wiki:TracQuery

Trac Ticket Queries

Table of Contents

In addition to reports, Trac provides support for custom ticket queries, which can be used to display tickets that meet specified criteria.

To configure and execute a custom query, switch to the View Tickets module from the navigation bar, and select the Custom Query link.

Filters

When you first go to the query page, the default filter will display tickets relevant to you:

  • If logged in then all open tickets, it will display open tickets assigned to you.
  • If not logged in but you have specified a name or email address in the preferences, then it will display all open tickets where your email (or name if email not defined) is in the CC list.
  • If not logged in and no name/email is defined in the preferences, then all open issues are displayed.

Current filters can be removed by clicking the button to the left with the minus sign on the label. New filters are added from the pulldown lists at the bottom corners of the filters box; 'And' conditions on the left, 'Or' conditions on the right. Filters with either a text box or a pulldown menu of options can be added multiple times to perform an Or on the criteria.

You can use the fields just below the filters box to group the results based on a field, or display the full description for each ticket.

After you have edited your filters, click the Update button to refresh your results.

Some shortcuts can be used to manipulate checkbox filters.

  • Clicking on a filter row label toggles all checkboxes.
  • Pressing the modifier key while clicking on a filter row label inverts the state of all checkboxes.
  • Pressing the modifier key while clicking on a checkbox selects the checkbox and deselects all other checkboxes in the filter.

The modifier key is platform and browser dependent. On Mac the modified key is Option/Alt or Command. On Linux the modifier key is Ctrl + Alt. Opera on Windows seems to use Ctrl + Alt, while Alt is effective for other Windows browsers.

Clicking on one of the query results will take you to that ticket. You can navigate through the results by clicking the Next Ticket or Previous Ticket links just below the main menu bar, or click the Back to Query link to return to the query page.

You can safely edit any of the tickets and continue to navigate through the results using the Next/Previous/Back to Query links after saving your results. When you return to the query any tickets which were edited will be displayed with italicized text. If one of the tickets was edited such that it no longer matches the query criteria , the text will also be greyed. Lastly, if a new ticket matching the query criteria has been created, it will be shown in bold.

The query results can be refreshed and cleared of these status indicators by clicking the Update button again.

Saving Queries

Trac allows you to save the query as a named query accessible from the reports module. To save a query ensure that you have Updated the view and then click the Save query button displayed beneath the results. You can also save references to queries in Wiki content, as described below.

Note: one way to easily build queries like the ones below, you can build and test the queries in the Custom report module and when ready - click Save query. This will build the query string for you. All you need to do is remove the extra line breaks.

Note: you must have the REPORT_CREATE permission in order to save queries to the list of default reports. The Save query button will only appear if you are logged in as a user that has been granted this permission. If your account does not have permission to create reports, you can still use the methods below to save a query.

You may want to save some queries so that you can come back to them later. You can do this by making a link to the query from any Wiki page. 

[query:status=new|assigned|reopened&version=1.0 Active tickets against 1.0]

Which is displayed as:

Active tickets against 1.0

This uses a very simple query language to specify the criteria, see Query Language.

Alternatively, you can copy the query string of a query and paste that into the Wiki link, including the leading ? character: 

[query:?status=new&status=assigned&status=reopened&group=owner Assigned tickets by owner]

Which is displayed as:

Assigned tickets by owner

Customizing the table format

You can also customize the columns displayed in the table format (format=table) by using col=<field>. You can specify multiple fields and what order they are displayed in by placing pipes (|) between the columns: 

[[TicketQuery(max=3,status=closed,order=id,desc=1,format=table,col=resolution|summary|owner|reporter)]]

This is displayed as:

Results (1 - 3 of 13588)

1 2 3 4 5 6 7 8 9 10 11 →
Ticket Resolution Summary Owner Reporter
#19988 duplicate Crash on Mac waking from sleep Tom Goddard a.fasemire@…
#19987 fixed Minimize: 'str' object is not callable Eric Pettersen etienne.reboul@…
#19986 duplicate Crash in swap_buffers exposing status line during Mac wakeup, macOS 26 Tom Goddard chimerax-bug-report@…
1 2 3 4 5 6 7 8 9 10 11 →

Full rows

In table format you can also have full rows by using rows=<field>: 

[[TicketQuery(max=3,status=closed,order=id,desc=1,format=table,col=resolution|summary|owner|reporter,rows=description)]]

This is displayed as:

Results (1 - 3 of 13588)

1 2 3 4 5 6 7 8 9 10 11 →
Ticket Resolution Summary Owner Reporter
#19988 duplicate Crash on Mac waking from sleep Tom Goddard a.fasemire@…
Description 
The following bug report has been submitted:
Platform:        macOS-15.7.4-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Thread 0x000000031c8fb000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031b8ef000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031a8e3000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003198d7000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003188cb000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003178bf000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003168b3000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003158a7000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031489b000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031388f000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000312883000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001fd0fe240 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 54)


{"app_name":"ChimeraX","timestamp":"2026-03-17 17:52:57.00 +0100","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.7.4 (24G517)","roots_installed":0,"name":"ChimeraX","incident_id":"37F77AC0-3A58-4AC0-9527-8D31C2802A6E"}
{
  "uptime" : 380000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac15,12",
  "coalitionID" : 952,
  "osVersion" : {
    "train" : "macOS 15.7.4",
    "build" : "24G517",
    "releaseType" : "User"
  },
  "captureTime" : "2026-03-17 17:52:29.6522 +0100",
  "codeSigningMonitor" : 1,
  "incident" : "37F77AC0-3A58-4AC0-9527-8D31C2802A6E",
  "pid" : 40923,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2026-03-17 16:52:42.8392 +0100",
  "procStartAbsTime" : 9052632721286,
  "procExitAbsTime" : 9138710442674,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"1285D59A-DC79-5D40-B366-2F3C3C4E451C","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "31E19731-CFC0-05F8-DC37-45557C23533F",
  "appleIntelligenceStatus" : {"state":"restricted","reasons":["siriAssetIsNotReady","assetIsNotReady"]},
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "EC65655E-BA96-4622-B5B0-4D24C1466F0D",
  "wakeTime" : 7023,
  "sleepWakeUUID" : "72A578B2-C187-41DB-9942-6578E7EC83F4",
  "sip" : "enabled",
  "vmRegionInfo" : "0x169 is not in any region.  Bytes before following region: 4303109783\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      1007c4000-1007c8000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":40923},
  "vmregioninfo" : "0x169 is not in any region.  Bytes before following region: 4303109783\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      1007c4000-1007c8000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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  "vmSummary" : "ReadOnly portion of Libraries: Total=2.0G resident=0K(0%) swapped_out_or_unallocated=2.0G(100%)\nWritable regions: Total=3.6G written=79.8M(2%) resident=2168K(0%) swapped_out=77.7M(2%) unallocated=3.5G(98%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               128K        1 \nActivity Tracing                   256K        1 \nCG image                           368K       20 \nColorSync                          624K       33 \nCoreAnimation                     1872K      112 \nCoreGraphics                        48K        3 \nCoreServices                      9616K        2 \nCoreUI image data                 4656K       33 \nFoundation                          32K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                             2.8G       97 \nMALLOC guard page                  288K       18 \nMach message                        64K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        608K       38 \nStack                            363.3M       39 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      323.6M      221 \nVM_ALLOCATE (reserved)            96.0M        3         reserved VM address space (unallocated)\n__AUTH                            5517K      696 \n__AUTH_CONST                      77.4M      943 \n__CTF                               824        1 \n__DATA                            34.9M     1112 \n__DATA_CONST                      37.5M     1130 \n__DATA_DIRTY                      2777K      342 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       654.1M      181 \n__OBJC_RO                         61.4M        1 \n__OBJC_RW                         2397K        1 \n__TEXT                             1.3G     1148 \n__TEXT (graphics)                 1696K        2 \n__TPRO_CONST                       128K        2 \ndyld private memory               5936K       48 \nmapped file                      280.2M       62 \npage table in kernel              2168K        1 \nshared memory                     3152K       21 \n===========                     =======  ======= \nTOTAL                              6.1G     6326 \nTOTAL, minus reserved VM space     6.0G     6326 \n",
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact
> map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_0.pdb"
> format pdb

Chain information for model_0.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> set bgColor white

> color byattribute a:bfactor

7847 atoms, 487 residues, atom bfactor range 0.245 to 2.81  

> worm bfactor

487 residues, residue bfactor range 0.245 to 2.81  

> graphics silhouettes true

> lighting intensity 0.7

> lighting intensity 0.9

> lighting intensity 1.5

> lighting intensity 1.2

> worm bfactor

487 residues, residue bfactor range 0.245 to 2.81  

> worm bfactor min:0.2 max:0.7

487 residues, residue bfactor range 0.245 to 2.81  

> ui tool show "Side View"

> cd "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact
> map/1IRA/CABSflex_Video/wiki_tutorial/flexible_mode/new_worms"

Current working directory is: /Users/ayomidefasemire/Documents/Doctoral/Side
projects/Contact map/1IRA/CABSflex_Video/wiki_tutorial/flexible_mode/new_worms  

> open spin_movie.cxc

> movie record size 3840,2160

> turn y 2 180

> wait 180

> movie stop

> movie encode output my_movie.mp4 quality highest

Movie saved to my_movie.mp4  
  
executed spin_movie.cxc  

> set bgColor white

> open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact
> map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_1.pdb"

Chain information for model_1.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact
> map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_2.pdb"

Chain information for model_2.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact
> map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_3.pdb"

Chain information for model_3.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact
> map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_4.pdb"

Chain information for model_4.pdb #5  
---  
Chain | Description  
A | No description available  
  

> open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact
> map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_5.pdb"

Chain information for model_5.pdb #6  
---  
Chain | Description  
A | No description available  
  

> open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact
> map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_6.pdb"

Chain information for model_6.pdb #7  
---  
Chain | Description  
A | No description available  
  

> open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact
> map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_7.pdb"

Chain information for model_7.pdb #8  
---  
Chain | Description  
A | No description available  
  

> open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact
> map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_8.pdb"

Chain information for model_8.pdb #9  
---  
Chain | Description  
A | No description available  
  

> open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact
> map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_9.pdb"

Chain information for model_9.pdb #10  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> worm bfactor min:0.2 max:0.7

4870 residues, residue bfactor range 0.245 to 2.81  

> color byattribute a:bfactor

78470 atoms, 4870 residues, atom bfactor range 0.245 to 2.81  

> open spin_movie.cxc

> movie record size 3840,2160

> turn y 2 180

> wait 180

> movie stop

> movie encode output my_movie.mp4 quality highest

Movie saved to my_movie.mp4  
  
executed spin_movie.cxc  

> close

> open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact
> map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1C9S_flexible/1C9S_flexible_with_rmsf/model_0.pdb"

Chain information for model_0.pdb #1  
---  
Chain | Description  
A D F H I K | No description available  
B E | No description available  
C | No description available  
G | No description available  
J | No description available  
  

> show atoms

> hide atoms

> show cartoons

Computing secondary structure  

> color byattribute a:bfactor

11824 atoms, 756 residues, atom bfactor range 0.07 to 1.05  

> worm bfactor

756 residues, residue bfactor range 0.07 to 1.05  

> worm bfactor min:0.2 max:0.7

756 residues, residue bfactor range 0.07 to 1.05  

> worm bfactor min:0.2 max:0.9

756 residues, residue bfactor range 0.07 to 1.05  

> save 19CS_worm.png width 2000 supersample 4

> lighting simple

> lighting intensity 1.2

> lighting intensity 1.5

> save 19CS_worm.png width 2000 supersample 4

> open spin_movie.cxc

> movie record size 3840,2160

> turn y 2 180

> wait 180

> movie stop

> movie encode output my_movie.mp4 quality highest

Movie saved to my_movie.mp4  
  
executed spin_movie.cxc  

> open spin_movie.cxc

> movie record size 3840,2160

> turn y 2 180

> wait 180

> movie stop

> movie encode output my_movie.mp4 quality highest

Movie saved to my_movie.mp4  
  
executed spin_movie.cxc  

> open spin_movie.cxc

> movie record size 3840,2160

> turn y 2 180

> wait 180

> movie stop

> movie encode output my_movie.mp4 quality highest

Movie saved to my_movie.mp4  
  
executed spin_movie.cxc  

> lighting depthCue false

> lighting depthCue true

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> save 19CS_worm.png width 2000 supersample 4

> close

> open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact
> map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1g0y_flexible/1g0y_flexible_with_rmsf/model_0.pdb"

Chain information for model_0.pdb #1  
---  
Chain | Description  
R | No description available  
  
Computing secondary structure  

> color byattribute a:bfactor

4982 atoms, 310 residues, atom bfactor range 0.18 to 1.39  

> worm bfactor min:0.2 max:0.9

310 residues, residue bfactor range 0.18 to 1.39  

> worm bfactor min:0.2 max:0.7

310 residues, residue bfactor range 0.18 to 1.39  

> worm bfactor min:0.2 max:0.9

310 residues, residue bfactor range 0.18 to 1.39  

> save 1GOY_worm.png width 2000 supersample 4

> open spin_movie.cxc

> movie record size 3840,2160

> turn y 2 180

> wait 180

> movie stop

> movie encode output my_movie.mp4 quality highest

Movie saved to my_movie.mp4  
  
executed spin_movie.cxc  

> open spin_movie.cxc

> movie record size 3840,2160

> turn y 2 180

> wait 180

> movie stop

> movie encode output my_movie.mp4 quality highest

Movie saved to my_movie.mp4  
  
executed spin_movie.cxc  

> open spin_movie.cxc

> movie record size 3840,2160

> turn y 2 180

> wait 180

> movie stop

> movie encode output my_movie.mp4 quality highest

Movie saved to my_movie.mp4  
  
executed spin_movie.cxc  

> close

> open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact
> map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1IJZ_flexible/1IJZ_flexible_with_rmsf/model_0.pdb"

Chain information for model_0.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> color byattribute a:bfactor

1770 atoms, 113 residues, atom bfactor range 0.473 to 1.74  

> worm bfactor min:0.2 max:0.9

113 residues, residue bfactor range 0.473 to 1.74  

> worm bfactor min:0.2 max:0.7

113 residues, residue bfactor range 0.473 to 1.74  

> worm bfactor min:0.2 max:0.8

113 residues, residue bfactor range 0.473 to 1.74  

> save 1IJZ_worm.png width 2000 supersample 4

> open spin_movie.cxc

> movie record size 3840,2160

> turn y 2 180

> wait 180

> movie stop

> movie encode output my_movie.mp4 quality highest

Movie saved to my_movie.mp4  
  
executed spin_movie.cxc  

> close

> open "/Users/ayomidefasemire/Documents/Doctoral/Side projects/Contact
> map/1IRA/CABSflex_Video/wiki_tutorial/dataset/1EOV_flexible/1EOV_flexible_with_rmsf/model_0.pdb"

Chain information for model_0.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> color byattribute a:bfactor

7847 atoms, 487 residues, atom bfactor range 0.245 to 2.81  

> worm bfactor min:0.2 max:0.9

487 residues, residue bfactor range 0.245 to 2.81  

> worm bfactor min:0.2 max:0.7

487 residues, residue bfactor range 0.245 to 2.81  

> worm bfactor min:0.2 max:0.8

487 residues, residue bfactor range 0.245 to 2.81  

> save 1EOV_worm.png width 2000 supersample 4

> open spin_movie.cxc

> movie record size 3840,2160

> turn y 2 180

> wait 180

> movie stop

> movie encode output my_movie.mp4 quality highest

Movie saved to my_movie.mp4  
  
executed spin_movie.cxc  

> open spin_movie.cxc

> movie record size 3840,2160

> turn y 2 180

> wait 180

> movie stop

> movie encode output my_movie.mp4 quality highest

Movie saved to my_movie.mp4  
  
executed spin_movie.cxc  


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

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




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple

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

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac15,12
      Model Number: MXCV3ZE/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.81.10
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.7.4 (24G517)
      Kernel Version: Darwin 24.6.0
      Time since boot: 14 days, 14 hours, 32 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        P24h-2L:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 75.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.24.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    MolecularDynamicsViewer: 1.6
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2
#19987 fixed Minimize: 'str' object is not callable Eric Pettersen etienne.reboul@…
Description 
The following bug report has been submitted:
Platform:        macOS-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.12.dev202603070142 (2026-03-07 01:42:04 UTC)
Description
I am trying to minimize a structure produced by AF3 but i have type error related to a string , which i guess is a bad type casting or failed transformation in another object.  I have attached the structure for reproducibility

Log:
UCSF ChimeraX version: 1.12.dev202603070142 (2026-03-07)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> cd /Users/ereboul/projects/NPF-ab-initio-
> modelling/repeat_unit_detection/NPF2.5/ChimeraX_manual_alignement

Current working directory is: /Users/ereboul/projects/NPF-ab-initio-
modelling/repeat_unit_detection/NPF2.5/ChimeraX_manual_alignement  

> open NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb

Chain information for NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select #1:25-115

1403 atoms, 1417 bonds, 91 residues, 1 model selected  

> name RU1A_1 sel

> select #1:328-433

1700 atoms, 1718 bonds, 106 residues, 1 model selected  

> name RU1A_2 sel

> select #1:136-229

1473 atoms, 1490 bonds, 94 residues, 1 model selected  

> name RU1B_1 sel

> select #1:441-540

1562 atoms, 1586 bonds, 100 residues, 1 model selected  

> name RU1B_2 sel

> select RU1A_1

1562 atoms, 1586 bonds, 100 residues, 1 model selected  

> save /path/to/output/RU1A_1.pdb selectedOnly true

Cannot save '/path/to/output/RU1A_1.pdb': Unable to open file
'/path/to/output/RU1A_1.pdb' for writing  

> select RU1B_1

1562 atoms, 1586 bonds, 100 residues, 1 model selected  

> save /path/to/output/RU1B_1.pdb selectedOnly true

Cannot save '/path/to/output/RU1B_1.pdb': Unable to open file
'/path/to/output/RU1B_1.pdb' for writing  

> select RU1A_2

1562 atoms, 1586 bonds, 100 residues, 1 model selected  

> save /path/to/output/RU1A_2.pdb selectedOnly true

Cannot save '/path/to/output/RU1A_2.pdb': Unable to open file
'/path/to/output/RU1A_2.pdb' for writing  

> select RU1B_2

1562 atoms, 1586 bonds, 100 residues, 1 model selected  

> save /path/to/output/RU1B_2.pdb selectedOnly true

Cannot save '/path/to/output/RU1B_2.pdb': Unable to open file
'/path/to/output/RU1B_2.pdb' for writing  

> select RU1A_1

1562 atoms, 1586 bonds, 100 residues, 1 model selected  

> save RU1A_1.pdb selectedOnly true

> select RU1B_1

1562 atoms, 1586 bonds, 100 residues, 1 model selected  

> save RU1B_1.pdb selectedOnly true

> select RU1A_2

1562 atoms, 1586 bonds, 100 residues, 1 model selected  

> save RU1A_2.pdb selectedOnly true

> select RU1B_2

1562 atoms, 1586 bonds, 100 residues, 1 model selected  

> save RU1B_2.pdb selectedOnly true

> close #1

> open RU1A_1.pdb

Summary of feedback from opening RU1A_1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
24 messages similar to the above omitted  
  
Chain information for RU1A_1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open RU1A_2.pdb

Summary of feedback from opening RU1A_2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
24 messages similar to the above omitted  
  
Chain information for RU1A_2.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open RU1B_1.pdb

Summary of feedback from opening RU1B_1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
24 messages similar to the above omitted  
  
Chain information for RU1B_1.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open RU1B_2.pdb

Summary of feedback from opening RU1B_2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
24 messages similar to the above omitted  
  
Chain information for RU1B_2.pdb #4  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #2/A

Alignment identifier is 2/A  

> sequence chain #3/A

Alignment identifier is 3/A  

> sequence chain #4/A

Alignment identifier is 4/A  

> close

> open NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb

Chain information for NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select #1:25-115

1403 atoms, 1417 bonds, 91 residues, 1 model selected  

> save RU1A_1.pdb selectedOnly true

> select clear

> open /Users/ereboul/projects/NPF-ab-initio-
> modelling/repeat_unit_detection/NPF2.5/ChimeraX_manual_alignement/RU1A_1.pdb

