 using 37364 points
correlation = 0.03002, correlation about mean = -0.02439, overlap = 0.01206
steps = 936, shift = 1.08, angle = 13.4 degrees
Position of hOAT1-TFV_OF.mrc (#39) relative to rOAT1-TVF_OF.mrc 2 (#19.3)
coordinates:
Matrix rotation and translation
0.98280665 -0.13043667 -0.13068041 37.39205996
0.11063752 0.98266445 -0.14876125 8.18112237
0.14781892 0.13174539 0.98020035 -34.01816129
Axis 0.60585490 -0.60151939 0.52068635
Axis point 0.00000000 261.98069292 24.54762139
Rotation angle (degrees) 13.38519605
Shift along axis 0.02026683
> fitmap #39 inMap #19.3
Fit map hOAT1-TFV_OF.mrc in map rOAT1-TVF_OF.mrc 2 using 37364 points
correlation = 0.03002, correlation about mean = -0.0244, overlap = 0.01206
steps = 48, shift = 0.0138, angle = 0.161 degrees
Position of hOAT1-TFV_OF.mrc (#39) relative to rOAT1-TVF_OF.mrc 2 (#19.3)
coordinates:
Matrix rotation and translation
0.98301413 -0.12857767 -0.13096186 37.15798588
0.10847145 0.98263409 -0.15054633 8.70610140
0.14804449 0.13378355 0.97989019 -34.26954280
Axis 0.61337235 -0.60188813 0.51137563
Axis point -0.00000000 260.45263984 27.89398858
Rotation angle (degrees) 13.40165031
Shift along axis 0.02697294
> fitmap #40 inMap #39
Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
atoms
average map value = 0.007219, steps = 132
shifted from previous position = 0.778
rotated from previous position = 13.4 degrees
atoms outside contour = 2889, contour level = 0.010308
Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
coordinates:
Matrix rotation and translation
0.99020454 -0.07852899 -0.11544767 25.97319443
0.07917768 0.99685998 0.00103677 -9.35919916
0.11500374 -0.01016749 0.99331302 -12.00484753
Axis -0.04009077 -0.82459474 0.56430155
Axis point 116.41047661 0.00000000 215.06686153
Rotation angle (degrees) 8.03257950
Shift along axis -0.09809308
> hide #!17 models
> hide #!39 models
> close #40
> open /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF-
> coot-1.pdb
Chain information for hOAT1-TFV_OF-coot-1.pdb #40
---
Chain | Description
A | No description available
> show #!39 models
> color #39 white models
> color #40 white
> hide #!39 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> color sel red
> select up
31 atoms, 32 bonds, 1 residue, 1 model selected
> color sel red
> show #!39 models
> color zone #39 near #40 distance 4.98
> color zone #39 near #40 distance 2
[Repeated 1 time(s)]
> volume #39 level 0.01241
> open /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF-
> coot-2.pdb
Chain information for hOAT1-TFV_OF-coot-2.pdb #41
---
Chain | Description
A | No description available
> hide #!40 models
> color #41 white
> color zone #39 near #41 distance 2
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 32 bonds, 1 residue, 1 model selected
> color sel red
> color zone #39 near #41 distance 2
> volume #39 level 0.01056
> color zone #39 near #41 distance 2.1
> color zone #39 near #41 distance 2.2
> color zone #39 near #41 distance 2.3
> color zone #39 near #41 distance 2.4
> color zone #39 near #41 distance 2.5
> color zone #39 near #41 distance 2.6
> color zone #39 near #41 distance 2.7
> color zone #39 near #41 distance 2.8
> color zone #39 near #41 distance 2.9
> color zone #39 near #41 distance 3
> color zone #39 near #41 distance 2.9
> color zone #39 near #41 distance 2.8
> color zone #39 near #41 distance 2.7
> color zone #39 near #41 distance 2.6
> color zone #39 near #41 distance 2.5
> color zone #39 near #41 distance 2.4
> color zone #39 near #41 distance 2.3
> color zone #39 near #41 distance 2.2
> color zone #39 near #41 distance 2.1
> color zone #39 near #41 distance 2
> color zone #39 near #41 distance 1.9
> color zone #39 near #41 distance 2
> color zone #39 near #41 distance 2.1
> color zone #39 near #41 distance 2.2
> color zone #39 near #41 distance 2.3
> color zone #39 near #41 distance 2.4
> color zone #39 near #41 distance 2.5
> volume splitbyzone #39
Opened hOAT1-TFV_OF.mrc 0 as #42.1, grid size 320,320,320, pixel 0.83, shown
at level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 1 as #42.2, grid size 320,320,320, pixel 0.83, shown
at level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0106, step 1, values float32
> close #42.1-2
> color #42.3 white models
> color #42.3 #ffffb2ff models
> color #42.3 #ffffb296 models
> volume #42.3 level 0.006989
> select add #41
4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected
> color #41 #aaffffff
> color #41 blue
> color #41 red
> color #41 #aa00ffff
> color #41 #0055ffff
> color #41 #55557fff
> color #41 #ff557fff
> color #41 #ffaaffff
> color (#!41 & sel) byhetero
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> show #!34 models
> hide #!41 models
> hide #!42 models
> hide #!42.3 models
> select subtract #41
Nothing selected
> hide #!34 models
> show #1 models
> show #!3.3 models
> hide #!3.3 models
> hide #!3 models
> hide #1 models
> show #!22.3 models
> show #21 models
> select add #21/A:601@O25
1 atom, 1 bond, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> view sel
> volume #22.3 level 0.01409
> hide #!22.3 models
> hide #!22 models
> hide #21 models
> show #!22.3 models
> hide #!22.3 models
> hide #!22 models
> show #!23 models
> hide #!23 models
> show #!25.3 models
> show #!24 models
> hide #!25.3 models
> hide #!25 models
> hide #!24 models
> show #1 models
> show #!3.3 models
> hide #!3.3 models
> hide #!3 models
> hide #1 models
> show #!5 models
> show #!6.3 models
> hide #!6.3 models
> hide #!6 models
> hide #!5 models
> show #8 models
> show #!9.3 models
> volume #9.3 level 0.003826
> select #8/A:230
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #8/A:227
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!9.3 models
> hide #!9 models
> hide #8 models
> show #!12 models
> show #!11.3 models
> color #11.3 #ffffb296 models
> hide #!12 models
> hide #!11.3 models
> hide #!11 models
> show #15 models
> show #!16.3 models
> hide #!16.3 models
> hide #!16 models
> hide #15 models
> show #!18 models
> show #!19.3 models
> hide #!18 models
> hide #!19 models
> hide #!19.3 models
> show #37 models
> show #!38.3 models
> hide #!38.3 models
> hide #!38 models
> hide #37 models
> close #40
> show #!41 models
> show #!42.3 models
> hide #!42.3 models
> hide #!42 models
> hide #!41 models
> show #!26 models
> show #!28.3 models
> select #26/A:230
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #26/A:200
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #26
3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected
> color (#!26 & sel) byhetero
> select clear
> select #26/A:223
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #26/A:227
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #26/A:223
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #26/A:200
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select #26/A:226
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #26/A:204
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!28.3 models
> hide #!28 models
> hide #!26 models
> show #!31.3 models
> show #30 models
> select add #30
4327 atoms, 4393 bonds, 591 residues, 1 model selected
> color sel byhetero
> select clear
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
——— End of log from Mon Feb 10 17:46:10 2025 ———
opened ChimeraX session
> hide #!31.3 models
> hide #!31 models
> hide #30 models
> show #!34 models
> show #!35 models
> show #!35.3 models
> volume #35.3 level 0.01175
> select #35.3
2 models selected
> view sel
> color #34 tan
> ui tool show "Side View"
> select add #34
3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 4 models selected
> color (#!34 & sel) byhetero
> select clear
> select #34/A:447
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #34/A:507
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
——— End of log from Tue Mar 11 12:00:09 2025 ———
opened ChimeraX session
> hide #!35.3 models
> hide #!35 models
> show #!17 models
> color #17 #ffffb2ff models
> color #17 #ffffb280 models
> ui tool show "Side View"
> color #17 #ffffb24d models
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
——— End of log from Thu Apr 10 14:06:06 2025 ———
opened ChimeraX session
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie1.mp4
Movie saved to /Users/dout2/Desktop/movie1.mp4
> select add #34
3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected
> show sel atoms
> select clear
> hide #!34 models
> hide #!17 models
> show #!6 models
> show #1 models
> view
> select #1/A:463
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:466
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:228
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:230
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:231
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:377
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:378
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:381
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:225
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:382
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!6 models
> show #!6 models
> hide #1 models
> show #1 models
> select add #1
3905 atoms, 3986 bonds, 515 residues, 1 model selected
> select subtract #1
Nothing selected
> hide #1 models
> hide #!6 models
> show #!18 models
> hide #!18 models
> show #1 models
> select #1/A:228
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:199
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:257
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:145
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:466
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:149
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:146
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:204
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:150
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:149
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:203
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:146
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:149
5 atoms, 4 bonds, 1 residue, 1 model selected
Drag select of 13 residues
> select #1/A:463
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:466@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel intraRes true ignoreHiddenModels true select true
> makePseudobonds false reveal true
26 contacts
> select clear
> select : 382
126 atoms, 112 bonds, 14 residues, 14 models selected
> select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #1 atoms
> hide #!6 target m
[Repeated 1 time(s)]
> hide #!4 target m
> select add #1
5716 atoms, 5702 bonds, 714 residues, 14 models selected
> select subtract #1
1811 atoms, 1716 bonds, 199 residues, 13 models selected
> select add #5
5446 atoms, 5448 bonds, 5 pseudobonds, 670 residues, 14 models selected
> select subtract #5
1672 atoms, 1584 bonds, 184 residues, 12 models selected
> select add #8
5445 atoms, 5437 bonds, 691 residues, 12 models selected
> select subtract #8
1533 atoms, 1452 bonds, 169 residues, 11 models selected
> select add #12
5186 atoms, 5201 bonds, 5 pseudobonds, 640 residues, 12 models selected
> select subtract #12
1394 atoms, 1320 bonds, 154 residues, 10 models selected
> hide #1 models
> show #1 models
> select add #15
5172 atoms, 5186 bonds, 654 residues, 10 models selected
> select subtract #15
1255 atoms, 1188 bonds, 139 residues, 9 models selected
> select add #18
4902 atoms, 4932 bonds, 5 pseudobonds, 610 residues, 10 models selected
> select subtract #18
1116 atoms, 1056 bonds, 124 residues, 8 models selected
> select add #21
4933 atoms, 4966 bonds, 625 residues, 8 models selected
> select subtract #21
977 atoms, 924 bonds, 109 residues, 7 models selected
> select add #24
4628 atoms, 4674 bonds, 5 pseudobonds, 580 residues, 8 models selected
> select subtract #24
838 atoms, 792 bonds, 94 residues, 6 models selected
> select add #26
4564 atoms, 4607 bonds, 1 pseudobond, 585 residues, 7 models selected
> select subtract #26
699 atoms, 660 bonds, 79 residues, 5 models selected
> select add #30
4885 atoms, 4921 bonds, 653 residues, 5 models selected
> select subtract #30
558 atoms, 528 bonds, 62 residues, 4 models selected
> select add #33
4744 atoms, 4789 bonds, 636 residues, 4 models selected
> select subtract #33
417 atoms, 396 bonds, 45 residues, 3 models selected
> select add #34
4065 atoms, 4140 bonds, 5 pseudobonds, 517 residues, 4 models selected
> select subtract #34
278 atoms, 264 bonds, 30 residues, 2 models selected
> select add #37
4514 atoms, 4613 bonds, 579 residues, 2 models selected
> select subtract #37
139 atoms, 132 bonds, 15 residues, 1 model selected
> select add #41
4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected
> select subtract #41
Nothing selected
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!3.3 models
> ui tool show "Side View"
> select #1/A:35@CG
1 atom, 1 residue, 1 model selected
> select : 35
112 atoms, 98 bonds, 14 residues, 14 models selected
> hide sel & #1 atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select : 35
112 atoms, 98 bonds, 14 residues, 14 models selected
> show sel & #1 atoms
> select clear
> select : 35
112 atoms, 98 bonds, 14 residues, 14 models selected
> hide sel & #1 atoms
> save /Users/dout2/Desktop/image1.png supersample 3
> save /Users/dout2/Desktop/rOAT1-AZT_OF_LigandDensity.png supersample 3
> select add #1
4009 atoms, 4077 bonds, 528 residues, 14 models selected
> select subtract #1
104 atoms, 91 bonds, 13 residues, 13 models selected
> select add #5
3870 atoms, 3948 bonds, 5 pseudobonds, 498 residues, 14 models selected
> select subtract #5
96 atoms, 84 bonds, 12 residues, 12 models selected
> select add #8
4000 atoms, 4062 bonds, 533 residues, 12 models selected
> select subtract #8
88 atoms, 77 bonds, 11 residues, 11 models selected
> select add #12
3872 atoms, 3951 bonds, 5 pseudobonds, 496 residues, 12 models selected
> select subtract #12
80 atoms, 70 bonds, 10 residues, 10 models selected
> select add #21
4028 atoms, 4105 bonds, 525 residues, 10 models selected
> select subtract #21
72 atoms, 63 bonds, 9 residues, 9 models selected
> select add #18
3850 atoms, 3932 bonds, 5 pseudobonds, 494 residues, 10 models selected
> select subtract #18
64 atoms, 56 bonds, 8 residues, 8 models selected
> select add #24
3846 atoms, 3931 bonds, 5 pseudobonds, 493 residues, 9 models selected
> select subtract #24
56 atoms, 49 bonds, 7 residues, 7 models selected
> select add #26
3913 atoms, 3989 bonds, 1 pseudobond, 512 residues, 8 models selected
> select subtract #26
48 atoms, 42 bonds, 6 residues, 6 models selected
> select add #30
4367 atoms, 4428 bonds, 596 residues, 6 models selected
> select subtract #30
40 atoms, 35 bonds, 5 residues, 5 models selected
> select add #33
4359 atoms, 4421 bonds, 595 residues, 5 models selected
> select subtract #33
32 atoms, 28 bonds, 4 residues, 4 models selected
> select add #34
3811 atoms, 3897 bonds, 5 pseudobonds, 490 residues, 5 models selected
> select subtract #34
24 atoms, 21 bonds, 3 residues, 3 models selected
> select add #37
4391 atoms, 4495 bonds, 566 residues, 3 models selected
> select subtract #37
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #41
4383 atoms, 4488 bonds, 1 pseudobond, 565 residues, 3 models selected
> select subtract #41
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!3.3 models
> hide #!3 models
> hide #1 models
> show #!5 models
> show #!6.3 models
> hide #!6.3 models
> hide #!6 models
> hide #!5 models
> show #8 models
> show #!9 models
> show #!9.3 models
> select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #8 atoms
> select: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
Unknown command: select:
382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
> select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #8 atoms
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #8 atoms
> select clear
> volume #9.3 level 0.00516
> save /Users/dout2/Desktop/rOAT1-PBD_IF_LigandDensity.png supersample 3
> hide #!9.3 models
> hide #!9 models
> hide #8 models
> show #15 models
> show #!16 models
> show #!16.3 models
> select #15/A:442
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #15 atoms
> select #1-50: 438
154 atoms, 154 bonds, 14 residues, 14 models selected
> select clear
> save /Users/dout2/Desktop/rOAT1-TFV_IF_LigandDensity.png supersample 3
> hide #!16.3 models
> hide #!16 models
> hide #15 models
> show #21 models
> show #!22 models
> show #!22.3 models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #21 atoms
> select clear
> save /Users/dout2/Desktop/rOAT1-AAI_IF_LigandDensity.png supersample 3
> volume #22.3 level 0.0128
> hide #!22.3 models
> hide #!22 models
> hide #21 models
> show #!27 models
> show #!28 models
> hide #!27 models
> show #!26 models
> show #!28.3 models
> volume #28.3 level 0.06828
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #!26 atoms
> select clear
> save /Users/dout2/Desktop/rOAT1-PAH_IF_LigandDensity.png supersample 3
> hide #!28.3 models
> hide #!28 models
> hide #!26 models
> show #30 models
> show #!31 models
> show #!31.3 models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #30 atoms
> select clear
> save /Users/dout2/Desktop/rOAT1-FBP_IF_LigandDensity.png supersample 3
> hide #!31.3 models
> hide #!31 models
> hide #30 models
> show #37 models
> show #!38 models
> show #!38.3 models
> select clear
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #37 atoms
> select clear
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> volume #38.3 level 0.006101
> volume #38.3 level 0.006864
> save /Users/dout2/Desktop/hOAT1-TFV_IF_LigandDensity.png supersample 3
> hide #!38.3 models
> hide #!38 models
> hide #37 models
> show #!2 models
> hide #!2 models
> show #1 models
> show #!3 models
> show #!3.3 models
> hide #!3.3 models
> hide #!3 models
> hide #1 models
> show #!5 models
> show #!6.3 models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #!5 atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #!5 atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> volume #6.3 level 0.0106
> save /Users/dout2/Desktop/rOAT1-AZT_OF_LigandDensity.png supersample 3
> hide #!5 models
> hide #!6 models
> hide #!6.3 models
> show #!11 models
> show #!12 models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #!12 atoms
> select clear
> show #!11.3 models
> select clear
> volume #11.3 level 0.009777
> select clear
> show #!10 models
> hide #!10 models
> select clear
> volume #11.3 level 0.01081
> select clear
> show #!10 models
> hide #!10 models
> save /Users/dout2/Desktop/rOAT1-PBD_OF_LigandDensity.png supersample 3
> hide #!12 models
> hide #!11 models
> show #!18 models
> show #!19 models
> show #!19.3 models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #!18 atoms
> select clear
> save /Users/dout2/Desktop/rOAT1-TFV_OF_LigandDensity.png supersample 3
> hide #!19 models
> hide #!18 models
> show #!24 models
> show #!25 models
> show #!25.3 models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #!24 atoms
> select clear
> save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
> hide #!25 models
> hide #!24 models
> show #!35 models
> show #!34 models
> show #!35.3 models
> hide #!35.3 models
> hide #!35 models
> hide #!34 models
> show #!41 models
> show #!42 models
> show #!42.3 models
> save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
> hide #!41 models
> hide #!42 models
> hide #!42.3 models
> show #!25 models
> show #!24 models
> save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
> hide #!24 models
> hide #!25 models
> show #!42.3 models
> show #!41 models
> select clear
[Repeated 1 time(s)]
> ui tool show Distances
> select clear
No distances to delete!
> save /Users/dout2/Desktop/hOAT1-TFV_OF_LigandDensity.png supersample 3
> view
> view orient
> open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j156_2.68A_outward-
> facing/postprocess.mrc
Opened postprocess.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
level 0.00432, step 2, values float32
> volume #40 step 1
> volume #40 level 0.008916
> hide #!41 models
> hide #!40 models
> select add #41
4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected
> select subtract #41
Nothing selected
> hide #!42 models
> show #!40 models
> rename #40 rOAT1-AKG_OF.mrc
> open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j156_2.68A_outward-
> facing/RealSpaceRefine_1/rOAT1-AKG_OF-coot-5_real_space_refined_001.pdb
Chain information for rOAT1-AKG_OF-coot-5_real_space_refined_001.pdb #43
---
Chain | Description
A | No description available
> select clear
> open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j122_2.63A_outward-
> occluded/postprocess.mrc
Opened postprocess.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
level 0.00378, step 2, values float32
> rename #44 rOAT1-AKG_OOC.mrc
> open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j122_2.63A_outward-
> occluded/RealSpaceRefine_3/rOAT1-AKG_OF-coot-4_real_space_refined_003.pdb
Chain information for rOAT1-AKG_OF-coot-4_real_space_refined_003.pdb #45
---
Chain | Description
A | No description available
> rename #45 rOAT1-AKG_OOC-coot-4_real_space_refined_003.pdb
> hide #!43 models
> hide #!40 models
> volume #44 step 1
> volume #44 level 0.01023
> select ::name="AKG"
20 atoms, 18 bonds, 2 residues, 2 models selected
> view sel
> color #44 #ffffb24d models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
2228 atoms, 2112 bonds, 244 residues, 16 models selected
> show sel & #!45 atoms
> select clear
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> color #44 #ffffb280 models
> color #44 #ffffb266 models
> color #44 #ffffb24d models
> select clear
> save /Users/dout2/Desktop/hOAT1-AKG_OOC_LigandDensity.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie2.mp4
Movie saved to /Users/dout2/Desktop/movie2.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie3.mp4
Movie saved to /Users/dout2/Desktop/movie3.mp4
> hide #!45 models
> hide #!44 models
> show #!43 models
> show #!40 models
> color #40 #b2b2b24d models
> select clear
> color #40 #ffffb24d models
> select clear
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
2228 atoms, 2112 bonds, 244 residues, 16 models selected
> show sel & #!43 atoms
> select clear
[Repeated 1 time(s)]
> volume #40 level 0.009283
> save /Users/dout2/Desktop/rOAT1-AKG_OF_LigandDensity.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie3.mp4
Movie saved to /Users/dout2/Desktop/movie3.mp4
> volume #40 level 0.01222
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie4.mp4
Movie saved to /Users/dout2/Desktop/movie4.mp4
> hide #!43 models
> hide #!40 models
> open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
> occluded/postprocess_rescaled.mrc
Opened postprocess_rescaled.mrc as #46, grid size 480,480,480, pixel 0.553,
shown at level 0.0038, step 2, values float32
> open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
> occluded/RealSpaceRefine_1/rOAT1-R466A_OO-coot-2_real_space_refined_001.pdb
Chain information for rOAT1-R466A_OO-coot-2_real_space_refined_001.pdb #47
---
Chain | Description
A | No description available
> select #46
4 models selected
> select clear
> view
> volume #46 step 1
> volume #46 level 0.01147
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
2367 atoms, 2244 bonds, 259 residues, 17 models selected
> view sel
> color #46 #b2ffff4d models
> select #46
4 models selected
> show #!47 atoms
> select clear
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> close #47
> open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
> occluded/RealSpaceRefine_2/rOAT1-R466A_OO-coot-3_real_space_refined_002.pdb
Chain information for rOAT1-R466A_OO-coot-3_real_space_refined_002.pdb #47
---
Chain | Description
A | No description available
> select add #46
4 models selected
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
2361 atoms, 2238 bonds, 259 residues, 17 models selected
> show sel & #!47 atoms
> select clear
> select #46
4 models selected
> select clear
> save /Users/dout2/Desktop/rOAT1-R466A_OF_LigandDensity.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie4.mp4
Movie saved to /Users/dout2/Desktop/movie4.mp4
> hide #!46 models
> show #!46 models
> save /Users/dout2/Desktop/rOAT1-R466A_OF_LigandDensity2.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie4.mp4
Movie saved to /Users/dout2/Desktop/movie4.mp4
> view
> color #46 #b2ffffff models
> color #46 #b2ffffab models
> color #46 #b2ffffff models
> select clear
[Repeated 1 time(s)]
> save /Users/dout2/Desktop/rOAT1-R466A_OF.png supersample 3
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
——— End of log from Thu Apr 10 15:43:35 2025 ———
opened ChimeraX session
> hide #!47 models
> hide #!46 models
> rename #46 rOAT1-R466A.mrc
> open
> /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-apo_20220519_cryoSPARC/J12_2.05A_clip-240/cryosparc_P4_J16__localfilter_240.mrc
Opened cryosparc_P4_J16__localfilter_240.mrc as #48, grid size 240,240,240,
pixel 0.553, shown at level 0.238, step 1, values float32
> open
> /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-apo_20220519_cryoSPARC/model/rOAT1-apo-
> coot-4_real_space_refined_004.pdb
Chain information for rOAT1-apo-coot-4_real_space_refined_004.pdb #49
---
Chain | Description
A | No description available
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> rename #48 rOAT1-Apo.mrc
> hide #49 models
> hide #!48 models
> hide #48.1 models
> show #49 models
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> show sel atoms
> size stickRadius 0.3
Changed 72733 bond radii
> select add #49
3942 atoms, 3966 bonds, 570 residues, 1 model selected
> hide sel cartoons
> select clear
Drag select of 10 atoms, 11 bonds
Drag select of 6 atoms, 9 bonds
Drag select of 8 atoms, 10 bonds
Drag select of 4 atoms, 4 bonds
> select up
36 atoms, 34 bonds, 4 residues, 1 model selected
> lighting flat
> graphics silhouettes false
> select clear
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> select clear
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> color sel orange
> color sel purple
> color sel hot pink
> size stickRadius 0.5
Changed 72733 bond radii
> size stickRadius 0.4
Changed 72733 bond radii
> select clear
> select add #49/A:466@CB
1 atom, 1 residue, 1 model selected
> select add #49/A:382@NZ
2 atoms, 2 residues, 1 model selected
> select up
20 atoms, 18 bonds, 2 residues, 1 model selected
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> color sel lime
> color sel purple
> select clear
> select add #49/A:382@NZ
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
20 atoms, 18 bonds, 2 residues, 1 model selected
> color sel byhetero
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> color sel purple
> select clear
> select #49/A:382@NZ
1 atom, 1 residue, 1 model selected
> select add #49/A:466@NH2
2 atoms, 2 residues, 1 model selected
> select add #49/A:466@NH1
3 atoms, 2 residues, 1 model selected
> select add #49/A:466@CZ
4 atoms, 2 residues, 1 model selected
> select add #49/A:466@NE
5 atoms, 2 residues, 1 model selected
> color sel byhetero
> select clear
> save /Users/dout2/Desktop/rOAT1-Apo_keyresidue.png supersample 3
> transparentBackground true
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> hide sel atoms
> select add #49
3942 atoms, 3966 bonds, 570 residues, 1 model selected
> show sel cartoons
> select clear
> view
> select add #49
3942 atoms, 3966 bonds, 570 residues, 1 model selected
> color sel gray
> color sel light gray
> color sel dark gray
> surface sel
> select clear
> save /Users/dout2/Desktop/rOAT1-Apo_bg.png supersample 3
> transparentBackground true
> open /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-0/model.cif
Summary of feedback from opening
/Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-0/model.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Chain information for model.cif #50
---
Chain | Description
A | .