Summary of feedback from opening /Users/ereboul/projects/NPF-ab-initio-
modelling/repeat_unit_detection/NPF2.5/ChimeraX_manual_alignement/RU1A_1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 11 11 ASN A 117 LEU A
119 1 3  
Start residue of secondary structure not found: HELIX 12 12 LYS A 136 ALA A
154 1 19  
24 messages similar to the above omitted  
  
Chain information for RU1A_1.pdb #2  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> close #2

> select #1:25-115

1403 atoms, 1417 bonds, 91 residues, 1 model selected  

> save RU1A_1.pdb selectedOnly true

> select #1:328-433

1700 atoms, 1718 bonds, 106 residues, 1 model selected  

> save RU1B_1.pdb selectedOnly true

> select #1:136-229

1473 atoms, 1490 bonds, 94 residues, 1 model selected  

> save RU1B_1.pdb selectedOnly true

> select #1:441-540

1562 atoms, 1586 bonds, 100 residues, 1 model selected  

> save RU1B_2.pdb selectedOnly true

> close #1

> open RU1A_1.pdb

Summary of feedback from opening RU1A_1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 11 11 ASN A 117 LEU A
119 1 3  
Start residue of secondary structure not found: HELIX 12 12 LYS A 136 ALA A
154 1 19  
24 messages similar to the above omitted  
  
Chain information for RU1A_1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open RU1A_2.pdb

No such file/path: RU1A_2.pdb  

> open RU1B_1.pdb

Summary of feedback from opening RU1B_1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
24 messages similar to the above omitted  
  
Chain information for RU1B_1.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open RU1B_2.pdb

Summary of feedback from opening RU1B_2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
24 messages similar to the above omitted  
  
Chain information for RU1B_2.pdb #3  
---  
Chain | Description  
A | No description available  
  

> matchmaker #1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RU1B_1.pdb, chain A (#2) with RU1A_1.pdb, chain A (#1), sequence
alignment score = 102.7  
RMSD between 27 pruned atom pairs is 0.755 angstroms; (across all 90 pairs:
5.828)  
  

> close

> open NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb

Chain information for NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select #1:25-115

1403 atoms, 1417 bonds, 91 residues, 1 model selected  

> save RU1A_1.pdb selectedOnly true

> select #1:328-433

1700 atoms, 1718 bonds, 106 residues, 1 model selected  

> save RU1A_2.pdb selectedOnly true

> select #1:136-229

1473 atoms, 1490 bonds, 94 residues, 1 model selected  

> save RU1B_1.pdb selectedOnly true

> select #1:441-540

1562 atoms, 1586 bonds, 100 residues, 1 model selected  

> save RU1B_2.pdb selectedOnly true

> close #1

> open RU1A_1.pdb

Summary of feedback from opening RU1A_1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 11 11 ASN A 117 LEU A
119 1 3  
Start residue of secondary structure not found: HELIX 12 12 LYS A 136 ALA A
154 1 19  
24 messages similar to the above omitted  
  
Chain information for RU1A_1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open RU1A_2.pdb

Summary of feedback from opening RU1A_2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
25 messages similar to the above omitted  
  
Chain information for RU1A_2.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open RU1B_1.pdb

Summary of feedback from opening RU1B_1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
24 messages similar to the above omitted  
  
Chain information for RU1B_1.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open RU1B_2.pdb

Summary of feedback from opening RU1B_2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
24 messages similar to the above omitted  
  
Chain information for RU1B_2.pdb #4  
---  
Chain | Description  
A | No description available  
  

> matchmaker #1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RU1A_2.pdb, chain A (#2) with RU1A_1.pdb, chain A (#1), sequence
alignment score = 106.8  
RMSD between 31 pruned atom pairs is 0.895 angstroms; (across all 88 pairs:
6.092)  
  

> matchmaker #3 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RU1B_2.pdb, chain A (#4) with RU1B_1.pdb, chain A (#3), sequence
alignment score = 107.6  
RMSD between 13 pruned atom pairs is 1.230 angstroms; (across all 86 pairs:
6.503)  
  

> select #2 & aligned

Expected a keyword  

> matchmaker #1 to #2 showAlignment true

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 RU1A_2.pdb, chain A (#2) with RU1A_1.pdb, chain A (#1), sequence
alignment score = 106.8  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: RU1A_1.pdb #1/A, RU1A_2.pdb
#2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 31 pruned atom pairs is 0.895 angstroms; (across all 88 pairs:
6.092)  
  

> hide #3 models

> hide #4 models

> select #2/A:402

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #2/A:402-426

370 atoms, 372 bonds, 25 residues, 1 model selected  

> select #2/A:363

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

> select #2/A:363-394 #1/A:57-88

995 atoms, 1004 bonds, 64 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region RU1A_2.pdb, chain A..RU1A_1.pdb, chain A
[39-70] RMSD: 8.630  
  

> select #2/A:328

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #2/A:328 #1/A:28

35 atoms, 33 bonds, 2 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region RU1A_2.pdb, chain A..RU1A_1.pdb, chain A
[4] RMSD: 0.688  
  

> hide #1 models

> hide #2 models

> show #3 models

> show #4 models

> matchmaker #3 to #4 showAlignment true

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 RU1B_2.pdb, chain A (#4) with RU1B_1.pdb, chain A (#3), sequence
alignment score = 107.6  
Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Hiding conservation header for alignment 2  
Chains used in RMSD evaluation for alignment 2: RU1B_1.pdb #3/A, RU1B_2.pdb
#4/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 13 pruned atom pairs is 1.230 angstroms; (across all 86 pairs:
6.503)  
  

> close #2

> close

> open *.pdb

Summary of feedback from opening RU1A_1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 11 11 ASN A 117 LEU A
119 1 3  
Start residue of secondary structure not found: HELIX 12 12 LYS A 136 ALA A
154 1 19  
24 messages similar to the above omitted  
  
Summary of feedback from opening RU1A_2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
25 messages similar to the above omitted  
  
Summary of feedback from opening RU1B_1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
24 messages similar to the above omitted  
  
Summary of feedback from opening RU1B_2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
24 messages similar to the above omitted  
  
Chain information for NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for RU1A_1.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for RU1A_2.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for RU1B_1.pdb #4  
---  
Chain | Description  
A | No description available  
  
Chain information for RU1B_2.pdb #5  
---  
Chain | Description  
A | No description available  
  

> close

> open /Users/ereboul/projects/NPF-ab-initio-modelling/neurosnap_boltz2_apo-
> NPF2.5/rank_1_chimerax_minimized.pdb /Users/ereboul/projects/NPF-ab-initio-
> modelling/neurosnap_boltz2_apo-NPF2.5/rank_2_chimerax_minimized.pdb
> /Users/ereboul/projects/NPF-ab-initio-modelling/neurosnap_boltz2_apo-
> NPF2.5/rank_7_chimerax_minimized.pdb

Chain information for rank_1_chimerax_minimized.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for rank_2_chimerax_minimized.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for rank_7_chimerax_minimized.pdb #3  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Find Cavities"

> kvfinder

23 cavities found for rank_1_chimerax_minimized.pdb #1  
rank_1_chimerax_minimized.pdb Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.1.13 |  | 837.43 | 711.31 | 3877 | 0 | 0  
1.1.3 |  | 807.19 | 699.71 | 3737 | 14.07 | 6.06  
1.1.12 |  | 227.02 | 201.07 | 1051 | 4.2 | 1.11  
1.1.9 |  | 126.58 | 147.25 | 586 | 4.84 | 2.32  
1.1.6 |  | 77.11 | 90.07 | 357 | 0 | 0  
1.1.4 |  | 76.25 | 83.08 | 353 | 4.24 | 1.7  
1.1.16 |  | 49.03 | 80.07 | 227 | 0 | 0  
1.1.15 |  | 43.63 | 66.31 | 202 | 0 | 0  
1.1.19 |  | 43.42 | 73.52 | 201 | 0 | 0  
1.1.14 |  | 36.5 | 54.73 | 169 | 1.7 | 0.37  
1.1.21 |  | 29.59 | 45.11 | 137 | 0 | 0  
1.1.20 |  | 28.51 | 44.2 | 132 | 0 | 0  
1.1.2 |  | 27.65 | 44.69 | 128 | 1.7 | 0.64  
1.1.7 |  | 25.92 | 45.52 | 120 | 1.34 | 0.37  
1.1.10 |  | 24.84 | 40.56 | 115 | 0 | 0  
1.1.23 |  | 21.82 | 40.63 | 101 | 0 | 0  
1.1.8 |  | 12.31 | 29.54 | 57 | 0 | 0  
1.1.11 |  | 12.31 | 29.54 | 57 | 0 | 0  
1.1.17 |  | 12.31 | 29.54 | 57 | 0 | 0  
1.1.18 |  | 12.1 | 21.07 | 56 | 0.6 | 0.19  
1.1.5 |  | 9.29 | 18.8 | 43 | 0.6 | 0.18  
1.1.22 |  | 8.86 | 19.3 | 41 | 1.2 | 0.35  
1.1.1 |  | 7.78 | 15.17 | 36 | 1.2 | 0.27  
  

Populating font family aliases took 109 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.  

31 cavities found for rank_2_chimerax_minimized.pdb #2  
rank_2_chimerax_minimized.pdb Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
2.1.17 |  | 722.09 | 660.9 | 3343 | 0 | 0  
2.1.2 |  | 339.98 | 345.67 | 1574 | 6.49 | 1.8  
2.1.5 |  | 183.38 | 215.19 | 849 | 8.38 | 3.6  
2.1.16 |  | 141.26 | 191.79 | 654 | 5.82 | 2.32  
2.1.24 |  | 112.97 | 152.87 | 523 | 0 | 0  
2.1.8 |  | 80.78 | 87.67 | 374 | 4.2 | 1.49  
2.1.12 |  | 66.31 | 84.35 | 307 | 2.08 | 0.59  
2.1.6 |  | 65.66 | 104.31 | 304 | 0 | 0  
2.1.26 |  | 59.62 | 79.55 | 276 | 0 | 0  
2.1.25 |  | 58.32 | 84.68 | 270 | 0 | 0  
2.1.21 |  | 52.27 | 77.56 | 242 | 0 | 0  
2.1.4 |  | 51.84 | 71.19 | 240 | 0 | 0  
2.1.10 |  | 44.28 | 64.98 | 205 | 2.68 | 0.85  
2.1.19 |  | 39.53 | 53.82 | 183 | 1.34 | 0.33  
2.1.9 |  | 27 | 44.51 | 125 | 0 | 0  
2.1.7 |  | 23.98 | 35.41 | 111 | 1.47 | 0.55  
2.1.15 |  | 17.28 | 36.68 | 80 | 0 | 0  
2.1.20 |  | 16.85 | 32.3 | 78 | 0 | 0  
2.1.29 |  | 16.85 | 27.01 | 78 | 1.8 | 0.57  
2.1.31 |  | 15.34 | 24.48 | 71 | 1.34 | 0.53  
2.1.22 |  | 13.61 | 25.27 | 63 | 1.2 | 0.27  
2.1.1 |  | 12.31 | 29.54 | 57 | 0 | 0  
2.1.3 |  | 12.31 | 29.54 | 57 | 0 | 0  
2.1.11 |  | 12.31 | 29.54 | 57 | 0 | 0  
2.1.13 |  | 12.31 | 29.54 | 57 | 0 | 0  
2.1.14 |  | 12.31 | 29.54 | 57 | 0 | 0  
2.1.23 |  | 12.31 | 29.54 | 57 | 0 | 0  
2.1.27 |  | 12.31 | 29.54 | 57 | 0 | 0  
2.1.28 |  | 11.23 | 20.82 | 52 | 0.85 | 0.22  
2.1.30 |  | 8.86 | 19.38 | 41 | 1.34 | 0.36  
2.1.18 |  | 8.21 | 15.44 | 38 | 0.6 | 0.21  
  
20 cavities found for rank_7_chimerax_minimized.pdb #3  
rank_7_chimerax_minimized.pdb Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
3.1.13 |  | 1598.4 | 1105.39 | 7400 | 18.14 | 5.62  
3.1.3 |  | 562.9 | 565.87 | 2606 | 16.05 | 7.27  
3.1.5 |  | 423.14 | 404.75 | 1959 | 9.14 | 3.19  
3.1.4 |  | 167.4 | 188.06 | 775 | 8.16 | 3.65  
3.1.15 |  | 57.24 | 80.85 | 265 | 0 | 0  
3.1.17 |  | 47.3 | 74.18 | 219 | 0 | 0  
3.1.1 |  | 28.3 | 48.73 | 131 | 0 | 0  
3.1.11 |  | 26.78 | 45.09 | 124 | 1.7 | 0.33  
3.1.6 |  | 26.14 | 44.82 | 121 | 0 | 0  
3.1.19 |  | 25.49 | 39.31 | 118 | 1.7 | 0.56  
3.1.12 |  | 19.01 | 38.34 | 88 | 0 | 0  
3.1.16 |  | 19.01 | 38.34 | 88 | 0 | 0  
3.1.14 |  | 16.85 | 32.3 | 78 | 0 | 0  
3.1.18 |  | 16.85 | 32.3 | 78 | 0 | 0  
3.1.7 |  | 12.96 | 23.28 | 60 | 1.2 | 0.35  
3.1.8 |  | 12.31 | 29.54 | 57 | 0 | 0  
3.1.9 |  | 12.31 | 29.54 | 57 | 0 | 0  
3.1.10 |  | 12.31 | 29.54 | 57 | 0 | 0  
3.1.20 |  | 9.94 | 20.83 | 46 | 1.04 | 0.44  
3.1.2 |  | 6.48 | 14.83 | 30 | 0.6 | 0.12  
  

> hide #!2 models

> hide #!3 models

> close #3

> close

> open /Users/ereboul/projects/NPF-ab-initio-modelling/neurosnap_boltz2_apo-
> NPF2.5/rank_1_chimerax_minimized.pdb /Users/ereboul/projects/NPF-ab-initio-
> modelling/neurosnap_boltz2_apo-NPF2.5/rank_2_chimerax_minimized.pdb
> /Users/ereboul/projects/NPF-ab-initio-modelling/neurosnap_boltz2_apo-
> NPF2.5/rank_7_chimerax_minimized.pdb

Chain information for rank_1_chimerax_minimized.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for rank_2_chimerax_minimized.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for rank_7_chimerax_minimized.pdb #3  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Find Cavities"

> kvfinder #1

23 cavities found for rank_1_chimerax_minimized.pdb #1  
rank_1_chimerax_minimized.pdb Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
1.1.13 |  | 837.43 | 711.31 | 3877 | 0 | 0  
1.1.3 |  | 807.19 | 699.71 | 3737 | 14.07 | 6.06  
1.1.12 |  | 227.02 | 201.07 | 1051 | 4.2 | 1.11  
1.1.9 |  | 126.58 | 147.25 | 586 | 4.84 | 2.32  
1.1.6 |  | 77.11 | 90.07 | 357 | 0 | 0  
1.1.4 |  | 76.25 | 83.08 | 353 | 4.24 | 1.7  
1.1.16 |  | 49.03 | 80.07 | 227 | 0 | 0  
1.1.15 |  | 43.63 | 66.31 | 202 | 0 | 0  
1.1.19 |  | 43.42 | 73.52 | 201 | 0 | 0  
1.1.14 |  | 36.5 | 54.73 | 169 | 1.7 | 0.37  
1.1.21 |  | 29.59 | 45.11 | 137 | 0 | 0  
1.1.20 |  | 28.51 | 44.2 | 132 | 0 | 0  
1.1.2 |  | 27.65 | 44.69 | 128 | 1.7 | 0.64  
1.1.7 |  | 25.92 | 45.52 | 120 | 1.34 | 0.37  
1.1.10 |  | 24.84 | 40.56 | 115 | 0 | 0  
1.1.23 |  | 21.82 | 40.63 | 101 | 0 | 0  
1.1.8 |  | 12.31 | 29.54 | 57 | 0 | 0  
1.1.11 |  | 12.31 | 29.54 | 57 | 0 | 0  
1.1.17 |  | 12.31 | 29.54 | 57 | 0 | 0  
1.1.18 |  | 12.1 | 21.07 | 56 | 0.6 | 0.19  
1.1.5 |  | 9.29 | 18.8 | 43 | 0.6 | 0.18  
1.1.22 |  | 8.86 | 19.3 | 41 | 1.2 | 0.35  
1.1.1 |  | 7.78 | 15.17 | 36 | 1.2 | 0.27  
  

> hide #2 models

> hide #3 models

> view #1.1.13 @< 3.5

> zoom 0.75

moved plane near -44.267412448592516 [-0.39958368 0.66184108 0.63427065]  
moved plane far -44.267412448592516 [-0.39958368 0.66184108 0.63427065]  

> surface #1.1.1-23 transparency 50

> ~surface #1.1

> surface #1.1.13

> show
> #!1/A:35,42-43,45-47,72,75-76,157-158,181-182,185-186,189,334,338-339,341-342,344-345,371,374-375,378,448,451-452,455,458-459,462-463,466,482-483,485-486,489-490

> select #!1/A:186

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

> select add #!1/A:459

41 atoms, 41 bonds, 2 residues, 1 model selected  

> select add #!1/A:182

61 atoms, 61 bonds, 3 residues, 1 model selected  

> show #2 models

> hide #!1 models

> ui tool show "Find Cavities"

> kvfinder #2 volumeCutoff 100

5 cavities found for rank_2_chimerax_minimized.pdb #2  
rank_2_chimerax_minimized.pdb Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
2.1.4 |  | 722.09 | 660.9 | 3343 | 0 | 0  
2.1.1 |  | 339.98 | 345.67 | 1574 | 6.49 | 1.8  
2.1.2 |  | 183.38 | 215.19 | 849 | 8.38 | 3.6  
2.1.3 |  | 141.26 | 191.79 | 654 | 5.82 | 2.32  
2.1.5 |  | 112.97 | 152.87 | 523 | 0 | 0  
  

> view #2.1.4 @< 3.5

> zoom 0.75

moved plane near -41.330234783346505 [-0.11106485 -0.12389558 0.98606008]  
moved plane far -41.330234783346505 [-0.11106485 -0.12389558 0.98606008]  

> surface #2.1.1-5 transparency 50

> ~surface #2.1

> surface #2.1.4

> show
> #!2/A:35,38-39,42-43,45-47,71-72,75-76,156-158,160-161,178,181-182,185-186,189,338,341-342,345,371,374-375,451,455,458-459,463,479,483,486,489-490

> show #!1 models

> hide #!2 models

> hide #!1 models

> show #3 models

> ui tool show "Find Cavities"

> kvfinder #3 volumeCutoff 100

4 cavities found for rank_7_chimerax_minimized.pdb #3  
rank_7_chimerax_minimized.pdb Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
3.1.4 |  | 1598.4 | 1105.39 | 7400 | 18.14 | 5.62  
3.1.1 |  | 562.9 | 565.87 | 2606 | 16.05 | 7.27  
3.1.3 |  | 423.14 | 404.75 | 1959 | 9.14 | 3.19  
3.1.2 |  | 167.4 | 188.06 | 775 | 8.16 | 3.65  
  

> hide #!3 models

> open /Users/ereboul/projects/NPF-ab-initio-
> modelling/neurosnap_boltz2_NF2.5-GA1/rank_2_minimized_chimerax.pdb

Chain information for rank_2_minimized_chimerax.pdb #4  
---  
Chain | Description  
A | No description available  
  

> show #!2 models

> show #!3 models

> ui tool show Matchmaker

> matchmaker #!1-2 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker rank_2_minimized_chimerax.pdb, chain A (#4) with
rank_1_chimerax_minimized.pdb, chain A (#1), sequence alignment score = 2727.6  
RMSD between 385 pruned atom pairs is 1.067 angstroms; (across all 560 pairs:
5.097)  
  
Matchmaker rank_2_minimized_chimerax.pdb, chain A (#4) with
rank_2_chimerax_minimized.pdb, chain A (#2), sequence alignment score = 2769.6  
RMSD between 507 pruned atom pairs is 0.723 angstroms; (across all 560 pairs:
4.085)  
  

> hide #!3 models

> show #!1 models

> show #!3 models

> ui tool show Matchmaker

> matchmaker #!1-3 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker rank_2_minimized_chimerax.pdb, chain A (#4) with
rank_1_chimerax_minimized.pdb, chain A (#1), sequence alignment score = 2727.6  
RMSD between 385 pruned atom pairs is 1.067 angstroms; (across all 560 pairs:
5.097)  
  
Matchmaker rank_2_minimized_chimerax.pdb, chain A (#4) with
rank_2_chimerax_minimized.pdb, chain A (#2), sequence alignment score = 2769.6  
RMSD between 507 pruned atom pairs is 0.723 angstroms; (across all 560 pairs:
4.085)  
  
Matchmaker rank_2_minimized_chimerax.pdb, chain A (#4) with
rank_7_chimerax_minimized.pdb, chain A (#3), sequence alignment score = 2771.4  
RMSD between 264 pruned atom pairs is 1.123 angstroms; (across all 560 pairs:
6.522)  
  

> hide #!3 models

> hide #4 models

> hide #!2 models

> close

> open *.pdb

Summary of feedback from opening RU1A_1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 11 11 ASN A 117 LEU A
119 1 3  
Start residue of secondary structure not found: HELIX 12 12 LYS A 136 ALA A
154 1 19  
24 messages similar to the above omitted  
  
Summary of feedback from opening RU1A_2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
25 messages similar to the above omitted  
  
Summary of feedback from opening RU1B_1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
24 messages similar to the above omitted  
  
Summary of feedback from opening RU1B_2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
24 messages similar to the above omitted  
  
Chain information for NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for RU1A_1.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for RU1A_2.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for RU1B_1.pdb #4  
---  
Chain | Description  
A | No description available  
  
Chain information for RU1B_2.pdb #5  
---  
Chain | Description  
A | No description available  
  

> hide #1 models

> show #1 models

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> select #1/A:7

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

> select #1/A:7-25

273 atoms, 276 bonds, 19 residues, 1 model selected  

> select #1/A:25

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1/A:25-115

1403 atoms, 1417 bonds, 91 residues, 1 model selected  

> show #2 models

> show #3 models

> show #4 models

> show #5 models

> hide #1 models

> close

> ui tool show "Molecular Dynamics Viewer"

Chain information for structure #1  
---  
Chain | Description  
A | No description available  
  

> open /Users/ereboul/projects/NPF-ab-initio-modelling/neurosnap_boltz2_apo-
> NPF2.5/rank_1_chimerax_minimized.pdb /Users/ereboul/projects/NPF-ab-initio-
> modelling/neurosnap_boltz2_apo-NPF2.5/rank_7_chimerax_minimized.pdb

Chain information for rank_1_chimerax_minimized.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for rank_7_chimerax_minimized.pdb #3  
---  
Chain | Description  
A | No description available  
  

> hide #3 models

> show #3 models

> hide #!1 models

> hide #3 models

> ui tool show "Find Cavities"

> kvfinder #2 volumeCutoff 100

4 cavities found for rank_1_chimerax_minimized.pdb #2  
rank_1_chimerax_minimized.pdb Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
2.1.4 |  | 837.43 | 711.31 | 3877 | 0 | 0  
2.1.1 |  | 807.19 | 699.71 | 3737 | 14.07 | 6.06  
2.1.3 |  | 227.02 | 201.07 | 1051 | 4.2 | 1.11  
2.1.2 |  | 126.58 | 147.25 | 586 | 4.84 | 2.32  
  

> view #2.1.4 @< 3.5

> zoom 0.75

moved plane near -37.78458045484981 [ 0.11486323 0.38519969 -0.91565694]  
moved plane far -37.78458045484981 [ 0.11486323 0.38519969 -0.91565694]  

> surface #2.1.1-4 transparency 50

> ~surface #2.1

> surface #2.1.4

> show
> #!2/A:35,42-43,45-47,72,75-76,157-158,181-182,185-186,189,334,338-339,341-342,344-345,371,374-375,378,448,451-452,455,458-459,462-463,466,482-483,485-486,489-490

> select #!2/A:186

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

> select add #!2/A:459

41 atoms, 41 bonds, 2 residues, 1 model selected  

> select add #!2/A:182

61 atoms, 61 bonds, 3 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #!2/A

Alignment identifier is 2/A  

> select #!2/A:178

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

> select #!2/A:178

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

> show (sel-residues & sidechain) target ab

> select #!2/A:181

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

> select add #!2/A:178

40 atoms, 40 bonds, 2 residues, 1 model selected  

> select add #!2/A:182

60 atoms, 60 bonds, 3 residues, 1 model selected  

> select #!2/A:186

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

> select #!2/A:178

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

> select #!2/A:178

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

> select #!2/A:186

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

> select #!2/A:186

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

> select #2:177

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

> show (sel-residues & sidechain) target ab

> select #!2/A:182

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

> close

> cd /Users/ereboul/projects/NPF-ab-initio-
> modelling/repeat_unit_detection/NPF2.5/ChimeraX_manual_alignement

Current working directory is: /Users/ereboul/projects/NPF-ab-initio-
modelling/repeat_unit_detection/NPF2.5/ChimeraX_manual_alignement  

> open NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb

Chain information for NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb #1  
---  
Chain | Description  
A | No description available  
  

> select #1:25-115

1403 atoms, 1417 bonds, 91 residues, 1 model selected  

> save RU1A_1.pdb selectedOnly true

> select #1:136-229

1473 atoms, 1490 bonds, 94 residues, 1 model selected  

> save RU1B.pdb selectedOnly true

> select #1:328-433

1700 atoms, 1718 bonds, 106 residues, 1 model selected  

> save RU2A.pdb selectedOnly true

> select #1:441-540

1562 atoms, 1586 bonds, 100 residues, 1 model selected  

> save RU2B.pdb selectedOnly true

> select #1:25-115

1403 atoms, 1417 bonds, 91 residues, 1 model selected  

> save RU1A.pdb selectedOnly true

> close #1

> open RU1A.pdb

Summary of feedback from opening RU1A.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 11 11 ASN A 117 LEU A
119 1 3  
Start residue of secondary structure not found: HELIX 12 12 LYS A 136 ALA A
154 1 19  
24 messages similar to the above omitted  
  
Chain information for RU1A.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open RU1B.pdb

Summary of feedback from opening RU1B.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
24 messages similar to the above omitted  
  
Chain information for RU1B.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open RU2A.pdb

Summary of feedback from opening RU2A.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
25 messages similar to the above omitted  
  
Chain information for RU2A.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open RU2B.pdb

Summary of feedback from opening RU2B.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 7 ALA A 12 1 6  
Start residue of secondary structure not found: HELIX 2 2 HIS A 13 SER A 16 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO A 18 LYS A 21 1
4  
Start residue of secondary structure not found: HELIX 4 4 TRP A 25 THR A 27 1
3  
Start residue of secondary structure not found: HELIX 5 5 LEU A 28 MET A 47 1
20  
24 messages similar to the above omitted  
  
Chain information for RU2B.pdb #4  
---  
Chain | Description  
A | No description available  
  

> matchmaker #1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RU1B.pdb, chain A (#2) with RU1A.pdb, chain A (#1), sequence
alignment score = 102.7  
RMSD between 27 pruned atom pairs is 0.755 angstroms; (across all 90 pairs:
5.828)  
  

> matchmaker #3 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RU2B.pdb, chain A (#4) with RU2A.pdb, chain A (#3), sequence
alignment score = 97.4  
RMSD between 14 pruned atom pairs is 1.317 angstroms; (across all 92 pairs:
6.853)  
  

> open /Users/ereboul/projects/NPF-ab-initio-
> modelling/repeat_unit_detection/NPF2.5/ChimeraX_manual_alignement/NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb

Chain information for NPF2.5_apo_boltz2_rank_7_chimerax_minimized.pdb #5  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #5/A

Alignment identifier is 5/A  

> select #5/A:230

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

> select #5/A:230-314

1359 atoms, 1372 bonds, 85 residues, 1 model selected  

> select #5/A:325

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #5/A:230-325

1540 atoms, 1554 bonds, 96 residues, 1 model selected  

> select #5/A:324

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #5/A:230-324

1521 atoms, 1535 bonds, 95 residues, 1 model selected  

> select #5/A:230

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

> select #5/A:230

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

> select #5/A:314

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

> select #5/A:314

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

> close #1-4

> color bfactor sel

11 atoms, 1 residues, atom bfactor range 73.5 to 73.5  

> color bfactor sel

11 atoms, 1 residues, atom bfactor range 73.5 to 73.5  

> select up

337 atoms, 338 bonds, 22 residues, 1 model selected  

> select up

8784 atoms, 8887 bonds, 560 residues, 1 model selected  

> color bfactor sel

8784 atoms, 560 residues, atom bfactor range 37.9 to 97.2  

> select #5:434–440

Expected an objects specifier or a keyword  

> select #5

8784 atoms, 8887 bonds, 560 residues, 1 model selected  

> select #5:434–440

Expected an objects specifier or a keyword  

> select #5:434-440

87 atoms, 88 bonds, 7 residues, 1 model selected  

> select /A:560

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select /A:541-560

340 atoms, 343 bonds, 20 residues, 1 model selected  

> close

> open
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_0.cif
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_1.cif
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_2.cif
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_3.cif
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_4.cif

Chain information for fold_dlc4_rnads_drb2_drb4_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
D E | .  
  
Chain information for fold_dlc4_rnads_drb2_drb4_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
C | .  
D E | .  
  
Chain information for fold_dlc4_rnads_drb2_drb4_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
D E | .  
  
Chain information for fold_dlc4_rnads_drb2_drb4_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
D E | .  
  
Chain information for fold_dlc4_rnads_drb2_drb4_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
D E | .  
  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  

> set bgColor #ffffff00

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> show protein target c

Computing secondary structure  
[Repeated 4 time(s)]

> hide protein target a

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 111575 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> hide #5 models

> hide #4 models

> hide #3 models

> hide #2 models

> hide #1 models

> show #2 models

> hide #2 models

> show #3 models

> hide #3 models

> show #4 models

> hide #4 models

> show #5 models

> hide #5 models

> show #2 models

> color bfactor #2

22315 atoms, 2623 residues, atom bfactor range 13.7 to 91.6  

> show #1 models

> hide #2 models

> color bfactor #1

22315 atoms, 2623 residues, atom bfactor range 14.7 to 91.1  

> hide #1 models

> show #2 models

> hide #2 models

> show #1 models

> hide #1 models

> show #2 models

> show #1 models

> hide #2 models

> hide #1 models

> show #1 models

> select #1/C:236

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

> select up

1116 atoms, 1137 bonds, 152 residues, 1 model selected  

> hide sel target c

> select #1/A:9

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

> select up

920 atoms, 936 bonds, 119 residues, 1 model selected  

> hide sel target c

> select #1/B:323

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

> select up

1782 atoms, 1829 bonds, 236 residues, 1 model selected  

> hide sel target c

> select #1/B

3332 atoms, 3409 bonds, 434 residues, 1 model selected  

> select #1/C

2697 atoms, 2760 bonds, 355 residues, 1 model selected  

> select #1/D

1424 atoms, 1593 bonds, 66 residues, 1 model selected  

> hide #1 models

> show #2 models

> select #2/D

1424 atoms, 1593 bonds, 66 residues, 1 model selected  

> hide #2 models

> show #3 models

> show #4 models

> hide #3 models

> show #5 models

> hide #4 models

> hide #5 models

> show #1 models

> select up

22315 atoms, 23065 bonds, 2623 residues, 1 model selected  

> hide #1 models

> show #2 models

> select #2/B

3332 atoms, 3409 bonds, 434 residues, 1 model selected  

> select up

22315 atoms, 23065 bonds, 2623 residues, 1 model selected  

> select down

3332 atoms, 3409 bonds, 434 residues, 1 model selected  

> select #2/A

13438 atoms, 13710 bonds, 1702 residues, 1 model selected  

> select up

22315 atoms, 23065 bonds, 2623 residues, 1 model selected  

> select down

13438 atoms, 13710 bonds, 1702 residues, 1 model selected  

> select clear

> close

> pwd

Current working directory is: /Users/ereboul/projects/NPF-ab-initio-
modelling/repeat_unit_detection/NPF2.5/ChimeraX_manual_alignement  

> cd ../../

Current working directory is: /Users/ereboul/projects/NPF-ab-initio-
modelling/repeat_unit_detection  

> cd ../

Current working directory is: /Users/ereboul/projects/NPF-ab-initio-modelling  

> open /Users/ereboul/projects/NPF-ab-initio-modelling/neurosnap_boltz2_apo-
> NPF2.5/rank_1_chimerax_minimized.pdb

Chain information for rank_1_chimerax_minimized.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open 4OH3

4oh3 title:  
Crystal structure of a nitrate transporter [more info...]  
  
Chain information for 4oh3 #2  
---  
Chain | Description | UniProt  
A B | Nitrate transporter 1.1 | PTR7_ARATH 1-590  
  
Non-standard residues in 4oh3 #2  
---  
LMT — dodecyl-β-D-maltoside  
NO3 — nitrate ion  
  
7992 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> ui tool show Matchmaker

> matchmaker #1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4oh3, chain A (#2) with rank_1_chimerax_minimized.pdb, chain A
(#1), sequence alignment score = 1132  
RMSD between 298 pruned atom pairs is 1.193 angstroms; (across all 493 pairs:
5.405)  
  

> select #2/B:84

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

> select up

202 atoms, 205 bonds, 28 residues, 1 model selected  

> select up

2026 atoms, 2067 bonds, 273 residues, 1 model selected  

> select up

2126 atoms, 2165 bonds, 292 residues, 1 model selected  

> select up

3078 atoms, 3138 bonds, 414 residues, 1 model selected  

> select up

3128 atoms, 3190 bonds, 420 residues, 1 model selected  

> select up

4062 atoms, 4150 bonds, 537 residues, 1 model selected  

> select #2/B

4090 atoms, 4178 bonds, 3 pseudobonds, 539 residues, 2 models selected  

> delete #2/B

> save /Users/ereboul/projects/NPF-ab-initio-modelling/NPF6.3_4OH3_crystal.pdb
> models #2

> ui tool show "Molecular Dynamics Viewer"

Chain information for structure #3  
---  
Chain | Description  
A | No description available  
  

> info #2

3 models  
#2, 4oh3, shown  
3958 atoms, 4046 bonds, 514 residues, 1 chains (A)  
3 missing structure  
#2.1, missing structure, shown, 3 pseudobonds  
#2.1.1, labels, shown, 6 triangles  

> close #3

> ui tool show "Molecular Dynamics Viewer"

Chain information for structure #3  
---  
Chain | Description  
A | No description available  
  

> delete solvent

> delete ligand

> delete #2 & ~protein

> close #3

> show #2 ribbons

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> select clear

[Repeated 2 time(s)]

> pwd

Current working directory is: /Users/ereboul/projects/NPF-ab-initio-modelling  

> cd MODELLER

Current working directory is: /Users/ereboul/projects/NPF-ab-initio-
modelling/MODELLER  

> select #2/A

3930 atoms, 4018 bonds, 3 pseudobonds, 512 residues, 2 models selected  

> hide #1 models

> ui tool show "Find Cavities"

> kvfinder #2 volumeCutoff 100

2 cavities found for 4oh3 #2  
4oh3 Cavities  
---  
ID |  | Volume | Area | Points | Maximum  
Depth | Average  
Depth  
2.2.1 |  | 1165.1 | 871.46 | 5394 | 12.01 | 2.97  
2.2.2 |  | 298.51 | 251.56 | 1382 | 6.43 | 1.39  
  

> view #2.2.2 @< 3.5

> zoom 0.75

moved plane near -41.243530436001585 [-0.72965792 -0.58301651 -0.35733888]  
moved plane far -41.243530436001585 [-0.72965792 -0.58301651 -0.35733888]  

> surface #2.2.1-2 transparency 50

> ~surface #2.2

> surface #2.2.2

> show
> #!2/A:56-57,60-61,64-67,71,131-133,135-140,361-362,364-366,368-369,534-536

> view #!2.2.1 @< 3.5

> zoom 0.75

moved plane near -62.466540726917366 [-0.76363139 -0.29706315 -0.5732544 ]  
moved plane far -62.466540726917366 [-0.76363139 -0.29706315 -0.5732544 ]  

> ~surface #2.2

> surface #!2.2.1

> show
> #!2/A:41,44-45,47-49,51-53,77-78,81-82,85-86,88-90,92-93,98,156-157,160,164-166,168,201,205,248-252,353,356,359-360,364,382,385,388-389,392-393,469,476,480,494,497-504,507,511

> select #2/A

3930 atoms, 4018 bonds, 3 pseudobonds, 512 residues, 2 models selected  

> close #2.2

> select #2/A

3930 atoms, 4018 bonds, 3 pseudobonds, 512 residues, 2 models selected  

> save 4oh3_clean.pdb selectedOnly true

> close #2

> show #1 models

> open 4oh3_clean.pdb

Summary of feedback from opening 4oh3_clean.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA A 2 LYS A 5 1 4  
Start residue of secondary structure not found: HELIX 2 2 SER A 6 ASP A 8 1 3  
Start residue of secondary structure not found: HELIX 3 3 GLY A 24 THR A 27 1
4  
Start residue of secondary structure not found: HELIX 4 4 LEU A 28 MET A 47 1
20  
End residue of secondary structure not found: HELIX 5 5 LEU A 49 GLU A 55 1 7  
Start residue of secondary structure not found: HELIX 6 6 ASN A 61 LEU A 78 1
18  
Start residue of secondary structure not found: HELIX 7 7 PRO A 79 PHE A 90 1
12  
Start residue of secondary structure not found: HELIX 8 8 ASN A 92 SER A 115 1
24  
Start residue of secondary structure not found: HELIX 9 9 ASN A 117 LEU A 119
1 3  
Start residue of secondary structure not found: HELIX 10 10 LYS A 136 ALA A
154 1 19  
1 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 12 12 ALA A 165 GLN A 167
1 3  
Start residue of secondary structure not found: HELIX 13 13 PRO A 171 ALA A
195 1 25  
Start residue of secondary structure not found: HELIX 14 14 ILE A 196 ASN A
202 1 7  
Start residue of secondary structure not found: HELIX 15 15 TRP A 205 PHE A
223 1 19  
Start residue of secondary structure not found: HELIX 16 16 ILE A 224 GLY A
226 1 3  
Start residue of secondary structure not found: HELIX 17 17 THR A 241 MET A
252 1 12  
17 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 35 35 VAL A 516 PHE A 540
1 25  
Start residue of secondary structure not found: HELIX 36 36 PRO A 555 ASP A
557 1 3  
  
Chain information for 4oh3_clean.pdb #2  
---  
Chain | Description  
A | No description available  
  
3930 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  
Computing secondary structure  

> info #2

2 models  
#2, 4oh3_clean.pdb, shown  
3930 atoms, 4018 bonds, 512 residues, 1 chains (A)  
3 missing structure  
#2.1, missing structure, shown, 3 pseudobonds  

> close

> open /Users/ereboul/Downloads/9KBZ.cif

Summary of feedback from opening /Users/ereboul/Downloads/9KBZ.cif  
---  
note | Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif  
  
9KBZ.cif title:  
Cryo-EM structure of DCL4-DRB4CTD-dsRNA complex [more info...]  
  
Chain information for 9KBZ.cif #1  
---  
Chain | Description | UniProt  
A | Dicer-like protein 4 | DCL4_ARATH 62-1702  
B | Double-stranded RNA-binding protein 4 | DRB4_ARATH 292-355  
C | RNA (57-MER) |   
D | RNA (55-MER) |   
  
Non-standard residues in 9KBZ.cif #1  
---  
MG — magnesium ion  
  

> open /Users/ereboul/Downloads/emd_62235.map

Opened emd_62235.map as #2, grid size 360,360,360, pixel 0.855, shown at level
0.144, step 2, values float32  

> volume #2 level 0.1708

> surface style mesh

> volume #2 level 0.3237

> volume #2 level 0.2068

> ui tool show "Show Sequence Viewer"

> sequence chain /C

Alignment identifier is 1/C  

> pwd

Current working directory is: /Users/ereboul/projects/NPF-ab-initio-
modelling/MODELLER  

> cd ../../

Current working directory is: /Users/ereboul/projects  

> cd drb2_modelling

Current working directory is: /Users/ereboul/projects/drb2_modelling  

> select clear

> select /C

1102 atoms, 1230 bonds, 52 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /D

Alignment identifier is 1/D  

> select clear

> select /D

1084 atoms, 1212 bonds, 51 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select clear

> select /A:126-1702

11290 atoms, 11519 bonds, 9 pseudobonds, 1423 residues, 2 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Destroying pre-existing alignment with identifier 1/B  
Alignment identifier is 1/B  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> open
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_0.cif
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_1.cif
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_2.cif
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_3.cif
> /Users/ereboul/Downloads/fold_dlc4_rnads_drb2_drb4/fold_dlc4_rnads_drb2_drb4_model_4.cif

Chain information for fold_dlc4_rnads_drb2_drb4_model_0.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
D E | .  
  