No chain in structure corresponds to chain ID given in local score info (chain
'B')
> hide #!49 models
> rename #50 rOAT1-AKG_IF_af3.cif
> select add #50
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> select clear
> select #50: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel purple
> size stickRadius 0.4
Changed 77114 bond radii
> select clear
> select add #50
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> hide sel cartoons
> select clear
[Repeated 1 time(s)]
> select #50/A:354@CG
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #50/B:1@C4
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select #50/A:382@NZ
1 atom, 1 residue, 1 model selected
> select add #50/A:466@NH1
2 atoms, 2 residues, 1 model selected
> select add #50/A:466@NH2
3 atoms, 2 residues, 1 model selected
> select add #50/A:466@NE
4 atoms, 2 residues, 1 model selected
> color sel byhetero
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_keyresidue.png supersample 3
> transparentBackground true
> select add #50
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> surface sel
> color (#!50 & sel) dark gray
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_bg.png supersample 3
> transparentBackground true
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> hide #!50 models
> show #!45 models
> show #!44 models
> hide #!44 models
> view
> view orient
> hide #!45 models
> show #!43 models
> show #!45 models
> hide #!45 models
> select add #43
3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 2 models selected
> color (#!43 & sel) dark gray
> surface (#!43 & sel)
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_OF_bg.png supersample 3
> transparentBackground true
> hide #43.2 models
> hide #43.1 models
> show #43.1 models
> select #43: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> select subtract #43.2
1 model selected
> select add #43
3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 2 models selected
> hide sel cartoons
> select clear
> select #43: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> select add #43
3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 3 models selected
> hide sel atoms
> select #43: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> show sel atoms
> select #43: akg
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #43/A:601@C2
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select clear
> select #43/A:466@NH2
1 atom, 1 residue, 1 model selected
> select add #43/A:466@NH1
2 atoms, 1 residue, 2 models selected
> select add #43/A:466@NE
3 atoms, 1 residue, 2 models selected
> select add #43/A:382@NZ
4 atoms, 2 residues, 2 models selected
> color (#!43 & sel) byhetero
> select clear
> select #43: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> color (#!43 & sel) purple
> select subtract #43/A:382@NZ
65 atoms, 63 bonds, 6 residues, 2 models selected
> select subtract #43/A:466@NH2
64 atoms, 62 bonds, 6 residues, 2 models selected
> select subtract #43/A:466@NH1
63 atoms, 61 bonds, 6 residues, 2 models selected
> select subtract #43/A:466@CD
62 atoms, 59 bonds, 6 residues, 2 models selected
> color (#!43 & sel) byhetero
> select #43: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> color (#!43 & sel) purple
> select subtract #43/A:382@NZ
65 atoms, 63 bonds, 6 residues, 2 models selected
> select subtract #43/A:466@NH1
64 atoms, 62 bonds, 6 residues, 2 models selected
> select subtract #43/A:466@NH2
63 atoms, 61 bonds, 6 residues, 2 models selected
> select clear
> select add #43/A:466@NH2
1 atom, 1 residue, 1 model selected
> select add #43/A:466@NH1
2 atoms, 1 residue, 2 models selected
> select add #43/A:382@NZ
3 atoms, 2 residues, 2 models selected
> color (#!43 & sel) byhetero
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_OF_residue.png supersample 3
> transparentBackground true
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> open /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-1/model.cif
Summary of feedback from opening
/Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-1/model.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Chain information for model.cif #51
---
Chain | Description
A | .
No chain in structure corresponds to chain ID given in local score info (chain
'B')
> hide #!43 models
> hide #43.1 models
> view
> rename #51 rOAT1-AKG_IF_af3_model1.cif
> rename #51 rOAT1-AKG_IF_af3_model1-1.cif
> select add #51
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> color sel dark gray
> surface sel
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_IF_bg.png supersample 3
> transparentBackground true
> hide #51.1 models
> select add #51
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #51: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> show sel atoms
> color (#!51 & sel) purple
> size stickRadius 0.4
Changed 81495 bond radii
> select clear
> select #51: AKG
Nothing selected
> show #!51 atoms
> undo
> select add #51
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> show sel atoms
> select #51/B:1@C3
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> select add #51
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> hide sel atoms
> select #51/B
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
> select clear
> select #51: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> show sel atoms
> select #51/A:382@NZ
1 atom, 1 residue, 1 model selected
> select add #51/A:466@NH1
2 atoms, 2 residues, 2 models selected
> select add #51/A:466@NH2
3 atoms, 2 residues, 2 models selected
> color (#!51 & sel) byhetero
> select #51/A:466@NE
1 atom, 1 residue, 1 model selected
> color (#!51 & sel) byhetero
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_IF_residue.png supersample 3
> transparentBackground true
> close #50
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
——— End of log from Sat Apr 12 21:31:41 2025 ———
opened ChimeraX session
> hide #!51 models
> show #!2 models
> show #1 models
> view
> lighting simple
> lighting soft
> lighting simple
> hide #!2 models
> select #1: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> view sel
> cofr sel
> select clear
> show #!2 models
> color #2 #ffffb2ff models
> color #2 #ffffb24f models
> color #2 #ffffb24e models
> color #2 #ffffb24d models
> select clear
> color #2 #a5ffb24d models
> color #2 #9effb24d models
> color #2 #9e43b24d models
> color #2 #9effb24d models
> color #2 #9effff4d models
> select clear
> size stickRadius 0.2
Changed 77114 bond radii
> select clear
> color #2 #942192ff models
> color #2 #9421924d models
> select clear
> color #2 #aa7942ff models
> color #2 #00fdffff models
> color #2 #00fdff4e models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> view sel
> ui tool show "Side View"
> volume #2 level 0.01002
> select clear
> select #1/A:223
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:207
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!2 models
> select #1/A:36
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!2 models
> select clear
> select #1/A:601@C4'
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
3891 atoms, 3986 bonds, 501 residues, 1 model selected
> select down
19 atoms, 20 bonds, 1 residue, 1 model selected
> cofr sel
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie1.mp4
Movie saved to /Users/dout2/Desktop/movie1.mp4
> hide #!2 models
> hide #1 models
> select add #1
3905 atoms, 3986 bonds, 515 residues, 1 model selected
> select subtract #1
Nothing selected
> show #1 models
> hide #1 models
> show #!5 models
> show #!4 models
> select clear
> volume #4 level 0.01053
> color #4 #fffb00ff models
> color #4 #ffffb2ff models
> color #4 #ffffb24d models
> select #4
4 models selected
> select clear
> select #1: 382, 353,438,230,442,466,207
74 atoms, 71 bonds, 7 residues, 1 model selected
> show #!5 atoms
> select add #5
3848 atoms, 3935 bonds, 5 pseudobonds, 493 residues, 3 models selected
> hide sel & #!5 atoms
> select #5: 382, 353,438,230,442,466,207,601
93 atoms, 91 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> select add #5
3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected
> show sel atoms
> select clear
> select #5/A:601@O4
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> cofr sel
> select #4
4 models selected
> volume #4 level 0.01089
> volume #4 level 0.01182
> volume #4 level 0.01292
> select clear
> volume #4 level 0.01311
> volume #4 level 0.01274
> volume #4 level 0.01126
> volume #4 level 0.01274
> volume #4 level 0.012
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie2.mp4
Movie saved to /Users/dout2/Desktop/movie2.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie3.mp4
Movie saved to /Users/dout2/Desktop/movie3.mp4
> view
> hide #!4 models
> select add #5
3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected
> hide sel atoms
> select #5: 382, 353,438,230,442,466,207,601
93 atoms, 91 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #8 models
> show #!7 models
> hide #8 models
> hide #!7 models
> show #!10 models
> show #!12 models
> color #10 darkgrey models
> color #10 silver models
> color #10 #c0c0c04d models
> select clear
> hide #!12 models
> show #!12 models
> hide #!10 models
> show #!10 models
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> volume #10 level 0.0124
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
37 atoms, 37 bonds, 1 residue, 1 model selected
> select #12: 382, 353,438,230,442,466,207,601
111 atoms, 108 bonds, 8 residues, 1 model selected
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select H
117 atoms, 10 residues, 9 models selected
> hide sel & #!12 atoms
> select clear
> select #12: 382, 353,438,230,442,466,207,601
111 atoms, 108 bonds, 8 residues, 1 model selected
> view sel
> cofr sel
> volume #10 level 0.009894
> volume #10 level 0.01073
> select clear
> select #12/B:601@C16
1 atom, 1 residue, 1 model selected
> select up
37 atoms, 37 bonds, 1 residue, 1 model selected
> view sel
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie4.mp4
Movie saved to /Users/dout2/Desktop/movie4.mp4
> select #10
4 models selected
> select clear
> hide #!12 models
> hide #!10 models
> show #8 models
> show #!7 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> color #7 #ff2f92ff models
> color #7 #ff2f924d models
> select #7
4 models selected
> select clear
> select #8: 382, 353,438,230,442,466,207,601
93 atoms, 90 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> open
> /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-PBD_20230217/cryosparc_P4_J55__localfilter_160.mrc
Opened cryosparc_P4_J55__localfilter_160.mrc as #50, grid size 160,160,160,
pixel 0.83, shown at level 0.131, step 1, values float32
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie1.mp4
Movie saved to /Users/dout2/Desktop/movie1.mp4
> hide #!7 models
> view
> show #!7 models
> rename #50 rOAT1-PBD_IF.mrc
> select add #50
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #50,1,0,0,82.163,0,1,0,34.821,0,0,1,72.008
> view matrix models #50,1,0,0,78.322,0,1,0,71.965,0,0,1,68.805
> view matrix models #50,1,0,0,68.336,0,1,0,66.309,0,0,1,66.361
> ui tool show "Fit in Map"
> fitmap #50 inMap #7
Fit map rOAT1-PBD_IF.mrc in map rOAT1-PBD_IF.mrc using 40907 points
correlation = 0.9052, correlation about mean = 0.7104, overlap = 318.4
steps = 88, shift = 2.7, angle = 7.48 degrees
Position of rOAT1-PBD_IF.mrc (#50) relative to rOAT1-PBD_IF.mrc (#7)
coordinates:
Matrix rotation and translation
0.99182552 0.09586728 -0.08421166 67.85108178
-0.09362983 0.99515083 0.03013765 73.24636935
0.08669251 -0.02200656 0.99599203 61.03836799
Axis -0.20020488 -0.65617735 -0.72756395
Axis point 63.93693297 -480.82614561 -0.00000000
Rotation angle (degrees) 7.48271681
Shift along axis -106.05604184
> hide #!7 models
> color #50 #b2b2b24d models
> select clear
> ui mousemode right translate
> select #8: 382, 353,438,230,442,466,207,601
93 atoms, 90 bonds, 8 residues, 1 model selected
> view sel
> cofr sel
> volume #50 level 0.2404
> select clear
> select #8: 382, 353,438,230,442,466,207,601
93 atoms, 90 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> volume #50 level 0.2822
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie2.mp4
Movie saved to /Users/dout2/Desktop/movie2.mp4
> hide #!50 models
> view
> hide #8 models
> show #!20 models
> show #21 models
> color #20 #ffffb2ff models
> color #20 #ffffb24d models
> select clear
> select #21: 382, 353,438,230,442,466,207,601
109 atoms, 109 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> select H
117 atoms, 10 residues, 9 models selected
> hide sel & #21 atoms
> select clear
> select #21: 382, 353,438,230,442,466,207,601
109 atoms, 109 bonds, 8 residues, 1 model selected
> view sel
> select clear
> color #20 #ffffb280 models
> select clear
> volume #20 level 0.01329
> select #21/A:602@O24
1 atom, 1 residue, 1 model selected
> select up
35 atoms, 38 bonds, 1 residue, 1 model selected
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie2.mp4
Movie saved to /Users/dout2/Desktop/movie2.mp4
> select #21: 382, 353,438,230,442,466,207,601,602
144 atoms, 147 bonds, 9 residues, 1 model selected
> select #20
4 models selected
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie3.mp4
Movie saved to /Users/dout2/Desktop/movie3.mp4
> hide #!20 models
> view
> hide #21 models
> show #!24 models
> show #!23 models
> color #23 #ffffb2ff models
> select clear
> hide #!23 models
> show #!23 models
> select #24: 382, 353,438,230,442,466,207,601,602
109 atoms, 109 bonds, 8 residues, 1 model selected
> view sel
> color #23 #ffffb280 models
> select clear
> select #24/A:601@O14
1 atom, 1 residue, 1 model selected
> select up
35 atoms, 38 bonds, 1 residue, 1 model selected
> cofr sel
> select #23
4 models selected
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie3.mp4
Movie saved to /Users/dout2/Desktop/movie3.mp4
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie4.mp4
Movie saved to /Users/dout2/Desktop/movie4.mp4
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> close session
> open /Users/dout2/Downloads/OAT1_ligand_Keyresidue.cxs
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.0151, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00516, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0108, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0128, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0683, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at level 0.0118, step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00686, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Opened rOAT1-AKG_OF.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
level 0.0122, step 1, values float32
Opened rOAT1-AKG_OOC.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
level 0.0102, step 1, values float32
Opened rOAT1-R466A.mrc as #46, grid size 480,480,480, pixel 0.553, shown at
level 0.0115, step 1, values float32
Opened rOAT1-Apo.mrc as #48, grid size 240,240,240, pixel 0.553, shown at step
1, values float32
opened ChimeraX session
> hide #15 models
> select subtract #15
Nothing selected
> show #!49 models
> hide #49.1 models
> select #49: 382, 353,438,230,442,466,207,601,602
74 atoms, 71 bonds, 7 residues, 1 model selected
> show sel atoms
> select add #49
3942 atoms, 3966 bonds, 570 residues, 2 models selected
> hide sel cartoons
> select clear
> size stickRadius 0.4
Changed 77114 bond radii
> select add #49
3942 atoms, 3966 bonds, 570 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel atoms
> hide sel atoms
> show sel cartoons
> select #49: 382, 353,438,230,442,466,207,601,602
74 atoms, 71 bonds, 7 residues, 1 model selected
> show sel atoms
> view
> hide sel cartoons
> select add #49
3942 atoms, 3966 bonds, 570 residues, 2 models selected
> hide sel cartoons
> color (#!49 & sel) purple
> select clear
> select add #49
3942 atoms, 3966 bonds, 570 residues, 1 model selected
> show sel cartoons
> select #49/A:223
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #49: 382, 353,438,230,442,466,207,601,602,203
79 atoms, 75 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select add #49
3942 atoms, 3966 bonds, 570 residues, 2 models selected
> hide sel cartoons
> select #49/A:223@CA
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 2 models selected
> hide sel atoms
> select add #49
3942 atoms, 3966 bonds, 570 residues, 2 models selected
> show sel cartoons
> select #49/A:223
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #49/A:224
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #49/A:223
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select add #49
3942 atoms, 3966 bonds, 570 residues, 2 models selected
> hide sel cartoons
> select #49/A:382@NZ
1 atom, 1 residue, 1 model selected
> select add #49/A:466@NH2
2 atoms, 2 residues, 2 models selected
> select add #49/A:466@NH1
3 atoms, 2 residues, 2 models selected
> select add #49/A:466@NE
4 atoms, 2 residues, 2 models selected
> color (#!49 & sel) byhetero
> select clear
> save /Users/dout2/Desktop/rOAT1-Apo_residues.png supersample 3
> transparentBackground true
> select clear
> save /Users/dout2/Desktop/rOAT1-Apo_residues.png supersample 3
> transparentBackground true
> hide #!49 models
> show #!51 models
> view
> show #!51 atoms
> select add #51
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> undo
> select add #51
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> show sel atoms
> select #51/A:207@CE
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> undo
> show sel cartoons
> select #51/A:223
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #51/A:208
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #51/A:211
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #51/A:207
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!51 & sel) purple
> select #51: 382, 353,438,230,442,466,207,601,602,203
79 atoms, 75 bonds, 8 residues, 1 model selected
> select add #51
4280 atoms, 4381 bonds, 552 residues, 2 models selected
> hide sel cartoons
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_IF_residues.png supersample 3
> transparentBackground true
> save /Users/dout2/Downloads/OAT1_ligand_Keyresidue.cxs includeMaps true
> hide #!51 models
> show #!43 models
> view
> select #43: 382, 353,438,230,442,466,207,601,602
84 atoms, 80 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> select #43/A:207@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> color (#!43 & sel) purple
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_OF_residues.png supersample 3
> transparentBackground true
> hide #!43 models
> show #!18 models
> select #18: 382, 353,438,230,442,466,207,601,602
105 atoms, 103 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> select #18/A:601@C05
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 32 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #18/A:207@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> color (#!18 & sel) purple
> select clear
> save /Users/dout2/Desktop/rOAT1-Apo_OF_residues.png supersample 3
> transparentBackground true
> select #18: 382, 353,438,230,442,466,207,601,602
105 atoms, 103 bonds, 8 residues, 1 model selected
> show sel atoms
> select #18/A:601@C05
1 atom, 1 residue, 1 model selected
> select #18/A:601@H051
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 32 bonds, 1 residue, 1 model selected
> select H
117 atoms, 10 residues, 9 models selected
> hide sel & #!18 atoms
> select clear
> save /Users/dout2/Desktop/rOAT1-TFV_OF_residues.png supersample 3
> transparentBackground true
> hide #!18 models
> show #15 models
> select #15: 382, 353,438,230,442,466,207,601,602
105 atoms, 103 bonds, 8 residues, 1 model selected
> show sel atoms
> select add #15
3917 atoms, 3998 bonds, 515 residues, 1 model selected
> hide sel cartoons
> select clear
> select add #15
3917 atoms, 3998 bonds, 515 residues, 1 model selected
> hide sel atoms
> select #15: 382, 353,438,230,442,466,207,601,602
105 atoms, 103 bonds, 8 residues, 1 model selected
> show sel atoms
> select #15/A:601@C07
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 32 bonds, 1 residue, 1 model selected
> select H
117 atoms, 10 residues, 9 models selected
> hide sel & #15 atoms
> select clear
> select #15/A:601@O19
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 32 bonds, 1 residue, 1 model selected
> select up
3903 atoms, 3998 bonds, 501 residues, 1 model selected
> select down
31 atoms, 32 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select clear
> select #15: 382, 353,438,230,442,466,207
74 atoms, 71 bonds, 7 residues, 1 model selected
> color sel purple
> select clear
> select #15/A:382@NZ
1 atom, 1 residue, 1 model selected
> select add #15/A:466@NH2
2 atoms, 2 residues, 1 model selected
> select add #15/A:466@NH1
3 atoms, 2 residues, 1 model selected
> select add #15/A:466@NE
4 atoms, 2 residues, 1 model selected
> color sel byhetero
> select clear
> select #15/A:601@N13
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 32 bonds, 1 residue, 1 model selected
> color sel cyan
> color sel byhetero
> select clear
> save /Users/dout2/Desktop/rOAT1-TFV_IF_residues.png supersample 3
> transparentBackground true
> save /Users/dout2/Downloads/OAT1_ligand_Keyresidue.cxs includeMaps true
> select add #15
3917 atoms, 3998 bonds, 515 residues, 1 model selected
> show sel cartoons
> select #15/A:227
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #15/A:223
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> select add #15
3917 atoms, 3998 bonds, 515 residues, 1 model selected
> hide sel cartoons
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> undo
> select add #15
3917 atoms, 3998 bonds, 515 residues, 1 model selected
> show sel cartoons
> select #15/A:223
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #15
3917 atoms, 3998 bonds, 515 residues, 1 model selected
> select clear
> select add #15
3917 atoms, 3998 bonds, 515 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select #15/A:203
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #15/A:223
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #15
3917 atoms, 3998 bonds, 515 residues, 1 model selected
> hide sel cartoons
> select clear
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/dout2/Downloads/OAT1_ligand_density.cxs
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.01, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.012, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00516, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.0107, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0108, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0133, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0128, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0683, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at level 0.0118, step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00686, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Opened rOAT1-AKG_OF.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
level 0.0122, step 1, values float32
Opened rOAT1-AKG_OOC.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
level 0.0102, step 1, values float32
Opened rOAT1-R466A.mrc as #46, grid size 480,480,480, pixel 0.553, shown at
level 0.0115, step 1, values float32
Opened rOAT1-Apo.mrc as #48, grid size 240,240,240, pixel 0.553, shown at step
1, values float32
Opened rOAT1-PBD_IF.mrc as #50, grid size 160,160,160, pixel 0.83, shown at
level 0.282, step 1, values float32
Log from Tue Apr 15 12:09:47 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/dout2/Downloads/OAT1_ligand_density.cxs
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.0151, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00516, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0108, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0128, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0683, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at level 0.0118, step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00686, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Opened rOAT1-AKG_OF.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
level 0.0122, step 1, values float32
Opened rOAT1-AKG_OOC.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
level 0.0102, step 1, values float32
Opened rOAT1-R466A.mrc as #46, grid size 480,480,480, pixel 0.553, shown at
level 0.0115, step 1, values float32
Opened rOAT1-Apo.mrc as #48, grid size 240,240,240, pixel 0.553, shown at step
1, values float32
Log from Sat Apr 12 21:31:41 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/dout2/Downloads/OAT1_ligand_density.cxs
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.0151, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00516, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0108, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0128, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0683, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at level 0.0118, step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00686, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Opened rOAT1-AKG_OF.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
level 0.0122, step 1, values float32
Opened rOAT1-AKG_OOC.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
level 0.0102, step 1, values float32
Opened postprocess_rescaled.mrc as #46, grid size 480,480,480, pixel 0.553,
shown at level 0.0115, step 1, values float32
Log from Thu Apr 10 15:43:35 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/dout2/Downloads/OAT1_ligand_density.cxs format session
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.0151, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0116, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00383, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0141, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0546, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at level 0.0118, step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Log from Thu Apr 10 14:06:06 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/dout2/Downloads/OAT1_ligand_density.cxs
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.0151, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0116, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00383, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0141, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0546, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at level 0.0118, step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Log from Tue Mar 11 12:00:09 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/dout2/Downloads/OAT1_ligand_density.cxs
Opened rOAT1-AZT_IF.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.0151, step 1, values float32
Opened rOAT1-AZT_IF.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT_OF.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0116, step 1, values float32
Opened rOAT1-PBD_IF.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00383, step 1, values float32
Opened rOAT1-PBD_OF.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-TFV_IF.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00563, step 2, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TVF_OF.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-AAI_IF.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0141, step 1, values float32
Opened rOAT1-AAI_OF.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-PAH.mrc as #27, grid size 160,160,160, pixel 0.83, shown at level
0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.0546, step 1, values float32
Opened rOAT1-FBP.mrc as #29, grid size 320,320,320, pixel 0.83, shown at level
0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0038, step 1, values float32
Opened rOAT1-CFM.mrc as #32, grid size 320,320,320, pixel 0.83, shown at level