Chain information for fold_dlc4_rnads_drb2_drb4_model_1.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
D E | .  
  
Chain information for fold_dlc4_rnads_drb2_drb4_model_2.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
D E | .  
  
Chain information for fold_dlc4_rnads_drb2_drb4_model_3.cif #6  
---  
Chain | Description  
A | .  
B | .  
C | .  
D E | .  
  
Chain information for fold_dlc4_rnads_drb2_drb4_model_4.cif #7  
---  
Chain | Description  
A | .  
B | .  
C | .  
D E | .  
  

> hide #!2 models

> ui tool show Matchmaker

> matchmaker #3-7 to #1

Computing secondary structure  
[Repeated 4 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 9KBZ.cif, chain A (#1) with fold_dlc4_rnads_drb2_drb4_model_0.cif,
chain A (#3), sequence alignment score = 7506.1  
RMSD between 489 pruned atom pairs is 1.251 angstroms; (across all 1423 pairs:
4.154)  
  
Matchmaker 9KBZ.cif, chain A (#1) with fold_dlc4_rnads_drb2_drb4_model_1.cif,
chain A (#4), sequence alignment score = 7500.4  
RMSD between 557 pruned atom pairs is 1.247 angstroms; (across all 1423 pairs:
5.431)  
  
Matchmaker 9KBZ.cif, chain A (#1) with fold_dlc4_rnads_drb2_drb4_model_2.cif,
chain A (#5), sequence alignment score = 7489.3  
RMSD between 655 pruned atom pairs is 1.266 angstroms; (across all 1423 pairs:
3.987)  
  
Matchmaker 9KBZ.cif, chain A (#1) with fold_dlc4_rnads_drb2_drb4_model_3.cif,
chain A (#6), sequence alignment score = 7483.3  
RMSD between 575 pruned atom pairs is 1.218 angstroms; (across all 1423 pairs:
4.163)  
  
Matchmaker 9KBZ.cif, chain A (#1) with fold_dlc4_rnads_drb2_drb4_model_4.cif,
chain A (#7), sequence alignment score = 7475.5  
RMSD between 673 pruned atom pairs is 1.258 angstroms; (across all 1423 pairs:
3.878)  
  

> hide protein target a

> hide RNA target a

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> select #1/C:33

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1102 atoms, 1230 bonds, 52 residues, 1 model selected  

> select up

13858 atoms, 14350 bonds, 1576 residues, 1 model selected  

> select down

1102 atoms, 1230 bonds, 52 residues, 1 model selected  

> select add #1/D:26

1124 atoms, 1254 bonds, 53 residues, 1 model selected  

> select up

2186 atoms, 2442 bonds, 103 residues, 1 model selected  

> show sel target ab

> surface sel

> hide dna target a

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide all target a

> show #1 target c

> show #3-7 target c

> hide #6 models

> hide #7 models

> hide #3 models

> hide #5 models

> close #3-7

> open
> /Users/ereboul/Downloads/fold_rna_ds_9kbz_dcl4_drb2_drb4/fold_rna_ds_9kbz_dcl4_drb2_drb4_model_0.cif
> /Users/ereboul/Downloads/fold_rna_ds_9kbz_dcl4_drb2_drb4/fold_rna_ds_9kbz_dcl4_drb2_drb4_model_1.cif
> /Users/ereboul/Downloads/fold_rna_ds_9kbz_dcl4_drb2_drb4/fold_rna_ds_9kbz_dcl4_drb2_drb4_model_2.cif
> /Users/ereboul/Downloads/fold_rna_ds_9kbz_dcl4_drb2_drb4/fold_rna_ds_9kbz_dcl4_drb2_drb4_model_3.cif
> /Users/ereboul/Downloads/fold_rna_ds_9kbz_dcl4_drb2_drb4/fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif

Chain information for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_0.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  
Chain information for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_1.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  
Chain information for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_2.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  
Chain information for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_3.cif #6  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  
Chain information for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  

> ui tool show Matchmaker

> matchmaker #3-7 to #1

Computing secondary structure  
[Repeated 4 time(s)]  Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 9KBZ.cif, chain A (#1) with
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_0.cif, chain A (#3), sequence alignment
score = 7501.3  
RMSD between 568 pruned atom pairs is 1.191 angstroms; (across all 1423 pairs:
3.888)  
  
Matchmaker 9KBZ.cif, chain A (#1) with
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_1.cif, chain A (#4), sequence alignment
score = 7507.3  
RMSD between 589 pruned atom pairs is 1.252 angstroms; (across all 1423 pairs:
3.219)  
  
Matchmaker 9KBZ.cif, chain A (#1) with
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_2.cif, chain A (#5), sequence alignment
score = 7512.4  
RMSD between 463 pruned atom pairs is 1.159 angstroms; (across all 1423 pairs:
4.254)  
  
Matchmaker 9KBZ.cif, chain A (#1) with
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_3.cif, chain A (#6), sequence alignment
score = 7471.2  
RMSD between 528 pruned atom pairs is 1.206 angstroms; (across all 1423 pairs:
4.336)  
  
Matchmaker 9KBZ.cif, chain A (#1) with
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif, chain A (#7), sequence alignment
score = 7507  
RMSD between 447 pruned atom pairs is 1.203 angstroms; (across all 1423 pairs:
4.576)  
  

> hide all target a

> show #3-7 target c

> hide #3 models

> hide #7 models

> show #7 models

> hide #6 models

> show #6 models

> hide #5 models

> show #5 models

> hide #4 models

> hide #6 models

> show #6 models

> hide #5 models

> hide #7 models

> hide #!1 models

> color bfactor #6

21838 atoms, 2602 residues, atom bfactor range 15.1 to 90.8  

> show #!1 models

> surface hidePatches (#!1 & sel)

> select clear

> show #7 models

> hide #7 models

> show #7 models

> hide #7 models

> show #7 models

> close #3-5

> hide #6 models

> hide #7 models

> show #7 models

> select #7/B:389

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

> select up

125 atoms, 126 bonds, 16 residues, 1 model selected  

> select up

3332 atoms, 3409 bonds, 434 residues, 1 model selected  

> select #7/C:208

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

> select up

159 atoms, 162 bonds, 21 residues, 1 model selected  

> select up

2697 atoms, 2760 bonds, 355 residues, 1 model selected  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> show nucleic target a

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel tube/slab shape box

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 43676 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> hide #7 models

> show #6 models

> select #1/B

379 atoms, 389 bonds, 47 residues, 1 model selected  

> select #6/D

1210 atoms, 1351 bonds, 57 residues, 1 model selected  

> select #6/B

3332 atoms, 3409 bonds, 434 residues, 1 model selected  

> select #1/B

379 atoms, 389 bonds, 47 residues, 1 model selected  

> select #6/C:323

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

> select up

48 atoms, 49 bonds, 6 residues, 1 model selected  

> select up

2697 atoms, 2760 bonds, 355 residues, 1 model selected  

> select #6/B:204

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

> select up

102 atoms, 106 bonds, 12 residues, 1 model selected  

> select up

3332 atoms, 3409 bonds, 434 residues, 1 model selected  

> hide #!1 models

> select #6/C:206

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

> select up

69 atoms, 71 bonds, 8 residues, 1 model selected  

> select up

2697 atoms, 2760 bonds, 355 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #6/C

Alignment identifier is 6/C  

> select #6/C:355

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

> select #6/C

2697 atoms, 2760 bonds, 355 residues, 1 model selected  

> show #7 models

> show #!1 models

> hide #7 models

> select #6/C:355

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

> select #6/C

2697 atoms, 2760 bonds, 355 residues, 1 model selected  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1/B

Alignment identifier is 1/B  

> select #1/B:307

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

> select #1/B

379 atoms, 389 bonds, 47 residues, 1 model selected  

> select #6/C:1

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

> select #6/C

2697 atoms, 2760 bonds, 355 residues, 1 model selected  

> select #6/C:307

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

> select #6/C:307-355

396 atoms, 407 bonds, 49 residues, 1 model selected  

> select #6/B:392

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

> select up

241 atoms, 241 bonds, 32 residues, 1 model selected  

> select up

3332 atoms, 3409 bonds, 434 residues, 1 model selected  

> hide #!1 models

> color sel byelement

> color sel orange

> select #6/A:682

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

> select up

63 atoms, 65 bonds, 7 residues, 1 model selected  

> select up

13430 atoms, 13702 bonds, 1701 residues, 1 model selected  

> color sel cornflower blue

> select #6/C:276

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

> select #6/C:175

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

> select up

233 atoms, 237 bonds, 31 residues, 1 model selected  

> select up

2697 atoms, 2760 bonds, 355 residues, 1 model selected  

> color sel forest green

> hide #6 models

> show #7 models

> show #6 models

> hide #6 models

> select #7/A:362

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

> select up

217 atoms, 217 bonds, 27 residues, 1 model selected  

> select up

13430 atoms, 13702 bonds, 1701 residues, 1 model selected  

> select #7/C:178

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

> select up

161 atoms, 162 bonds, 20 residues, 1 model selected  

> select up

2697 atoms, 2760 bonds, 355 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #7/C

Alignment identifier is 7/C  

> show #!1 models

> select #1/B

379 atoms, 389 bonds, 47 residues, 1 model selected  

> select #7/C:307

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

> select #7/C:307-355

396 atoms, 407 bonds, 49 residues, 1 model selected  

> select #1/B

379 atoms, 389 bonds, 47 residues, 1 model selected  

> color sel red

> select #7/C:307

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

> select #7/C:307-355

396 atoms, 407 bonds, 49 residues, 1 model selected  

> ui tool show "Minimize Structure"

> minimize #7 logEnergy true

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Deleting residues with incomplete backbones  
Summary of feedback from adding hydrogens to
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7  
---  
notes | Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain A determined from SEQRES records  
Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain B
determined from SEQRES records  
Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain C
determined from SEQRES records  
Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain D
determined from SEQRES records  
Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain E
determined from SEQRES records  
Chain-initial residues that are actual N termini:
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/A ARG 1,
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/B MET 1,
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/C MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/A CYS 1701,
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/B ILE 434,
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/C PRO 355  
Chain-final residues that are not actual C termini:  
2549 hydrogen bonds  
20715 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/tool.py", line 101, in minimize  
run(self.session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 43, in cmd_minimize  
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 129, in prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/dock_prep.py", line 56, in run_for_dock_prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/dock_prep.py", line 58, in run_for_dock_prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 156, in run_steps  
callback()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 128, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 45, in <lambda>  
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 89, in _minimize  
raise LimitationError(c_error_template(c_term, "can't find C atom"))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: 'str' object is not callable  
  
TypeError: 'str' object is not callable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 89, in _minimize  
raise LimitationError(c_error_template(c_term, "can't find C atom"))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> ui tool show Clashes

> hide #!1 models

> clashes interModel false ignoreHiddenModels true select true reveal true

480 clashes  

> select clear

> ui tool show "Minimize Structure"

[Repeated 1 time(s)]

> minimize #7 logEnergy true

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Deleting residues with incomplete backbones  
Summary of feedback from adding hydrogens to
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7  
---  
notes | Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain A determined from SEQRES records  
Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain B
determined from SEQRES records  
Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain C
determined from SEQRES records  
Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain D
determined from SEQRES records  
Termini for fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif (#7) chain E
determined from SEQRES records  
Chain-initial residues that are actual N termini:
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/A ARG 1,
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/B MET 1,
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/C MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/A CYS 1701,
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/B ILE 434,
fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif #7/C PRO 355  
Chain-final residues that are not actual C termini:  
2349 hydrogen bonds  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/tool.py", line 101, in minimize  
run(self.session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 43, in cmd_minimize  
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 129, in prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/dock_prep.py", line 56, in run_for_dock_prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/dock_prep.py", line 58, in run_for_dock_prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 156, in run_steps  
callback()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 128, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 45, in <lambda>  
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 89, in _minimize  
raise LimitationError(c_error_template(c_term, "can't find C atom"))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: 'str' object is not callable  
  
TypeError: 'str' object is not callable  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 89, in _minimize  
raise LimitationError(c_error_template(c_term, "can't find C atom"))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4 Max
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PySide6 6.10.1, Qt 6.10.1
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac16,9
      Model Number: Z1CD000KXFN/A
      Chip: Apple M4 Max
      Total Number of Cores: 14 (10 Performance and 4 Efficiency)
      Memory: 36 GB
      System Firmware Version: 13822.81.10
      OS Loader Version: 13822.81.10

Software:

    System Software Overview:

      System Version: macOS 26.3.1 (25D2128)
      Kernel Version: Darwin 25.3.0
      Time since boot: 4 jours, 22 heures et 30 minutes

Graphics/Displays:

    Apple M4 Max:

      Chipset Model: Apple M4 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        LS32D80xU:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.1.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.5
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.64.1
    ChimeraX-AtomicLibrary: 14.2.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12.dev202603070142
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.8.2
    ChimeraX-Label: 1.3
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.18
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.6
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.5.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.18
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    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: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.50.3
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.4
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.20
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    MolecularDynamicsViewer: 1.6
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.17.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 2.4.3
    numpy: 1.26.4
    OpenMM: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.6
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.9.4
    plotly: 6.5.2
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.13.1
    pydantic_core: 2.41.5
    pydata-sphinx-theme: 0.16.1
    pydicom: 2.4.4
    Pygments: 2.18.0
    pyKVFinder: 0.9.0
    pynmrstar: 3.5.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PySide6: 6.10.1
    PySide6_Addons: 6.10.1
    PySide6_Essentials: 6.10.1
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.22
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.1
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    shiboken6: 6.10.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.3.2
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tomlkit: 0.14.0
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    urllib3: 2.6.3
    uvicorn: 0.41.0
    wcwidth: 0.6.0
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.23.0
File attachment: fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif

fold_rna_ds_9kbz_dcl4_drb2_drb4_model_4.cif​

#19986 duplicate Crash in swap_buffers exposing status line during Mac wakeup, macOS 26 Tom Goddard chimerax-bug-report@…
Description 
The following bug report has been submitted:
Platform:        macOS-26.1-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Current thread 0x00000001fd396080 (most recent call first):
  File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
  File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
  File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 166 in status
  File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 98 in _expose_event
  File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
  File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
  File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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, PIL._imaging, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._imagingmath (total: 55)


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===== Log before crash start =====
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/king/Desktop/project/alphafold/1qj8.pdb

Chain information for 1qj8.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> view orient

> view initial

> graphics axis true

Expected a keyword  

> view

> view x

Expected an objects specifier or a view name or a keyword  

> shape rectangle width 80 height 80 color tan

> move z 10 models #2

> move z -100 models #2

> undo

> move x -100 models #2

> move y -100 models #2

> move y 20 models #2

> open /Users/king/Desktop/project/alphafold/ompx/AF-P0A917-F1-model_v6.pdb

AF-P0A917-F1-model_v6.pdb title:  
Alphafold monomer V2.0 prediction for outer membrane protein X (P0A917) [more
info...]  
  
Chain information for AF-P0A917-F1-model_v6.pdb #3  
---  
Chain | Description | UniProt  
A | outer membrane protein X | OMPX_ECOLI 1-171  
  
Computing secondary structure  

> matchmaker #3 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 1qj8.pdb, chain A (#1) with AF-P0A917-F1-model_v6.pdb, chain A
(#3), sequence alignment score = 791.7  
RMSD between 148 pruned atom pairs is 0.559 angstroms; (across all 148 pairs:
0.559)  
  

> hide #2 models

> show #2 models

> hide #3 models

> show #3 models

> hide #1 models

> select add #3

1314 atoms, 1346 bonds, 171 residues, 1 model selected  

> color sel lime

> color sel cyan

> color sel gray

> color sel light gray

> ui tool show "Show Sequence Viewer"

> select :36-44

139 atoms, 130 bonds, 27 residues, 2 models selected  

> color (#3 & sel) red

> select :70-85

258 atoms, 259 bonds, 35 residues, 2 models selected  

> color (#3 & sel) orange

> select :110-129

330 atoms, 335 bonds, 44 residues, 2 models selected  

> color (#3 & sel) forest green

> select :154-160

64 atoms, 61 bonds, 9 residues, 2 models selected  

> color (#3 & sel) blue

> move y 20 models #2

> move y -10 models #2

> show #1 models

> hide #3 models

> show #3 models

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> hide #3 models

> select: 36-44

Unknown command: select: 36-44  

> select: 36-44.A

Unknown command: select: 36-44.A  

> select #3/A:17-70

397 atoms, 403 bonds, 54 residues, 1 model selected  

> select #3/A:17-20

23 atoms, 22 bonds, 4 residues, 1 model selected  

> select #3/A:17-20

23 atoms, 22 bonds, 4 residues, 1 model selected  

> select #3/A:23

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

> select #3/A:23-28

37 atoms, 36 bonds, 6 residues, 1 model selected  

> select #3/A:29-30

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

> select #3/A:29-31

15 atoms, 14 bonds, 3 residues, 1 model selected  

> select #3/A:33-34

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

> select #3/A:33-34

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

> select #3/A:36

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

> select #3/A:36-41

43 atoms, 42 bonds, 6 residues, 1 model selected  

> select #3/A:36

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

> select #3/A:36-45

72 atoms, 71 bonds, 10 residues, 1 model selected  

> select #3/A:36

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

> select #3/A:36-44

68 atoms, 67 bonds, 9 residues, 1 model selected  

> color #1-2 red

> undo

> select #3/A:24-37,44-55,60-74,80-97,100-117,121-138,144-155,158-171

950 atoms, 968 bonds, 121 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> select #1/A:7

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

> select #1/A:7-12

40 atoms, 40 bonds, 6 residues, 1 model selected  

> select #1/A:14

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

> select #1/A:14-19

43 atoms, 42 bonds, 6 residues, 1 model selected  

> select #1/A:21

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

> select #1/A:21-24

27 atoms, 27 bonds, 4 residues, 1 model selected  

> select #1/A:32

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

> select #1/A:32-38

50 atoms, 50 bonds, 7 residues, 1 model selected  

> select #1/A:36

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

> select #1/A:36-45

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

> select #1/A:29

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

> select #1/A:29-32

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

> select #1/A:27-32

62 atoms, 63 bonds, 6 residues, 1 model selected  

> select #1/A:27-32

62 atoms, 63 bonds, 6 residues, 1 model selected  

> select #1/A:37

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

> select #1/A:37-40

27 atoms, 26 bonds, 4 residues, 1 model selected  

> select #1/A:25

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

> select #1/A:16-25

73 atoms, 73 bonds, 10 residues, 1 model selected  

> select #1/A:16-17

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

> select #1/A:14-17

27 atoms, 26 bonds, 4 residues, 1 model selected  

> select #1/A:14

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

> select #1/A:10-14

33 atoms, 32 bonds, 5 residues, 1 model selected  

> hide #1 models

> show #3 models

> show #1 models

> select #1/A:13

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

> select #1/A:13-17

35 atoms, 34 bonds, 5 residues, 1 model selected  

> hide #3 models

> select #1/A:13

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

> select #1/A:13-21

68 atoms, 67 bonds, 9 residues, 1 model selected  

> color sel red

> select #1/A:47

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

> select #1/A:47-62

129 atoms, 130 bonds, 16 residues, 1 model selected  

> color sel orange

> select #1/A:87

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

> select #1/A:87-106

168 atoms, 173 bonds, 20 residues, 1 model selected  

> color sel forest green

> select #1/A:131

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

> select #1/A:131-137

58 atoms, 57 bonds, 7 residues, 1 model selected  

> color sel blue

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

Unsupported scale factor (0.000000) detected on Display0  

> save /Users/king/Desktop/project/alphafold/ompx/3.15.cxs

Desktop color scheme is light  

> hide #1 models

> show #3 models

> measure center #2

Center of area of surface rectangle #2 = (-6.48, -9.04, 15.06)  
Desktop color scheme is dark  
Desktop color scheme is light  

> select #1/A:2-14,21-31,37-51,57-74,77-94,98-115,121-132,135-147

922 atoms, 938 bonds, 118 residues, 1 model selected  

> select #1/A:131-137

58 atoms, 57 bonds, 7 residues, 1 model selected  

> select #1/A:31

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

> select #1/A:31-32

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

> select #1/A:2-14,21-31,37-51,57-74,77-94,98-115,121-132,135-147

922 atoms, 938 bonds, 118 residues, 1 model selected  

> select #1/A:54

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

> select #1/A:54-55

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

> Select ~sel

Unknown command: Select ~sel  

> style #3 stick

Changed 1314 atom styles  

> style #3 stick

Changed 1314 atom styles  

> style #3 sphere

Changed 1314 atom styles  

> style #3 sphere

Changed 1314 atom styles  

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> open "/Users/king/Desktop/project/alphafold/ompx/exp - 2M06.cif"

exp - 2M06.cif title:  
NMR structure of OmpX in phopspholipid nanodiscs [more info...]  
  
Chain information for exp - 2M06.cif  
---  
Chain | Description | UniProt  
4.1/A 4.2/A 4.3/A 4.4/A 4.5/A 4.6/A 4.7/A 4.8/A 4.9/A 4.10/A 4.11/A 4.12/A 4.13/A 4.14/A 4.15/A 4.16/A 4.17/A 4.18/A 4.19/A 4.20/A | Outer membrane protein X | OMPX_ECOLI 1-148  
  

> ui tool show "Show Sequence Viewer"

> select #4.1/A:1-148

2229 atoms, 2260 bonds, 148 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #4.1/A #4.2/A #4.3/A #4.4/A #4.5/A #4.6/A #4.7/A #4.8/A
> #4.9/A #4.10/A #4.11/A #4.12/A #4.13/A #4.14/A #4.15/A #4.16/A #4.17/A
> #4.18/A #4.19/A #4.20/A

Alignment identifier is 1  

> matchmaker #4.1 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 1qj8.pdb, chain A (#1) with exp - 2M06.cif, chain A (#4.1),
sequence alignment score = 716.1  
RMSD between 89 pruned atom pairs is 1.352 angstroms; (across all 148 pairs:
4.602)  
  

> matchmaker #4.1 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.1), sequence alignment score = 718.6  
RMSD between 98 pruned atom pairs is 1.232 angstroms; (across all 148 pairs:
4.317)  
  

> hide #2 models

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> select #3/A:1

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

> select #3/A:1-22

149 atoms, 149 bonds, 22 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #4.1/A #4.2/A #4.3/A #4.4/A #4.5/A #4.6/A #4.7/A #4.8/A
> #4.9/A #4.10/A #4.11/A #4.12/A #4.13/A #4.14/A #4.15/A #4.16/A #4.17/A
> #4.18/A #4.19/A #4.20/A

Alignment identifier is 1  

> select #4.1/A:1 #4.2/A:1 #4.3/A:1 #4.4/A:1 #4.5/A:1 #4.6/A:1 #4.7/A:1
> #4.8/A:1 #4.9/A:1 #4.10/A:1 #4.11/A:1 #4.12/A:1 #4.13/A:1 #4.14/A:1
> #4.15/A:1 #4.16/A:1 #4.17/A:1 #4.18/A:1 #4.19/A:1 #4.20/A:1

240 atoms, 220 bonds, 20 residues, 20 models selected  

> select #4.1/A #4.2/A #4.3/A #4.4/A #4.5/A #4.6/A #4.7/A #4.8/A #4.9/A
> #4.10/A #4.11/A #4.12/A #4.13/A #4.14/A #4.15/A #4.16/A #4.17/A #4.18/A
> #4.19/A #4.20/A

44580 atoms, 45200 bonds, 2960 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [1-148] RMSD: 36.163  
  

> color sel purple

> color sel dark gray

> color sel black

> color sel hot pink

> color sel light sea green

> select #4.1/A:13 #4.2/A:13 #4.3/A:13 #4.4/A:13 #4.5/A:13 #4.6/A:13 #4.7/A:13
> #4.8/A:13 #4.9/A:13 #4.10/A:13 #4.11/A:13 #4.12/A:13 #4.13/A:13 #4.14/A:13
> #4.15/A:13 #4.16/A:13 #4.17/A:13 #4.18/A:13 #4.19/A:13 #4.20/A:13

240 atoms, 220 bonds, 20 residues, 20 models selected  

> select #4.1/A:13-21 #4.2/A:13-21 #4.3/A:13-21 #4.4/A:13-21 #4.5/A:13-21
> #4.6/A:13-21 #4.7/A:13-21 #4.8/A:13-21 #4.9/A:13-21 #4.10/A:13-21
> #4.11/A:13-21 #4.12/A:13-21 #4.13/A:13-21 #4.14/A:13-21 #4.15/A:13-21
> #4.16/A:13-21 #4.17/A:13-21 #4.18/A:13-21 #4.19/A:13-21 #4.20/A:13-21

2660 atoms, 2640 bonds, 180 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [13-21] RMSD: 35.183  
  

> color sel dim gray

> show #2 models

> select #4.1/A:47 #4.2/A:47 #4.3/A:47 #4.4/A:47 #4.5/A:47 #4.6/A:47 #4.7/A:47
> #4.8/A:47 #4.9/A:47 #4.10/A:47 #4.11/A:47 #4.12/A:47 #4.13/A:47 #4.14/A:47
> #4.15/A:47 #4.16/A:47 #4.17/A:47 #4.18/A:47 #4.19/A:47 #4.20/A:47

300 atoms, 280 bonds, 20 residues, 20 models selected  

> select #4.1/A:47-62 #4.2/A:47-62 #4.3/A:47-62 #4.4/A:47-62 #4.5/A:47-62
> #4.6/A:47-62 #4.7/A:47-62 #4.8/A:47-62 #4.9/A:47-62 #4.10/A:47-62
> #4.11/A:47-62 #4.12/A:47-62 #4.13/A:47-62 #4.14/A:47-62 #4.15/A:47-62
> #4.16/A:47-62 #4.17/A:47-62 #4.18/A:47-62 #4.19/A:47-62 #4.20/A:47-62

4920 atoms, 4940 bonds, 320 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [47-62] RMSD: 41.843  
  

> color sel dim gray

> color sel dark gray

> color sel dim gray

> select #4.1/A:87 #4.2/A:87 #4.3/A:87 #4.4/A:87 #4.5/A:87 #4.6/A:87 #4.7/A:87
> #4.8/A:87 #4.9/A:87 #4.10/A:87 #4.11/A:87 #4.12/A:87 #4.13/A:87 #4.14/A:87
> #4.15/A:87 #4.16/A:87 #4.17/A:87 #4.18/A:87 #4.19/A:87 #4.20/A:87

420 atoms, 420 bonds, 20 residues, 20 models selected  

> select #4.1/A:87-106 #4.2/A:87-106 #4.3/A:87-106 #4.4/A:87-106 #4.5/A:87-106
> #4.6/A:87-106 #4.7/A:87-106 #4.8/A:87-106 #4.9/A:87-106 #4.10/A:87-106
> #4.11/A:87-106 #4.12/A:87-106 #4.13/A:87-106 #4.14/A:87-106 #4.15/A:87-106
> #4.16/A:87-106 #4.17/A:87-106 #4.18/A:87-106 #4.19/A:87-106 #4.20/A:87-106

6320 atoms, 6440 bonds, 400 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [87-106] RMSD: 38.635  
  

> color sel dim gray

> select #4.1/A:131 #4.2/A:131 #4.3/A:131 #4.4/A:131 #4.5/A:131 #4.6/A:131
> #4.7/A:131 #4.8/A:131 #4.9/A:131 #4.10/A:131 #4.11/A:131 #4.12/A:131
> #4.13/A:131 #4.14/A:131 #4.15/A:131 #4.16/A:131 #4.17/A:131 #4.18/A:131
> #4.19/A:131 #4.20/A:131

480 atoms, 460 bonds, 20 residues, 20 models selected  

> select #4.1/A:131-137 #4.2/A:131-137 #4.3/A:131-137 #4.4/A:131-137
> #4.5/A:131-137 #4.6/A:131-137 #4.7/A:131-137 #4.8/A:131-137 #4.9/A:131-137
> #4.10/A:131-137 #4.11/A:131-137 #4.12/A:131-137 #4.13/A:131-137
> #4.14/A:131-137 #4.15/A:131-137 #4.16/A:131-137 #4.17/A:131-137
> #4.18/A:131-137 #4.19/A:131-137 #4.20/A:131-137

2440 atoms, 2420 bonds, 140 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [131-137] RMSD: 31.999  
  

> color sel dim gray

> select #4.1/A:55-56 #4.2/A:55-56 #4.3/A:55-56 #4.4/A:55-56 #4.5/A:55-56
> #4.6/A:55-56 #4.7/A:55-56 #4.8/A:55-56 #4.9/A:55-56 #4.10/A:55-56
> #4.11/A:55-56 #4.12/A:55-56 #4.13/A:55-56 #4.14/A:55-56 #4.15/A:55-56
> #4.16/A:55-56 #4.17/A:55-56 #4.18/A:55-56 #4.19/A:55-56 #4.20/A:55-56

380 atoms, 360 bonds, 40 residues, 20 models selected  

> select #4.1/A:55-56 #4.2/A:55-56 #4.3/A:55-56 #4.4/A:55-56 #4.5/A:55-56
> #4.6/A:55-56 #4.7/A:55-56 #4.8/A:55-56 #4.9/A:55-56 #4.10/A:55-56
> #4.11/A:55-56 #4.12/A:55-56 #4.13/A:55-56 #4.14/A:55-56 #4.15/A:55-56
> #4.16/A:55-56 #4.17/A:55-56 #4.18/A:55-56 #4.19/A:55-56 #4.20/A:55-56

380 atoms, 360 bonds, 40 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [55-56] RMSD: 44.406  
  

> select #4.1/A:93 #4.2/A:93 #4.3/A:93 #4.4/A:93 #4.5/A:93 #4.6/A:93 #4.7/A:93
> #4.8/A:93 #4.9/A:93 #4.10/A:93 #4.11/A:93 #4.12/A:93 #4.13/A:93 #4.14/A:93
> #4.15/A:93 #4.16/A:93 #4.17/A:93 #4.18/A:93 #4.19/A:93 #4.20/A:93

280 atoms, 260 bonds, 20 residues, 20 models selected  

> select #4.1/A:93-96 #4.2/A:93-96 #4.3/A:93-96 #4.4/A:93-96 #4.5/A:93-96
> #4.6/A:93-96 #4.7/A:93-96 #4.8/A:93-96 #4.9/A:93-96 #4.10/A:93-96
> #4.11/A:93-96 #4.12/A:93-96 #4.13/A:93-96 #4.14/A:93-96 #4.15/A:93-96
> #4.16/A:93-96 #4.17/A:93-96 #4.18/A:93-96 #4.19/A:93-96 #4.20/A:93-96

1280 atoms, 1300 bonds, 80 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [93-96] RMSD: 41.957  
  

> select #4.1/A:94 #4.2/A:94 #4.3/A:94 #4.4/A:94 #4.5/A:94 #4.6/A:94 #4.7/A:94
> #4.8/A:94 #4.9/A:94 #4.10/A:94 #4.11/A:94 #4.12/A:94 #4.13/A:94 #4.14/A:94
> #4.15/A:94 #4.16/A:94 #4.17/A:94 #4.18/A:94 #4.19/A:94 #4.20/A:94

300 atoms, 280 bonds, 20 residues, 20 models selected  

> select #4.1/A:94-95 #4.2/A:94-95 #4.3/A:94-95 #4.4/A:94-95 #4.5/A:94-95
> #4.6/A:94-95 #4.7/A:94-95 #4.8/A:94-95 #4.9/A:94-95 #4.10/A:94-95
> #4.11/A:94-95 #4.12/A:94-95 #4.13/A:94-95 #4.14/A:94-95 #4.15/A:94-95
> #4.16/A:94-95 #4.17/A:94-95 #4.18/A:94-95 #4.19/A:94-95 #4.20/A:94-95

720 atoms, 720 bonds, 40 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [94-95] RMSD: 42.035  
  

> select #4.1/A:96 #4.2/A:96 #4.3/A:96 #4.4/A:96 #4.5/A:96 #4.6/A:96 #4.7/A:96
> #4.8/A:96 #4.9/A:96 #4.10/A:96 #4.11/A:96 #4.12/A:96 #4.13/A:96 #4.14/A:96
> #4.15/A:96 #4.16/A:96 #4.17/A:96 #4.18/A:96 #4.19/A:96 #4.20/A:96

280 atoms, 280 bonds, 20 residues, 20 models selected  

> select #4.1/A:96-97 #4.2/A:96-97 #4.3/A:96-97 #4.4/A:96-97 #4.5/A:96-97
> #4.6/A:96-97 #4.7/A:96-97 #4.8/A:96-97 #4.9/A:96-97 #4.10/A:96-97
> #4.11/A:96-97 #4.12/A:96-97 #4.13/A:96-97 #4.14/A:96-97 #4.15/A:96-97
> #4.16/A:96-97 #4.17/A:96-97 #4.18/A:96-97 #4.19/A:96-97 #4.20/A:96-97

560 atoms, 560 bonds, 40 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [96-97] RMSD: 40.494  
  

> select #4.1/A:95 #4.2/A:95 #4.3/A:95 #4.4/A:95 #4.5/A:95 #4.6/A:95 #4.7/A:95
> #4.8/A:95 #4.9/A:95 #4.10/A:95 #4.11/A:95 #4.12/A:95 #4.13/A:95 #4.14/A:95
> #4.15/A:95 #4.16/A:95 #4.17/A:95 #4.18/A:95 #4.19/A:95 #4.20/A:95

420 atoms, 420 bonds, 20 residues, 20 models selected  

> select #4.1/A:95-96 #4.2/A:95-96 #4.3/A:95-96 #4.4/A:95-96 #4.5/A:95-96
> #4.6/A:95-96 #4.7/A:95-96 #4.8/A:95-96 #4.9/A:95-96 #4.10/A:95-96
> #4.11/A:95-96 #4.12/A:95-96 #4.13/A:95-96 #4.14/A:95-96 #4.15/A:95-96
> #4.16/A:95-96 #4.17/A:95-96 #4.18/A:95-96 #4.19/A:95-96 #4.20/A:95-96

700 atoms, 720 bonds, 40 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [95-96] RMSD: 41.225  
  

> select #4.1/A:96 #4.2/A:96 #4.3/A:96 #4.4/A:96 #4.5/A:96 #4.6/A:96 #4.7/A:96
> #4.8/A:96 #4.9/A:96 #4.10/A:96 #4.11/A:96 #4.12/A:96 #4.13/A:96 #4.14/A:96
> #4.15/A:96 #4.16/A:96 #4.17/A:96 #4.18/A:96 #4.19/A:96 #4.20/A:96

280 atoms, 280 bonds, 20 residues, 20 models selected  

> select #4.1/A:95-96 #4.2/A:95-96 #4.3/A:95-96 #4.4/A:95-96 #4.5/A:95-96
> #4.6/A:95-96 #4.7/A:95-96 #4.8/A:95-96 #4.9/A:95-96 #4.10/A:95-96
> #4.11/A:95-96 #4.12/A:95-96 #4.13/A:95-96 #4.14/A:95-96 #4.15/A:95-96
> #4.16/A:95-96 #4.17/A:95-96 #4.18/A:95-96 #4.19/A:95-96 #4.20/A:95-96

700 atoms, 720 bonds, 40 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [95-96] RMSD: 41.225  
  

> select #4.1/A:96 #4.2/A:96 #4.3/A:96 #4.4/A:96 #4.5/A:96 #4.6/A:96 #4.7/A:96
> #4.8/A:96 #4.9/A:96 #4.10/A:96 #4.11/A:96 #4.12/A:96 #4.13/A:96 #4.14/A:96
> #4.15/A:96 #4.16/A:96 #4.17/A:96 #4.18/A:96 #4.19/A:96 #4.20/A:96

280 atoms, 280 bonds, 20 residues, 20 models selected  

> select #4.1/A:95-96 #4.2/A:95-96 #4.3/A:95-96 #4.4/A:95-96 #4.5/A:95-96
> #4.6/A:95-96 #4.7/A:95-96 #4.8/A:95-96 #4.9/A:95-96 #4.10/A:95-96
> #4.11/A:95-96 #4.12/A:95-96 #4.13/A:95-96 #4.14/A:95-96 #4.15/A:95-96
> #4.16/A:95-96 #4.17/A:95-96 #4.18/A:95-96 #4.19/A:95-96 #4.20/A:95-96

700 atoms, 720 bonds, 40 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [95-96] RMSD: 41.225  
  

> select #4.1/A:96 #4.2/A:96 #4.3/A:96 #4.4/A:96 #4.5/A:96 #4.6/A:96 #4.7/A:96
> #4.8/A:96 #4.9/A:96 #4.10/A:96 #4.11/A:96 #4.12/A:96 #4.13/A:96 #4.14/A:96
> #4.15/A:96 #4.16/A:96 #4.17/A:96 #4.18/A:96 #4.19/A:96 #4.20/A:96

280 atoms, 280 bonds, 20 residues, 20 models selected  

> select #4.1/A:96-97 #4.2/A:96-97 #4.3/A:96-97 #4.4/A:96-97 #4.5/A:96-97
> #4.6/A:96-97 #4.7/A:96-97 #4.8/A:96-97 #4.9/A:96-97 #4.10/A:96-97
> #4.11/A:96-97 #4.12/A:96-97 #4.13/A:96-97 #4.14/A:96-97 #4.15/A:96-97
> #4.16/A:96-97 #4.17/A:96-97 #4.18/A:96-97 #4.19/A:96-97 #4.20/A:96-97

560 atoms, 560 bonds, 40 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [96-97] RMSD: 40.494  
  

> select #4.1/A:96 #4.2/A:96 #4.3/A:96 #4.4/A:96 #4.5/A:96 #4.6/A:96 #4.7/A:96
> #4.8/A:96 #4.9/A:96 #4.10/A:96 #4.11/A:96 #4.12/A:96 #4.13/A:96 #4.14/A:96
> #4.15/A:96 #4.16/A:96 #4.17/A:96 #4.18/A:96 #4.19/A:96 #4.20/A:96

280 atoms, 280 bonds, 20 residues, 20 models selected  

> select #4.1/A:96 #4.2/A:96 #4.3/A:96 #4.4/A:96 #4.5/A:96 #4.6/A:96 #4.7/A:96
> #4.8/A:96 #4.9/A:96 #4.10/A:96 #4.11/A:96 #4.12/A:96 #4.13/A:96 #4.14/A:96
> #4.15/A:96 #4.16/A:96 #4.17/A:96 #4.18/A:96 #4.19/A:96 #4.20/A:96

280 atoms, 280 bonds, 20 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [96] RMSD: 41.038  
  

> matchmaker #4.1 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.1), sequence alignment score = 718.6  
RMSD between 98 pruned atom pairs is 1.232 angstroms; (across all 148 pairs:
4.317)  
  