0.0119, step 1, values float32
Opened rOAT1-TVF-Cl_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83,
shown at step 1, values float32
Opened hOAT1-TFV_IF.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32
Opened hOAT1-TFV_OF.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00699, step 1, values float32
Log from Mon Feb 10 17:46:10 2025UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
Opened relion_locres_filtered.mrc as #3, grid size 320,320,320, pixel 0.83,
shown at level 0.00928, step 1, values float32
Log from Wed Dec 11 13:28:04 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> format session
Opened relion_locres_filtered.mrc as #3, grid size 320,320,320, pixel 0.83,
shown at level 0.00928, step 1, values float32
Log from Tue Dec 10 11:33:02 2024 Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
> hOCT1-VB1_3_real_space_refined_002.pdb"
Chain information for hOCT1-VB1_3_real_space_refined_002.pdb #1
---
Chain | Description
A | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 1650, resource id:
35652789, major code: 40 (TranslateCoords), minor code: 0
> select ::name="VIB"
18 atoms, 19 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> save
> "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
> hOCT1-noVB1.pdb" relModel #1
QXcbConnection: XCB error: 3 (BadWindow), sequence: 7992, resource id:
35652794, major code: 40 (TranslateCoords), minor code: 0
> close session
> open
> "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
> hOCT1-noVB1.pdb"
Chain information for hOCT1-noVB1.pdb #1
---
Chain | Description
A | No description available
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt
Summary of feedback from opening
/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1
Ignored bad PDB record found on line 2
REMARK SMILES IDX 15 1 14 2 10 3 9 4 8 5 7 6 11 7 12 8 13 9 6 11 5 12 4 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 16 14 3 15 18 16 2 17 1 18 17 19
Ignored bad PDB record found on line 4
REMARK H PARENT 13 10 17 20 17 21
Ignored bad PDB record found on line 5
REMARK Flexibility Score: inf
15 messages similar to the above omitted
Opened ligand.pdbqt containing 1 structures (21 atoms, 22 bonds)
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt
Summary of feedback from opening
/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/ligand.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1
Ignored bad PDB record found on line 2
REMARK SMILES IDX 15 1 14 2 10 3 9 4 8 5 7 6 11 7 12 8 13 9 6 11 5 12 4 13
Ignored bad PDB record found on line 3
REMARK SMILES IDX 16 14 3 15 18 16 2 17 1 18 17 19
Ignored bad PDB record found on line 4
REMARK H PARENT 13 10 17 20 17 21
Ignored bad PDB record found on line 5
REMARK Flexibility Score: inf
15 messages similar to the above omitted
Opened ligand.pdbqt containing 1 structures (21 atoms, 22 bonds)
QXcbConnection: XCB error: 3 (BadWindow), sequence: 6676, resource id:
35652851, major code: 40 (TranslateCoords), minor code: 0
> hide #3 models
> show #3 models
> hide #3 models
> close #2-3
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/vina_dock.pdbqt
Summary of feedback from opening
/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/vina_dock.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.139 0.000 0.000
Ignored bad PDB record found on line 3
REMARK INTER + INTRA: -8.396
Ignored bad PDB record found on line 4
REMARK INTER: -7.934
Ignored bad PDB record found on line 5
REMARK INTRA: -0.463
Ignored bad PDB record found on line 6
REMARK UNBOUND: -0.463
495 messages similar to the above omitted
Opened vina_dock.pdbqt containing 20 structures (420 atoms, 440 bonds)
> viewdockx #2.1-20
> set bgColor white
> select #2.9/?:1@@serial_number=16
1 atom, 1 residue, 1 model selected
> select up
21 atoms, 22 bonds, 1 residue, 1 model selected
> view sel
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job320/note.txt
Unrecognized file suffix '.txt'
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job320/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #3, grid size 320,320,320, pixel 0.83,
shown at level 0.00146, step 2, values float32
> color #3 #b2b2b296 models
> volume #3 step 1
> ui tool show "Side View"
> volume #3 level 0.01472
> select add #1
3482 atoms, 3578 bonds, 1 pseudobond, 448 residues, 3 models selected
> show sel atoms
JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
properties of undefined (reading 'id')
> hide #2.1-20 models
> show #2.1 models
> select clear
> volume #3 level 0.01037
> show #2.2 models
> show #2.3 models
> hide #2.2 models
> hide #2.1 models
> volume #3 level 0.009064
> volume #3 level 0.009281
> hide #2.3 models
> show #2.4 models
> hide #2.4 models
> show #2.5 models
> close #1
> open
> "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_2/
> hOCT1-noVB1.pdb"
Chain information for hOCT1-noVB1.pdb #1
---
Chain | Description
A | No description available
> select add #1
3461 atoms, 3556 bonds, 1 pseudobond, 447 residues, 2 models selected
> show sel atoms
> select clear
> hide #2.5 models
> show #2.6 models
> hide #2.6 models
> show #2.7 models
> hide #2.7 models
> show #2.8 models
> hide #2.8 models
> show #2.9 models
> hide #2.9 models
> show #2.10 models
> hide #2.10 models
> show #2.10 models
> hide #2.10 models
> show #2.11 models
> hide #2.11 models
> show #2.12 models
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> includeMaps true
> lighting soft
> lighting simple
> color #3 #b2b2b264 models
> hide #2.12 models
> show #2.13 models
> hide #2.13 models
> show #2.14 models
> hide #2.14 models
> show #2.15 models
> hide #2.15 models
> show #2.15 models
> hide #2.15 models
> show #2.16 models
> hide #2.16 models
> show #2.17 models
> hide #2.17 models
> show #2.18 models
> hide #2.18 models
> show #2.19 models
> hide #2.19 models
> show #2.20 models
> hide #2.20 models
> show #2.19 models
> hide #2.19 models
> show #2.20 models
> hide #2.20 models
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.3 models
> hide #2.3 models
> show #2.3 models
> hide #2.3 models
> show #2.4 models
> hide #2.4 models
> show #2.5 models
> hide #2.5 models
> show #2.6 models
> hide #2.6 models
> show #2.7 models
> hide #2.7 models
> show #2.7 models
> hide #2.7 models
> show #2.8 models
> hide #2.8 models
> show #2.9 models
> hide #2.9 models
> show #2.10 models
> select down
Nothing selected
> hide #2.10 models
> show #2.10 models
> hide #2.10 models
> show #2.11 models
> hide #2.11 models
> show #2.12 models
> hide #2.12 models
> show #2.13 models
> hide #2.13 models
> show #2.14 models
> hide #2.14 models
> show #2.15 models
> hide #2.15 models
> show #2.15 models
> hide #2.15 models
> show #2.15 models
> hide #2.15 models
> show #2.16 models
> hide #2.16 models
> show #2.16 models
> hide #2.16 models
> show #2.17 models
> hide #2.17 models
> show #2.17 models
> hide #2.17 models
> show #2.18 models
> hide #2.18 models
> show #2.19 models
> hide #2.19 models
> show #2.20 models
> volume #3 level 0.01124
> hide #2.20 models
> show #2.20 models
> hide #2.20 models
> show #2.20 models
> hide #2.20 models
> show #2.19 models
> hide #2.19 models
> show #2.18 models
> hide #2.18 models
> show #2.19 models
> hide #2.19 models
> show #2.18 models
> volume #3 level 0.008629
> hide #2.18 models
> show #2.18 models
> hide #2.18 models
> show #2.17 models
> hide #2.17 models
> show #2.16 models
> hide #2.16 models
> show #2.15 models
> hide #2.15 models
> show #2.14 models
> hide #2.14 models
> show #2.13 models
> hide #2.13 models
> show #2.12 models
> hide #2.12 models
> show #2.11 models
> hide #2.11 models
> show #2.10 models
> hide #2.10 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.3 models
> hide #2.3 models
> show #2.4 models
> hide #2.4 models
> show #2.5 models
> hide #2.5 models
> show #2.6 models
> hide #2.6 models
> show #2.7 models
> hide #2.7 models
> show #2.8 models
> hide #2.8 models
> show #2.9 models
> hide #2.9 models
> show #2.9 models
> hide #2.9 models
> show #2.9 models
> hide #2.9 models
> show #2.10 models
> hide #2.10 models
> show #2.11 models
> hide #2.11 models
> show #2.12 models
> hide #2.12 models
> show #2.13 models
> hide #2.13 models
> show #2.12 models
> hide #2.12 models
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.3 models
> hide #2.3 models
> show #2.4 models
> hide #2.4 models
> show #2.5 models
> hide #2.5 models
> show #2.6 models
> hide #2.6 models
> show #2.7 models
> hide #2.7 models
> show #2.8 models
> hide #2.8 models
> show #2.8 models
> hide #2.8 models
> show #2.9 models
> hide #2.9 models
> show #2.10 models
> hide #2.10 models
> show #2.11 models
> hide #2.11 models
> show #2.12 models
> hide #2.12 models
> show #2.1 models
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 35492, resource id:
35652978, major code: 40 (TranslateCoords), minor code: 0
> volume #3 level 0.009281
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.3 models
> hide #2.3 models
> show #2.4 models
> show #2.5 models
> hide #2.4 models
> hide #2.5 models
> show #2.18 models
> hide #2.18 models
> show #2.18 models
> hide #2.18 models
> show #2.17 models
> hide #2.17 models
> show #2.16 models
> hide #2.16 models
> show #2.15 models
> hide #2.15 models
> show #2.14 models
> hide #2.14 models
> show #2.13 models
> hide #2.13 models
> show #2.12 models
> hide #2.12 models
> show #2.12 models
> hide #2.12 models
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 32670, resource id:
35652988, major code: 40 (TranslateCoords), minor code: 0
——— End of log from Tue Dec 10 11:33:02 2024 ———
opened ChimeraX session
JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined
JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 7404, resource id:
35653140, major code: 40 (TranslateCoords), minor code: 0
QXcbConnection: XCB error: 3 (BadWindow), sequence: 7416, resource id:
35653135, major code: 40 (TranslateCoords), minor code: 0
> show #2.11 models
> hide #2.11 models
> show #2.12 models
> hide #2.12 models
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/hOCT1-VB1/Analysis.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 60442, resource id:
35653379, major code: 40 (TranslateCoords), minor code: 0
——— End of log from Wed Dec 11 13:28:04 2024 ———
opened ChimeraX session
JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined
JS console(:1:error): Uncaught ReferenceError: vdxtable is not defined
> show #2.11 models
> show #2.12 models
> hide #2.11 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_7/hOCT1VB1007.pdb
Chain information for hOCT1VB1007.pdb #4
---
Chain | Description
A | No description available
> open
> "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_8/
> hOCT1-VB_Dock2_real_space_refined_008.pdb"
Chain information for hOCT1-VB_Dock2_real_space_refined_008.pdb #5
---
Chain | Description
A | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 17659, resource id:
35653657, major code: 40 (TranslateCoords), minor code: 0
> close session
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/P3_J149_fsc_iteration_010_after_fsc_mask_auto_tightening.pdf
QXcbConnection: XCB error: 3 (BadWindow), sequence: 50929, resource id:
35654568, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/cryosparc_P3_J154__localfilter_240.mrc
Opened cryosparc_P3_J154__localfilter_240.mrc as #1, grid size 240,240,240,
pixel 0.553, shown at level 0.207, step 1, values float32
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_20220303_cryoSPARC/J149_2.26A_clip-240/cryosparc_P3_J154__localfilter_240_VB1.mrc
Opened cryosparc_P3_J154__localfilter_240_VB1.mrc as #2, grid size
240,240,240, pixel 0.553, shown at level 0.000117, step 1, values float32
> volume #2 level 0.3318
Drag select of 2 cryosparc_P3_J154__localfilter_240_VB1.mrc
> view orient
> select clear
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_RSF_014_VB1.pdb
Summary of feedback from opening
/home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_RSF_014_VB1.pdb
---
warnings | Cannot find LINK/SSBOND residue CYS (50 )
Cannot find LINK/SSBOND residue CYS (62 )
Cannot find LINK/SSBOND residue CYS (89 )
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/RealSpaceRefine_6/mOCT1-VB1-coot-11_real_space_refined_006.pdb
Chain information for mOCT1-VB1-coot-11_real_space_refined_006.pdb #4
---
Chain | Description
A | No description available
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-VB1_Model/mOCT1-VB1_real_space_refined_014.pdb
Chain information for mOCT1-VB1_real_space_refined_014.pdb #5
---
Chain | Description
A | No description available
> close #3#4
> volume #2 color #ffffb296
> volume #2 color #ffffb2c8
> volume #2 level 0.4304
> volume #2 level 0.3677
> select /A:601@C15
1 atom, 1 residue, 1 model selected
> select up
18 atoms, 19 bonds, 1 residue, 1 model selected
> view sel
> select clear
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-ABC_Model/mOCT1-ABC_real_space_refined_009.pdb
Chain information for mOCT1-ABC_real_space_refined_009.pdb #3
---
Chain | Description
A | No description available
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-ABC_20220411_cryoSPARC/J142_2.25A_clip-240/cryosparc_P3_J150__localfilter_240.mrc
Opened cryosparc_P3_J150__localfilter_240.mrc as #4, grid size 240,240,240,
pixel 0.553, shown at level 0.229, step 1, values float32
> volume #4 level 0.7041
> hide #!2 models
> hide #!3 models
> hide #!5 models
> show #!3 models
> select ::name="ABC"
42 atoms, 48 bonds, 2 residues, 1 model selected
> view sel
> volume #4 level 0.5273
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!3 models
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 57982, resource id:
35654641, major code: 40 (TranslateCoords), minor code: 0
> hide #!1 models
> rename #1 mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
> rename #2 mOCT1-VB1_cryosparc_P3_J154__localfilter_240_VB1.mrc
> rename #4 mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc
> show #!3 models
> select clear
> hide #!4 models
> select ::name="ABC"
42 atoms, 48 bonds, 2 residues, 1 model selected
> select add #3
3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected
> color (#!3 & sel) white
> select clear
> select ::name="ABC"
42 atoms, 48 bonds, 2 residues, 1 model selected
> color sel red
> show #!4 models
> ui tool show "Color Zone"
> color zone #4 near #3 distance 3.32
> volume splitbyzone #4
Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 0 as #6.1, grid size
240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32
Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 1 as #6.2, grid size
240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32
Opened mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 2 as #6.3, grid size
240,240,240, pixel 0.553, shown at level 0.527, step 1, values float32
> hide #!3 models
> select add #3
3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected
> select subtract #3
Nothing selected
> hide #!6.1 models
> hide #!6.3 models
> show #!6.3 models
> hide #!6.2 models
> close #6.1-2
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 18121, resource id:
35654647, major code: 40 (TranslateCoords), minor code: 0
> show #!3 models
> color #3 #fffffbff
> color #3 #ddddaaff
> color #3 #dda0deff
> color #3 plum
> select add #3
3550 atoms, 3613 bonds, 1 pseudobond, 490 residues, 2 models selected
> color (#!3 & sel) byhetero
> color #6.3 #ddddaaff models
> color #6.3 plum models
> color #6.3 #ffffb2ff models
Drag select of 6.3 mOCT1-ABC_cryosparc_P3_J150__localfilter_240.mrc 2 , 5
atoms, 5 residues, 5 bonds
> select clear
> color #6.3 #ffffb2c8 models
> select ::name="ABC"
42 atoms, 48 bonds, 2 residues, 1 model selected
> view sel
> select #3/A:234
11 atoms, 10 bonds, 1 residue, 1 model selected
> color #6.3 #ffffb296 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!6 models
> hide #!6.3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!3 models
> hide #!3 models
> select #5/A:36
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!5 models
> hide #!2 models
> show #!1 models
> view
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 5156, resource id:
35654673, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-3TC_20240411/job207/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #7, grid size 320,320,320, pixel 0.83,
shown at level 0.00144, step 2, values float32
> volume #7 level 0.01204
> select add #7
12 atoms, 12 bonds, 1 residue, 3 models selected
> select add #5
3526 atoms, 3584 bonds, 1 pseudobond, 489 residues, 4 models selected
> select subtract #5
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,-67.025,0,1,0,-62.171,0,0,1,-62.016
> view matrix models #7,1,0,0,-65.422,0,1,0,-60.829,0,0,1,-69.057
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.44906,0.62428,0.63923,-47.882,-0.83076,-0.55508,-0.041522,263.31,0.32891,-0.5497,0.76789,-6.0495
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.44906,0.62428,0.63923,-43.112,-0.83076,-0.55508,-0.041522,259.52,0.32891,-0.5497,0.76789,-3.3226
> view matrix models
> #7,-0.44906,0.62428,0.63923,-46.691,-0.83076,-0.55508,-0.041522,257.64,0.32891,-0.5497,0.76789,-5.4256
> view matrix models
> #7,-0.44906,0.62428,0.63923,-43.086,-0.83076,-0.55508,-0.041522,254.57,0.32891,-0.5497,0.76789,-5.2175
> ui tool show "Fit in Map"
> fitmap #7 inMap #1
Fit map relion_locres_filtered.mrc in map
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc using 3812 points
correlation = 0.2373, correlation about mean = 0.07089, overlap = 11.07
steps = 116, shift = 1.21, angle = 8.84 degrees
Position of relion_locres_filtered.mrc (#7) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
-0.36461695 0.73265397 0.57469351 -59.14787422
-0.87490183 -0.48082660 0.05790126 236.29988230
0.31874951 -0.48168862 0.81631784 -18.80617873
Axis -0.31464704 0.14924672 -0.93740208
Axis point 41.71559551 127.71968026 0.00000000
Rotation angle (degrees) 120.96824033
Shift along axis 71.50663710
> rename #7 mOCT1-3TC
> select clear
[Repeated 1 time(s)]
> rename #7 mOCT1-3TC.mrc
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-3TC_Model/RealSpaceRefine_6/mOCT1-3TC-
> coot-14_real_space_refined_006.pdb
Chain information for mOCT1-3TC-coot-14_real_space_refined_006.pdb #8
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #!8 to #5
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 mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1-3TC-
coot-14_real_space_refined_006.pdb, chain A (#8), sequence alignment score =
2352.2
RMSD between 450 pruned atom pairs is 0.409 angstroms; (across all 450 pairs:
0.409)
> hide #!1 models
> hide #!7 models
> show #!1 models
> hide #!8 models
> show #!7 models
> select add #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.49719,-0.57211,-0.6523,173.98,0.80196,0.58997,0.093813,-133.23,0.33116,-0.56976,0.75214,0.34956
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.49719,-0.57211,-0.6523,164.87,0.80196,0.58997,0.093813,-137.47,0.33116,-0.56976,0.75214,-2.3096
> fitmap #7 inMap #1
Fit map mOCT1-3TC.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 3812 points
correlation = 0.9181, correlation about mean = 0.7496, overlap = 65.08
steps = 160, shift = 6.4, angle = 20.1 degrees
Position of mOCT1-3TC.mrc (#7) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
0.27009123 -0.75134279 -0.60210857 210.67160095
0.83888334 0.49056205 -0.23584655 -78.20606144
0.47257322 -0.44139877 0.76278546 -39.17036140
Axis -0.10648785 -0.55674686 0.82382842
Axis point 169.78551241 113.86943556 0.00000000
Rotation angle (degrees) 74.82789173
Shift along axis -11.16264322
> fitmap #8 inMap #7
Fit molecule mOCT1-3TC-coot-14_real_space_refined_006.pdb (#8) to map
mOCT1-3TC.mrc (#7) using 7048 atoms
average map value = 0.01706, steps = 60
shifted from previous position = 0.0823
rotated from previous position = 0.357 degrees
atoms outside contour = 4146, contour level = 0.012041
Position of mOCT1-3TC-coot-14_real_space_refined_006.pdb (#8) relative to
mOCT1-3TC.mrc (#7) coordinates:
Matrix rotation and translation
0.99999991 -0.00005602 -0.00043067 0.07339565
0.00005621 0.99999991 0.00043709 -0.06044298
0.00043064 -0.00043712 0.99999982 0.02180230
Axis -0.70938425 -0.69891365 0.09106970
Axis point 0.00000000 51.44490735 150.82453668
Rotation angle (degrees) 0.03530433
Shift along axis -0.00783577
> show #!8 models
> hide #!8 models
> select subtract #7
Nothing selected
> hide #!1 models
> show #!8 models
> select ::name="3TC"
26 atoms, 27 bonds, 1 residue, 1 model selected
> select add #8
7048 atoms, 7109 bonds, 1 pseudobond, 486 residues, 2 models selected
> color (#!8 & sel) white
> select ::name="3TC"
26 atoms, 27 bonds, 1 residue, 1 model selected
> color sel red
> view sel
> volume #7 step 1
> color zone #7 near #8 distance 4.98
> volume splitbyzone #7
Opened mOCT1-3TC.mrc 0 as #9.1, grid size 320,320,320, pixel 0.83, shown at
level 0.012, step 1, values float32
Opened mOCT1-3TC.mrc 1 as #9.2, grid size 320,320,320, pixel 0.83, shown at
level 0.012, step 1, values float32
Opened mOCT1-3TC.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.012, step 1, values float32
> close #9.2
> close #9.1
> color #9.3 white models
> color #9.3 #ffffb2ff models
> color #9.3 #ffffb296 models
> select #8/A:447
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #8
7048 atoms, 7109 bonds, 1 pseudobond, 486 residues, 2 models selected
> color #8 #bb22ffff
> color #8 #b2fffbff
> color #8 #b2ffb2ff
> color (#!8 & sel) byhetero
> select clear
[Repeated 1 time(s)]
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
> hide #!9.3 models
> hide #!9 models
> hide #!8 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-AZT_20240413/job307/relion_locres_filtered_flipz.mrc
Opened relion_locres_filtered_flipz.mrc as #10, grid size 320,320,320, pixel
0.83, shown at level 0.00125, step 2, values float32
> show #!1 models
> view
> volume #1 level 0.3063
> volume #10 step 1
> volume #10 level 0.01019
> rename #10 mOCT1-AZT.mrc
> select add #10
2 models selected
> view matrix models #10,1,0,0,-48.383,0,1,0,-77.671,0,0,1,-67.093
> view matrix models #10,1,0,0,-54.836,0,1,0,-59.483,0,0,1,-63.826
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.55307,0.83192,0.044939,-108.96,-0.78881,0.54024,-0.29312,148.24,-0.26813,0.12666,0.95502,-37.718
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.55307,0.83192,0.044939,-120.39,-0.78881,0.54024,-0.29312,136.85,-0.26813,0.12666,0.95502,-39.969
> view matrix models
> #10,0.55307,0.83192,0.044939,-121.53,-0.78881,0.54024,-0.29312,137.41,-0.26813,0.12666,0.95502,-39.609
> fitmap #10 inMap #1
Fit map mOCT1-AZT.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 33175 points
correlation = 0.9169, correlation about mean = 0.7611, overlap = 495.2
steps = 172, shift = 3.01, angle = 24.4 degrees
Position of mOCT1-AZT.mrc (#10) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
0.17958596 0.98366820 0.01207312 -89.49221412
-0.89232990 0.16805236 -0.41893408 218.60375344
-0.41412105 0.06446147 0.90793639 -7.62218964
Axis 0.24369569 0.21485858 -0.94575272
Axis point 81.50821029 166.97786454 0.00000000
Rotation angle (degrees) 82.65824965
Shift along axis 32.36873253
> view
> view orient
> ui tool show "Side View"
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-AZT_Model/RealSpaceRefine_4/mOCT1-AZT_14_real_space_refined_004.pdb
Chain information for mOCT1-AZT_14_real_space_refined_004.pdb #11
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #!11 to #5
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 mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with
mOCT1-AZT_14_real_space_refined_004.pdb, chain A (#11), sequence alignment
score = 2367.3
RMSD between 449 pruned atom pairs is 0.415 angstroms; (across all 449 pairs:
0.415)
> fitmap #11 inMap #10
Fit molecule mOCT1-AZT_14_real_space_refined_004.pdb (#11) to map
mOCT1-AZT.mrc (#10) using 7017 atoms
average map value = 0.01592, steps = 48
shifted from previous position = 0.0651
rotated from previous position = 0.278 degrees
atoms outside contour = 3029, contour level = 0.010186
Position of mOCT1-AZT_14_real_space_refined_004.pdb (#11) relative to
mOCT1-AZT.mrc (#10) coordinates:
Matrix rotation and translation
-0.89530533 -0.39092164 -0.21356179 331.89133766
0.43778783 -0.68362766 -0.58394781 243.21431714
0.08228108 -0.61630634 0.78319622 99.39179726
Axis -0.03674901 -0.33598352 0.94115067
Axis point 137.92729950 180.24940846 0.00000000
Rotation angle (degrees) 153.87927506
Shift along axis -0.37002346
> hide #!1 models
> select ::name="AZZ"
19 atoms, 20 bonds, 1 residue, 1 model selected
> hide #!10 models
> select add #11
7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected
> select subtract #11
Nothing selected
> select add #11
7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected
> color (#!11 & sel) white
> color #11 #aaaaffff
> color (#!11 & sel) white
> select ::name="AZZ"
19 atoms, 20 bonds, 1 residue, 1 model selected
> color sel red
> color zone #10 near #11 distance 4.98
> show #!10 models
> volume splitbyzone #10
Opened mOCT1-AZT.mrc 0 as #12.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0102, step 1, values float32
Opened mOCT1-AZT.mrc 1 as #12.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0102, step 1, values float32
Opened mOCT1-AZT.mrc 2 as #12.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0102, step 1, values float32
> close #12.2
> close #12.1
> color #12.3 #ff0000fe models
> color #12.3 #ff000096 models
> color #12.3 #ffffff96 models
> color #12.3 #ffffb296 models
> color #11 #aaffffff
> color #11 #aaaaffff
> select add #11
7017 atoms, 7080 bonds, 1 pseudobond, 483 residues, 2 models selected
> color (#!11 & sel) byhetero
> select clear
> show #!3 models
> hide #!3 models
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
> hide #!12.3 models
> hide #!12 models
> hide #!11 models
> show #!1 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-MTF_20240702/job350/postprocess.mrc
Opened postprocess.mrc as #13, grid size 320,320,320, pixel 0.83, shown at
level 0.00595, step 2, values float32
> volume #13 step 1
> volume #13 level 0.02012
> select add #13
2 models selected
> view matrix models #13,1,0,0,-56.643,0,1,0,-72.238,0,0,1,-68.565
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.02465,-0.61986,0.78433,49.618,-0.43145,0.70114,0.56768,-50.105,-0.9018,-0.35239,-0.25015,252.26
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.02465,-0.61986,0.78433,42.91,-0.43145,0.70114,0.56768,-47.812,-0.9018,-0.35239,-0.25015,260.75
> view matrix models
> #13,0.02465,-0.61986,0.78433,45.137,-0.43145,0.70114,0.56768,-48.218,-0.9018,-0.35239,-0.25015,267.86
> rename #13 mOCT1-MTF.mrc
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/mOCT1-MTF_20240603/RealSpaceRefine_3/mOCT1_MTF-
> coot-9_real_space_refined_003.pdb
Chain information for mOCT1_MTF-coot-9_real_space_refined_003.pdb #14
---
Chain | Description
A | No description available
> fitmap #13 inMap #1
Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 17817 points
correlation = 0.2983, correlation about mean = 0.07385, overlap = 82.29
steps = 200, shift = 2.4, angle = 7.61 degrees
Position of mOCT1-MTF.mrc (#13) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
-0.05771312 -0.64461025 0.76232987 59.74942259
-0.34050237 0.73052504 0.59193860 -66.21901607
-0.93847075 -0.22541250 -0.26165220 256.68697920
Axis -0.42762978 0.88984156 0.15910615
Axis point 123.33045199 0.00000000 117.21732044
Rotation angle (degrees) 107.12276965
Shift along axis -43.63458901
> select subtract #13
Nothing selected
> select add #13
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.50114,0.40107,-0.76681,42.081,-0.045209,-0.87277,-0.48604,255.79,-0.86419,0.27824,-0.41924,198.29
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.50114,0.40107,-0.76681,41.903,-0.045209,-0.87277,-0.48604,247.49,-0.86419,0.27824,-0.41924,198.18
> view matrix models
> #13,0.50114,0.40107,-0.76681,53.046,-0.045209,-0.87277,-0.48604,251.12,-0.86419,0.27824,-0.41924,198.38
> fitmap #13 inMap #1
Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 17817 points
correlation = 0.2273, correlation about mean = 0.06656, overlap = 59.06
steps = 120, shift = 2.59, angle = 4.72 degrees
Position of mOCT1-MTF.mrc (#13) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
0.43566959 0.38627366 -0.81300964 69.55864121
-0.07375796 -0.88487887 -0.45994473 251.91510217
-0.89707959 0.26034986 -0.35702406 194.41028021
Axis 0.83873143 0.09789343 -0.53567385
Axis point 0.00000000 97.27212052 153.57991582
Rotation angle (degrees) 154.57081238
Shift along axis -21.13865268
> view matrix models
> #13,0.43567,0.38627,-0.81301,67.4,-0.073758,-0.88488,-0.45994,259.27,-0.89708,0.26035,-0.35702,197.15
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.3307,0.47313,-0.81657,68.962,0.20831,-0.88051,-0.42581,219.2,-0.92046,-0.029281,-0.38974,244.12
> view matrix models
> #13,0.3796,0.48184,-0.78977,58.246,0.18592,-0.87598,-0.44507,223.83,-0.90628,0.022112,-0.42211,239.42
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.3796,0.48184,-0.78977,53.846,0.18592,-0.87598,-0.44507,217.81,-0.90628,0.022112,-0.42211,235.11
> fitmap #13 inMap #1
Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 17817 points
correlation = 0.2652, correlation about mean = 0.06679, overlap = 73.72
steps = 92, shift = 1.81, angle = 5.01 degrees
Position of mOCT1-MTF.mrc (#13) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
0.31415893 0.53789144 -0.78228958 53.81386032
0.19698588 -0.84300825 -0.50053338 220.95415625
-0.92870918 0.00314703 -0.37079559 234.49017112
Axis 0.80514260 0.23405449 -0.54494394
Axis point 0.00000000 81.07236056 158.23174632
Rotation angle (degrees) 161.77257653
Shift along axis -32.74085292
> view matrix models
> #13,0.31416,0.53789,-0.78229,60.198,0.19699,-0.84301,-0.50053,217.39,-0.92871,0.003147,-0.3708,234.22
> fitmap #13 inMap #1
Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 17817 points
correlation = 0.2449, correlation about mean = 0.05515, overlap = 65.5
steps = 80, shift = 1.45, angle = 5.73 degrees
Position of mOCT1-MTF.mrc (#13) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
0.28419679 0.60053681 -0.74738728 50.81854511
0.27816291 -0.79764719 -0.53514891 205.19579930
-0.91752798 -0.05580782 -0.39373584 245.12613641
Axis 0.79598780 0.28253351 -0.53533003
Axis point 0.00000000 71.54715698 160.41463451
Rotation angle (degrees) 162.47642045
Shift along axis -32.79775064
> view matrix models
> #13,0.2842,0.60054,-0.74739,49.177,0.27816,-0.79765,-0.53515,206.5,-0.91753,-0.055808,-0.39374,243.99
> fitmap #13 inMap #1
Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 17817 points
correlation = 0.3559, correlation about mean = 0.151, overlap = 107.2
steps = 88, shift = 2.33, angle = 2.34 degrees
Position of mOCT1-MTF.mrc (#13) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
0.29378487 0.57675594 -0.76226180 52.65591556
0.29516509 -0.81321822 -0.50155130 203.18767751
-0.90915787 -0.07764488 -0.40914943 245.95334709
Axis 0.80029578 0.27732609 -0.53161726
Axis point 0.00000000 73.19686532 158.33534093
Rotation angle (degrees) 164.64234082
Shift along axis -32.26349399
> view matrix models
> #13,0.29378,0.57676,-0.76226,50.19,0.29517,-0.81322,-0.50155,203.5,-0.90916,-0.077645,-0.40915,251.78
> fitmap #13 inMap #1
Fit map mOCT1-MTF.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 17817 points
correlation = 0.9033, correlation about mean = 0.6277, overlap = 419.6
steps = 52, shift = 1.52, angle = 1.92 degrees
Position of mOCT1-MTF.mrc (#13) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
0.29574252 0.60146473 -0.74214321 45.38180479
0.29484975 -0.79643687 -0.52796964 204.44935424
-0.90862533 -0.06267767 -0.41288198 249.74597785
Axis 0.80005949 0.28626242 -0.52721784
Axis point 0.00000000 72.71544700 159.79227740
Rotation angle (degrees) 163.09499009
Shift along axis -36.83622428
> ui tool show Matchmaker
> matchmaker #!14 to #5
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 mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with mOCT1_MTF-
coot-9_real_space_refined_003.pdb, chain A (#14), sequence alignment score =
2355.8
RMSD between 450 pruned atom pairs is 0.377 angstroms; (across all 450 pairs:
0.377)
> select add #14
7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 4 models selected
> select subtract #13
7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected
> hide #!1 models
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 5891, resource id:
35654810, major code: 40 (TranslateCoords), minor code: 0
> color #14 #95cacdff
> select ::name="MF8"
22 atoms, 21 bonds, 1 residue, 1 model selected
> select add #14
7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected
> select subtract #14
Nothing selected
> select add #14
7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected
> color (#!14 & sel) white
> select ::name="MF8"
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel red
> color zone #10 near #11 distance 4.98
> color zone #13 near #14 distance 4.98
> hide #!14 models
> show #!14 models
> volume #13 level 0.0238
> volume #13 level 0.02122
> volume #13 level 0.01423
> volume splitbyzone #13
Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0142, step 1, values float32
Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0142, step 1, values float32
Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0142, step 1, values float32
> close #15.1
> close #15.2
> volume #15.3 level 0.009273
> volume #15.3 level 0.01703
> close #15#15.3
> select add #14
7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected
> show #!13 models
> color zone #13 near #14 distance 4.88
> color zone #13 near #14 distance 4.78
> color zone #13 near #14 distance 4.68
> color zone #13 near #14 distance 4.58
> color zone #13 near #14 distance 4.48
> color zone #13 near #14 distance 4.38
> color zone #13 near #14 distance 4.28
> color zone #13 near #14 distance 4.18
> color zone #13 near #14 distance 4.08
> color zone #13 near #14 distance 3.98
> color zone #13 near #14 distance 3.88
> color zone #13 near #14 distance 3.78
> color zone #13 near #14 distance 3.68
> color zone #13 near #14 distance 3.58
> color zone #13 near #14 distance 3.48
> color zone #13 near #14 distance 3.38
[Repeated 1 time(s)]
> volume splitbyzone #13
Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0142, step 1, values float32
Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0142, step 1, values float32
Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0142, step 1, values float32
> close #15.1-2
> volume #15.3 level 0.009634
> color zone #13 near #14 distance 3.28
> color zone #13 near #14 distance 3.18
> color zone #13 near #14 distance 3.08
> close #15#15.3
> show #!13 models
> select add #13
7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 4 models selected
> select subtract #13
7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected
> color zone #13 near #14 distance 2.98
> color zone #13 near #14 distance 2.88
> color zone #13 near #14 distance 2.78
> color zone #13 near #14 distance 2.68
> color zone #13 near #14 distance 2.58
> color zone #13 near #14 distance 2.48
> volume #13 level 0.01681
> fitmap #14 inMap #13
Fit molecule mOCT1_MTF-coot-9_real_space_refined_003.pdb (#14) to map
mOCT1-MTF.mrc (#13) using 7044 atoms
average map value = 0.01572, steps = 48
shifted from previous position = 0.0765
rotated from previous position = 0.266 degrees
atoms outside contour = 4386, contour level = 0.016807
Position of mOCT1_MTF-coot-9_real_space_refined_003.pdb (#14) relative to
mOCT1-MTF.mrc (#13) coordinates:
Matrix rotation and translation
0.99946408 0.01781074 -0.02746495 0.87693504
-0.01720783 0.99960910 0.02203450 -1.16466203
0.02784666 -0.02155008 0.99937988 -1.14535630
Axis -0.55418255 -0.70329295 -0.44526478
Axis point 28.72708736 -0.00000000 48.38067452
Rotation angle (degrees) 2.25364092
Shift along axis 0.84310332
> color zone #13 near #14 distance 2.48
[Repeated 1 time(s)]
> color single #13
> color zone #13 near #14 distance 2.48
> color zone #13 near #14 distance 2.38
> color zone #13 near #14 distance 2.28
> color zone #13 near #14 distance 2.18
> color zone #13 near #14 distance 2.08
> color zone #13 near #14 distance 1.98
> color zone #13 near #14 distance 1.88
> color zone #13 near #14 distance 1.78
> color zone #13 near #14 distance 1.68
> color zone #13 near #14 distance 1.58
> color zone #13 near #14 distance 1.48
> color zone #13 near #14 distance 1.38
> color zone #13 near #14 distance 1.48
> color zone #13 near #14 distance 1.58
> color zone #13 near #14 distance 1.68
> color zone #13 near #14 distance 1.78
> color zone #13 near #14 distance 1.88
> color zone #13 near #14 distance 1.98
> volume #13 level 0.01957
> color zone #13 near #14 distance 1.98
> volume splitbyzone #13
Opened mOCT1-MTF.mrc 0 as #15.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0196, step 1, values float32
Opened mOCT1-MTF.mrc 1 as #15.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0196, step 1, values float32
Opened mOCT1-MTF.mrc 2 as #15.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0196, step 1, values float32
> close #15.1-2
> color #15.3 yellow models
> color #15.3 white models
> color #15.3 #ffffb2ff models
> color #15.3 #ffffb296 models
> volume #15.3 level 0.01524
> volume #15.3 level 0.0119
> select subtract #14
Nothing selected
> select add #14
7044 atoms, 7103 bonds, 1 pseudobond, 486 residues, 2 models selected
> color #14 #55dd44ff
> color #14 #5d42cdff
> color #14 #5858cdff
> color #14 #7d76cdff
> color #14 #9d7bcdff
> color #14 #cd75baff
> color #14 #9381cdff
> color (#!14 & sel) byhetero
> select clear
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
> hide #!15.3 models
> hide #!15 models
> hide #!14 models
> show #!1 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/job321/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #16, grid size 320,320,320, pixel 0.83,
shown at level 0.00147, step 2, values float32
> volume #13 level 0.01846
> volume #16 step 1
> volume #16 level 0.01137
> select add #16
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.91726,-0.046522,0.39555,-35.801,-0.13266,0.90075,0.41357,-25.02,-0.37554,-0.43183,0.82006,127.4
> view matrix models
> #16,0.97308,0.0084656,-0.23031,32.94,-0.035652,0.99283,-0.11414,20.659,0.2277,0.11927,0.9664,-40.203
> view matrix models
> #16,0.95291,-0.013325,0.30296,-32.366,-0.094841,0.93583,0.33946,-24.554,-0.28805,-0.35221,0.89049,96.605
> view matrix models
> #16,0.68405,0.72927,0.015283,-53.826,0.65561,-0.6055,-0.45117,179.02,-0.31977,0.31864,-0.89231,251.74
> view matrix models
> #16,-0.14871,0.82898,-0.53915,114.85,0.43367,-0.43531,-0.78894,230.9,-0.88872,-0.35114,-0.29476,331.38
> view matrix models
> #16,-0.59154,0.6904,-0.41646,173.56,0.69281,0.17103,-0.70054,108.52,-0.41243,-0.70292,-0.57948,352.16
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.59154,0.6904,-0.41646,98.473,0.69281,0.17103,-0.70054,82.195,-0.41243,-0.70292,-0.57948,295.09
> view matrix models
> #16,-0.59154,0.6904,-0.41646,115.7,0.69281,0.17103,-0.70054,51.467,-0.41243,-0.70292,-0.57948,297.87
> view matrix models
> #16,-0.59154,0.6904,-0.41646,109.24,0.69281,0.17103,-0.70054,49.803,-0.41243,-0.70292,-0.57948,297.08
> view matrix models
> #16,-0.59154,0.6904,-0.41646,112.5,0.69281,0.17103,-0.70054,41.909,-0.41243,-0.70292,-0.57948,292.69
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.52634,0.62911,-0.57201,132.47,0.46428,-0.35094,-0.81319,152.81,-0.71233,-0.69359,-0.10737,267.76
> view matrix models
> #16,-0.56071,0.74447,-0.36245,94.475,0.40226,-0.13769,-0.90511,145.91,-0.72373,-0.6533,-0.22227,279.35
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.56071,0.74447,-0.36245,91.988,0.40226,-0.13769,-0.90511,152.84,-0.72373,-0.6533,-0.22227,276.37
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.69312,0.68147,-0.23491,100.24,0.41746,0.11382,-0.90154,118.42,-0.58764,-0.72294,-0.36338,286.3
> rename #16 hOCT1-VB1.mrc
> fitmap #16 inMap #1
Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 29501 points
correlation = 0.336, correlation about mean = 0.1558, overlap = 114.4
steps = 148, shift = 3.34, angle = 5.64 degrees
Position of hOCT1-VB1.mrc (#16) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
-0.66774800 0.66848229 -0.32748134 111.59775010
0.47076725 0.03845367 -0.88141903 115.78397104
-0.57662015 -0.74273329 -0.34037693 282.67572866
Axis 0.39969377 0.71802066 -0.56981683
Axis point 39.62225841 0.00000000 179.67701786
Rotation angle (degrees) 170.00920250
Shift along axis -33.33317846
> ui mousemode right "translate selected models"
> view matrix models
> #16,-0.66775,0.66848,-0.32748,111.72,0.47077,0.038454,-0.88142,115.95,-0.57662,-0.74273,-0.34038,288.9
> fitmap #16 inMap #1
Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 29501 points
correlation = 0.7772, correlation about mean = 0.5328, overlap = 352.7
steps = 60, shift = 1.34, angle = 1.92 degrees
Position of hOCT1-VB1.mrc (#16) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
-0.68896253 0.65809895 -0.30370448 111.90845021
0.45027206 0.06027049 -0.89085495 116.65862228
-0.56796628 -0.75051532 -0.33784768 287.44343290
Axis 0.38522072 0.72537689 -0.57046767
Axis point 41.86637964 0.00000000 181.62562393
Rotation angle (degrees) 169.50470225
Shift along axis -36.24626372
> view matrix models
> #16,-0.68896,0.6581,-0.3037,110.15,0.45027,0.06027,-0.89085,119.19,-0.56797,-0.75052,-0.33785,287.46
> fitmap #16 inMap #1
Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 29501 points
correlation = 0.7772, correlation about mean = 0.5327, overlap = 352.7
steps = 72, shift = 3.09, angle = 0.0182 degrees
Position of hOCT1-VB1.mrc (#16) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
-0.68902052 0.65795875 -0.30387662 111.96278841
0.45022908 0.06002731 -0.89089309 116.69902951
-0.56793001 -0.75065771 -0.33759222 287.41226501
Axis 0.38519550 0.72529614 -0.57058737
Axis point 41.87016659 0.00000000 181.64241189
Rotation angle (degrees) 169.51189271
Shift along axis -36.22489055
> fitmap #16 inMap #1
Fit map hOCT1-VB1.mrc in map mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc
using 29501 points
correlation = 0.7772, correlation about mean = 0.5328, overlap = 352.7
steps = 36, shift = 0.00448, angle = 0.00722 degrees
Position of hOCT1-VB1.mrc (#16) relative to
mOCT1-VB1_cryosparc_P3_J154__localfilter_240.mrc (#1) coordinates:
Matrix rotation and translation
-0.68898476 0.65802671 -0.30381055 111.93916561
0.45024501 0.06010903 -0.89087953 116.68451889
-0.56796077 -0.75059160 -0.33768744 287.42460080
Axis 0.38521270 0.72532270 -0.57054198
Axis point 41.86758112 0.00000000 181.63640339
Rotation angle (degrees) 169.50839167
Shift along axis -36.23348002
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241031Krios_hOCT1-VB1/RealSpaceRefine_10/hOCT1-VB_Dock2_real_space_refined_010.pdb
Chain information for hOCT1-VB_Dock2_real_space_refined_010.pdb #17
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #!17 to #5
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 mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with
hOCT1-VB_Dock2_real_space_refined_010.pdb, chain A (#17), sequence alignment
score = 1980
RMSD between 416 pruned atom pairs is 0.792 angstroms; (across all 446 pairs:
1.346)
> fitmap #17 inMap #16
Fit molecule hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) to map
hOCT1-VB1.mrc (#16) using 3479 atoms
average map value = 0.02025, steps = 64
shifted from previous position = 0.153
rotated from previous position = 0.521 degrees
atoms outside contour = 1063, contour level = 0.011373
Position of hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) relative to
hOCT1-VB1.mrc (#16) coordinates:
Matrix rotation and translation
0.99999651 0.00186028 0.00187897 -0.40239474
-0.00185675 0.99999652 -0.00187607 0.55801929
-0.00188246 0.00187257 0.99999648 0.09469763
Axis 0.57831092 0.58028383 -0.57343453
Axis point 61.09212114 0.00000000 225.59585813
Rotation angle (degrees) 0.18569746
Shift along axis 0.03679741
> fitmap #17 inMap #16
Fit molecule hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) to map
hOCT1-VB1.mrc (#16) using 3479 atoms
average map value = 0.02025, steps = 28
shifted from previous position = 0.0153
rotated from previous position = 0.0146 degrees
atoms outside contour = 1064, contour level = 0.011373
Position of hOCT1-VB_Dock2_real_space_refined_010.pdb (#17) relative to
hOCT1-VB1.mrc (#16) coordinates:
Matrix rotation and translation
0.99999599 0.00211002 0.00188874 -0.43726655
-0.00210638 0.99999592 -0.00192887 0.59237860
-0.00189280 0.00192488 0.99999636 0.07510223
Axis 0.56254941 0.55200867 -0.61548727
Axis point 271.69369003 217.02489508 0.00000000
Rotation angle (degrees) 0.19625280
Shift along axis 0.03478962
> hide #!1 models
> select add #17
3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected
> select subtract #16
3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected
> color (#!17 & sel) white
> select clear
> select ::name="VIB"
18 atoms, 19 bonds, 1 residue, 1 model selected
> color sel red
> color zone #16 near #17 distance 4.98
> color zone #16 near #17 distance 4.88
> color zone #16 near #17 distance 4.78
> color zone #16 near #17 distance 4.68
> color zone #16 near #17 distance 4.58
> color zone #16 near #17 distance 4.48
> color zone #16 near #17 distance 4.38
> color zone #16 near #17 distance 4.28
> color zone #16 near #17 distance 4.18
> color zone #16 near #17 distance 4.08
> color zone #16 near #17 distance 3.98
> color zone #16 near #17 distance 3.88
> color zone #16 near #17 distance 3.78
> color zone #16 near #17 distance 3.68
> color zone #16 near #17 distance 3.58
> color zone #16 near #17 distance 3.48
> color zone #16 near #17 distance 3.38
> color zone #16 near #17 distance 3.28
> color sel white
> select ::name="VIB"
18 atoms, 19 bonds, 1 residue, 1 model selected
> color sel red
> select add #16
18 atoms, 19 bonds, 1 residue, 3 models selected
> select add #17
3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected
> select subtract #17
2 models selected
> color #16.1 white
> color zone #16 near #17 distance 3.28
> color zone #16 near #17 distance 3.18
> color zone #16 near #17 distance 3.08
> color zone #16 near #17 distance 2.98
> color zone #16 near #17 distance 2.88
> color zone #16 near #17 distance 2.98
> color zone #16 near #17 distance 3.08
> color zone #16 near #17 distance 3.18
> color zone #16 near #17 distance 3.28
> color zone #16 near #17 distance 3.38
[Repeated 1 time(s)]
> volume splitbyzone #16
Opened hOCT1-VB1.mrc 0 as #18.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0114, step 1, values float32
Opened hOCT1-VB1.mrc 1 as #18.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0114, step 1, values float32
Opened hOCT1-VB1.mrc 2 as #18.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0114, step 1, values float32
> close #18.1-2
> color #18.3 yellow models
> color #18.3 white models
> color #18.3 #ffffb2ff models
> color #18.3 #ffffb296 models
> select add #17
3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 4 models selected
> select subtract #16
3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected
> color #17 #6622bbff
> color #17 #62be40ff
> color (#!17 & sel) byhetero
Drag select of 1 atoms, 1 bonds
> volume #18.3 level 0.006511
> volume #18.3 level 0.01112
> close #18#18.3
> select add #17
3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected
> color (#!17 & sel) white
> select ::name="VIB"
18 atoms, 19 bonds, 1 residue, 1 model selected
> color sel red
> show #!16 models
> color zone #16 near #17 distance 3.28
> color zone #16 near #17 distance 3.18
> color zone #16 near #17 distance 3.08
> color zone #16 near #17 distance 2.98
> color zone #16 near #17 distance 2.88
> color zone #16 near #17 distance 2.78
> color zone #16 near #17 distance 2.68
> color zone #16 near #17 distance 2.58
> color zone #16 near #17 distance 2.48
> color zone #16 near #17 distance 2.38
> color zone #16 near #17 distance 2.28
> color zone #16 near #17 distance 2.18
> color zone #16 near #17 distance 2.08
> color zone #16 near #17 distance 1.98
> color zone #16 near #17 distance 1.88
> color zone #16 near #17 distance 1.78
> color zone #16 near #17 distance 1.68
> color zone #16 near #17 distance 1.78
> color zone #16 near #17 distance 1.88
> color zone #16 near #17 distance 1.98
> color zone #16 near #17 distance 2.08
> volume splitbyzone #16
Opened hOCT1-VB1.mrc 0 as #18.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0114, step 1, values float32
Opened hOCT1-VB1.mrc 1 as #18.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0114, step 1, values float32
Opened hOCT1-VB1.mrc 2 as #18.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0114, step 1, values float32
> close #18.1-2
> color #18.3 white models
> color #18.3 #ffffb2ff models
> select add #18.3
18 atoms, 19 bonds, 1 residue, 3 models selected
> color #18.3 #ffffb296 models
> select subtract #18.3
18 atoms, 19 bonds, 1 residue, 1 model selected
> select add #17
3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected
> select subtract #17
Nothing selected
> select add #17
3479 atoms, 3575 bonds, 1 pseudobond, 448 residues, 2 models selected
> color #17 #6622bbff
> color #17 #62be40ff
> color (#!17 & sel) byhetero
> view
> hide #!18.3 models
> hide #!18 models
> hide #!17 models
> select subtract #17
Nothing selected
> show #!1 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241004Krios_hOCT1-AZT/job154/postprocess_masked.mrc
Opened postprocess_masked.mrc as #19, grid size 320,320,320, pixel 0.83, shown
at level 2.83e-06, step 2, values float32
> volume #19 step 1
> volume #19 level 0.0131
> select add #19
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #19,-0.93986,0.28611,-0.18654,253.04,-0.10485,-0.76147,-0.63967,340.05,-0.32506,-0.58164,0.74567,158.04
> ui mousemode right "translate selected models"
> view matrix models
> #19,-0.93986,0.28611,-0.18654,175.89,-0.10485,-0.76147,-0.63967,293,-0.32506,-0.58164,0.74567,91.801
> view matrix models
> #19,-0.93986,0.28611,-0.18654,185.27,-0.10485,-0.76147,-0.63967,269.77,-0.32506,-0.58164,0.74567,91.027
> view matrix models
> #19,-0.93986,0.28611,-0.18654,178.6,-0.10485,-0.76147,-0.63967,268.3,-0.32506,-0.58164,0.74567,89.593
> rename #19 hOCT1-AZT.mrc
> fitmap #19 inMap #16
Fit map hOCT1-AZT.mrc in map hOCT1-VB1.mrc using 23475 points
correlation = 0.9652, correlation about mean = 0.8232, overlap = 14.07
steps = 112, shift = 2.59, angle = 19.3 degrees
Position of hOCT1-AZT.mrc (#19) relative to hOCT1-VB1.mrc (#16) coordinates:
Matrix rotation and translation
0.86934918 -0.02079803 -0.49376051 87.20318527
-0.45396874 0.36123943 -0.81450504 253.58267245
0.19530587 0.93224113 0.30460154 -57.13169181
Axis 0.90642923 -0.35757337 -0.22478286
Axis point 0.00000000 185.25380563 166.58335969
Rotation angle (degrees) 74.47879004
Shift along axis 1.21133072
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/20241004Krios_hOCT1-AZT/RealSpaceRefine_6/hOCT1_AZT-
> coot-2_real_space_refined_006.pdb
Chain information for hOCT1_AZT-coot-2_real_space_refined_006.pdb #20
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #!20 to #5
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 mOCT1-VB1_real_space_refined_014.pdb, chain A (#5) with hOCT1_AZT-
coot-2_real_space_refined_006.pdb, chain A (#20), sequence alignment score =
1978
RMSD between 414 pruned atom pairs is 0.849 angstroms; (across all 446 pairs:
1.482)
> hide #!1 models
> color #19 white models
> select add #20
3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 4 models selected
> color #20 white
> hide #!19 models
> select subtract #19
3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> color sel red
> color zone #19 near #20 distance 4.98
> show #!19 models
> select add #19
19 atoms, 20 bonds, 1 residue, 3 models selected
> select subtract #19
19 atoms, 20 bonds, 1 residue, 1 model selected
> color zone #19 near #20 distance 4.88
> color zone #19 near #20 distance 4.78
> color zone #19 near #20 distance 4.68
> color zone #19 near #20 distance 4.58
> color zone #19 near #20 distance 4.48
> color zone #19 near #20 distance 4.38
> color zone #19 near #20 distance 4.28
> color zone #19 near #20 distance 4.18
> color zone #19 near #20 distance 4.08
> color zone #19 near #20 distance 3.98
> color zone #19 near #20 distance 3.88
> color zone #19 near #20 distance 3.78
> color zone #19 near #20 distance 3.68
> color zone #19 near #20 distance 3.58
> color zone #19 near #20 distance 3.48
> volume #19 level 0.01039
> color zone #19 near #20 distance 3.38
> color zone #19 near #20 distance 3.28
> color zone #19 near #20 distance 3.18
> color zone #19 near #20 distance 3.08
> color zone #19 near #20 distance 2.98
> color zone #19 near #20 distance 2.88
> color zone #19 near #20 distance 2.78
> color zone #19 near #20 distance 2.68
> color zone #19 near #20 distance 2.58
> color zone #19 near #20 distance 2.48
> color zone #19 near #20 distance 2.38
> color zone #19 near #20 distance 2.28
> color zone #19 near #20 distance 2.18
> color zone #19 near #20 distance 2.08
> color zone #19 near #20 distance 1.98
> color zone #19 near #20 distance 1.88
> color zone #19 near #20 distance 1.78
> color zone #19 near #20 distance 1.88
> color zone #19 near #20 distance 1.98
> color zone #19 near #20 distance 2.08
[Repeated 1 time(s)]
> volume splitbyzone #19
Opened hOCT1-AZT.mrc 0 as #21.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
Opened hOCT1-AZT.mrc 1 as #21.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
Opened hOCT1-AZT.mrc 2 as #21.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
> close #21.1-2
> select add #20
3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected
> select subtract #20
Nothing selected
> select add #20
3578 atoms, 3672 bonds, 1 pseudobond, 463 residues, 2 models selected
> color #20 #773333ff
> color #20 #733551ff
> color (#!20 & sel) byhetero
> select clear
> color #21.3 #ff000096 models
> color #21.3 #ffffff96 models
> color #21.3 #ffffb296 models
> volume #21.3 level 0.008896
> hide #!21.3 models
> hide #!21 models
> hide #!20 models
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 59019, resource id:
35654939, major code: 40 (TranslateCoords), minor code: 0
> show #!3 models
> show #!6.3 models
> select ::name="ABC"
42 atoms, 48 bonds, 2 residues, 1 model selected
> view sel
> select clear
> hide #!6.3 models
> hide #!6 models
> hide #!3 models
> show #!2 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> show #!8 models
> show #!9.3 models
> hide #!9.3 models
> hide #!9 models
> hide #!8 models
> show #!11 models
> show #!12.3 models
> hide #!12.3 models
> hide #!12 models
> hide #!11 models
> show #!14 models
> show #!15 models
> hide #!15 models
> show #!15.3 models
> hide #!14 models
> hide #!15 models
> hide #!15.3 models
> show #!17 models
> show #!18.3 models
> hide #!18.3 models
> hide #!18 models
> hide #!17 models
> show #!20 models
> show #!21.3 models
> save "/home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1 structures ligand
> density.cxs" includeMaps true
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/OCT1_structures_ligand_density.cxs
> includeMaps true
[Repeated 1 time(s)]
> close session
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/0-coot-
> history.scm
Unrecognized file suffix '.scm'
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.cif
Summary of feedback from opening
/home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 187
Missing entity information. Treating each chain as a separate entity.