> info atoms sel

atom id #4.1/A:96@N idatm_type Npl  
atom id #4.1/A:96@CA idatm_type C3  
atom id #4.1/A:96@C idatm_type C2  
atom id #4.1/A:96@O idatm_type O2  
atom id #4.1/A:96@CB idatm_type C3  
atom id #4.1/A:96@CG idatm_type C3  
atom id #4.1/A:96@CD idatm_type C3  
atom id #4.1/A:96@HA idatm_type HC  
atom id #4.1/A:96@HB2 idatm_type HC  
atom id #4.1/A:96@HB3 idatm_type HC  
atom id #4.1/A:96@HG2 idatm_type HC  
atom id #4.1/A:96@HG3 idatm_type HC  
atom id #4.1/A:96@HD2 idatm_type HC  
atom id #4.1/A:96@HD3 idatm_type HC  
atom id #4.2/A:96@N idatm_type Npl  
atom id #4.2/A:96@CA idatm_type C3  
atom id #4.2/A:96@C idatm_type C2  
atom id #4.2/A:96@O idatm_type O2  
atom id #4.2/A:96@CB idatm_type C3  
atom id #4.2/A:96@CG idatm_type C3  
atom id #4.2/A:96@CD idatm_type C3  
atom id #4.2/A:96@HA idatm_type HC  
atom id #4.2/A:96@HB2 idatm_type HC  
atom id #4.2/A:96@HB3 idatm_type HC  
atom id #4.2/A:96@HG2 idatm_type HC  
atom id #4.2/A:96@HG3 idatm_type HC  
atom id #4.2/A:96@HD2 idatm_type HC  
atom id #4.2/A:96@HD3 idatm_type HC  
atom id #4.3/A:96@N idatm_type Npl  
atom id #4.3/A:96@CA idatm_type C3  
atom id #4.3/A:96@C idatm_type C2  
atom id #4.3/A:96@O idatm_type O2  
atom id #4.3/A:96@CB idatm_type C3  
atom id #4.3/A:96@CG idatm_type C3  
atom id #4.3/A:96@CD idatm_type C3  
atom id #4.3/A:96@HA idatm_type HC  
atom id #4.3/A:96@HB2 idatm_type HC  
atom id #4.3/A:96@HB3 idatm_type HC  
atom id #4.3/A:96@HG2 idatm_type HC  
atom id #4.3/A:96@HG3 idatm_type HC  
atom id #4.3/A:96@HD2 idatm_type HC  
atom id #4.3/A:96@HD3 idatm_type HC  
atom id #4.4/A:96@N idatm_type Npl  
atom id #4.4/A:96@CA idatm_type C3  
atom id #4.4/A:96@C idatm_type C2  
atom id #4.4/A:96@O idatm_type O2  
atom id #4.4/A:96@CB idatm_type C3  
atom id #4.4/A:96@CG idatm_type C3  
atom id #4.4/A:96@CD idatm_type C3  
atom id #4.4/A:96@HA idatm_type HC  
atom id #4.4/A:96@HB2 idatm_type HC  
atom id #4.4/A:96@HB3 idatm_type HC  
atom id #4.4/A:96@HG2 idatm_type HC  
atom id #4.4/A:96@HG3 idatm_type HC  
atom id #4.4/A:96@HD2 idatm_type HC  
atom id #4.4/A:96@HD3 idatm_type HC  
atom id #4.5/A:96@N idatm_type Npl  
atom id #4.5/A:96@CA idatm_type C3  
atom id #4.5/A:96@C idatm_type C2  
atom id #4.5/A:96@O idatm_type O2  
atom id #4.5/A:96@CB idatm_type C3  
atom id #4.5/A:96@CG idatm_type C3  
atom id #4.5/A:96@CD idatm_type C3  
atom id #4.5/A:96@HA idatm_type HC  
atom id #4.5/A:96@HB2 idatm_type HC  
atom id #4.5/A:96@HB3 idatm_type HC  
atom id #4.5/A:96@HG2 idatm_type HC  
atom id #4.5/A:96@HG3 idatm_type HC  
atom id #4.5/A:96@HD2 idatm_type HC  
atom id #4.5/A:96@HD3 idatm_type HC  
atom id #4.6/A:96@N idatm_type Npl  
atom id #4.6/A:96@CA idatm_type C3  
atom id #4.6/A:96@C idatm_type C2  
atom id #4.6/A:96@O idatm_type O2  
atom id #4.6/A:96@CB idatm_type C3  
atom id #4.6/A:96@CG idatm_type C3  
atom id #4.6/A:96@CD idatm_type C3  
atom id #4.6/A:96@HA idatm_type HC  
atom id #4.6/A:96@HB2 idatm_type HC  
atom id #4.6/A:96@HB3 idatm_type HC  
atom id #4.6/A:96@HG2 idatm_type HC  
atom id #4.6/A:96@HG3 idatm_type HC  
atom id #4.6/A:96@HD2 idatm_type HC  
atom id #4.6/A:96@HD3 idatm_type HC  
atom id #4.7/A:96@N idatm_type Npl  
atom id #4.7/A:96@CA idatm_type C3  
atom id #4.7/A:96@C idatm_type C2  
atom id #4.7/A:96@O idatm_type O2  
atom id #4.7/A:96@CB idatm_type C3  
atom id #4.7/A:96@CG idatm_type C3  
atom id #4.7/A:96@CD idatm_type C3  
atom id #4.7/A:96@HA idatm_type HC  
atom id #4.7/A:96@HB2 idatm_type HC  
atom id #4.7/A:96@HB3 idatm_type HC  
atom id #4.7/A:96@HG2 idatm_type HC  
atom id #4.7/A:96@HG3 idatm_type HC  
atom id #4.7/A:96@HD2 idatm_type HC  
atom id #4.7/A:96@HD3 idatm_type HC  
atom id #4.8/A:96@N idatm_type Npl  
atom id #4.8/A:96@CA idatm_type C3  
atom id #4.8/A:96@C idatm_type C2  
atom id #4.8/A:96@O idatm_type O2  
atom id #4.8/A:96@CB idatm_type C3  
atom id #4.8/A:96@CG idatm_type C3  
atom id #4.8/A:96@CD idatm_type C3  
atom id #4.8/A:96@HA idatm_type HC  
atom id #4.8/A:96@HB2 idatm_type HC  
atom id #4.8/A:96@HB3 idatm_type HC  
atom id #4.8/A:96@HG2 idatm_type HC  
atom id #4.8/A:96@HG3 idatm_type HC  
atom id #4.8/A:96@HD2 idatm_type HC  
atom id #4.8/A:96@HD3 idatm_type HC  
atom id #4.9/A:96@N idatm_type Npl  
atom id #4.9/A:96@CA idatm_type C3  
atom id #4.9/A:96@C idatm_type C2  
atom id #4.9/A:96@O idatm_type O2  
atom id #4.9/A:96@CB idatm_type C3  
atom id #4.9/A:96@CG idatm_type C3  
atom id #4.9/A:96@CD idatm_type C3  
atom id #4.9/A:96@HA idatm_type HC  
atom id #4.9/A:96@HB2 idatm_type HC  
atom id #4.9/A:96@HB3 idatm_type HC  
atom id #4.9/A:96@HG2 idatm_type HC  
atom id #4.9/A:96@HG3 idatm_type HC  
atom id #4.9/A:96@HD2 idatm_type HC  
atom id #4.9/A:96@HD3 idatm_type HC  
atom id #4.10/A:96@N idatm_type Npl  
atom id #4.10/A:96@CA idatm_type C3  
atom id #4.10/A:96@C idatm_type C2  
atom id #4.10/A:96@O idatm_type O2  
atom id #4.10/A:96@CB idatm_type C3  
atom id #4.10/A:96@CG idatm_type C3  
atom id #4.10/A:96@CD idatm_type C3  
atom id #4.10/A:96@HA idatm_type HC  
atom id #4.10/A:96@HB2 idatm_type HC  
atom id #4.10/A:96@HB3 idatm_type HC  
atom id #4.10/A:96@HG2 idatm_type HC  
atom id #4.10/A:96@HG3 idatm_type HC  
atom id #4.10/A:96@HD2 idatm_type HC  
atom id #4.10/A:96@HD3 idatm_type HC  
atom id #4.11/A:96@N idatm_type Npl  
atom id #4.11/A:96@CA idatm_type C3  
atom id #4.11/A:96@C idatm_type C2  
atom id #4.11/A:96@O idatm_type O2  
atom id #4.11/A:96@CB idatm_type C3  
atom id #4.11/A:96@CG idatm_type C3  
atom id #4.11/A:96@CD idatm_type C3  
atom id #4.11/A:96@HA idatm_type HC  
atom id #4.11/A:96@HB2 idatm_type HC  
atom id #4.11/A:96@HB3 idatm_type HC  
atom id #4.11/A:96@HG2 idatm_type HC  
atom id #4.11/A:96@HG3 idatm_type HC  
atom id #4.11/A:96@HD2 idatm_type HC  
atom id #4.11/A:96@HD3 idatm_type HC  
atom id #4.12/A:96@N idatm_type Npl  
atom id #4.12/A:96@CA idatm_type C3  
atom id #4.12/A:96@C idatm_type C2  
atom id #4.12/A:96@O idatm_type O2  
atom id #4.12/A:96@CB idatm_type C3  
atom id #4.12/A:96@CG idatm_type C3  
atom id #4.12/A:96@CD idatm_type C3  
atom id #4.12/A:96@HA idatm_type HC  
atom id #4.12/A:96@HB2 idatm_type HC  
atom id #4.12/A:96@HB3 idatm_type HC  
atom id #4.12/A:96@HG2 idatm_type HC  
atom id #4.12/A:96@HG3 idatm_type HC  
atom id #4.12/A:96@HD2 idatm_type HC  
atom id #4.12/A:96@HD3 idatm_type HC  
atom id #4.13/A:96@N idatm_type Npl  
atom id #4.13/A:96@CA idatm_type C3  
atom id #4.13/A:96@C idatm_type C2  
atom id #4.13/A:96@O idatm_type O2  
atom id #4.13/A:96@CB idatm_type C3  
atom id #4.13/A:96@CG idatm_type C3  
atom id #4.13/A:96@CD idatm_type C3  
atom id #4.13/A:96@HA idatm_type HC  
atom id #4.13/A:96@HB2 idatm_type HC  
atom id #4.13/A:96@HB3 idatm_type HC  
atom id #4.13/A:96@HG2 idatm_type HC  
atom id #4.13/A:96@HG3 idatm_type HC  
atom id #4.13/A:96@HD2 idatm_type HC  
atom id #4.13/A:96@HD3 idatm_type HC  
atom id #4.14/A:96@N idatm_type Npl  
atom id #4.14/A:96@CA idatm_type C3  
atom id #4.14/A:96@C idatm_type C2  
atom id #4.14/A:96@O idatm_type O2  
atom id #4.14/A:96@CB idatm_type C3  
atom id #4.14/A:96@CG idatm_type C3  
atom id #4.14/A:96@CD idatm_type C3  
atom id #4.14/A:96@HA idatm_type HC  
atom id #4.14/A:96@HB2 idatm_type HC  
atom id #4.14/A:96@HB3 idatm_type HC  
atom id #4.14/A:96@HG2 idatm_type HC  
atom id #4.14/A:96@HG3 idatm_type HC  
atom id #4.14/A:96@HD2 idatm_type HC  
atom id #4.14/A:96@HD3 idatm_type HC  
atom id #4.15/A:96@N idatm_type Npl  
atom id #4.15/A:96@CA idatm_type C3  
atom id #4.15/A:96@C idatm_type C2  
atom id #4.15/A:96@O idatm_type O2  
atom id #4.15/A:96@CB idatm_type C3  
atom id #4.15/A:96@CG idatm_type C3  
atom id #4.15/A:96@CD idatm_type C3  
atom id #4.15/A:96@HA idatm_type HC  
atom id #4.15/A:96@HB2 idatm_type HC  
atom id #4.15/A:96@HB3 idatm_type HC  
atom id #4.15/A:96@HG2 idatm_type HC  
atom id #4.15/A:96@HG3 idatm_type HC  
atom id #4.15/A:96@HD2 idatm_type HC  
atom id #4.15/A:96@HD3 idatm_type HC  
atom id #4.16/A:96@N idatm_type Npl  
atom id #4.16/A:96@CA idatm_type C3  
atom id #4.16/A:96@C idatm_type C2  
atom id #4.16/A:96@O idatm_type O2  
atom id #4.16/A:96@CB idatm_type C3  
atom id #4.16/A:96@CG idatm_type C3  
atom id #4.16/A:96@CD idatm_type C3  
atom id #4.16/A:96@HA idatm_type HC  
atom id #4.16/A:96@HB2 idatm_type HC  
atom id #4.16/A:96@HB3 idatm_type HC  
atom id #4.16/A:96@HG2 idatm_type HC  
atom id #4.16/A:96@HG3 idatm_type HC  
atom id #4.16/A:96@HD2 idatm_type HC  
atom id #4.16/A:96@HD3 idatm_type HC  
atom id #4.17/A:96@N idatm_type Npl  
atom id #4.17/A:96@CA idatm_type C3  
atom id #4.17/A:96@C idatm_type C2  
atom id #4.17/A:96@O idatm_type O2  
atom id #4.17/A:96@CB idatm_type C3  
atom id #4.17/A:96@CG idatm_type C3  
atom id #4.17/A:96@CD idatm_type C3  
atom id #4.17/A:96@HA idatm_type HC  
atom id #4.17/A:96@HB2 idatm_type HC  
atom id #4.17/A:96@HB3 idatm_type HC  
atom id #4.17/A:96@HG2 idatm_type HC  
atom id #4.17/A:96@HG3 idatm_type HC  
atom id #4.17/A:96@HD2 idatm_type HC  
atom id #4.17/A:96@HD3 idatm_type HC  
atom id #4.18/A:96@N idatm_type Npl  
atom id #4.18/A:96@CA idatm_type C3  
atom id #4.18/A:96@C idatm_type C2  
atom id #4.18/A:96@O idatm_type O2  
atom id #4.18/A:96@CB idatm_type C3  
atom id #4.18/A:96@CG idatm_type C3  
atom id #4.18/A:96@CD idatm_type C3  
atom id #4.18/A:96@HA idatm_type HC  
atom id #4.18/A:96@HB2 idatm_type HC  
atom id #4.18/A:96@HB3 idatm_type HC  
atom id #4.18/A:96@HG2 idatm_type HC  
atom id #4.18/A:96@HG3 idatm_type HC  
atom id #4.18/A:96@HD2 idatm_type HC  
atom id #4.18/A:96@HD3 idatm_type HC  
atom id #4.19/A:96@N idatm_type Npl  
atom id #4.19/A:96@CA idatm_type C3  
atom id #4.19/A:96@C idatm_type C2  
atom id #4.19/A:96@O idatm_type O2  
atom id #4.19/A:96@CB idatm_type C3  
atom id #4.19/A:96@CG idatm_type C3  
atom id #4.19/A:96@CD idatm_type C3  
atom id #4.19/A:96@HA idatm_type HC  
atom id #4.19/A:96@HB2 idatm_type HC  
atom id #4.19/A:96@HB3 idatm_type HC  
atom id #4.19/A:96@HG2 idatm_type HC  
atom id #4.19/A:96@HG3 idatm_type HC  
atom id #4.19/A:96@HD2 idatm_type HC  
atom id #4.19/A:96@HD3 idatm_type HC  
atom id #4.20/A:96@N idatm_type Npl  
atom id #4.20/A:96@CA idatm_type C3  
atom id #4.20/A:96@C idatm_type C2  
atom id #4.20/A:96@O idatm_type O2  
atom id #4.20/A:96@CB idatm_type C3  
atom id #4.20/A:96@CG idatm_type C3  
atom id #4.20/A:96@CD idatm_type C3  
atom id #4.20/A:96@HA idatm_type HC  
atom id #4.20/A:96@HB2 idatm_type HC  
atom id #4.20/A:96@HB3 idatm_type HC  
atom id #4.20/A:96@HG2 idatm_type HC  
atom id #4.20/A:96@HG3 idatm_type HC  
atom id #4.20/A:96@HD2 idatm_type HC  
atom id #4.20/A:96@HD3 idatm_type HC  

> select #4.1/A:96@CA

1 atom, 1 residue, 1 model selected  

> getcrd sel

Atom #4.1/A:96@CA -18.334 10.893 34.466  

> select #4.1/A:95 #4.2/A:95 #4.3/A:95 #4.4/A:95 #4.5/A:95 #4.6/A:95 #4.7/A:95
> #4.8/A:95 #4.9/A:95 #4.10/A:95 #4.11/A:95 #4.12/A:95 #4.13/A:95 #4.14/A:95
> #4.15/A:95 #4.16/A:95 #4.17/A:95 #4.18/A:95 #4.19/A:95 #4.20/A:95

420 atoms, 420 bonds, 20 residues, 20 models selected  

> select #4.1/A:95-97 #4.2/A:95-97 #4.3/A:95-97 #4.4/A:95-97 #4.5/A:95-97
> #4.6/A:95-97 #4.7/A:95-97 #4.8/A:95-97 #4.9/A:95-97 #4.10/A:95-97
> #4.11/A:95-97 #4.12/A:95-97 #4.13/A:95-97 #4.14/A:95-97 #4.15/A:95-97
> #4.16/A:95-97 #4.17/A:95-97 #4.18/A:95-97 #4.19/A:95-97 #4.20/A:95-97

980 atoms, 1000 bonds, 60 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [95-97] RMSD: 40.802  
  

> select #4.1/A:95-97@CA

3 atoms, 3 residues, 1 model selected  

> getcrd sel

Atom #4.1/A:95@CA -16.810 7.491 33.455  
Atom #4.1/A:96@CA -18.334 10.893 34.466  
Atom #4.1/A:97@CA -19.007 13.197 31.524  

> select #4.2/A:95-97@CA

3 atoms, 3 residues, 1 model selected  

> select #4.2/A:95-97@CA

3 atoms, 3 residues, 1 model selected  

> getcrd sel

Atom #4.2/A:95@CA 109.794 28.151 16.339  
Atom #4.2/A:96@CA 109.739 25.108 18.656  
Atom #4.2/A:97@CA 106.810 22.772 18.048  

> select #4/A:95-97@CA

60 atoms, 60 residues, 20 models selected  

> getcrd sel

Atom #4.1/A:95@CA -16.810 7.491 33.455  
Atom #4.1/A:96@CA -18.334 10.893 34.466  
Atom #4.1/A:97@CA -19.007 13.197 31.524  
Atom #4.2/A:95@CA 109.794 28.151 16.339  
Atom #4.2/A:96@CA 109.739 25.108 18.656  
Atom #4.2/A:97@CA 106.810 22.772 18.048  
Atom #4.3/A:95@CA 110.699 29.628 12.611  
Atom #4.3/A:96@CA 108.529 26.523 13.418  
Atom #4.3/A:97@CA 105.582 26.659 15.796  
Atom #4.4/A:95@CA 103.648 31.500 5.466  
Atom #4.4/A:96@CA 103.619 29.311 8.598  
Atom #4.4/A:97@CA 100.616 27.096 9.262  
Atom #4.5/A:95@CA 104.363 29.918 8.170  
Atom #4.5/A:96@CA 102.971 26.346 8.683  
Atom #4.5/A:97@CA 99.260 25.567 8.729  
Atom #4.6/A:95@CA 109.573 30.681 12.363  
Atom #4.6/A:96@CA 107.739 27.538 13.557  
Atom #4.6/A:97@CA 104.059 27.008 12.823  
Atom #4.7/A:95@CA 113.653 24.535 18.998  
Atom #4.7/A:96@CA 111.080 21.691 19.072  
Atom #4.7/A:97@CA 107.402 22.547 18.697  
Atom #4.8/A:95@CA 111.939 29.866 14.122  
Atom #4.8/A:96@CA 109.404 27.244 15.301  
Atom #4.8/A:97@CA 105.727 27.546 14.434  
Atom #4.9/A:95@CA 106.596 29.887 11.782  
Atom #4.9/A:96@CA 105.046 26.406 12.311  
Atom #4.9/A:97@CA 101.334 25.657 12.275  
Atom #4.10/A:95@CA 107.295 27.966 15.380  
Atom #4.10/A:96@CA 104.470 28.606 17.935  
Atom #4.10/A:97@CA 102.390 25.547 18.783  
Atom #4.11/A:95@CA 110.434 27.749 16.442  
Atom #4.11/A:96@CA 108.241 28.023 19.609  
Atom #4.11/A:97@CA 105.856 25.100 20.018  
Atom #4.12/A:95@CA 106.554 31.782 10.055  
Atom #4.12/A:96@CA 105.297 30.030 13.217  
Atom #4.12/A:97@CA 102.697 27.352 12.551  
Atom #4.13/A:95@CA 108.269 30.749 12.396  
Atom #4.13/A:96@CA 106.559 27.953 14.389  
Atom #4.13/A:97@CA 103.228 26.719 13.053  
Atom #4.14/A:95@CA 111.710 28.652 15.347  
Atom #4.14/A:96@CA 109.537 25.653 16.348  
Atom #4.14/A:97@CA 105.976 25.550 15.045  
Atom #4.15/A:95@CA 108.124 31.418 11.681  
Atom #4.15/A:96@CA 107.320 29.241 14.725  
Atom #4.15/A:97@CA 104.420 26.861 14.171  
Atom #4.16/A:95@CA 108.360 30.489 11.340  
Atom #4.16/A:96@CA 107.851 27.402 13.553  
Atom #4.16/A:97@CA 104.363 25.920 13.739  
Atom #4.17/A:95@CA 105.062 28.644 10.027  
Atom #4.17/A:96@CA 103.653 25.073 9.510  
Atom #4.17/A:97@CA 99.946 24.334 9.224  
Atom #4.18/A:95@CA 113.847 25.092 19.639  
Atom #4.18/A:96@CA 111.540 22.034 19.771  
Atom #4.18/A:97@CA 107.781 22.531 19.629  
Atom #4.19/A:95@CA 104.795 30.988 6.341  
Atom #4.19/A:96@CA 103.611 28.565 9.079  
Atom #4.19/A:97@CA 100.711 26.284 8.176  
Atom #4.20/A:95@CA 107.984 28.414 14.620  
Atom #4.20/A:96@CA 106.225 25.048 14.054  
Atom #4.20/A:97@CA 102.491 24.599 13.598  