Bad residue range for struct_conf "3" near line 98
Bad residue range for struct_conf "4" near line 99
Bad residue range for struct_conf "5" near line 100
Bad residue range for struct_conf "6" near line 101
Bad residue range for struct_conf "7" near line 102
15 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "2 1" near line 183
Invalid sheet range for struct_sheet_range "3 1" near line 184
Invalid sheet range for struct_sheet_range "4 1" near line 186
Missing or incomplete sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' near line 4361
Chain information for rOAT1-AZT_coot-4_real_space_refined_002.cif #1
---
Chain | Description
A | No description available
> close session
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AZT_20240729/RealSpaceRefine_2/rOAT1-AZT_coot-4_real_space_refined_002.pdb
Chain information for rOAT1-AZT_coot-4_real_space_refined_002.pdb #1
---
Chain | Description
A | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 10568, resource id:
35655077, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/inward_j156_2.7A/postprocess.mrc
Opened postprocess.mrc as #2, grid size 320,320,320, pixel 0.83, shown at
level 0.00421, step 2, values float32
> rename #2 rOAT1-AZT.mrc
> volume #2 step 1
> volume #2 level 0.01415
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> select add #1
3905 atoms, 3986 bonds, 515 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.81264,-0.025153,-0.58222,300.85,0.24435,0.8923,-0.37961,31.685,0.52906,-0.45075,-0.71897,210.07
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.81264,-0.025153,-0.58222,320.11,0.24435,0.8923,-0.37961,31.387,0.52906,-0.45075,-0.71897,214.5
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.62181,-0.74054,-0.25487,347.35,-0.028985,0.34697,-0.93743,205.98,0.78263,-0.57551,-0.23722,138.33
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.62181,-0.74054,-0.25487,344.94,-0.028985,0.34697,-0.93743,211.72,0.78263,-0.57551,-0.23722,135.34
> view matrix models
> #1,-0.62181,-0.74054,-0.25487,347.37,-0.028985,0.34697,-0.93743,211.37,0.78263,-0.57551,-0.23722,136.41
> ui tool show "Fit in Map"
> fitmap #1 inMap #2
Fit molecule rOAT1-AZT_coot-4_real_space_refined_002.pdb (#1) to map
rOAT1-AZT.mrc (#2) using 3905 atoms
average map value = 0.01965, steps = 108
shifted from previous position = 2.32
rotated from previous position = 12.8 degrees
atoms outside contour = 1436, contour level = 0.014154
Position of rOAT1-AZT_coot-4_real_space_refined_002.pdb (#1) relative to
rOAT1-AZT.mrc (#2) coordinates:
Matrix rotation and translation
-0.62427498 -0.78041245 -0.03517318 323.27181278
-0.15760640 0.16991691 -0.97277359 257.26632447
0.76514114 -0.60173470 -0.22907287 142.60270901
Axis 0.34360458 -0.74113973 0.57675627
Axis point 193.37147122 0.00000000 235.15956508
Rotation angle (degrees) 147.32171525
Shift along axis 2.65438788
> select subtract #1
Nothing selected
> select add #1
3905 atoms, 3986 bonds, 515 residues, 1 model selected
> color sel white
> select ::name="AZZ"
19 atoms, 20 bonds, 1 residue, 1 model selected
> color sel red
> ui tool show "Color Zone"
> color zone #2 near #1 distance 4.98
> volume #2 level 0.0105
> color zone #2 near #1 distance 4.88
> color zone #2 near #1 distance 4.78
> color zone #2 near #1 distance 4.68
> color zone #2 near #1 distance 4.58
> color zone #2 near #1 distance 4.48
> color zone #2 near #1 distance 4.38
> color zone #2 near #1 distance 4.28
> color zone #2 near #1 distance 4.18
> color zone #2 near #1 distance 4.08
> color zone #2 near #1 distance 3.98
> color zone #2 near #1 distance 3.88
> color zone #2 near #1 distance 3.78
> color zone #2 near #1 distance 3.68
> color zone #2 near #1 distance 3.58
> color zone #2 near #1 distance 3.48
> color zone #2 near #1 distance 3.38
> color zone #2 near #1 distance 3.28
> color zone #2 near #1 distance 3.18
> color zone #2 near #1 distance 3.08
> color zone #2 near #1 distance 2.98
> color zone #2 near #1 distance 2.88
> color zone #2 near #1 distance 2.78
> color zone #2 near #1 distance 2.68
> color zone #2 near #1 distance 2.58
> color zone #2 near #1 distance 2.48
> color zone #2 near #1 distance 2.38
> color zone #2 near #1 distance 2.28
> color zone #2 near #1 distance 2.18
> color zone #2 near #1 distance 2.08
> color zone #2 near #1 distance 1.98
> color zone #2 near #1 distance 1.88
> color zone #2 near #1 distance 1.78
> volume #2 level 0.008069
> volume splitbyzone #2
Opened rOAT1-AZT.mrc 0 as #3.1, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT.mrc 1 as #3.2, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
Opened rOAT1-AZT.mrc 2 as #3.3, grid size 320,320,320, pixel 0.83, shown at
level 0.00807, step 1, values float32
> close #3.1-2
> color #3.3 white models
> color #3.3 #ffffb2ff models
> select add #1
3905 atoms, 3986 bonds, 515 residues, 1 model selected
> color #1 #dd22bbff
> color #1 tan
> color sel byhetero
> color #3.3 #ffffb296 models
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 355, resource id:
35655128, major code: 40 (TranslateCoords), minor code: 0
QXcbConnection: XCB error: 3 (BadWindow), sequence: 366, resource id:
35655123, major code: 40 (TranslateCoords), minor code: 0
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 14345, resource id:
35655133, major code: 40 (TranslateCoords), minor code: 0
> rename #1 rOAT1-AZT_IF.pdb
> rename #2 rOAT1-AZT_IF.mrc
> rename #3 "rOAT1-AZT_IF.mrc split"
> rename #3.3 "rOAT1-AZT_IF.mrc 2"
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 23455, resource id:
35655148, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/run_class001.mrc
Opened run_class001.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.00134, step 2, values float32
> close #4
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/postprocess.mrc
Opened postprocess.mrc as #4, grid size 320,320,320, pixel 0.83, shown at
level 0.00459, step 2, values float32
> volume #4 step 1
> volume #4 level 0.01366
> rename #4 rOAT1-AZT_OF.mrc
> open
> /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PBD_LMNG_combined_20230419_20230217_OF/rOAT1-PBD_OF-
> coot-7_real_space_refined_008.pdb
Chain information for rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb #5
---
Chain | Description
A | No description available
> select subtract #1
Nothing selected
> select add #5
3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected
> hide #!3 models
> hide #!3.3 models
> hide #1 models
> view matrix models #5,1,0,0,68.569,0,1,0,64.41,0,0,1,67.632
> view matrix models #5,1,0,0,67.083,0,1,0,66.14,0,0,1,66.95
> fitmap #5 inMap #4
Fit molecule rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb (#5) to map
rOAT1-AZT_OF.mrc (#4) using 3792 atoms
average map value = 0.01938, steps = 84
shifted from previous position = 0.803
rotated from previous position = 4.35 degrees
atoms outside contour = 1323, contour level = 0.013659
Position of rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb (#5) relative to
rOAT1-AZT_OF.mrc (#4) coordinates:
Matrix rotation and translation
0.99822969 -0.04531644 -0.03852150 72.45731875
0.04345449 0.99790785 -0.04787105 67.21065914
0.04061025 0.04611237 0.99811044 61.32293455
Axis 0.62004547 -0.52206316 0.58565662
Axis point 0.00000000 -669.59173064 1932.22009801
Rotation angle (degrees) 4.34647273
Shift along axis 45.75280586
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/rOAT1-AZT_OF.pdb
> models #5 relModel #4
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/inward_j156_2.7A/rOAT1-AZT_IF.pdb
> models #1
> close #5
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/postprocess.mrc
Opened rOAT1-AZT_OF.mrc as #5, grid size 320,320,320, pixel 0.83, shown at
level 0.00459, step 2, values float32
> close #5
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240803_rOAT1-AZT/outward_j170_2.7A/rOAT1-AZT_OF-
> coot-0_real_space_refined_003.pdb
Chain information for rOAT1-AZT_OF-coot-0_real_space_refined_003.pdb #5
---
Chain | Description
A | No description available
> select add #4
2 models selected
> select subtract #4
Nothing selected
> select add #5
3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected
> select clear
> select add #5
3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected
> color #5 white
> color #4 white models
> color #2 white models
> select #5/A:601@O4
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> color sel red
> color zone #4 near #5 distance 4.98
> color zone #4 near #5 distance 4.88
> color zone #4 near #5 distance 4.78
> color zone #4 near #5 distance 4.68
> color zone #4 near #5 distance 4.58
> color zone #4 near #5 distance 4.48
> color zone #4 near #5 distance 4.38
> color zone #4 near #5 distance 4.28
> color zone #4 near #5 distance 4.18
> color zone #4 near #5 distance 4.08
> color zone #4 near #5 distance 3.98
> color zone #4 near #5 distance 3.88
> color zone #4 near #5 distance 3.78
> color zone #4 near #5 distance 3.68
> color zone #4 near #5 distance 3.58
> color zone #4 near #5 distance 3.48
> color zone #4 near #5 distance 3.38
> color zone #4 near #5 distance 3.28
> color zone #4 near #5 distance 3.18
> color zone #4 near #5 distance 3.08
> color zone #4 near #5 distance 2.98
> color zone #4 near #5 distance 2.88
> color zone #4 near #5 distance 2.78
> color zone #4 near #5 distance 2.68
> color zone #4 near #5 distance 2.58
> color zone #4 near #5 distance 2.48
> color zone #4 near #5 distance 2.38
> color zone #4 near #5 distance 2.28
> color zone #4 near #5 distance 2.18
> color zone #4 near #5 distance 2.08
> color zone #4 near #5 distance 1.98
> color zone #4 near #5 distance 1.88
> color zone #4 near #5 distance 1.78
> color zone #4 near #5 distance 1.68
> color zone #4 near #5 distance 1.58
> color zone #4 near #5 distance 1.48
> color zone #4 near #5 distance 1.58
> color zone #4 near #5 distance 1.68
> color zone #4 near #5 distance 1.78
> color zone #4 near #5 distance 1.88
> volume splitbyzone #4
Opened rOAT1-AZT_OF.mrc 0 as #6.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 1 as #6.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
Opened rOAT1-AZT_OF.mrc 2 as #6.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0137, step 1, values float32
> close #6.1-2
> volume #6.3 level 0.0116
> select add #5
3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected
> select subtract #5
Nothing selected
> color #6.3 yellow models
> color #6.3 white models
> color #6.3 #ffffb2ff models
> select add #5
3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected
> color #5 #ffaa88ff
> color #5 salmon
> color (#!5 & sel) byhetero
> color #6.3 #ffffb296 models
> select clear
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> show #!2 models
> hide #!5 models
> hide #!6 models
> hide #!6.3 models
> volume #2 level 0.01456
> color #2 #a5a5a5ff models
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/inward_j261_2.6A/postprocess.mrc
Opened postprocess.mrc as #7, grid size 320,320,320, pixel 0.83, shown at
level 0.00408, step 2, values float32
> rename #7 rOAT1-PBD_IF.mrc
> volume #2 level 0.01983
> volume #2 level 0.0151
> hide #!7 models
> volume #7 level 0.01185
> volume #7 step 1
> volume #7 level 0.01094
> hide #!2 models
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/inward_j261_2.6A/rOAT1-PBD-
> coot-6.pdb
Chain information for rOAT1-PBD-coot-6.pdb #8
---
Chain | Description
A | No description available
> select add #8
3912 atoms, 3985 bonds, 522 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,55.004,0,1,0,73.737,0,0,1,58.702
> view matrix models #8,1,0,0,66.378,0,1,0,64.897,0,0,1,63.973
> fitmap #8 inMap #7
Fit molecule rOAT1-PBD-coot-6.pdb (#8) to map rOAT1-PBD_IF.mrc (#7) using 3912
atoms
average map value = 0.02737, steps = 56
shifted from previous position = 2.6
rotated from previous position = 0.396 degrees
atoms outside contour = 571, contour level = 0.010939
Position of rOAT1-PBD-coot-6.pdb (#8) relative to rOAT1-PBD_IF.mrc (#7)
coordinates:
Matrix rotation and translation
0.99998387 0.00531886 -0.00199304 66.36205660
-0.00532668 0.99997806 -0.00393867 67.06308709
0.00197205 0.00394922 0.99999026 65.65327743
Axis 0.57034742 -0.28670293 -0.76974363
Axis point 10937.66555565 -15865.74627304 0.00000000
Rotation angle (degrees) 0.39620277
Shift along axis -31.91394767
> rename #8 rOAT1-PBD_IF.pdb
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 51376, resource id:
35655645, major code: 40 (TranslateCoords), minor code: 0
QXcbConnection: XCB error: 3 (BadWindow), sequence: 51388, resource id:
35655640, major code: 40 (TranslateCoords), minor code: 0
> color #8 white
> hide #!7 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 19 bonds, 1 residue, 1 model selected
> color sel red
> show #!7 models
> color zone #7 near #8 distance 4.98
> color zone #7 near #8 distance 4.88
> color zone #7 near #8 distance 4.78
> color zone #7 near #8 distance 4.68
> color zone #7 near #8 distance 4.58
> color zone #7 near #8 distance 4.48
> color zone #7 near #8 distance 4.38
> color zone #7 near #8 distance 4.28
> color zone #7 near #8 distance 4.18
> color zone #7 near #8 distance 4.08
> color zone #7 near #8 distance 3.98
> color zone #7 near #8 distance 3.88
> color zone #7 near #8 distance 3.78
> color zone #7 near #8 distance 3.68
> volume #7 level 0.02515
> volume #7 level 0.01677
> volume #7 level 0.0124
> volume #7 level 0.01476
> color zone #7 near #8 distance 3.58
> color zone #7 near #8 distance 3.48
> color zone #7 near #8 distance 3.38
> color zone #7 near #8 distance 3.28
> color zone #7 near #8 distance 3.18
> color zone #7 near #8 distance 3.08
> color zone #7 near #8 distance 2.98
> color zone #7 near #8 distance 2.88
> color zone #7 near #8 distance 2.78
> color zone #7 near #8 distance 2.68
> color zone #7 near #8 distance 2.58
> color zone #7 near #8 distance 2.48
> color zone #7 near #8 distance 2.38
> color zone #7 near #8 distance 2.28
> volume #7 level 0.01112
> color zone #7 near #8 distance 2.18
> color zone #7 near #8 distance 2.08
> color zone #7 near #8 distance 1.98
> color zone #7 near #8 distance 1.88
> color zone #7 near #8 distance 1.98
> color zone #7 near #8 distance 2.08
> volume splitbyzone #7
Opened rOAT1-PBD_IF.mrc 0 as #9.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 1 as #9.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
Opened rOAT1-PBD_IF.mrc 2 as #9.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0111, step 1, values float32
> close #9.1-2
> color #9.3 #ff000096 models
> color #9.3 #ffff0096 models
> color #9.3 #ffffff96 models
> color #9.3 #ffffb296 models
> select add #8
3912 atoms, 3985 bonds, 522 residues, 1 model selected
> color #8 #ffffddff
> color #8 gold
> select clear
> select add #8
3912 atoms, 3985 bonds, 522 residues, 1 model selected
> color sel byhetero
> select clear
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 19133, resource id:
35655670, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/outward_j272_3.0A/postprocess.mrc
Opened postprocess.mrc as #10, grid size 320,320,320, pixel 0.83, shown at
level 0.00409, step 2, values float32
QXcbConnection: XCB error: 3 (BadWindow), sequence: 23804, resource id:
35655680, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20230419_rOAT1-PBD/outward_j272_3.0A/rOAT1-PBD_OF-
> coot-0.pdb
Chain information for rOAT1-PBD_OF-coot-0.pdb #11
---
Chain | Description
A | No description available
> hide #!9 models
> hide #8 models
> rename #10 rOAT1-PBD_OF
> rename #10 rOAT1-PBD_OF.mrc
> show #!2 models
> volume #10 level 0.004712
> volume #10 step 1
> volume #10 level 0.01128
> hide #!2 models
> select add #11
3872 atoms, 3966 bonds, 500 residues, 1 model selected
> view matrix models #11,1,0,0,65.11,0,1,0,69.986,0,0,1,61.035
> view matrix models #11,1,0,0,68.61,0,1,0,68.058,0,0,1,65.073
> view matrix models #11,1,0,0,67.516,0,1,0,68.105,0,0,1,67.386
> fitmap #11 inMap #10
Fit molecule rOAT1-PBD_OF-coot-0.pdb (#11) to map rOAT1-PBD_OF.mrc (#10) using
3872 atoms
average map value = 0.01531, steps = 56
shifted from previous position = 2.42
rotated from previous position = 0.764 degrees
atoms outside contour = 1505, contour level = 0.011277
Position of rOAT1-PBD_OF-coot-0.pdb (#11) relative to rOAT1-PBD_OF.mrc (#10)
coordinates:
Matrix rotation and translation
0.99995211 0.00939248 0.00274947 65.65298070
-0.00936721 0.99991506 -0.00906240 67.47749964
-0.00283436 0.00903621 0.99995516 65.83404461
Axis 0.67891074 0.20945939 -0.70370943
Axis point 6981.74049553 -6059.62250131 0.00000000
Rotation angle (degrees) 0.76372650
Shift along axis 12.37827175
> show sel atoms
> hide #!10 models
> show #!10 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-PBD_LMNG_combined_20230419_20230217_OF/rOAT1-PBD_OF-
> coot-7_real_space_refined_008.pdb
Chain information for rOAT1-PBD_OF-coot-7_real_space_refined_008.pdb #12
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #!12 to #11
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 rOAT1-PBD_OF-coot-0.pdb, chain A (#11) with rOAT1-PBD_OF-
coot-7_real_space_refined_008.pdb, chain A (#12), sequence alignment score =
2423.1
RMSD between 470 pruned atom pairs is 0.696 angstroms; (across all 485 pairs:
1.080)
> hide #11 models
> select subtract #11
Nothing selected
> show #11 models
> hide #!12 models
> hide #!10 models
> show #!12 models
> close #11
> color #12 #bb4455ff
> color #12 #b4503bff
QXcbConnection: XCB error: 3 (BadWindow), sequence: 15705, resource id:
35655708, major code: 40 (TranslateCoords), minor code: 0
> show #!10 models
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 19760, resource id:
35655718, major code: 40 (TranslateCoords), minor code: 0
QXcbConnection: XCB error: 3 (BadWindow), sequence: 19772, resource id:
35655713, major code: 40 (TranslateCoords), minor code: 0
> color #10 #ffb2ff96 models
> volume #10 level 0.009218
> volume #10 level 0.008059
> color #10 #ffb2ffff models
> select add #12
3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected
> hide #!10 models
> color #12 white
> select clear
> select #12/B:601@C11
1 atom, 1 residue, 1 model selected
> select up
37 atoms, 37 bonds, 1 residue, 1 model selected
> color sel red
> color #10 white models
> select add #10
37 atoms, 37 bonds, 1 residue, 3 models selected
> select subtract #10
37 atoms, 37 bonds, 1 residue, 1 model selected
> show #!10 models
> color zone #10 near #12 distance 2
> color zone #10 near #12 distance 1.9
> color zone #10 near #12 distance 1.8
> color zone #10 near #12 distance 1.7
> color zone #10 near #12 distance 1.8
> color zone #10 near #12 distance 1.9
> color zone #10 near #12 distance 2
[Repeated 1 time(s)]
> volume splitbyzone #10
Opened rOAT1-PBD_OF.mrc 0 as #11.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 1 as #11.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #11.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
> volume splitbyzone #10
Opened rOAT1-PBD_OF.mrc 0 as #13.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 1 as #13.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
Opened rOAT1-PBD_OF.mrc 2 as #13.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00806, step 1, values float32
> close #11.1-2
> hide #!12 models
> hide #!11.3 models
> hide #!11 models
> select add #12
3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected
> select subtract #12
Nothing selected
> close #13.1-2
> show #!12 models
> color #11.3 white models
> color #11.3 #ffffb2ff models
> color #13.3 white models
> color #13.3 #ffffb2ff models
> select add #12
3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected
> color #12 #bb4455ff
> color #12 #b4503bff
> color (#!12 & sel) byhetero
> select #12/A:440
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #12
3792 atoms, 3881 bonds, 5 pseudobonds, 486 residues, 2 models selected
> select subtract #12
Nothing selected
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> hide #!13 models
> hide #!13.3 models
> hide #!12 models
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/inward_j152_2.7A/postprocess.mrc
Opened postprocess.mrc as #14, grid size 320,320,320, pixel 0.83, shown at
level 0.00408, step 2, values float32
QXcbConnection: XCB error: 3 (BadWindow), sequence: 27239, resource id:
35655778, major code: 40 (TranslateCoords), minor code: 0
> show #!2 models
> hide #!2 models
> rename #14 rOAT1-TFV_IF.mrc
> show #1 models
> hide #!14 models
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF.pdb
> models #1 relModel #14
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_5/rOAT1-TFV_IF-
> coot-2_real_space_refined_005.pdb
Chain information for rOAT1-TFV_IF-coot-2_real_space_refined_005.pdb #15
---
Chain | Description
A | No description available
> hide #1 models
> show #!14 models
> color #15 white
> color #14 white models
> select ::name="TFV"
31 atoms, 32 bonds, 1 residue, 1 model selected
> color sel red
> color zone #14 near #15 distance 4.68
> color zone #14 near #15 distance 4.58
> color zone #14 near #15 distance 4.48
> color zone #14 near #15 distance 4.38
> color zone #14 near #15 distance 4.28
> color zone #14 near #15 distance 4.18
> color zone #14 near #15 distance 4.08
> color zone #14 near #15 distance 3.98
> color zone #14 near #15 distance 3.88
> color zone #14 near #15 distance 3.78
> color zone #14 near #15 distance 3.68
> color zone #14 near #15 distance 3.58
> color zone #14 near #15 distance 3.48
> color zone #14 near #15 distance 3.38
> color zone #14 near #15 distance 3.28
> color zone #14 near #15 distance 3.18
> color zone #14 near #15 distance 3.08
> color zone #14 near #15 distance 2.98
> color zone #14 near #15 distance 2.88
> color zone #14 near #15 distance 2.78
> color zone #14 near #15 distance 2.68
> volume #14 level 0.007613
> color zone #14 near #15 distance 2.78
> color zone #14 near #15 distance 2.88
> color zone #14 near #15 distance 2.98
> color zone #14 near #15 distance 2.88
> color zone #14 near #15 distance 2.78
> color zone #14 near #15 distance 2.68
> color zone #14 near #15 distance 2.58
> color zone #14 near #15 distance 2.48
> color zone #14 near #15 distance 2.38
> volume #14 level 0.005915
> volume #14 level 0.005632
> volume splitbyzone #14
Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
> close #16.1-2
> color zone #14 near #15 distance 2.09
> close #16#16.3
> show #!14 models
> color zone #14 near #15 distance 1.99
> color zone #14 near #15 distance 2.09
> color zone #14 near #15 distance 2.19
> color zone #14 near #15 distance 2.29
> color zone #14 near #15 distance 2.39
> color zone #14 near #15 distance 2.29
> volume splitbyzone #14
Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
> close #16.1-2
> select add #15
3917 atoms, 3998 bonds, 515 residues, 1 model selected
> color #16.3 #ff5500ff models
> color #16.3 #aa0000ff models
> color #16.3 #ff5500ff models
> color #16.3 #ff557fff models
> color #15 #ff557fff
> color #16.3 white models
> color #16.3 #ffffb2ff models
> color #16.3 #ffffb296 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF-
> coot-3.pdb
Chain information for rOAT1-TFV_IF-coot-3.pdb #17
---
Chain | Description
A | No description available
> close #17#16#16.3
> close #15
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/IF/rOAT1-TFV_IF-
> coot-3.pdb
Chain information for rOAT1-TFV_IF-coot-3.pdb #15
---
Chain | Description
A | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 28850, resource id:
35656402, major code: 40 (TranslateCoords), minor code: 0
> show #!14 models
> select add #15
3917 atoms, 3998 bonds, 515 residues, 1 model selected
> select subtract #15
Nothing selected
> select add #15
3917 atoms, 3998 bonds, 515 residues, 1 model selected
> color #15 white
> color zone #14 near #15 distance 2.29
> select ::name="TFV"
31 atoms, 32 bonds, 1 residue, 1 model selected
> color sel red
> color zone #14 near #15 distance 2.29
> color zone #14 near #15 distance 2.19
> color zone #14 near #15 distance 2.09
> color zone #14 near #15 distance 1.99
> color zone #14 near #15 distance 1.89
> color zone #14 near #15 distance 1.79
> color zone #14 near #15 distance 1.69
> color zone #14 near #15 distance 1.59
> color zone #14 near #15 distance 1.49
> color zone #14 near #15 distance 1.39
> color zone #14 near #15 distance 1.29
> color zone #14 near #15 distance 1.19
> color zone #14 near #15 distance 1.09
> color zone #14 near #15 distance 1.19
> color zone #14 near #15 distance 1.29
> color zone #14 near #15 distance 1.39
> color zone #14 near #15 distance 1.49
> color zone #14 near #15 distance 1.59
> color zone #14 near #15 distance 1.69
> color zone #14 near #15 distance 1.79
> color zone #14 near #15 distance 1.89
> color zone #14 near #15 distance 1.99
> color zone #14 near #15 distance 2.09
[Repeated 1 time(s)]
> volume splitbyzone #14
Opened rOAT1-TFV_IF.mrc 0 as #16.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TFV_IF.mrc 1 as #16.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
Opened rOAT1-TFV_IF.mrc 2 as #16.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00563, step 1, values float32
> close #16.1-2
> color #16.3 white models
> color #16.3 #ffffb2ff models
> color #16.3 #ffffb296 models
> color #15 #ff5500ff
> color #15 #ff557fff
> select add #15
3917 atoms, 3998 bonds, 515 residues, 1 model selected
> color sel byhetero
> select clear
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/postprocess.mrc
Opened postprocess.mrc as #17, grid size 320,320,320, pixel 0.83, shown at
level 0.00401, step 2, values float32
> rename #17 rOAT1-TVF_OF.mrc
> hide #15 models
> hide #!16 models
> show #8 models
> hide #8 models
> show #!11.3 models
> hide #!11 models
> hide #!11.3 models
> show #!12 models
> volume #17 step 1
> volume #17 level 0.01305
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF.pdb
> models #12 relModel #17
> hide #!16.3 models
> hide #!12 models
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20240831_rOAT1-TFV/outward_j170_2.7A/rOAT1-TFV_OF.pdb
Chain information for rOAT1-TFV_OF.pdb #18
---
Chain | Description
A | No description available
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> close #18
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_7/rOAT1-TFV_OF-
> coot-1_real_space_refined_007.pdb
Chain information for rOAT1-TFV_OF-coot-1_real_space_refined_007.pdb #18
---
Chain | Description
A | No description available
> select add #18
3786 atoms, 3876 bonds, 5 pseudobonds, 486 residues, 2 models selected
> color #18 white
> color #17 white models
> select #18/A:601@H131
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 32 bonds, 1 residue, 1 model selected
> color sel red
> volume #17 level 0.011
> color zone #17 near #18 distance 4.98
> color zone #17 near #18 distance 4.88
> color zone #17 near #18 distance 4.78
> color zone #17 near #18 distance 4.68
> color zone #17 near #18 distance 4.58
> color zone #17 near #18 distance 4.48
> color zone #17 near #18 distance 4.38
> color zone #17 near #18 distance 4.28
> color zone #17 near #18 distance 4.18
> color zone #17 near #18 distance 4.08
> color zone #17 near #18 distance 3.98
> color zone #17 near #18 distance 3.88
> color zone #17 near #18 distance 3.78
> color zone #17 near #18 distance 3.68
> color zone #17 near #18 distance 3.58
> color zone #17 near #18 distance 3.48
> color zone #17 near #18 distance 3.38
> color zone #17 near #18 distance 3.28
> color zone #17 near #18 distance 3.18
> color zone #17 near #18 distance 3.08
> color zone #17 near #18 distance 2.98
> volume splitbyzone #17