> select #4.1/A:54 #4.2/A:54 #4.3/A:54 #4.4/A:54 #4.5/A:54 #4.6/A:54 #4.7/A:54
> #4.8/A:54 #4.9/A:54 #4.10/A:54 #4.11/A:54 #4.12/A:54 #4.13/A:54 #4.14/A:54
> #4.15/A:54 #4.16/A:54 #4.17/A:54 #4.18/A:54 #4.19/A:54 #4.20/A:54

220 atoms, 200 bonds, 20 residues, 20 models selected  

> select #4.1/A:54-56 #4.2/A:54-56 #4.3/A:54-56 #4.4/A:54-56 #4.5/A:54-56
> #4.6/A:54-56 #4.7/A:54-56 #4.8/A:54-56 #4.9/A:54-56 #4.10/A:54-56
> #4.11/A:54-56 #4.12/A:54-56 #4.13/A:54-56 #4.14/A:54-56 #4.15/A:54-56
> #4.16/A:54-56 #4.17/A:54-56 #4.18/A:54-56 #4.19/A:54-56 #4.20/A:54-56

600 atoms, 580 bonds, 60 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [54-56] RMSD: 44.340  
  

> select #4.1/A:54 #4.2/A:54 #4.3/A:54 #4.4/A:54 #4.5/A:54 #4.6/A:54 #4.7/A:54
> #4.8/A:54 #4.9/A:54 #4.10/A:54 #4.11/A:54 #4.12/A:54 #4.13/A:54 #4.14/A:54
> #4.15/A:54 #4.16/A:54 #4.17/A:54 #4.18/A:54 #4.19/A:54 #4.20/A:54

220 atoms, 200 bonds, 20 residues, 20 models selected  

> select #4.1/A:53-54 #4.2/A:53-54 #4.3/A:53-54 #4.4/A:53-54 #4.5/A:53-54
> #4.6/A:53-54 #4.7/A:53-54 #4.8/A:53-54 #4.9/A:53-54 #4.10/A:53-54
> #4.11/A:53-54 #4.12/A:53-54 #4.13/A:53-54 #4.14/A:53-54 #4.15/A:53-54
> #4.16/A:53-54 #4.17/A:53-54 #4.18/A:53-54 #4.19/A:53-54 #4.20/A:53-54

440 atoms, 420 bonds, 40 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [53-54] RMSD: 44.192  
  

> select #4.1/A:52 #4.2/A:52 #4.3/A:52 #4.4/A:52 #4.5/A:52 #4.6/A:52 #4.7/A:52
> #4.8/A:52 #4.9/A:52 #4.10/A:52 #4.11/A:52 #4.12/A:52 #4.13/A:52 #4.14/A:52
> #4.15/A:52 #4.16/A:52 #4.17/A:52 #4.18/A:52 #4.19/A:52 #4.20/A:52

200 atoms, 180 bonds, 20 residues, 20 models selected  

> select #4.1/A:52-54 #4.2/A:52-54 #4.3/A:52-54 #4.4/A:52-54 #4.5/A:52-54
> #4.6/A:52-54 #4.7/A:52-54 #4.8/A:52-54 #4.9/A:52-54 #4.10/A:52-54
> #4.11/A:52-54 #4.12/A:52-54 #4.13/A:52-54 #4.14/A:52-54 #4.15/A:52-54
> #4.16/A:52-54 #4.17/A:52-54 #4.18/A:52-54 #4.19/A:52-54 #4.20/A:52-54

640 atoms, 620 bonds, 60 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [52-54] RMSD: 43.994  
  

> select #4.1/A:53-54 #4.2/A:53-54 #4.3/A:53-54 #4.4/A:53-54 #4.5/A:53-54
> #4.6/A:53-54 #4.7/A:53-54 #4.8/A:53-54 #4.9/A:53-54 #4.10/A:53-54
> #4.11/A:53-54 #4.12/A:53-54 #4.13/A:53-54 #4.14/A:53-54 #4.15/A:53-54
> #4.16/A:53-54 #4.17/A:53-54 #4.18/A:53-54 #4.19/A:53-54 #4.20/A:53-54

440 atoms, 420 bonds, 40 residues, 20 models selected  

> select #4.1/A:53-55 #4.2/A:53-55 #4.3/A:53-55 #4.4/A:53-55 #4.5/A:53-55
> #4.6/A:53-55 #4.7/A:53-55 #4.8/A:53-55 #4.9/A:53-55 #4.10/A:53-55
> #4.11/A:53-55 #4.12/A:53-55 #4.13/A:53-55 #4.14/A:53-55 #4.15/A:53-55
> #4.16/A:53-55 #4.17/A:53-55 #4.18/A:53-55 #4.19/A:53-55 #4.20/A:53-55

580 atoms, 560 bonds, 60 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [53-55] RMSD: 44.459  
  