Opened rOAT1-TVF_OF.mrc 0 as #19.1, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 1 as #19.2, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #19.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
> close #19.1-2
> color #19.3 white models
> color #19.3 #ffffb2ff models
> select add #18
3786 atoms, 3876 bonds, 5 pseudobonds, 486 residues, 2 models selected
> color #18 #337744ff
> color #18 #374c02ff
> color (#!18 & sel) byhetero
> select clear
> color #19.3 #ffffb296 models
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/inward_j112_2.6A/postprocess.mrc
Opened postprocess.mrc as #20, grid size 320,320,320, pixel 0.83, shown at
level 0.00494, step 2, values float32
> volume #20 step 1
> hide #!19 models
> hide #!18 models
> rename #20 rOAT1-AAI_IF.mrc
> volume #20 level 0.0194
QXcbConnection: XCB error: 3 (BadWindow), sequence: 35473, resource id:
35656688, major code: 40 (TranslateCoords), minor code: 0
> show #!2 models
> hide #!2 models
> show #1 models
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/IF/rOAT1-AAI_IF.pdb
> models #1 relModel #20
> hide #1 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/IF/rOAT1-AAI_IF.pdb
Chain information for rOAT1-AAI_IF.pdb #21
---
Chain | Description
A | No description available
> close #21
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_1/rOAT1-AAI_IF_real_space_refined_001.pdb
Chain information for rOAT1-AAI_IF_real_space_refined_001.pdb #21
---
Chain | Description
A | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 12758, resource id:
35656914, major code: 40 (TranslateCoords), minor code: 0
> close #21
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_3/rOAT1-AAI_IF-
> coot-1_real_space_refined_003_initial.geo
Unrecognized file suffix '.geo'
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_3/rOAT1-AAI_IF-
> coot-1_real_space_refined_003.pdb
Chain information for rOAT1-AAI_IF-coot-1_real_space_refined_003.pdb #21
---
Chain | Description
A | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 49188, resource id:
35657106, major code: 40 (TranslateCoords), minor code: 0
> select add #21
3956 atoms, 4042 bonds, 516 residues, 1 model selected
> color #21 white
> color #20 white models
> select clear
> select #21/A:602@O24
1 atom, 1 residue, 1 model selected
> select up
35 atoms, 38 bonds, 1 residue, 1 model selected
> select #21/A:601@O20
1 atom, 1 residue, 1 model selected
> select add #21/A:602@C23
2 atoms, 2 residues, 1 model selected
> select up
70 atoms, 76 bonds, 2 residues, 1 model selected
> color sel red
> color zone #20 near #21 distance 4.98
> color zone #20 near #21 distance 4.88
> color zone #20 near #21 distance 4.78
> color zone #20 near #21 distance 4.68
> color zone #20 near #21 distance 4.58
> color zone #20 near #21 distance 4.48
> color zone #20 near #21 distance 4.38
> color zone #20 near #21 distance 4.28
> color zone #20 near #21 distance 4.18
> color zone #20 near #21 distance 4.08
> color zone #20 near #21 distance 3.98
> color zone #20 near #21 distance 3.88
> color zone #20 near #21 distance 3.78
> color zone #20 near #21 distance 3.68
> color zone #20 near #21 distance 3.58
> color zone #20 near #21 distance 3.48
> color zone #20 near #21 distance 3.38
> color zone #20 near #21 distance 3.28
> color zone #20 near #21 distance 3.18
> color zone #20 near #21 distance 3.08
> color zone #20 near #21 distance 2.98
> color zone #20 near #21 distance 2.88
> volume splitbyzone #20
Opened rOAT1-AAI_IF.mrc 0 as #22.1, grid size 320,320,320, pixel 0.83, shown
at level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 1 as #22.2, grid size 320,320,320, pixel 0.83, shown
at level 0.0194, step 1, values float32
Opened rOAT1-AAI_IF.mrc 2 as #22.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0194, step 1, values float32
> close #22.1-2
> color #22.3 yellow models
> color #22.3 white models
> color #22.3 #ffffb2ff models
> color #22.3 #ffffb296 models
> select add #21
3956 atoms, 4042 bonds, 516 residues, 1 model selected
> color #21 #668855ff
> color #21 #685d73ff
> color sel byhetero
> select clear
[Repeated 1 time(s)]
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 7603, resource id:
35657141, major code: 40 (TranslateCoords), minor code: 0
QXcbConnection: XCB error: 3 (BadWindow), sequence: 7615, resource id:
35657136, major code: 40 (TranslateCoords), minor code: 0
> hide #!22.3 models
> hide #!22 models
> hide #21 models
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/outward_j122_2.5A/postprocess.mrc
Opened postprocess.mrc as #23, grid size 320,320,320, pixel 0.83, shown at
level 0.00494, step 2, values float32
> volume #23 level 0.01307
> volume #23 step 1
> volume #23 level 0.01684
> show #1 models
> hide #1 models
> show #!5 models
> rename #23 rOAT1-AAI_OF.mrc
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20250129_rOAT1-AAI/outward_j122_2.5A/rOAT1-AAI_OF.pdb
> models #5 relModel #23
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-AAI/RealSpaceRefine_4/rOAT1-AAI_OF-
> coot-1_real_space_refined_004.pdb
Chain information for rOAT1-AAI_OF-coot-1_real_space_refined_004.pdb #24
---
Chain | Description
A | No description available
> color #23 white models
> color #24 white
> hide #!5 models
> select add #24/A:601@O24
1 atom, 1 residue, 1 model selected
> select add #24/A:230@OH
2 atoms, 2 residues, 1 model selected
> select clear
> select add #24/A:601@O24
1 atom, 1 residue, 1 model selected
> select up
35 atoms, 38 bonds, 1 residue, 1 model selected
> color sel red
> color zone #23 near #24 distance 4.98
> volume splitbyzone #23
Opened rOAT1-AAI_OF.mrc 0 as #25.1, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 1 as #25.2, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
Opened rOAT1-AAI_OF.mrc 2 as #25.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0168, step 1, values float32
> close #25.1-2
> select add #24
3790 atoms, 3882 bonds, 5 pseudobonds, 486 residues, 2 models selected
> select subtract #24
Nothing selected
> color #25.3 white models
> color #25.3 #ffffb2ff models
> select add #24
3790 atoms, 3882 bonds, 5 pseudobonds, 486 residues, 2 models selected
> color #24 #1177ccff
> color #24 #17c127ff
> color (#!24 & sel) byhetero
> select #24/A:438@CE2
1 atom, 1 residue, 1 model selected
Drag select of 1 atoms, 1 bonds
> select clear
> color #25.3 #ffffb296 models
> select clear
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> open
> /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/rOAT1-PAH-
> coot-7_real_space_refined_007.pdb
Chain information for rOAT1-PAH-coot-7_real_space_refined_007.pdb #26
---
Chain | Description
A | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 7338, resource id:
35657291, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/PROJECTS/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/cryosparc_P4_J89__localfilter_160.mrc
Opened cryosparc_P4_J89__localfilter_160.mrc as #27, grid size 160,160,160,
pixel 0.83, shown at level 0.134, step 1, values float32
> hide #!24 models
> hide #!25.3 models
> hide #!25 models
> view
> show #!2 models
> select add #26
3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected
> select add #27
3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 4 models selected
> view matrix models
> #26,1,0,0,55.434,0,1,0,82.728,0,0,1,62.865,#27,1,0,0,55.434,0,1,0,82.728,0,0,1,62.865
> view matrix models
> #26,1,0,0,67.067,0,1,0,66.938,0,0,1,64.563,#27,1,0,0,67.067,0,1,0,66.938,0,0,1,64.563
> rename #27 rOAT1-PAH
> rename #27 rOAT1-PAH.mrc
> view
> fitmap #26 inMap #27
Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
rOAT1-PAH.mrc (#27) using 3865 atoms
average map value = 0.3441, steps = 44
shifted from previous position = 0.0131
rotated from previous position = 0.0158 degrees
atoms outside contour = 699, contour level = 0.13428
Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
rOAT1-PAH.mrc (#27) coordinates:
Matrix rotation and translation
0.99999996 -0.00021122 0.00016567 0.00535685
0.00021123 0.99999998 -0.00006568 0.00053709
-0.00016566 0.00006571 0.99999998 -0.00148379
Axis 0.23771757 0.59945172 0.76429575
Axis point -1.23064203 24.84299856 0.00000000
Rotation angle (degrees) 0.01583428
Shift along axis 0.00046132
> hide #!2 models
> color #27 white models
> color #26 white
> hide #!26 models
> select subtract #27
3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected
> select subtract #26
Nothing selected
> hide #!27 models
> show #!26 models
> select #26/B:601@C07
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 23 bonds, 1 residue, 1 model selected
> color sel red
> show #!27 models
> color zone #27 near #26 distance 4.98
> color zone #27 near #26 distance 4.88
> color zone #27 near #26 distance 4.78
> color zone #27 near #26 distance 4.68
> color zone #27 near #26 distance 4.58
> color zone #27 near #26 distance 4.48
> color zone #27 near #26 distance 4.38
> color zone #27 near #26 distance 4.28
> color zone #27 near #26 distance 4.18
> color zone #27 near #26 distance 4.08
> color zone #27 near #26 distance 3.98
> color zone #27 near #26 distance 3.88
> color zone #27 near #26 distance 3.78
> color zone #27 near #26 distance 3.68
> color zone #27 near #26 distance 3.58
> color zone #27 near #26 distance 3.48
> color zone #27 near #26 distance 3.38
> color zone #27 near #26 distance 3.28
> color zone #27 near #26 distance 3.18
> color zone #27 near #26 distance 3.08
> color zone #27 near #26 distance 2.98
> color zone #27 near #26 distance 2.88
> color zone #27 near #26 distance 2.78
> color zone #27 near #26 distance 2.68
> color zone #27 near #26 distance 2.58
> color zone #27 near #26 distance 2.48
> color zone #27 near #26 distance 2.38
> color zone #27 near #26 distance 2.28
> volume #27 level 0.1207
> color zone #27 near #26 distance 2.18
> color zone #27 near #26 distance 2.08
> hide #!27 models
> show #!27 models
> fitmap #26 inMap #27
Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
rOAT1-PAH.mrc (#27) using 3865 atoms
average map value = 0.3441, steps = 44
shifted from previous position = 0.00509
rotated from previous position = 0.0145 degrees
atoms outside contour = 605, contour level = 0.12073
Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
rOAT1-PAH.mrc (#27) coordinates:
Matrix rotation and translation
1.00000000 -0.00003177 0.00004592 0.00408484
0.00003177 1.00000000 0.00006809 -0.00110606
-0.00004592 -0.00006809 1.00000000 0.00040828
Axis -0.77323345 0.52146975 0.36080373
Axis point 0.00000000 25.00840435 -11.23310139
Rotation angle (degrees) 0.00504562
Shift along axis -0.00358800
> fitmap #26 inMap #27
Fit molecule rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) to map
rOAT1-PAH.mrc (#27) using 3865 atoms
average map value = 0.3441, steps = 40
shifted from previous position = 0.0153
rotated from previous position = 0.0197 degrees
atoms outside contour = 607, contour level = 0.12073
Position of rOAT1-PAH-coot-7_real_space_refined_007.pdb (#26) relative to
rOAT1-PAH.mrc (#27) coordinates:
Matrix rotation and translation
0.99999998 -0.00017402 -0.00004728 0.01145050
0.00017401 0.99999996 -0.00023139 -0.00012574
0.00004732 0.00023138 0.99999997 -0.01696563
Axis 0.78875519 -0.16123857 0.59318410
Axis point 0.00000000 70.72803400 -1.26127659
Rotation angle (degrees) 0.01680827
Shift along axis -0.00101183
> volume splitbyzone #27
Opened rOAT1-PAH.mrc 0 as #28.1, grid size 160,160,160, pixel 0.83, shown at
level 0.121, step 1, values float32
Opened rOAT1-PAH.mrc 1 as #28.2, grid size 160,160,160, pixel 0.83, shown at
level 0.121, step 1, values float32
Opened rOAT1-PAH.mrc 2 as #28.3, grid size 160,160,160, pixel 0.83, shown at
level 0.121, step 1, values float32
> close #28.1-2
> volume #28.3 level 0.05463
> color #28.3 white models
> color #28.3 #ffffb2ff models
> color #28.3 #ffffb296 models
> select add #26
3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected
> color #26 #bf3434ff
> select subtract #26
Nothing selected
> hide #!26 models
> hide #!28 models
> hide #!28.3 models
> show #!28 models
> show #!28.3 models
> hide #!28 models
> show #!28 models
> show #!26 models
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 59852, resource id:
35657337, major code: 40 (TranslateCoords), minor code: 0
> hide #!26 models
> hide #!28 models
> hide #!28.3 models
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20220525_rOAT1-FBP/inward_j46_2.8A/postprocess.mrc
Opened postprocess.mrc as #29, grid size 320,320,320, pixel 0.83, shown at
level 0.0068, step 2, values float32
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-FBP_model/rOAT1-FBP_Model04_RSR_004.pdb
Chain information for rOAT1-FBP_Model04_RSR_004.pdb #30
---
Chain | Description
A | No description available
> show #!2 models
> volume #29 step 1
> volume #29 level 0.01695
> select add #30
4327 atoms, 4393 bonds, 591 residues, 1 model selected
> view matrix models #30,1,0,0,75.395,0,1,0,59.328,0,0,1,65.467
> view matrix models #30,1,0,0,69.37,0,1,0,69.752,0,0,1,66.8
> view matrix models #30,1,0,0,64.899,0,1,0,72.303,0,0,1,66.211
> view matrix models #30,1,0,0,67.675,0,1,0,68.154,0,0,1,64.823
> rename #29 rOAT1-FBP.mrc
> fitmap #30 inMap #29
Fit molecule rOAT1-FBP_Model04_RSR_004.pdb (#30) to map rOAT1-FBP.mrc (#29)
using 4327 atoms
average map value = 0.02366, steps = 64
shifted from previous position = 2.15
rotated from previous position = 1.57 degrees
atoms outside contour = 1497, contour level = 0.016951
Position of rOAT1-FBP_Model04_RSR_004.pdb (#30) relative to rOAT1-FBP.mrc
(#29) coordinates:
Matrix rotation and translation
0.99965949 -0.01809184 -0.01880406 69.16631575
0.01825291 0.99979787 0.00842953 64.90387685
0.01864775 -0.00876989 0.99978765 65.39100171
Axis -0.31300664 -0.68157330 0.66142625
Axis point -4271.01743380 0.00000000 3378.83285764
Rotation angle (degrees) 1.57437238
Shift along axis -22.63494048
> fitmap #29 inMap #28.3
Fit map rOAT1-FBP.mrc in map rOAT1-PAH.mrc 2 using 25401 points
correlation = 0.04397, correlation about mean = 0.03331, overlap = 0.1449
steps = 2000, shift = 8.88, angle = 34.9 degrees
Position of rOAT1-FBP.mrc (#29) relative to rOAT1-PAH.mrc 2 (#28.3)
coordinates:
Matrix rotation and translation
0.83021101 -0.04922054 -0.55527201 36.70411652
0.13130357 0.98533433 0.10897540 -101.23145590
0.54176475 -0.16338178 0.82449824 -98.97434819
Axis -0.23793623 -0.95839145 0.15770918
Axis point 214.13564799 0.00000000 31.76591481
Rotation angle (degrees) 34.91302477
Shift along axis 72.67695975
> fitmap #29 inMap #28.3
Fit map rOAT1-FBP.mrc in map rOAT1-PAH.mrc 2 using 25401 points
correlation = 0.06352, correlation about mean = 0.0448, overlap = 0.3215
steps = 1976, shift = 9.79, angle = 47.5 degrees
Position of rOAT1-FBP.mrc (#29) relative to rOAT1-PAH.mrc 2 (#28.3)
coordinates:
Matrix rotation and translation
0.44591506 0.03168285 -0.89451437 128.47676238
-0.42572042 0.88660402 -0.18081879 31.25418163
0.78735118 0.46144286 0.40883812 -156.17744024
Axis 0.34576253 -0.90543486 -0.24624374
Axis point 186.53313716 0.00000000 6.98625710
Rotation angle (degrees) 68.24252592
Shift along axis 54.58154231
> fitmap #29 inMap #2
Fit map rOAT1-FBP.mrc in map rOAT1-AZT_IF.mrc using 25401 points
correlation = 0.2561, correlation about mean = 0.04268, overlap = 2.051
steps = 232, shift = 3.32, angle = 8.56 degrees
Position of rOAT1-FBP.mrc (#29) relative to rOAT1-AZT_IF.mrc (#2) coordinates:
Matrix rotation and translation
0.54964589 -0.00012465 -0.83539774 175.75622877
-0.44507129 0.84621907 -0.29295875 119.06565669
0.70696602 0.53283512 0.46506536 -99.09845418
Axis 0.45744920 -0.85439368 -0.24647856
Axis point 210.95352936 0.00000000 94.96801349
Rotation angle (degrees) 64.50291620
Shift along axis 3.09624573
> select add #29
4327 atoms, 4393 bonds, 591 residues, 3 models selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!27 models
> view matrix models
> #29,0.54965,-0.00012465,-0.8354,176.85,-0.44507,0.84622,-0.29296,120.37,0.70697,0.53284,0.46507,-99.177,#30,0.99966,-0.018092,-0.018804,70.259,0.018253,0.9998,0.0084295,66.206,0.018648,-0.0087699,0.99979,65.312
> select subtract #30
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #29,0.93603,-0.13155,0.32642,-36.684,0.29946,0.78494,-0.54239,70.054,-0.18487,0.60545,0.77412,-40.4
> view matrix models
> #29,0.99097,-0.1328,0.018694,4.0787,0.13411,0.98118,-0.13891,3.4116,0.00010362,0.14016,0.99013,-37.407
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.99097,-0.1328,0.018694,17.811,0.13411,0.98118,-0.13891,8.06,0.00010362,0.14016,0.99013,-17.751
> view matrix models
> #29,0.99097,-0.1328,0.018694,18.852,0.13411,0.98118,-0.13891,3.5023,0.00010362,0.14016,0.99013,-19.331
> fitmap #29 inMap #2
Fit map rOAT1-FBP.mrc in map rOAT1-AZT_IF.mrc using 25401 points
correlation = 0.937, correlation about mean = 0.7119, overlap = 14.98
steps = 260, shift = 2.93, angle = 16.7 degrees
Position of rOAT1-FBP.mrc (#29) relative to rOAT1-AZT_IF.mrc (#2) coordinates:
Matrix rotation and translation
0.99338416 0.10541244 -0.04556454 -5.89234048
-0.10461957 0.99432199 0.01945563 14.33237930
0.04735669 -0.01455997 0.99877192 -4.89753719
Axis -0.14650897 -0.40022199 -0.90463113
Axis point 131.78683646 64.78395429 0.00000000
Rotation angle (degrees) 6.66633138
Shift along axis -0.44238796
> fitmap #30 inMap #29
Fit molecule rOAT1-FBP_Model04_RSR_004.pdb (#30) to map rOAT1-FBP.mrc (#29)
using 4327 atoms
average map value = 0.02366, steps = 84
shifted from previous position = 1.18
rotated from previous position = 6.66 degrees
atoms outside contour = 1496, contour level = 0.016951
Position of rOAT1-FBP_Model04_RSR_004.pdb (#30) relative to rOAT1-FBP.mrc
(#29) coordinates:
Matrix rotation and translation
0.99966027 -0.01808767 -0.01876641 69.16021058
0.01824668 0.99979876 0.00833662 64.90031908
0.01861185 -0.00867622 0.99978914 65.39198117
Axis -0.31026139 -0.68166338 0.66262576
Axis point -4271.35731029 0.00000000 3392.84555643
Rotation angle (degrees) 1.57107230
Shift along axis -22.36750269
> select subtract #29
Nothing selected
> hide #!27 models
> color #29 white models
> color #30 white
> select ::name="FBP"
18 atoms, 19 bonds, 1 residue, 1 model selected
> color sel red
> color zone #29 near #30 distance 4.98
> volume #29 level 0.01043
> volume splitbyzone #29
Opened rOAT1-FBP.mrc 0 as #31.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 1 as #31.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
> close #31.1-2
> volume #31.3 level 0.002491
> volume #31.3 level 0.005476
> close #31#31.3
> show #!29 models
> color zone #29 near #30 distance 2
[Repeated 1 time(s)]
> volume splitbyzone #29
Opened rOAT1-FBP.mrc 0 as #31.1, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 1 as #31.2, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
Opened rOAT1-FBP.mrc 2 as #31.3, grid size 320,320,320, pixel 0.83, shown at
level 0.0104, step 1, values float32
> close #31.1-2
> volume #31.3 level 0.003802
> color #31.3 white models
> color #31.3 #ffffb2ff models
> color #31.3 #ffffb20f models
> color #31.3 #ffffb296 models
> select add #30
4327 atoms, 4393 bonds, 591 residues, 1 model selected
> color #30 #889944ff
> color #30 #894a08ff
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> hide #!31.3 models
> hide #!31 models
> select subtract #30
Nothing selected
> hide #30 models
> show #!2 models
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20220609_rOAT1-CFM/inward_j194_2.7A/postprocess.mrc
Opened postprocess.mrc as #32, grid size 320,320,320, pixel 0.83, shown at
level 0.00396, step 2, values float32
QXcbConnection: XCB error: 3 (BadWindow), sequence: 4668, resource id:
35657387, major code: 40 (TranslateCoords), minor code: 0
> volume #32 step 1
> volume #32 level 0.01186
> rename #32 rOAT1-CFM.mrc
> fitmap #31.3 inMap #32
Fit map rOAT1-FBP.mrc 2 in map rOAT1-CFM.mrc using 186 points
correlation = 0.7788, correlation about mean = 0.1794, overlap = 0.008643
steps = 80, shift = 1.06, angle = 39.7 degrees
Position of rOAT1-FBP.mrc 2 (#31.3) relative to rOAT1-CFM.mrc (#32)
coordinates:
Matrix rotation and translation
0.74404465 0.65679786 0.12253212 -67.09990326
-0.66239846 0.70118044 0.26376935 89.56606533
0.08732602 -0.27742126 0.95677145 29.93219993
Axis -0.37942983 0.02468307 -0.92489121
Axis point 75.79903236 131.70903838 0.00000000
Rotation angle (degrees) 45.49284979
Shift along axis -0.01355792
> fitmap #31.3 inMap #2
Fit map rOAT1-FBP.mrc 2 in map rOAT1-AZT_IF.mrc using 186 points
correlation = 0.8514, correlation about mean = 0.3895, overlap = 0.01295
steps = 76, shift = 0.987, angle = 35 degrees
Position of rOAT1-FBP.mrc 2 (#31.3) relative to rOAT1-AZT_IF.mrc (#2)
coordinates:
Matrix rotation and translation
0.98357109 0.17790518 -0.03062105 -15.98050765
-0.17592201 0.98266732 0.05844983 19.75924781
0.04048883 -0.05210265 0.99782061 1.12732183
Axis -0.29288928 -0.18839308 -0.93740275
Axis point 102.41456930 99.44616144 0.00000000
Rotation angle (degrees) 10.87852675
Shift along axis -0.09874061
> fitmap #32 inMap #2
Fit map rOAT1-CFM.mrc in map rOAT1-AZT_IF.mrc using 30016 points
correlation = 0.9542, correlation about mean = 0.7898, overlap = 13.57
steps = 72, shift = 2.43, angle = 7.06 degrees
Position of rOAT1-CFM.mrc (#32) relative to rOAT1-AZT_IF.mrc (#2) coordinates:
Matrix rotation and translation
0.99240829 0.11776796 -0.03544703 -8.88787383
-0.11778889 0.99303752 0.00150464 18.44106769
0.03537743 0.00268205 0.99937042 -5.69387210
Axis 0.00478670 -0.28793162 -0.95763901
Axis point 151.76616064 85.25679566 0.00000000
Rotation angle (degrees) 7.06459913
Shift along axis 0.10036409
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM_IF.pdb
> models #30 relModel #32
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM_IF.pdb
Chain information for rOAT1-CFM_IF.pdb #33
---
Chain | Description
A | No description available
> color #33 #ffff7fff
> color #33 #55aaffff
> select add #33
4327 atoms, 4393 bonds, 591 residues, 1 model selected
> view matrix models #33,1,0,0,-3.2206,0,1,0,10.827,0,0,1,-3.1224
> view matrix models #33,1,0,0,-4.4307,0,1,0,11.668,0,0,1,-3.5924
> view matrix models #33,1,0,0,-4.3326,0,1,0,9.3726,0,0,1,-2.8036
> fitmap #33 inMap #32
Fit molecule rOAT1-CFM_IF.pdb (#33) to map rOAT1-CFM.mrc (#32) using 4327
atoms
average map value = 0.0191, steps = 80
shifted from previous position = 1.1
rotated from previous position = 7.12 degrees
atoms outside contour = 1362, contour level = 0.01186
Position of rOAT1-CFM_IF.pdb (#33) relative to rOAT1-CFM.mrc (#32)
coordinates:
Matrix rotation and translation
0.99999299 -0.00023005 -0.00373680 -4.70643521
0.00021365 0.99999035 -0.00438786 8.58155234
0.00373777 0.00438703 0.99998339 -3.97966882
Axis 0.76069466 -0.64796926 0.03846397
Axis point 0.00000000 827.85989235 581.48051316
Rotation angle (degrees) 0.33046593
Shift along axis -9.29381608
> save /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-CFM/rOAT1-CFM.pdb
> models #33 relModel #32
QXcbConnection: XCB error: 3 (BadWindow), sequence: 60371, resource id:
35657459, major code: 40 (TranslateCoords), minor code: 0
> hide #33 models
> hide #!32 models
> select subtract #33
Nothing selected
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!2 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/rOAT1-TFV/RealSpaceRefine_7/rOAT1-TFV-
> Cl_OF-coot-2.pdb
Chain information for rOAT1-TFV-Cl_OF-coot-2.pdb #34
---
Chain | Description
A | No description available
> select ::name="CL"
1 atom, 1 residue, 1 model selected
> hide #!17 models
> show sel atoms
> show #!17 models
> style sel stick
Changed 1 atom style
> color zone #17 near #34 distance 2.98
> select add #34
3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected
> color #34 white
> color zone #17 near #34 distance 2.98
> select ::name="CL"
1 atom, 1 residue, 1 model selected
> color sel red
> color zone #17 near #34 distance 2.98
> volume splitbyzone #17
Opened rOAT1-TVF_OF.mrc 0 as #35.1, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 1 as #35.2, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
Opened rOAT1-TVF_OF.mrc 2 as #35.3, grid size 320,320,320, pixel 0.83, shown
at level 0.011, step 1, values float32
> rename #35 "rOAT1-TVF-Cl_OF.mrc split"
> close #35.1-2
> rename #35.3 "rOAT1-TVF-Cl_OF.mrc 2"
> hide #!35.3 models
> select #34/B:1@CL
1 atom, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel interModel false ignoreHiddenModels true select true
6 contacts
> ui tool show Contacts
> contacts sel intraRes true ignoreHiddenModels true select true
15 contacts
> show sel atoms
> color #34 yellow
> show sel atoms
> close #36
> select add #34
3787 atoms, 3876 bonds, 11 pseudobonds, 487 residues, 3 models selected
> color #34 white
> hide sel atoms
> select ::name="CL"
1 atom, 1 residue, 1 model selected
> show sel atoms
> hide #35.3.1 models
> show #35.3.1 models
> close #34.2
> hide #!35.3 models
> hide #35.3.1 models
> hide #!35 models
> hide #34.1 models
> select #34/B:1@CL
1 atom, 1 residue, 1 model selected
> select #34/A:216
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #34/A:511
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #34: 219
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #34: 273
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #34/A:4
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #34/A:511
15 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> select add #34/A:512
23 atoms, 21 bonds, 3 residues, 1 model selected
> show sel atoms
> select #34/B:1@CL
1 atom, 1 residue, 1 model selected
> color sel lime
> color #35.3.1 white
> color #35.3.1 #ffffb2ff
> color #35.3.1 #ffffb296
> select #34/B:1@CL
1 atom, 1 residue, 1 model selected
> select add #34
3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected
> color #34 #374c02ff
> select #34/B:1@CL
1 atom, 1 residue, 1 model selected
> color sel lime
> select add #34
3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected
> color (#!34 & sel) byhetero
> select #34/A:2
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select #34/A:3
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #34/A:215
18 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> select #34/B:1@CL
1 atom, 1 residue, 1 model selected
> show #35.3.1 models
> view sel
> hide #35.3.1 models
> hide #!35.3 models
> hide #!35 models
> hide #!34 models
> select add #34
3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected
> select subtract #34
Nothing selected
> show #1 models
> view
> hide #1 models
> show #21 models
> select add #21/A:602@C12
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
44 atoms, 46 bonds, 2 residues, 1 model selected
> select clear
> select #21/A:602@O14
1 atom, 1 residue, 1 model selected
> select add #21/A:601@C04
2 atoms, 2 residues, 1 model selected
> select up
70 atoms, 76 bonds, 2 residues, 1 model selected
> view sel
> show #!22.3 models
> hide #!22.3 models
> hide #!22 models
> hide #21 models
> select add #21
3956 atoms, 4042 bonds, 516 residues, 1 model selected
> select subtract #21
Nothing selected
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 40781, resource id:
35657669, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/postprocess.mrc
Opened postprocess.mrc as #36, grid size 320,320,320, pixel 0.83, shown at
level 0.00418, step 2, values float32
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1_AF-Q4U2R8-F1-model_v4.pdb
hOAT1_AF-Q4U2R8-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for solute carrier family 22 member 6
(Q4U2R8) [more info...]
Chain information for hOAT1_AF-Q4U2R8-F1-model_v4.pdb #37
---
Chain | Description | UniProt
A | solute carrier family 22 member 6 | S22A6_HUMAN 1-563
> rename #36 hOAT1-TFV.mrc
> volume #36 step 1
> volume #36 level 0.008515
> rename #37 hOAT1-TFV_IF.pdb
> view
> show #!2 models
> hide #!2 models
> ui tool show Matchmaker
> matchmaker #37 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rOAT1-AZT_IF.pdb, chain A (#1) with hOAT1-TFV_IF.pdb, chain A
(#37), sequence alignment score = 2359.6
RMSD between 490 pruned atom pairs is 0.806 angstroms; (across all 500 pairs:
0.862)
> matchmaker #37 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rOAT1-AZT_IF.pdb, chain A (#1) with hOAT1-TFV_IF.pdb, chain A
(#37), sequence alignment score = 2359.6
RMSD between 490 pruned atom pairs is 0.806 angstroms; (across all 500 pairs:
0.862)
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1-TVF_IF.pdb
> models #37 relModel #36
> rename #36 hOAT1-TFV_IF.mrc
> hide #37 models
> hide #!36 models
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/inward_j62_3.2A/hOAT1_AF-Q4U2R8-F1-model_v4.pdb
hOAT1_AF-Q4U2R8-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for solute carrier family 22 member 6
(Q4U2R8) [more info...]
Chain information for hOAT1_AF-Q4U2R8-F1-model_v4.pdb #38
---
Chain | Description | UniProt
A | solute carrier family 22 member 6 | S22A6_HUMAN 1-563
> close #38
> close #37
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/RealSpaceRefine_2/hOAT1-TVF_IF-
> coot-1_real_space_refined_002.pdb
Chain information for hOAT1-TVF_IF-coot-1_real_space_refined_002.pdb #37
---
Chain | Description
A | No description available
> show #!36 models
> color #36 white models
> color #37 white
> hide #!36 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select #37/A:601@C08
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 32 bonds, 1 residue, 1 model selected
> color sel red
> show #!36 models
> color zone #36 near #37 distance 4.98
> color zone #36 near #37 distance 2
[Repeated 1 time(s)]
> color zone #36 near #37 distance 1.9
> color zone #36 near #37 distance 1.8
> color zone #36 near #37 distance 1.7
> volume splitbyzone #36
Opened hOAT1-TFV_IF.mrc 0 as #38.1, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 1 as #38.2, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32
Opened hOAT1-TFV_IF.mrc 2 as #38.3, grid size 320,320,320, pixel 0.83, shown
at level 0.00852, step 1, values float32
> close #38.1-2
> color #38.3 white models
> color #38.3 #ffffb2ff models
> color #38.3 #ffffb296 models
> color #37 #aaff7fff
> select add #37
4375 atoms, 4481 bonds, 564 residues, 1 model selected
> color sel byhetero
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
QXcbConnection: XCB error: 3 (BadWindow), sequence: 48690, resource id:
35657985, major code: 40 (TranslateCoords), minor code: 0
> hide #!38.3 models
> hide #!38 models
> select subtract #37
Nothing selected
> show #!34 models
Drag select of 25 atoms, 383 residues, 24 bonds
> select up
2906 atoms, 2958 bonds, 383 residues, 2 models selected
> select clear
> select add #37/A:326
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> hide #!34 models
> select add #37
4375 atoms, 4481 bonds, 564 residues, 1 model selected
> select subtract #37
Nothing selected
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
> models #37 relModel #36
QXcbConnection: XCB error: 3 (BadWindow), sequence: 16970, resource id:
35658005, major code: 40 (TranslateCoords), minor code: 0
QXcbConnection: XCB error: 3 (BadWindow), sequence: 16981, resource id:
35657995, major code: 40 (TranslateCoords), minor code: 0
> open
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/20241127_hOAT1-TFV/outward_j68_3.1A/postprocess.mrc
Opened postprocess.mrc as #39, grid size 320,320,320, pixel 0.83, shown at
level 0.00436, step 2, values float32
QXcbConnection: XCB error: 3 (BadWindow), sequence: 18302, resource id:
35658010, major code: 40 (TranslateCoords), minor code: 0
> rename #39 hOAT1-TFV_OF.mrc
> volume #39 step 1
> volume #39 level 0.01031
> hide #!39 models
> open
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
Chain information for hOAT1-TFV_OF.pdb #40
---
Chain | Description
A | No description available
> hide #37 models
> select #40: 320-600
1850 atoms, 1888 bonds, 244 residues, 1 model selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> ui tool show Matchmaker
> matchmaker #40 & sel to #18
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 rOAT1-TFV_OF-coot-1_real_space_refined_007.pdb, chain A (#18) with
hOAT1-TFV_OF.pdb, chain A (#40), sequence alignment score = 866.1
RMSD between 164 pruned atom pairs is 0.748 angstroms; (across all 200 pairs:
7.198)
> matchmaker #40 to #15
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 rOAT1-TFV_IF-coot-3.pdb, chain A (#15) with hOAT1-TFV_OF.pdb, chain
A (#40), sequence alignment score = 2368.6
RMSD between 493 pruned atom pairs is 0.665 angstroms; (across all 500 pairs:
0.719)
> show #!18 models
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> view matrix models
> #40,0.99727,-0.025813,-0.069217,13.221,0.025375,0.99965,-0.0072002,-1.7643,0.069379,0.0054242,0.99758,-8.8122
> undo
> ui mousemode right "move picked models"
> view matrix models #18,1,0,0,0.019269,0,1,0,-0.04277,0,0,1,0.28987
> undo
> ui mousemode right pivot
> ui tool show Matchmaker
> matchmaker #40 & sel to #5 & sel
No 'to' model specified
> select clear
> hide #!18 models
> show #!18 models
> select #18,40: 320-600
3274 atoms, 3340 bonds, 2 pseudobonds, 433 residues, 3 models selected
> ui tool show Matchmaker
> matchmaker #40 & sel to #5 & sel
No 'to' model specified
> matchmaker #40 & sel to #5 & sel
No 'to' model specified
> matchmaker #40 & sel to #5 & sel
No 'to' model specified
> ui mousemode right "translate selected atoms"
> select #40: 320-600
1850 atoms, 1888 bonds, 244 residues, 1 model selected
> hide #!18 models
> show #!18 models
> hide #40 models
> hide #!18 models
> show #40 models
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
> models #40 relModel #39
QXcbConnection: XCB error: 3 (BadWindow), sequence: 34583, resource id:
35658147, major code: 40 (TranslateCoords), minor code: 0
> fitmap #40 inMap #39
Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
atoms
average map value = 0.007219, steps = 88
shifted from previous position = 0.909
rotated from previous position = 8.49 degrees
atoms outside contour = 2887, contour level = 0.010308
Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
coordinates:
Matrix rotation and translation
0.99019825 -0.07829950 -0.11565728 27.38037598
0.07892080 0.99688057 0.00079533 -10.70816731
0.11523422 -0.00991530 0.99328886 -13.08861468
Axis -0.03831490 -0.82596303 0.56242070
Axis point 128.86145300 0.00000000 225.96021530
Rotation angle (degrees) 8.03460025
Shift along axis 0.43416611
> save
> /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF.pdb
> models #40 relModel #39
> undo
> select clear
> show #!39 models
> fitmap #40 inMap #39
Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
atoms
average map value = 0.007218, steps = 28
shifted from previous position = 0.0175
rotated from previous position = 0.016 degrees
atoms outside contour = 2888, contour level = 0.010308
Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
coordinates:
Matrix rotation and translation
0.99020256 -0.07845145 -0.11551732 27.36683659
0.07909202 0.99686685 0.00096497 -10.76110579
0.11507968 -0.01009202 0.99330500 -13.04322773
Axis -0.03956067 -0.82505023 0.56367284
Axis point 128.67057833 0.00000000 226.14572082
Rotation angle (degrees) 8.03322105
Shift along axis 0.44368911
> fitmap #40 inMap #39
Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
atoms
average map value = 0.007219, steps = 44
shifted from previous position = 0.00455
rotated from previous position = 0.00258 degrees
atoms outside contour = 2889, contour level = 0.010308
Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
coordinates:
Matrix rotation and translation
0.99020340 -0.07846932 -0.11549800 27.37049731
0.07911379 0.99686509 0.00099928 -10.76639922
0.11505751 -0.01012698 0.99330721 -13.03687370
Axis -0.03980982 -0.82492871 0.56383314
Axis point 128.62890621 0.00000000 226.21984207
Rotation angle (degrees) 8.03295687
Shift along axis 0.44127588
> select add #40
4375 atoms, 4481 bonds, 564 residues, 1 model selected
> fitmap #40 inMap #39
Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
atoms
average map value = 0.007219, steps = 60
shifted from previous position = 2.24
rotated from previous position = 0.00666 degrees
atoms outside contour = 2889, contour level = 0.010308
Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
coordinates:
Matrix rotation and translation
0.99020164 -0.07840067 -0.11555975 25.97288245
0.07903810 0.99687116 0.00093711 -9.32824593
0.11512471 -0.01006155 0.99330009 -12.03377088
Axis -0.03935047 -0.82533103 0.56327634
Axis point 116.53468443 0.00000000 214.84157931
Rotation angle (degrees) 8.03353574
Shift along axis -0.10149276
> show #!17 models
> fitmap #39 inMap #19.3
Fit map hOAT1-TFV_OF.mrc in map rOAT1-TVF_OF.mrc 2 using 37364 points
correlation = 0.03002, correlation about mean = -0.02439, overlap = 0.01206
steps = 936, shift = 1.08, angle = 13.4 degrees
Position of hOAT1-TFV_OF.mrc (#39) relative to rOAT1-TVF_OF.mrc 2 (#19.3)
coordinates:
Matrix rotation and translation
0.98280665 -0.13043667 -0.13068041 37.39205996
0.11063752 0.98266445 -0.14876125 8.18112237
0.14781892 0.13174539 0.98020035 -34.01816129
Axis 0.60585490 -0.60151939 0.52068635
Axis point 0.00000000 261.98069292 24.54762139
Rotation angle (degrees) 13.38519605
Shift along axis 0.02026683
> fitmap #39 inMap #19.3
Fit map hOAT1-TFV_OF.mrc in map rOAT1-TVF_OF.mrc 2 using 37364 points
correlation = 0.03002, correlation about mean = -0.0244, overlap = 0.01206
steps = 48, shift = 0.0138, angle = 0.161 degrees
Position of hOAT1-TFV_OF.mrc (#39) relative to rOAT1-TVF_OF.mrc 2 (#19.3)
coordinates:
Matrix rotation and translation
0.98301413 -0.12857767 -0.13096186 37.15798588
0.10847145 0.98263409 -0.15054633 8.70610140
0.14804449 0.13378355 0.97989019 -34.26954280
Axis 0.61337235 -0.60188813 0.51137563
Axis point -0.00000000 260.45263984 27.89398858
Rotation angle (degrees) 13.40165031
Shift along axis 0.02697294
> fitmap #40 inMap #39
Fit molecule hOAT1-TFV_OF.pdb (#40) to map hOAT1-TFV_OF.mrc (#39) using 4375
atoms
average map value = 0.007219, steps = 132
shifted from previous position = 0.778
rotated from previous position = 13.4 degrees
atoms outside contour = 2889, contour level = 0.010308
Position of hOAT1-TFV_OF.pdb (#40) relative to hOAT1-TFV_OF.mrc (#39)
coordinates:
Matrix rotation and translation
0.99020454 -0.07852899 -0.11544767 25.97319443
0.07917768 0.99685998 0.00103677 -9.35919916
0.11500374 -0.01016749 0.99331302 -12.00484753
Axis -0.04009077 -0.82459474 0.56430155
Axis point 116.41047661 0.00000000 215.06686153
Rotation angle (degrees) 8.03257950
Shift along axis -0.09809308
> hide #!17 models
> hide #!39 models
> close #40
> open /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF-
> coot-1.pdb
Chain information for hOAT1-TFV_OF-coot-1.pdb #40
---
Chain | Description
A | No description available
> show #!39 models
> color #39 white models
> color #40 white
> hide #!39 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> color sel red
> select up
31 atoms, 32 bonds, 1 residue, 1 model selected
> color sel red
> show #!39 models
> color zone #39 near #40 distance 4.98
> color zone #39 near #40 distance 2
[Repeated 1 time(s)]
> volume #39 level 0.01241
> open /home/dout2/isilon/USERS/dout2/SLC22_MapModel/hOAT1-PBD/hOAT1-TFV_OF-
> coot-2.pdb
Chain information for hOAT1-TFV_OF-coot-2.pdb #41
---
Chain | Description
A | No description available
> hide #!40 models
> color #41 white
> color zone #39 near #41 distance 2
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 32 bonds, 1 residue, 1 model selected
> color sel red
> color zone #39 near #41 distance 2
> volume #39 level 0.01056
> color zone #39 near #41 distance 2.1
> color zone #39 near #41 distance 2.2
> color zone #39 near #41 distance 2.3
> color zone #39 near #41 distance 2.4
> color zone #39 near #41 distance 2.5
> color zone #39 near #41 distance 2.6
> color zone #39 near #41 distance 2.7
> color zone #39 near #41 distance 2.8
> color zone #39 near #41 distance 2.9
> color zone #39 near #41 distance 3
> color zone #39 near #41 distance 2.9
> color zone #39 near #41 distance 2.8
> color zone #39 near #41 distance 2.7
> color zone #39 near #41 distance 2.6
> color zone #39 near #41 distance 2.5
> color zone #39 near #41 distance 2.4
> color zone #39 near #41 distance 2.3
> color zone #39 near #41 distance 2.2
> color zone #39 near #41 distance 2.1
> color zone #39 near #41 distance 2
> color zone #39 near #41 distance 1.9
> color zone #39 near #41 distance 2
> color zone #39 near #41 distance 2.1
> color zone #39 near #41 distance 2.2
> color zone #39 near #41 distance 2.3
> color zone #39 near #41 distance 2.4
> color zone #39 near #41 distance 2.5
> volume splitbyzone #39
Opened hOAT1-TFV_OF.mrc 0 as #42.1, grid size 320,320,320, pixel 0.83, shown
at level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 1 as #42.2, grid size 320,320,320, pixel 0.83, shown
at level 0.0106, step 1, values float32
Opened hOAT1-TFV_OF.mrc 2 as #42.3, grid size 320,320,320, pixel 0.83, shown
at level 0.0106, step 1, values float32
> close #42.1-2
> color #42.3 white models
> color #42.3 #ffffb2ff models
> color #42.3 #ffffb296 models
> volume #42.3 level 0.006989
> select add #41
4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected
> color #41 #aaffffff
> color #41 blue
> color #41 red
> color #41 #aa00ffff
> color #41 #0055ffff
> color #41 #55557fff
> color #41 #ff557fff
> color #41 #ffaaffff
> color (#!41 & sel) byhetero
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
> show #!34 models
> hide #!41 models
> hide #!42 models
> hide #!42.3 models
> select subtract #41
Nothing selected
> hide #!34 models
> show #1 models
> show #!3.3 models
> hide #!3.3 models
> hide #!3 models
> hide #1 models
> show #!22.3 models
> show #21 models
> select add #21/A:601@O25
1 atom, 1 bond, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> view sel
> volume #22.3 level 0.01409
> hide #!22.3 models
> hide #!22 models
> hide #21 models
> show #!22.3 models
> hide #!22.3 models
> hide #!22 models
> show #!23 models
> hide #!23 models
> show #!25.3 models
> show #!24 models
> hide #!25.3 models
> hide #!25 models
> hide #!24 models
> show #1 models
> show #!3.3 models
> hide #!3.3 models
> hide #!3 models
> hide #1 models
> show #!5 models
> show #!6.3 models
> hide #!6.3 models
> hide #!6 models
> hide #!5 models
> show #8 models
> show #!9.3 models
> volume #9.3 level 0.003826
> select #8/A:230
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #8/A:227
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!9.3 models
> hide #!9 models
> hide #8 models
> show #!12 models
> show #!11.3 models
> color #11.3 #ffffb296 models
> hide #!12 models
> hide #!11.3 models
> hide #!11 models
> show #15 models
> show #!16.3 models
> hide #!16.3 models
> hide #!16 models
> hide #15 models
> show #!18 models
> show #!19.3 models
> hide #!18 models
> hide #!19 models
> hide #!19.3 models
> show #37 models
> show #!38.3 models
> hide #!38.3 models
> hide #!38 models
> hide #37 models
> close #40
> show #!41 models
> show #!42.3 models
> hide #!42.3 models
> hide #!42 models
> hide #!41 models
> show #!26 models
> show #!28.3 models
> select #26/A:230
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select #26/A:200
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #26
3865 atoms, 3947 bonds, 1 pseudobond, 506 residues, 2 models selected
> color (#!26 & sel) byhetero
> select clear
> select #26/A:223
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #26/A:227
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #26/A:223
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #26/A:200
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select #26/A:226
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #26/A:204
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!28.3 models
> hide #!28 models
> hide #!26 models
> show #!31.3 models
> show #30 models
> select add #30
4327 atoms, 4393 bonds, 591 residues, 1 model selected
> color sel byhetero
> select clear
> save
> /home/dout2/isilon/PROJECTS/OAT1/new_structures_20250209/OAT1_ligand_density.cxs
> includeMaps true
——— End of log from Mon Feb 10 17:46:10 2025 ———
opened ChimeraX session
> hide #!31.3 models
> hide #!31 models
> hide #30 models
> show #!34 models
> show #!35 models
> show #!35.3 models
> volume #35.3 level 0.01175
> select #35.3
2 models selected
> view sel
> color #34 tan
> ui tool show "Side View"
> select add #34
3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 4 models selected
> color (#!34 & sel) byhetero
> select clear
> select #34/A:447
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #34/A:507
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
——— End of log from Tue Mar 11 12:00:09 2025 ———
opened ChimeraX session
> hide #!35.3 models
> hide #!35 models
> show #!17 models
> color #17 #ffffb2ff models
> color #17 #ffffb280 models
> ui tool show "Side View"
> color #17 #ffffb24d models
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
——— End of log from Thu Apr 10 14:06:06 2025 ———
opened ChimeraX session
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie1.mp4
Movie saved to /Users/dout2/Desktop/movie1.mp4
> select add #34
3787 atoms, 3876 bonds, 5 pseudobonds, 487 residues, 2 models selected
> show sel atoms
> select clear
> hide #!34 models
> hide #!17 models
> show #!6 models
> show #1 models
> view
> select #1/A:463
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:466
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:228
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:230
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:231
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:377
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:378
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:381
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:225
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:382
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!6 models
> show #!6 models
> hide #1 models
> show #1 models
> select add #1
3905 atoms, 3986 bonds, 515 residues, 1 model selected
> select subtract #1
Nothing selected
> hide #1 models
> hide #!6 models
> show #!18 models
> hide #!18 models
> show #1 models
> select #1/A:228
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/A:199
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:257
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:145
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:466
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:149
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:146
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:204
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:150
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:149
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:203
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:146
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:149
5 atoms, 4 bonds, 1 residue, 1 model selected
Drag select of 13 residues
> select #1/A:463
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:466@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel intraRes true ignoreHiddenModels true select true
> makePseudobonds false reveal true
26 contacts
> select clear
> select : 382
126 atoms, 112 bonds, 14 residues, 14 models selected
> select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #1 atoms
> hide #!6 target m
[Repeated 1 time(s)]
> hide #!4 target m
> select add #1
5716 atoms, 5702 bonds, 714 residues, 14 models selected
> select subtract #1
1811 atoms, 1716 bonds, 199 residues, 13 models selected
> select add #5
5446 atoms, 5448 bonds, 5 pseudobonds, 670 residues, 14 models selected
> select subtract #5
1672 atoms, 1584 bonds, 184 residues, 12 models selected
> select add #8
5445 atoms, 5437 bonds, 691 residues, 12 models selected
> select subtract #8
1533 atoms, 1452 bonds, 169 residues, 11 models selected
> select add #12
5186 atoms, 5201 bonds, 5 pseudobonds, 640 residues, 12 models selected
> select subtract #12
1394 atoms, 1320 bonds, 154 residues, 10 models selected
> hide #1 models
> show #1 models
> select add #15
5172 atoms, 5186 bonds, 654 residues, 10 models selected
> select subtract #15
1255 atoms, 1188 bonds, 139 residues, 9 models selected
> select add #18
4902 atoms, 4932 bonds, 5 pseudobonds, 610 residues, 10 models selected
> select subtract #18
1116 atoms, 1056 bonds, 124 residues, 8 models selected
> select add #21
4933 atoms, 4966 bonds, 625 residues, 8 models selected
> select subtract #21
977 atoms, 924 bonds, 109 residues, 7 models selected
> select add #24
4628 atoms, 4674 bonds, 5 pseudobonds, 580 residues, 8 models selected
> select subtract #24
838 atoms, 792 bonds, 94 residues, 6 models selected
> select add #26
4564 atoms, 4607 bonds, 1 pseudobond, 585 residues, 7 models selected
> select subtract #26
699 atoms, 660 bonds, 79 residues, 5 models selected
> select add #30
4885 atoms, 4921 bonds, 653 residues, 5 models selected
> select subtract #30
558 atoms, 528 bonds, 62 residues, 4 models selected
> select add #33
4744 atoms, 4789 bonds, 636 residues, 4 models selected
> select subtract #33
417 atoms, 396 bonds, 45 residues, 3 models selected
> select add #34
4065 atoms, 4140 bonds, 5 pseudobonds, 517 residues, 4 models selected
> select subtract #34
278 atoms, 264 bonds, 30 residues, 2 models selected
> select add #37
4514 atoms, 4613 bonds, 579 residues, 2 models selected
> select subtract #37
139 atoms, 132 bonds, 15 residues, 1 model selected
> select add #41
4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected
> select subtract #41
Nothing selected
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!3.3 models
> ui tool show "Side View"
> select #1/A:35@CG
1 atom, 1 residue, 1 model selected
> select : 35
112 atoms, 98 bonds, 14 residues, 14 models selected
> hide sel & #1 atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select : 35
112 atoms, 98 bonds, 14 residues, 14 models selected
> show sel & #1 atoms
> select clear
> select : 35
112 atoms, 98 bonds, 14 residues, 14 models selected
> hide sel & #1 atoms
> save /Users/dout2/Desktop/image1.png supersample 3
> save /Users/dout2/Desktop/rOAT1-AZT_OF_LigandDensity.png supersample 3
> select add #1
4009 atoms, 4077 bonds, 528 residues, 14 models selected
> select subtract #1
104 atoms, 91 bonds, 13 residues, 13 models selected
> select add #5
3870 atoms, 3948 bonds, 5 pseudobonds, 498 residues, 14 models selected
> select subtract #5
96 atoms, 84 bonds, 12 residues, 12 models selected
> select add #8
4000 atoms, 4062 bonds, 533 residues, 12 models selected
> select subtract #8
88 atoms, 77 bonds, 11 residues, 11 models selected
> select add #12
3872 atoms, 3951 bonds, 5 pseudobonds, 496 residues, 12 models selected
> select subtract #12
80 atoms, 70 bonds, 10 residues, 10 models selected
> select add #21
4028 atoms, 4105 bonds, 525 residues, 10 models selected
> select subtract #21
72 atoms, 63 bonds, 9 residues, 9 models selected
> select add #18
3850 atoms, 3932 bonds, 5 pseudobonds, 494 residues, 10 models selected
> select subtract #18
64 atoms, 56 bonds, 8 residues, 8 models selected
> select add #24
3846 atoms, 3931 bonds, 5 pseudobonds, 493 residues, 9 models selected
> select subtract #24
56 atoms, 49 bonds, 7 residues, 7 models selected
> select add #26
3913 atoms, 3989 bonds, 1 pseudobond, 512 residues, 8 models selected
> select subtract #26
48 atoms, 42 bonds, 6 residues, 6 models selected
> select add #30
4367 atoms, 4428 bonds, 596 residues, 6 models selected
> select subtract #30
40 atoms, 35 bonds, 5 residues, 5 models selected
> select add #33
4359 atoms, 4421 bonds, 595 residues, 5 models selected
> select subtract #33
32 atoms, 28 bonds, 4 residues, 4 models selected
> select add #34
3811 atoms, 3897 bonds, 5 pseudobonds, 490 residues, 5 models selected
> select subtract #34
24 atoms, 21 bonds, 3 residues, 3 models selected
> select add #37
4391 atoms, 4495 bonds, 566 residues, 3 models selected
> select subtract #37
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #41
4383 atoms, 4488 bonds, 1 pseudobond, 565 residues, 3 models selected
> select subtract #41
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!3.3 models
> hide #!3 models
> hide #1 models
> show #!5 models
> show #!6.3 models
> hide #!6.3 models
> hide #!6 models
> hide #!5 models
> show #8 models
> show #!9 models
> show #!9.3 models
> select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #8 atoms
> select: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
Unknown command: select:
382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
> select : 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #8 atoms
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #8 atoms
> select clear
> volume #9.3 level 0.00516
> save /Users/dout2/Desktop/rOAT1-PBD_IF_LigandDensity.png supersample 3
> hide #!9.3 models
> hide #!9 models
> hide #8 models
> show #15 models
> show #!16 models
> show #!16.3 models
> select #15/A:442
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #15 atoms
> select #1-50: 438
154 atoms, 154 bonds, 14 residues, 14 models selected
> select clear
> save /Users/dout2/Desktop/rOAT1-TFV_IF_LigandDensity.png supersample 3
> hide #!16.3 models
> hide #!16 models
> hide #15 models
> show #21 models
> show #!22 models
> show #!22.3 models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #21 atoms
> select clear
> save /Users/dout2/Desktop/rOAT1-AAI_IF_LigandDensity.png supersample 3
> volume #22.3 level 0.0128
> hide #!22.3 models
> hide #!22 models
> hide #21 models
> show #!27 models
> show #!28 models
> hide #!27 models
> show #!26 models
> show #!28.3 models
> volume #28.3 level 0.06828
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #!26 atoms
> select clear
> save /Users/dout2/Desktop/rOAT1-PAH_IF_LigandDensity.png supersample 3
> hide #!28.3 models
> hide #!28 models
> hide #!26 models
> show #30 models
> show #!31 models
> show #!31.3 models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #30 atoms
> select clear
> save /Users/dout2/Desktop/rOAT1-FBP_IF_LigandDensity.png supersample 3
> hide #!31.3 models
> hide #!31 models
> hide #30 models
> show #37 models
> show #!38 models
> show #!38.3 models
> select clear
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #37 atoms
> select clear
> show #!36 models
> hide #!36 models
> show #!36 models
> hide #!36 models
> volume #38.3 level 0.006101
> volume #38.3 level 0.006864
> save /Users/dout2/Desktop/hOAT1-TFV_IF_LigandDensity.png supersample 3
> hide #!38.3 models
> hide #!38 models
> hide #37 models
> show #!2 models
> hide #!2 models
> show #1 models
> show #!3 models
> show #!3.3 models
> hide #!3.3 models
> hide #!3 models
> hide #1 models
> show #!5 models
> show #!6.3 models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #!5 atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
[Repeated 1 time(s)]
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #!5 atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> volume #6.3 level 0.0106
> save /Users/dout2/Desktop/rOAT1-AZT_OF_LigandDensity.png supersample 3
> hide #!5 models
> hide #!6 models
> hide #!6.3 models
> show #!11 models
> show #!12 models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #!12 atoms
> select clear
> show #!11.3 models
> select clear
> volume #11.3 level 0.009777
> select clear
> show #!10 models
> hide #!10 models
> select clear
> volume #11.3 level 0.01081
> select clear
> show #!10 models
> hide #!10 models
> save /Users/dout2/Desktop/rOAT1-PBD_OF_LigandDensity.png supersample 3
> hide #!12 models
> hide #!11 models
> show #!18 models
> show #!19 models
> show #!19.3 models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #!18 atoms
> select clear
> save /Users/dout2/Desktop/rOAT1-TFV_OF_LigandDensity.png supersample 3
> hide #!19 models
> hide #!18 models
> show #!24 models
> show #!25 models
> show #!25.3 models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
1950 atoms, 1848 bonds, 214 residues, 14 models selected
> show sel & #!24 atoms
> select clear
> save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
> hide #!25 models
> hide #!24 models
> show #!35 models
> show #!34 models
> show #!35.3 models
> hide #!35.3 models
> hide #!35 models
> hide #!34 models
> show #!41 models
> show #!42 models
> show #!42.3 models
> save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
> hide #!41 models
> hide #!42 models
> hide #!42.3 models
> show #!25 models
> show #!24 models
> save /Users/dout2/Desktop/rOAT1-AAI_OF_LigandDensity.png supersample 3
> hide #!24 models
> hide #!25 models
> show #!42.3 models
> show #!41 models
> select clear
[Repeated 1 time(s)]
> ui tool show Distances
> select clear
No distances to delete!
> save /Users/dout2/Desktop/hOAT1-TFV_OF_LigandDensity.png supersample 3
> view
> view orient
> open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j156_2.68A_outward-
> facing/postprocess.mrc
Opened postprocess.mrc as #40, grid size 320,320,320, pixel 0.83, shown at
level 0.00432, step 2, values float32
> volume #40 step 1
> volume #40 level 0.008916
> hide #!41 models
> hide #!40 models
> select add #41
4375 atoms, 4481 bonds, 1 pseudobond, 564 residues, 2 models selected
> select subtract #41
Nothing selected
> hide #!42 models
> show #!40 models
> rename #40 rOAT1-AKG_OF.mrc
> open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j156_2.68A_outward-
> facing/RealSpaceRefine_1/rOAT1-AKG_OF-coot-5_real_space_refined_001.pdb
Chain information for rOAT1-AKG_OF-coot-5_real_space_refined_001.pdb #43
---
Chain | Description
A | No description available
> select clear
> open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j122_2.63A_outward-
> occluded/postprocess.mrc
Opened postprocess.mrc as #44, grid size 320,320,320, pixel 0.83, shown at
level 0.00378, step 2, values float32
> rename #44 rOAT1-AKG_OOC.mrc
> open /Users/dout2/Downloads/20250226_rOAT1-AKG/r3d_j122_2.63A_outward-
> occluded/RealSpaceRefine_3/rOAT1-AKG_OF-coot-4_real_space_refined_003.pdb
Chain information for rOAT1-AKG_OF-coot-4_real_space_refined_003.pdb #45
---
Chain | Description
A | No description available
> rename #45 rOAT1-AKG_OOC-coot-4_real_space_refined_003.pdb
> hide #!43 models
> hide #!40 models
> volume #44 step 1
> volume #44 level 0.01023
> select ::name="AKG"
20 atoms, 18 bonds, 2 residues, 2 models selected
> view sel
> color #44 #ffffb24d models
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
2228 atoms, 2112 bonds, 244 residues, 16 models selected
> show sel & #!45 atoms
> select clear
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> color #44 #ffffb280 models
> color #44 #ffffb266 models
> color #44 #ffffb24d models
> select clear
> save /Users/dout2/Desktop/hOAT1-AKG_OOC_LigandDensity.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie2.mp4
Movie saved to /Users/dout2/Desktop/movie2.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie3.mp4
Movie saved to /Users/dout2/Desktop/movie3.mp4
> hide #!45 models
> hide #!44 models
> show #!43 models
> show #!40 models
> color #40 #b2b2b24d models
> select clear
> color #40 #ffffb24d models
> select clear
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
2228 atoms, 2112 bonds, 244 residues, 16 models selected
> show sel & #!43 atoms
> select clear
[Repeated 1 time(s)]
> volume #40 level 0.009283
> save /Users/dout2/Desktop/rOAT1-AKG_OF_LigandDensity.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie3.mp4
Movie saved to /Users/dout2/Desktop/movie3.mp4
> volume #40 level 0.01222
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie4.mp4
Movie saved to /Users/dout2/Desktop/movie4.mp4
> hide #!43 models
> hide #!40 models
> open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
> occluded/postprocess_rescaled.mrc
Opened postprocess_rescaled.mrc as #46, grid size 480,480,480, pixel 0.553,
shown at level 0.0038, step 2, values float32
> open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
> occluded/RealSpaceRefine_1/rOAT1-R466A_OO-coot-2_real_space_refined_001.pdb
Chain information for rOAT1-R466A_OO-coot-2_real_space_refined_001.pdb #47
---
Chain | Description
A | No description available
> select #46
4 models selected
> select clear
> view
> volume #46 step 1
> volume #46 level 0.01147
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
2367 atoms, 2244 bonds, 259 residues, 17 models selected
> view sel
> color #46 #b2ffff4d models
> select #46
4 models selected
> show #!47 atoms
> select clear
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> close #47
> open /Users/dout2/Downloads/20250328_rOAT1-R466A/r3d_j052_2.71A_outward-
> occluded/RealSpaceRefine_2/rOAT1-R466A_OO-coot-3_real_space_refined_002.pdb
Chain information for rOAT1-R466A_OO-coot-3_real_space_refined_002.pdb #47
---
Chain | Description
A | No description available
> select add #46
4 models selected
> select #1-50: 382,35,353,354,142,469,350,466,462,463,346,438,230,378,234
2361 atoms, 2238 bonds, 259 residues, 17 models selected
> show sel & #!47 atoms
> select clear
> select #46
4 models selected
> select clear
> save /Users/dout2/Desktop/rOAT1-R466A_OF_LigandDensity.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie4.mp4
Movie saved to /Users/dout2/Desktop/movie4.mp4
> hide #!46 models
> show #!46 models
> save /Users/dout2/Desktop/rOAT1-R466A_OF_LigandDensity2.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie4.mp4
Movie saved to /Users/dout2/Desktop/movie4.mp4
> view
> color #46 #b2ffffff models
> color #46 #b2ffffab models
> color #46 #b2ffffff models
> select clear
[Repeated 1 time(s)]
> save /Users/dout2/Desktop/rOAT1-R466A_OF.png supersample 3
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
——— End of log from Thu Apr 10 15:43:35 2025 ———
opened ChimeraX session
> hide #!47 models
> hide #!46 models
> rename #46 rOAT1-R466A.mrc
> open
> /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-apo_20220519_cryoSPARC/J12_2.05A_clip-240/cryosparc_P4_J16__localfilter_240.mrc
Opened cryosparc_P4_J16__localfilter_240.mrc as #48, grid size 240,240,240,
pixel 0.553, shown at level 0.238, step 1, values float32
> open
> /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-apo_20220519_cryoSPARC/model/rOAT1-apo-
> coot-4_real_space_refined_004.pdb
Chain information for rOAT1-apo-coot-4_real_space_refined_004.pdb #49
---
Chain | Description
A | No description available
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> rename #48 rOAT1-Apo.mrc
> hide #49 models
> hide #!48 models
> hide #48.1 models
> show #49 models
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> show sel atoms
> size stickRadius 0.3
Changed 72733 bond radii
> select add #49
3942 atoms, 3966 bonds, 570 residues, 1 model selected
> hide sel cartoons
> select clear
Drag select of 10 atoms, 11 bonds
Drag select of 6 atoms, 9 bonds
Drag select of 8 atoms, 10 bonds
Drag select of 4 atoms, 4 bonds
> select up
36 atoms, 34 bonds, 4 residues, 1 model selected
> lighting flat
> graphics silhouettes false
> select clear
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> select clear
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> color sel orange
> color sel purple
> color sel hot pink
> size stickRadius 0.5
Changed 72733 bond radii
> size stickRadius 0.4
Changed 72733 bond radii
> select clear
> select add #49/A:466@CB
1 atom, 1 residue, 1 model selected
> select add #49/A:382@NZ
2 atoms, 2 residues, 1 model selected
> select up
20 atoms, 18 bonds, 2 residues, 1 model selected
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> color sel lime
> color sel purple
> select clear
> select add #49/A:382@NZ
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
20 atoms, 18 bonds, 2 residues, 1 model selected
> color sel byhetero
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> color sel purple
> select clear
> select #49/A:382@NZ
1 atom, 1 residue, 1 model selected
> select add #49/A:466@NH2
2 atoms, 2 residues, 1 model selected
> select add #49/A:466@NH1
3 atoms, 2 residues, 1 model selected
> select add #49/A:466@CZ
4 atoms, 2 residues, 1 model selected
> select add #49/A:466@NE
5 atoms, 2 residues, 1 model selected
> color sel byhetero
> select clear
> save /Users/dout2/Desktop/rOAT1-Apo_keyresidue.png supersample 3
> transparentBackground true
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> ui tool show "Color Actions"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #49: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> hide sel atoms
> select add #49
3942 atoms, 3966 bonds, 570 residues, 1 model selected
> show sel cartoons
> select clear
> view
> select add #49
3942 atoms, 3966 bonds, 570 residues, 1 model selected
> color sel gray
> color sel light gray
> color sel dark gray
> surface sel
> select clear
> save /Users/dout2/Desktop/rOAT1-Apo_bg.png supersample 3
> transparentBackground true
> open /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-0/model.cif
Summary of feedback from opening
/Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-0/model.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Chain information for model.cif #50
---
Chain | Description
A | .
No chain in structure corresponds to chain ID given in local score info (chain
'B')
> hide #!49 models
> rename #50 rOAT1-AKG_IF_af3.cif
> select add #50
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> select clear
> select #50: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel purple
> size stickRadius 0.4
Changed 77114 bond radii
> select clear
> select add #50
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> hide sel cartoons
> select clear
[Repeated 1 time(s)]
> select #50/A:354@CG
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #50/B:1@C4
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select #50/A:382@NZ
1 atom, 1 residue, 1 model selected
> select add #50/A:466@NH1
2 atoms, 2 residues, 1 model selected
> select add #50/A:466@NH2
3 atoms, 2 residues, 1 model selected
> select add #50/A:466@NE
4 atoms, 2 residues, 1 model selected
> color sel byhetero
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_keyresidue.png supersample 3
> transparentBackground true
> select add #50
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> surface sel
> color (#!50 & sel) dark gray
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_bg.png supersample 3
> transparentBackground true
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> hide #!50 models
> show #!45 models
> show #!44 models
> hide #!44 models
> view
> view orient
> hide #!45 models
> show #!43 models
> show #!45 models
> hide #!45 models
> select add #43
3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 2 models selected
> color (#!43 & sel) dark gray
> surface (#!43 & sel)
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_OF_bg.png supersample 3
> transparentBackground true
> hide #43.2 models
> hide #43.1 models
> show #43.1 models
> select #43: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> select subtract #43.2
1 model selected
> select add #43
3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 2 models selected
> hide sel cartoons
> select clear
> select #43: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> select add #43
3807 atoms, 3899 bonds, 3 pseudobonds, 492 residues, 3 models selected
> hide sel atoms
> select #43: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> show sel atoms
> select #43: akg
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #43/A:601@C2
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select clear
> select #43/A:466@NH2
1 atom, 1 residue, 1 model selected
> select add #43/A:466@NH1
2 atoms, 1 residue, 2 models selected
> select add #43/A:466@NE
3 atoms, 1 residue, 2 models selected
> select add #43/A:382@NZ
4 atoms, 2 residues, 2 models selected
> color (#!43 & sel) byhetero
> select clear
> select #43: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> color (#!43 & sel) purple
> select subtract #43/A:382@NZ
65 atoms, 63 bonds, 6 residues, 2 models selected
> select subtract #43/A:466@NH2
64 atoms, 62 bonds, 6 residues, 2 models selected
> select subtract #43/A:466@NH1
63 atoms, 61 bonds, 6 residues, 2 models selected
> select subtract #43/A:466@CD
62 atoms, 59 bonds, 6 residues, 2 models selected
> color (#!43 & sel) byhetero
> select #43: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> color (#!43 & sel) purple
> select subtract #43/A:382@NZ
65 atoms, 63 bonds, 6 residues, 2 models selected
> select subtract #43/A:466@NH1
64 atoms, 62 bonds, 6 residues, 2 models selected
> select subtract #43/A:466@NH2
63 atoms, 61 bonds, 6 residues, 2 models selected
> select clear
> select add #43/A:466@NH2
1 atom, 1 residue, 1 model selected
> select add #43/A:466@NH1
2 atoms, 1 residue, 2 models selected
> select add #43/A:382@NZ
3 atoms, 2 residues, 2 models selected
> color (#!43 & sel) byhetero
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_OF_residue.png supersample 3
> transparentBackground true
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> open /Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-1/model.cif
Summary of feedback from opening
/Users/dout2/Downloads/af3/roat1-AKG_model/seed-1_sample-1/model.cif
---
warning | Unable to fetch template for 'LIG_B': will connect using distance criteria
Chain information for model.cif #51
---
Chain | Description
A | .
No chain in structure corresponds to chain ID given in local score info (chain
'B')
> hide #!43 models
> hide #43.1 models
> view
> rename #51 rOAT1-AKG_IF_af3_model1.cif
> rename #51 rOAT1-AKG_IF_af3_model1-1.cif
> select add #51
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> color sel dark gray
> surface sel
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_IF_bg.png supersample 3
> transparentBackground true
> hide #51.1 models
> select add #51
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #51: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> show sel atoms
> color (#!51 & sel) purple
> size stickRadius 0.4
Changed 81495 bond radii
> select clear
> select #51: AKG
Nothing selected
> show #!51 atoms
> undo
> select add #51
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> show sel atoms
> select #51/B:1@C3
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 1 residue, 1 model selected
> select add #51
4280 atoms, 4381 bonds, 552 residues, 1 model selected
> hide sel atoms
> select #51/B
10 atoms, 9 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> color sel byhetero
> select clear
> select #51: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> show sel atoms
> select #51/A:382@NZ
1 atom, 1 residue, 1 model selected
> select add #51/A:466@NH1
2 atoms, 2 residues, 2 models selected
> select add #51/A:466@NH2
3 atoms, 2 residues, 2 models selected
> color (#!51 & sel) byhetero
> select #51/A:466@NE
1 atom, 1 residue, 1 model selected
> color (#!51 & sel) byhetero
> select clear
> save /Users/dout2/Desktop/rOAT1-AKG_IF_residue.png supersample 3
> transparentBackground true
> close #50
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
——— End of log from Sat Apr 12 21:31:41 2025 ———
opened ChimeraX session
> hide #!51 models
> show #!2 models
> show #1 models
> view
> lighting simple
> lighting soft
> lighting simple
> hide #!2 models
> select #1: 382, 353,438,230,442,466
66 atoms, 64 bonds, 6 residues, 1 model selected
> view sel
> cofr sel
> select clear
> show #!2 models
> color #2 #ffffb2ff models
> color #2 #ffffb24f models
> color #2 #ffffb24e models
> color #2 #ffffb24d models
> select clear
[Repeated 1 time(s)]
> color #2 #a5ffb24d models
> color #2 #9effb24d models
> color #2 #9e43b24d models
> color #2 #9effb24d models
> color #2 #9effff4d models
> select clear
> size stickRadius 0.2
Changed 77114 bond radii
> select clear
> color #2 #942192ff models
> color #2 #9421924d models
> select clear
> color #2 #aa7942ff models
> color #2 #00fdffff models
> color #2 #00fdff4e models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> view sel
> ui tool show "Side View"
> volume #2 level 0.01002
> select clear
> select #1/A:223
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #1/A:207
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!2 models
> select #1/A:36
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!2 models
> select clear
> select #1/A:601@C4'
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> select up
3891 atoms, 3986 bonds, 501 residues, 1 model selected
> select down
19 atoms, 20 bonds, 1 residue, 1 model selected
> cofr sel
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie1.mp4
Movie saved to /Users/dout2/Desktop/movie1.mp4
> hide #!2 models
> hide #1 models
> select add #1
3905 atoms, 3986 bonds, 515 residues, 1 model selected
> select subtract #1
Nothing selected
> show #1 models
> hide #1 models
> show #!5 models
> show #!4 models
> select clear
> volume #4 level 0.01053
> color #4 #fffb00ff models
> color #4 #ffffb2ff models
> color #4 #ffffb24d models
> select #4
4 models selected
> select clear
> select #1: 382, 353,438,230,442,466,207
74 atoms, 71 bonds, 7 residues, 1 model selected
> show #!5 atoms
> select add #5
3848 atoms, 3935 bonds, 5 pseudobonds, 493 residues, 3 models selected
> hide sel & #!5 atoms
> select #5: 382, 353,438,230,442,466,207,601
93 atoms, 91 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> select add #5
3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected
> show sel atoms
> select clear
> select #5/A:601@O4
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 20 bonds, 1 residue, 1 model selected
> cofr sel
> select #4
4 models selected
> volume #4 level 0.01089
> volume #4 level 0.01182
> volume #4 level 0.01292
> select clear
> volume #4 level 0.01311
> volume #4 level 0.01274
> volume #4 level 0.01126
> volume #4 level 0.01274
> volume #4 level 0.012
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie2.mp4
Movie saved to /Users/dout2/Desktop/movie2.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie3.mp4
Movie saved to /Users/dout2/Desktop/movie3.mp4
> view
> hide #!4 models
> select add #5
3774 atoms, 3864 bonds, 5 pseudobonds, 486 residues, 2 models selected
> hide sel atoms
> select #5: 382, 353,438,230,442,466,207,601
93 atoms, 91 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #8 models
> show #!7 models
> hide #8 models
> hide #!7 models
> show #!10 models
> show #!12 models
> color #10 darkgrey models
> color #10 silver models
> color #10 #c0c0c04d models
> select clear
> hide #!12 models
> show #!12 models
> hide #!10 models
> show #!10 models
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
> volume #10 level 0.0124
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
37 atoms, 37 bonds, 1 residue, 1 model selected
> select #12: 382, 353,438,230,442,466,207,601
111 atoms, 108 bonds, 8 residues, 1 model selected
> show sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select H
117 atoms, 10 residues, 9 models selected
> hide sel & #!12 atoms
> select clear
> select #12: 382, 353,438,230,442,466,207,601
111 atoms, 108 bonds, 8 residues, 1 model selected
> view sel
> cofr sel
> volume #10 level 0.009894
> volume #10 level 0.01073
> select clear
[Repeated 1 time(s)]
> select #12/B:601@C16
1 atom, 1 residue, 1 model selected
> select up
37 atoms, 37 bonds, 1 residue, 1 model selected
> view sel
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie4.mp4
Movie saved to /Users/dout2/Desktop/movie4.mp4
> select #10
4 models selected
> select clear
> hide #!12 models
> hide #!10 models
> show #8 models
> show #!7 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> color #7 #ff2f92ff models
> color #7 #ff2f924d models
> select #7
4 models selected
> select clear
> select #8: 382, 353,438,230,442,466,207,601
93 atoms, 90 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> open
> /Users/dout2/Documents/Manuscripts/rOAT1_2023/cryoEM/rOAT1-PBD_20230217/cryosparc_P4_J55__localfilter_160.mrc
Opened cryosparc_P4_J55__localfilter_160.mrc as #50, grid size 160,160,160,
pixel 0.83, shown at level 0.131, step 1, values float32
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie1.mp4
Movie saved to /Users/dout2/Desktop/movie1.mp4
> hide #!7 models
> view
> show #!7 models
> rename #50 rOAT1-PBD_IF.mrc
> select add #50
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #50,1,0,0,82.163,0,1,0,34.821,0,0,1,72.008
> view matrix models #50,1,0,0,78.322,0,1,0,71.965,0,0,1,68.805
> view matrix models #50,1,0,0,68.336,0,1,0,66.309,0,0,1,66.361
> ui tool show "Fit in Map"
> fitmap #50 inMap #7
Fit map rOAT1-PBD_IF.mrc in map rOAT1-PBD_IF.mrc using 40907 points
correlation = 0.9052, correlation about mean = 0.7104, overlap = 318.4
steps = 88, shift = 2.7, angle = 7.48 degrees
Position of rOAT1-PBD_IF.mrc (#50) relative to rOAT1-PBD_IF.mrc (#7)
coordinates:
Matrix rotation and translation
0.99182552 0.09586728 -0.08421166 67.85108178
-0.09362983 0.99515083 0.03013765 73.24636935
0.08669251 -0.02200656 0.99599203 61.03836799
Axis -0.20020488 -0.65617735 -0.72756395
Axis point 63.93693297 -480.82614561 -0.00000000
Rotation angle (degrees) 7.48271681
Shift along axis -106.05604184
> hide #!7 models
> color #50 #b2b2b24d models
> select clear
> ui mousemode right translate
> select #8: 382, 353,438,230,442,466,207,601
93 atoms, 90 bonds, 8 residues, 1 model selected
> view sel
> cofr sel
> volume #50 level 0.2404
> select clear
> select #8: 382, 353,438,230,442,466,207,601
93 atoms, 90 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> volume #50 level 0.2822
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie2.mp4
Movie saved to /Users/dout2/Desktop/movie2.mp4
> hide #!50 models
> view
> hide #8 models
> show #!20 models
> show #21 models
> color #20 #ffffb2ff models
> color #20 #ffffb24d models
> select clear
> select #21: 382, 353,438,230,442,466,207,601
109 atoms, 109 bonds, 8 residues, 1 model selected
> show sel atoms
> select clear
> select H
117 atoms, 10 residues, 9 models selected
> hide sel & #21 atoms
> select clear
> select #21: 382, 353,438,230,442,466,207,601
109 atoms, 109 bonds, 8 residues, 1 model selected
> view sel
> select clear
> color #20 #ffffb280 models
> select clear
> volume #20 level 0.01329
> select #21/A:602@O24
1 atom, 1 residue, 1 model selected
> select up
35 atoms, 38 bonds, 1 residue, 1 model selected
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie2.mp4
Movie saved to /Users/dout2/Desktop/movie2.mp4
> select #21: 382, 353,438,230,442,466,207,601,602
144 atoms, 147 bonds, 9 residues, 1 model selected
> select #20
4 models selected
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie3.mp4
Movie saved to /Users/dout2/Desktop/movie3.mp4
> hide #!20 models
> view
> hide #21 models
> show #!24 models
> show #!23 models
> color #23 #ffffb2ff models
> select clear
> hide #!23 models
> show #!23 models
> select #24: 382, 353,438,230,442,466,207,601,602
109 atoms, 109 bonds, 8 residues, 1 model selected
> view sel
> color #23 #ffffb280 models
> select clear
> select #24/A:601@O14
1 atom, 1 residue, 1 model selected
> select up
35 atoms, 38 bonds, 1 residue, 1 model selected
> cofr sel
> select #23
4 models selected
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie3.mp4
Movie saved to /Users/dout2/Desktop/movie3.mp4
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/dout2/Desktop/movie4.mp4
Movie saved to /Users/dout2/Desktop/movie4.mp4
> save /Users/dout2/Downloads/OAT1_ligand_density.cxs includeMaps true
——— End of log from Tue Apr 15 12:09:47 2025 ———
opened ChimeraX session
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,5
Model Number: MPHG3LL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 16 hours, 13 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
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
R240HY:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
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