> getcrd sel

Atom #4.1/A:53@N -3.377 -15.004 31.500  
Atom #4.1/A:53@CA -2.718 -14.903 32.797  
Atom #4.1/A:53@C -3.629 -14.186 33.795  
Atom #4.1/A:53@O -4.200 -14.816 34.685  
Atom #4.1/A:53@CB -1.382 -14.162 32.660  
Atom #4.1/A:53@OG -0.348 -15.107 32.419  
Atom #4.1/A:53@H -4.276 -14.627 31.390  
Atom #4.1/A:53@HA -2.523 -15.901 33.164  
Atom #4.1/A:53@HB2 -1.432 -13.475 31.832  
Atom #4.1/A:53@HB3 -1.181 -13.609 33.568  
Atom #4.1/A:53@HG -0.123 -15.069 31.487  
Atom #4.1/A:54@N -3.763 -12.871 33.642  
Atom #4.1/A:54@CA -4.644 -12.095 34.509  
Atom #4.1/A:54@C -6.101 -12.529 34.344  
Atom #4.1/A:54@O -6.857 -12.570 35.316  
Atom #4.1/A:54@CB -4.518 -10.607 34.181  
Atom #4.1/A:54@OG -3.152 -10.224 34.272  
Atom #4.1/A:54@H -3.261 -12.414 32.935  
Atom #4.1/A:54@HA -4.349 -12.250 35.537  
Atom #4.1/A:54@HB2 -4.868 -10.423 33.178  
Atom #4.1/A:54@HB3 -5.116 -10.035 34.877  
Atom #4.1/A:54@HG -2.938 -9.704 33.494  
Atom #4.1/A:55@N -6.487 -12.853 33.114  
Atom #4.1/A:55@CA -7.864 -13.255 32.828  
Atom #4.1/A:55@C -8.723 -12.112 32.264  
Atom #4.1/A:55@O -9.862 -12.347 31.858  
Atom #4.1/A:55@H -5.835 -12.821 32.382  
Atom #4.1/A:55@HA2 -7.848 -14.062 32.112  
Atom #4.1/A:55@HA3 -8.317 -13.611 33.741  
Atom #4.2/A:53@N 124.160 28.109 -6.855  
Atom #4.2/A:53@CA 125.246 29.083 -6.794  
Atom #4.2/A:53@C 125.207 29.843 -5.470  
Atom #4.2/A:53@O 126.245 30.103 -4.861  
Atom #4.2/A:53@CB 125.130 30.070 -7.955  
Atom #4.2/A:53@OG 125.070 29.347 -9.177  
Atom #4.2/A:53@H 123.509 28.155 -7.586  
Atom #4.2/A:53@HA 126.188 28.562 -6.872  
Atom #4.2/A:53@HB2 124.230 30.655 -7.848  
Atom #4.2/A:53@HB3 125.986 30.730 -7.950  
Atom #4.2/A:53@HG 124.423 28.645 -9.076  
Atom #4.2/A:54@N 124.002 30.196 -5.031  
Atom #4.2/A:54@CA 123.827 30.858 -3.740  
Atom #4.2/A:54@C 124.188 29.931 -2.575  
Atom #4.2/A:54@O 124.644 30.393 -1.529  
Atom #4.2/A:54@CB 122.378 31.319 -3.589  
Atom #4.2/A:54@OG 121.535 30.180 -3.475  
Atom #4.2/A:54@H 123.215 30.009 -5.584  
Atom #4.2/A:54@HA 124.469 31.726 -3.704  
Atom #4.2/A:54@HB2 122.277 31.920 -2.699  
Atom #4.2/A:54@HB3 122.098 31.910 -4.451  
Atom #4.2/A:54@HG 121.622 29.665 -4.281  
Atom #4.2/A:55@N 123.983 28.627 -2.755  
Atom #4.2/A:55@CA 124.258 27.661 -1.692  
Atom #4.2/A:55@C 123.004 27.245 -0.908  
Atom #4.2/A:55@O 123.101 26.442 0.020  
Atom #4.2/A:55@H 123.640 28.309 -3.616  
Atom #4.2/A:55@HA2 124.697 26.778 -2.133  
Atom #4.2/A:55@HA3 124.969 28.096 -1.005  
Atom #4.3/A:53@N 123.845 24.514 -10.895  
Atom #4.3/A:53@CA 123.421 25.767 -11.520  
Atom #4.3/A:53@C 121.901 25.911 -11.516  
Atom #4.3/A:53@O 121.209 25.377 -12.383  
Atom #4.3/A:53@CB 123.945 25.838 -12.956  
Atom #4.3/A:53@OG 123.239 24.908 -13.765  
Atom #4.3/A:53@H 124.530 24.542 -10.194  
Atom #4.3/A:53@HA 123.845 26.588 -10.962  
Atom #4.3/A:53@HB2 123.795 26.830 -13.349  
Atom #4.3/A:53@HB3 125.003 25.612 -12.960  
Atom #4.3/A:53@HG 122.314 25.165 -13.775  
Atom #4.3/A:54@N 121.388 26.649 -10.537  
Atom #4.3/A:54@CA 119.951 26.877 -10.434  
Atom #4.3/A:54@C 119.645 27.862 -9.310  
Atom #4.3/A:54@O 118.964 28.866 -9.518  
Atom #4.3/A:54@CB 119.231 25.554 -10.166  
Atom #4.3/A:54@OG 117.855 25.813 -9.923  
Atom #4.3/A:54@H 121.987 27.048 -9.871  
Atom #4.3/A:54@HA 119.593 27.286 -11.367  
Atom #4.3/A:54@HB2 119.321 24.909 -11.024  
Atom #4.3/A:54@HB3 119.680 25.071 -9.308  
Atom #4.3/A:54@HG 117.350 25.437 -10.648  
Atom #4.3/A:55@N 120.155 27.565 -8.119  
Atom #4.3/A:55@CA 119.934 28.430 -6.960  
Atom #4.3/A:55@C 118.765 27.974 -6.075  
Atom #4.3/A:55@O 118.555 28.536 -5.000  
Atom #4.3/A:55@H 120.689 26.750 -8.015  
Atom #4.3/A:55@HA2 120.834 28.445 -6.363  
Atom #4.3/A:55@HA3 119.734 29.432 -7.310  
Atom #4.4/A:53@N 123.889 28.568 -6.558  
Atom #4.4/A:53@CA 124.898 29.595 -6.307  
Atom #4.4/A:53@C 124.513 30.477 -5.118  
Atom #4.4/A:53@O 125.380 30.945 -4.381  
Atom #4.4/A:53@CB 125.072 30.466 -7.552  
Atom #4.4/A:53@OG 123.890 31.228 -7.757  
Atom #4.4/A:53@H 123.450 28.527 -7.433  
Atom #4.4/A:53@HA 125.839 29.111 -6.090  
Atom #4.4/A:53@HB2 125.904 31.137 -7.413  
Atom #4.4/A:53@HB3 125.266 29.833 -8.407  
Atom #4.4/A:53@HG 124.085 32.142 -7.536  
Atom #4.4/A:54@N 123.214 30.703 -4.933  
Atom #4.4/A:54@CA 122.736 31.506 -3.811  
Atom #4.4/A:54@C 123.203 30.930 -2.473  
Atom #4.4/A:54@O 123.470 31.675 -1.530  
Atom #4.4/A:54@CB 121.209 31.569 -3.831  
Atom #4.4/A:54@OG 120.766 32.486 -2.840  
Atom #4.4/A:54@H 122.566 30.324 -5.562  
Atom #4.4/A:54@HA 123.124 32.509 -3.911  
Atom #4.4/A:54@HB2 120.871 31.905 -4.798  
Atom #4.4/A:54@HB3 120.808 30.583 -3.637  
Atom #4.4/A:54@HG 120.994 32.126 -1.979  
Atom #4.4/A:55@N 123.303 29.605 -2.392  
Atom #4.4/A:55@CA 123.723 28.949 -1.154  
Atom #4.4/A:55@C 122.556 28.357 -0.350  
Atom #4.4/A:55@O 122.767 27.854 0.753  
Atom #4.4/A:55@H 123.090 29.058 -3.177  
Atom #4.4/A:55@HA2 124.410 28.153 -1.401  
Atom #4.4/A:55@HA3 124.239 29.670 -0.538  
Atom #4.5/A:53@N 126.519 24.396 -6.072  
Atom #4.5/A:53@CA 127.097 25.608 -6.640  
Atom #4.5/A:53@C 127.078 26.732 -5.610  
Atom #4.5/A:53@O 128.126 27.176 -5.140  
Atom #4.5/A:53@CB 126.312 26.037 -7.881  
Atom #4.5/A:53@OG 125.987 24.887 -8.651  
Atom #4.5/A:53@H 125.974 24.459 -5.261  
Atom #4.5/A:53@HA 128.120 25.409 -6.925  
Atom #4.5/A:53@HB2 125.402 26.530 -7.586  
Atom #4.5/A:53@HB3 126.913 26.721 -8.465  
Atom #4.5/A:53@HG 125.127 25.033 -9.054  
Atom #4.5/A:54@N 125.878 27.187 -5.264  
Atom #4.5/A:54@CA 125.726 28.239 -4.263  
Atom #4.5/A:54@C 126.294 27.808 -2.910  
Atom #4.5/A:54@O 126.841 28.628 -2.172  
Atom #4.5/A:54@CB 124.247 28.590 -4.102  
Atom #4.5/A:54@OG 123.712 28.949 -5.370  
Atom #4.5/A:54@H 125.080 26.807 -5.686  
Atom #4.5/A:54@HA 126.255 29.118 -4.599  
Atom #4.5/A:54@HB2 123.708 27.738 -3.722  
Atom #4.5/A:54@HB3 124.148 29.413 -3.406  
Atom #4.5/A:54@HG 124.031 28.315 -6.016  
Atom #4.5/A:55@N 126.164 26.523 -2.589  
Atom #4.5/A:55@CA 126.628 26.010 -1.299  
Atom #4.5/A:55@C 125.490 25.790 -0.291  
Atom #4.5/A:55@O 125.724 25.239 0.786  
Atom #4.5/A:55@H 125.748 25.908 -3.228  
Atom #4.5/A:55@HA2 127.132 25.069 -1.463  
Atom #4.5/A:55@HA3 127.332 26.712 -0.879  
Atom #4.6/A:53@N 117.359 28.993 -8.076  
Atom #4.6/A:53@CA 118.136 30.162 -8.479  
Atom #4.6/A:53@C 118.715 30.877 -7.261  
Atom #4.6/A:53@O 119.848 31.358 -7.296  
Atom #4.6/A:53@CB 117.249 31.128 -9.266  
Atom #4.6/A:53@OG 118.055 32.171 -9.798  
Atom #4.6/A:53@H 116.416 28.929 -8.333  
Atom #4.6/A:53@HA 118.946 29.840 -9.115  
Atom #4.6/A:53@HB2 116.770 30.605 -10.077  
Atom #4.6/A:53@HB3 116.493 31.536 -8.609  
Atom #4.6/A:53@HG 117.684 33.009 -9.512  
Atom #4.6/A:54@N 117.935 30.945 -6.187  
Atom #4.6/A:54@CA 118.393 31.589 -4.960  
Atom #4.6/A:54@C 119.671 30.935 -4.436  
Atom #4.6/A:54@O 120.548 31.613 -3.900  
Atom #4.6/A:54@CB 117.304 31.503 -3.890  
Atom #4.6/A:54@OG 116.100 32.055 -4.405  
Atom #4.6/A:54@H 117.036 30.556 -6.219  
Atom #4.6/A:54@HA 118.593 32.630 -5.165  
Atom #4.6/A:54@HB2 117.134 30.473 -3.625  
Atom #4.6/A:54@HB3 117.622 32.049 -3.011  
Atom #4.6/A:54@HG 115.364 31.622 -3.966  
Atom #4.6/A:55@N 119.775 29.618 -4.593  
Atom #4.6/A:55@CA 120.950 28.888 -4.122  
Atom #4.6/A:55@C 120.811 28.414 -2.672  
Atom #4.6/A:55@O 121.815 28.129 -2.018  
Atom #4.6/A:55@H 119.049 29.129 -5.034  
Atom #4.6/A:55@HA2 121.102 28.027 -4.756  
Atom #4.6/A:55@HA3 121.814 29.532 -4.197  
Atom #4.7/A:53@N 126.048 27.507 -4.972  
Atom #4.7/A:53@CA 126.715 28.635 -4.330  
Atom #4.7/A:53@C 125.702 29.532 -3.620  
Atom #4.7/A:53@O 125.967 30.043 -2.533  
Atom #4.7/A:53@CB 127.480 29.451 -5.371  
Atom #4.7/A:53@OG 128.371 28.595 -6.074  
Atom #4.7/A:53@H 126.140 27.380 -5.940  
Atom #4.7/A:53@HA 127.417 28.257 -3.600  
Atom #4.7/A:53@HB2 126.788 29.890 -6.071  
Atom #4.7/A:53@HB3 128.029 30.241 -4.875  
Atom #4.7/A:53@HG 129.268 28.836 -5.829  
Atom #4.7/A:54@N 124.541 29.721 -4.243  
Atom #4.7/A:54@CA 123.491 30.545 -3.656  
Atom #4.7/A:54@C 122.115 30.008 -4.040  
Atom #4.7/A:54@O 121.948 29.418 -5.107  
Atom #4.7/A:54@CB 123.630 31.990 -4.137  
Atom #4.7/A:54@OG 122.681 32.801 -3.459  
Atom #4.7/A:54@H 124.388 29.297 -5.113  
Atom #4.7/A:54@HA 123.587 30.524 -2.580  
Atom #4.7/A:54@HB2 124.622 32.352 -3.922  
Atom #4.7/A:54@HB3 123.462 32.027 -5.205  
Atom #4.7/A:54@HG 122.899 32.791 -2.524  
Atom #4.7/A:55@N 121.134 30.215 -3.167  
Atom #4.7/A:55@CA 119.776 29.749 -3.441  
Atom #4.7/A:55@C 119.557 28.287 -3.036  
Atom #4.7/A:55@O 118.636 27.640 -3.535  
Atom #4.7/A:55@H 121.324 30.686 -2.329  
Atom #4.7/A:55@HA2 119.080 30.369 -2.895  
Atom #4.7/A:55@HA3 119.578 29.851 -4.497  
Atom #4.8/A:53@N 122.482 28.122 -7.538  
Atom #4.8/A:53@CA 123.563 29.068 -7.801  
Atom #4.8/A:53@C 124.035 29.731 -6.507  
Atom #4.8/A:53@O 125.228 29.978 -6.328  
Atom #4.8/A:53@CB 123.090 30.140 -8.781  
Atom #4.8/A:53@OG 122.110 30.952 -8.148  
Atom #4.8/A:53@H 121.599 28.276 -7.933  
Atom #4.8/A:53@HA 124.392 28.535 -8.243  
Atom #4.8/A:53@HB2 123.923 30.758 -9.076  
Atom #4.8/A:53@HB3 122.673 29.663 -9.659  
Atom #4.8/A:53@HG 122.415 31.862 -8.177  
Atom #4.8/A:54@N 123.097 30.017 -5.609  
Atom #4.8/A:54@CA 123.434 30.618 -4.322  
Atom #4.8/A:54@C 124.351 29.705 -3.507  
Atom #4.8/A:54@O 125.236 30.180 -2.796  
Atom #4.8/A:54@CB 122.158 30.897 -3.528  
Atom #4.8/A:54@OG 121.284 31.694 -4.315  
Atom #4.8/A:54@H 122.159 29.820 -5.815  
Atom #4.8/A:54@HA 123.943 31.553 -4.498  
Atom #4.8/A:54@HB2 121.667 29.967 -3.290  
Atom #4.8/A:54@HB3 122.412 31.410 -2.611  
Atom #4.8/A:54@HG 121.221 32.559 -3.905  
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Atom #4.9/A:53@N 117.089 25.641 -10.837  
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Atom #4.9/A:53@C 115.234 27.243 -10.810  
Atom #4.9/A:53@O 115.272 28.432 -11.129  
Atom #4.9/A:53@CB 115.029 25.080 -12.042  
Atom #4.9/A:53@OG 114.283 25.512 -13.172  
Atom #4.9/A:53@H 117.196 25.914 -9.902  
Atom #4.9/A:53@HA 116.393 26.660 -12.507  
Atom #4.9/A:53@HB2 115.587 24.197 -12.305  
Atom #4.9/A:53@HB3 114.366 24.848 -11.220  
Atom #4.9/A:53@HG 113.857 24.742 -13.557  
Atom #4.9/A:54@N 114.549 26.797 -9.762  
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Atom #4.9/A:54@C 114.721 28.693 -8.184  
Atom #4.9/A:54@O 114.343 29.838 -7.936  
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Atom #4.9/A:54@OG 113.903 26.275 -6.978  
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Atom #4.9/A:54@HA 113.105 28.269 -9.516  
Atom #4.9/A:54@HB2 112.360 27.574 -7.315  
Atom #4.9/A:54@HB3 112.395 26.174 -8.382  
Atom #4.9/A:54@HG 113.795 25.325 -7.073  
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Atom #4.10/A:53@H 122.700 28.409 -8.003  
Atom #4.10/A:53@HA 125.409 28.808 -7.371  
Atom #4.10/A:53@HB2 125.171 30.969 -8.436  
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Atom #4.10/A:53@HG 123.431 32.023 -8.034  
Atom #4.10/A:54@N 123.274 30.345 -5.395  
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Atom #4.10/A:54@C 123.683 30.137 -2.966  
Atom #4.10/A:54@O 124.226 30.645 -1.985  
Atom #4.10/A:54@CB 121.692 31.367 -3.835  
Atom #4.10/A:54@OG 120.951 30.169 -3.644  
Atom #4.10/A:54@H 122.463 30.100 -5.887  
Atom #4.10/A:54@HA 123.730 31.928 -4.131  
Atom #4.10/A:54@HB2 121.620 31.971 -2.946  
Atom #4.10/A:54@HB3 121.299 31.923 -4.676  
Atom #4.10/A:54@HG 120.734 30.099 -2.712  
Atom #4.10/A:55@N 123.523 28.822 -3.097  
Atom #4.10/A:55@CA 123.977 27.895 -2.060  
Atom #4.10/A:55@C 122.869 27.487 -1.079  
Atom #4.10/A:55@O 123.125 26.716 -0.153  
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Atom #4.10/A:55@HA2 124.361 27.005 -2.537  
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Atom #4.11/A:53@N 121.022 28.907 -6.595  
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Atom #4.11/A:53@C 122.692 30.444 -5.640  
Atom #4.11/A:53@O 123.900 30.674 -5.583  
Atom #4.11/A:53@CB 121.487 31.014 -7.750  
Atom #4.11/A:53@OG 120.852 30.471 -8.900  
Atom #4.11/A:53@H 120.109 29.063 -6.917  
Atom #4.11/A:53@HA 122.838 29.378 -7.487  
Atom #4.11/A:53@HB2 120.760 31.557 -7.171  
Atom #4.11/A:53@HB3 122.283 31.684 -8.042  
Atom #4.11/A:53@HG 121.323 30.787 -9.675  
Atom #4.11/A:54@N 121.866 30.669 -4.623  
Atom #4.11/A:54@CA 122.351 31.204 -3.355  
Atom #4.11/A:54@C 123.436 30.311 -2.752  
Atom #4.11/A:54@O 124.375 30.803 -2.127  
Atom #4.11/A:54@CB 121.192 31.332 -2.367  
Atom #4.11/A:54@OG 120.164 32.119 -2.954  
Atom #4.11/A:54@H 120.911 30.471 -4.726  
Atom #4.11/A:54@HA 122.768 32.186 -3.528  
Atom #4.11/A:54@HB2 120.799 30.355 -2.137  
Atom #4.11/A:54@HB3 121.548 31.797 -1.457  
Atom #4.11/A:54@HG 120.332 33.038 -2.734  
Atom #4.11/A:55@N 123.305 29.001 -2.941  
Atom #4.11/A:55@CA 124.277 28.054 -2.393  
Atom #4.11/A:55@C 123.791 27.354 -1.116  
Atom #4.11/A:55@O 124.471 26.459 -0.613  
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Atom #4.11/A:55@HA2 124.486 27.303 -3.140  
Atom #4.11/A:55@HA3 125.192 28.584 -2.171  
Atom #4.12/A:53@N 121.966 27.696 -5.640  
Atom #4.12/A:53@CA 122.058 28.943 -6.390  
Atom #4.12/A:53@C 121.526 30.101 -5.553  
Atom #4.12/A:53@O 122.237 31.072 -5.292  
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Atom #4.12/A:53@OG 121.129 30.125 -8.268  
Atom #4.12/A:53@H 121.463 27.677 -4.799  
Atom #4.12/A:53@HA 123.092 29.132 -6.635  
Atom #4.12/A:53@HB2 121.764 28.184 -8.378  
Atom #4.12/A:53@HB3 120.277 28.425 -7.467  
Atom #4.12/A:53@HG 120.289 30.496 -7.990  
Atom #4.12/A:54@N 120.269 29.990 -5.136  
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Atom #4.12/A:54@C 120.362 31.146 -2.942  
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Atom #4.12/A:54@CB 118.181 30.672 -4.059  
Atom #4.12/A:54@OG 118.095 29.504 -3.255  
Atom #4.12/A:54@H 119.744 29.205 -5.398  
Atom #4.12/A:54@HA 119.707 31.962 -4.806  
Atom #4.12/A:54@HB2 117.695 31.487 -3.549  
Atom #4.12/A:54@HB3 117.697 30.509 -5.013  
Atom #4.12/A:54@HG 117.212 29.140 -3.354  
Atom #4.12/A:55@N 120.985 30.066 -2.471  
Atom #4.12/A:55@CA 121.656 30.078 -1.171  
Atom #4.12/A:55@C 120.855 29.372 -0.068  
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Atom #4.12/A:55@H 120.992 29.247 -3.008  
Atom #4.12/A:55@HA2 122.612 29.586 -1.273  
Atom #4.12/A:55@HA3 121.824 31.103 -0.876  
Atom #4.13/A:53@N 123.856 24.949 -4.680  
Atom #4.13/A:53@CA 123.899 26.405 -4.757  
Atom #4.13/A:53@C 124.485 26.987 -3.475  
Atom #4.13/A:53@O 124.213 26.495 -2.379  
Atom #4.13/A:53@CB 122.489 26.959 -4.972  
Atom #4.13/A:53@OG 122.565 28.364 -5.169  
Atom #4.13/A:53@H 123.572 24.521 -3.845  
Atom #4.13/A:53@HA 124.519 26.698 -5.591  
Atom #4.13/A:53@HB2 122.048 26.504 -5.844  
Atom #4.13/A:53@HB3 121.880 26.732 -4.107  
Atom #4.13/A:53@HG 122.273 28.554 -6.064  
Atom #4.13/A:54@N 125.292 28.034 -3.617  
Atom #4.13/A:54@CA 125.912 28.665 -2.458  
Atom #4.13/A:54@C 124.863 29.361 -1.598  
Atom #4.13/A:54@O 123.882 29.901 -2.109  
Atom #4.13/A:54@CB 126.954 29.686 -2.916  
Atom #4.13/A:54@OG 127.936 29.030 -3.705  
Atom #4.13/A:54@H 125.473 28.385 -4.513  
Atom #4.13/A:54@HA 126.403 27.907 -1.867  
Atom #4.13/A:54@HB2 126.479 30.451 -3.508  
Atom #4.13/A:54@HB3 127.412 30.143 -2.048  
Atom #4.13/A:54@HG 128.375 29.693 -4.244  
Atom #4.13/A:55@N 125.079 29.343 -0.286  
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Atom #4.13/A:55@C 122.844 29.256 0.845  
Atom #4.13/A:55@O 122.045 29.641 1.698  
Atom #4.13/A:55@H 125.863 28.873 0.065  
Atom #4.13/A:55@HA2 124.658 30.105 1.600  
Atom #4.13/A:55@HA3 123.949 30.996 0.264  
Atom #4.14/A:53@N 124.649 26.942 -4.554  
Atom #4.14/A:53@CA 124.684 28.038 -5.516  
Atom #4.14/A:53@C 123.828 29.200 -5.024  
Atom #4.14/A:53@O 124.344 30.270 -4.698  
Atom #4.14/A:53@CB 124.168 27.559 -6.873  
Atom #4.14/A:53@OG 122.921 26.901 -6.694  
Atom #4.14/A:53@H 124.047 26.999 -3.783  
Atom #4.14/A:53@HA 125.704 28.374 -5.628  
Atom #4.14/A:53@HB2 124.029 28.404 -7.529  
Atom #4.14/A:53@HB3 124.890 26.884 -7.312  
Atom #4.14/A:53@HG 123.048 25.968 -6.885  
Atom #4.14/A:54@N 122.520 28.981 -4.970  
Atom #4.14/A:54@CA 121.600 29.996 -4.464  
Atom #4.14/A:54@C 121.940 30.394 -3.025  
Atom #4.14/A:54@O 121.748 31.544 -2.633  
Atom #4.14/A:54@CB 120.165 29.470 -4.519  
Atom #4.14/A:54@OG 119.870 29.055 -5.846  
Atom #4.14/A:54@H 122.163 28.120 -5.277  
Atom #4.14/A:54@HA 121.670 30.873 -5.092  
Atom #4.14/A:54@HB2 120.061 28.627 -3.855  
Atom #4.14/A:54@HB3 119.485 30.252 -4.210  
Atom #4.14/A:54@HG 119.021 28.608 -5.835  
Atom #4.14/A:55@N 122.443 29.440 -2.244  
Atom #4.14/A:55@CA 122.765 29.691 -0.840  
Atom #4.14/A:55@C 121.723 29.116 0.132  
Atom #4.14/A:55@O 121.936 29.141 1.344  
Atom #4.14/A:55@H 122.602 28.549 -2.619  
Atom #4.14/A:55@HA2 123.724 29.247 -0.619  
Atom #4.14/A:55@HA3 122.832 30.758 -0.685  
Atom #4.15/A:53@N 122.088 27.873 -8.952  
Atom #4.15/A:53@CA 123.099 28.916 -9.099  
Atom #4.15/A:53@C 123.183 29.780 -7.841  
Atom #4.15/A:53@O 124.267 30.212 -7.449  
Atom #4.15/A:53@CB 122.764 29.798 -10.301  
Atom #4.15/A:53@OG 121.582 30.537 -10.024  
Atom #4.15/A:53@H 121.328 27.846 -9.568  
Atom #4.15/A:53@HA 124.059 28.451 -9.267  
Atom #4.15/A:53@HB2 123.574 30.485 -10.486  
Atom #4.15/A:53@HB3 122.622 29.174 -11.174  
Atom #4.15/A:53@HG 121.375 31.066 -10.797  
Atom #4.15/A:54@N 122.038 30.029 -7.211  
Atom #4.15/A:54@CA 122.005 30.810 -5.978  
Atom #4.15/A:54@C 122.827 30.140 -4.877  
Atom #4.15/A:54@O 123.474 30.816 -4.077  
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Atom #4.15/A:54@OG 119.786 31.535 -6.557  
Atom #4.15/A:54@H 121.200 29.681 -7.581  
Atom #4.15/A:54@HA 122.418 31.788 -6.173  
Atom #4.15/A:54@HB2 120.151 30.012 -5.242  
Atom #4.15/A:54@HB3 120.540 31.619 -4.637  
Atom #4.15/A:54@HG 119.314 30.820 -6.991  
Atom #4.15/A:55@N 122.800 28.810 -4.839  
Atom #4.15/A:55@CA 123.531 28.065 -3.815  
Atom #4.15/A:55@C 122.661 27.674 -2.611  
Atom #4.15/A:55@O 123.183 27.169 -1.617  
Atom #4.15/A:55@H 122.280 28.321 -5.510  
Atom #4.15/A:55@HA2 123.928 27.164 -4.259  
Atom #4.15/A:55@HA3 124.353 28.672 -3.466  
Atom #4.16/A:53@N 120.770 23.661 -11.882  
Atom #4.16/A:53@CA 119.637 24.577 -11.822  
Atom #4.16/A:53@C 120.113 26.010 -11.602  
Atom #4.16/A:53@O 121.313 26.283 -11.596  
Atom #4.16/A:53@CB 118.698 24.166 -10.687  
Atom #4.16/A:53@OG 119.321 24.447 -9.441  
Atom #4.16/A:53@H 121.612 23.909 -11.447  
Atom #4.16/A:53@HA 119.097 24.527 -12.756  
Atom #4.16/A:53@HB2 117.779 24.725 -10.754  
Atom #4.16/A:53@HB3 118.479 23.110 -10.770  
Atom #4.16/A:53@HG 118.695 24.242 -8.743  
Atom #4.16/A:54@N 119.161 26.922 -11.423  
Atom #4.16/A:54@CA 119.486 28.330 -11.200  
Atom #4.16/A:54@C 119.870 28.628 -9.744  
Atom #4.16/A:54@O 119.845 29.786 -9.328  
Atom #4.16/A:54@CB 118.291 29.199 -11.592  
Atom #4.16/A:54@OG 117.301 29.117 -10.576  
Atom #4.16/A:54@H 118.221 26.643 -11.440  
Atom #4.16/A:54@HA 120.319 28.594 -11.834  
Atom #4.16/A:54@HB2 118.606 30.225 -11.695  
Atom #4.16/A:54@HB3 117.892 28.853 -12.536  
Atom #4.16/A:54@HG 116.515 28.721 -10.959  
Atom #4.16/A:55@N 120.221 27.602 -8.968  
Atom #4.16/A:55@CA 120.610 27.803 -7.572  
Atom #4.16/A:55@C 119.512 27.419 -6.571  
Atom #4.16/A:55@O 119.751 27.445 -5.363  
Atom #4.16/A:55@H 120.214 26.695 -9.335  
Atom #4.16/A:55@HA2 121.486 27.204 -7.368  
Atom #4.16/A:55@HA3 120.863 28.844 -7.427  
Atom #4.17/A:53@N 125.488 25.126 -6.745  
Atom #4.17/A:53@CA 125.820 26.337 -7.487  
Atom #4.17/A:53@C 125.574 27.571 -6.626  
Atom #4.17/A:53@O 126.509 28.279 -6.255  
Atom #4.17/A:53@CB 124.974 26.419 -8.759  
Atom #4.17/A:53@OG 125.601 25.662 -9.786  
Atom #4.17/A:53@H 125.017 25.201 -5.889  
Atom #4.17/A:53@HA 126.864 26.303 -7.764  
Atom #4.17/A:53@HB2 123.994 26.013 -8.571  
Atom #4.17/A:53@HB3 124.879 27.454 -9.059  
Atom #4.17/A:53@HG 126.534 25.887 -9.793  
Atom #4.17/A:54@N 124.306 27.821 -6.313  
Atom #4.17/A:54@CA 123.945 28.959 -5.470  
Atom #4.17/A:54@C 124.536 28.835 -4.064  
Atom #4.17/A:54@O 124.816 29.844 -3.415  
Atom #4.17/A:54@CB 122.423 29.068 -5.374  
Atom #4.17/A:54@OG 121.920 27.956 -4.645  
Atom #4.17/A:54@H 123.601 27.233 -6.655  
Atom #4.17/A:54@HA 124.324 29.861 -5.926  
Atom #4.17/A:54@HB2 122.155 29.975 -4.859  
Atom #4.17/A:54@HB3 122.002 29.086 -6.369  
Atom #4.17/A:54@HG 121.816 28.224 -3.729  
Atom #4.17/A:55@N 124.726 27.604 -3.590  
Atom #4.17/A:55@CA 125.273 27.381 -2.251  
Atom #4.17/A:55@C 124.205 27.018 -1.209  
Atom #4.17/A:55@O 124.542 26.758 -0.054  
Atom #4.17/A:55@H 124.496 26.833 -4.150  
Atom #4.17/A:55@HA2 125.991 26.576 -2.302  
Atom #4.17/A:55@HA3 125.779 28.278 -1.930  
Atom #4.18/A:53@N 117.476 29.475 -6.589  
Atom #4.18/A:53@CA 118.191 30.742 -6.702  
Atom #4.18/A:53@C 118.388 31.389 -5.331  
Atom #4.18/A:53@O 119.423 32.003 -5.071  
Atom #4.18/A:53@CB 117.414 31.699 -7.608  
Atom #4.18/A:53@OG 118.200 32.858 -7.845  
Atom #4.18/A:53@H 116.617 29.364 -7.049  
Atom #4.18/A:53@HA 119.159 30.558 -7.142  
Atom #4.18/A:53@HB2 117.204 31.217 -8.549  
Atom #4.18/A:53@HB3 116.482 31.967 -7.129  
Atom #4.18/A:53@HG 118.214 33.377 -7.037  
Atom #4.18/A:54@N 117.393 31.251 -4.459  
Atom #4.18/A:54@CA 117.464 31.844 -3.127  
Atom #4.18/A:54@C 118.713 31.381 -2.378  
Atom #4.18/A:54@O 119.306 32.147 -1.619  
Atom #4.18/A:54@CB 116.220 31.462 -2.325  
Atom #4.18/A:54@OG 116.222 32.172 -1.093  
Atom #4.18/A:54@H 116.597 30.740 -4.717  
Atom #4.18/A:54@HA 117.495 32.918 -3.225  
Atom #4.18/A:54@HB2 115.334 31.724 -2.880  
Atom #4.18/A:54@HB3 116.224 30.395 -2.144  
Atom #4.18/A:54@HG 115.605 31.738 -0.500  
Atom #4.18/A:55@N 119.110 30.130 -2.591  
Atom #4.18/A:55@CA 120.284 29.584 -1.914  
Atom #4.18/A:55@C 119.948 28.962 -0.553  
Atom #4.18/A:55@O 120.830 28.816 0.293  
Atom #4.18/A:55@H 118.606 29.563 -3.212  
Atom #4.18/A:55@HA2 120.729 28.827 -2.543  
Atom #4.18/A:55@HA3 121.001 30.378 -1.765  
Atom #4.19/A:53@N 118.659 28.910 -7.794  
Atom #4.19/A:53@CA 119.558 29.984 -8.204  
Atom #4.19/A:53@C 120.391 30.482 -7.023  
Atom #4.19/A:53@O 121.567 30.811 -7.182  
Atom #4.19/A:53@CB 118.749 31.146 -8.782  
Atom #4.19/A:53@OG 117.929 30.664 -9.837  
Atom #4.19/A:53@H 117.694 29.009 -7.935  
Atom #4.19/A:53@HA 120.223 29.611 -8.968  
Atom #4.19/A:53@HB2 118.123 31.572 -8.015  
Atom #4.19/A:53@HB3 119.427 31.905 -9.149  
Atom #4.19/A:53@HG 118.458 30.640 -10.638  
Atom #4.19/A:54@N 119.780 30.535 -5.843  
Atom #4.19/A:54@CA 120.484 30.989 -4.647  
Atom #4.19/A:54@C 121.688 30.099 -4.330  
Atom #4.19/A:54@O 122.695 30.576 -3.807  
Atom #4.19/A:54@CB 119.529 30.993 -3.454  
Atom #4.19/A:54@OG 119.183 29.653 -3.129  
Atom #4.19/A:54@H 118.842 30.263 -5.775  
Atom #4.19/A:54@HA 120.833 31.997 -4.813  
Atom #4.19/A:54@HB2 120.008 31.450 -2.605  
Atom #4.19/A:54@HB3 118.642 31.559 -3.709  
Atom #4.19/A:54@HG 118.246 29.632 -2.917  
Atom #4.19/A:55@N 121.584 28.810 -4.644  
Atom #4.19/A:55@CA 122.680 27.878 -4.385  
Atom #4.19/A:55@C 122.661 27.320 -2.957  
Atom #4.19/A:55@O 123.687 26.851 -2.465  
Atom #4.19/A:55@H 120.759 28.480 -5.056  
Atom #4.19/A:55@HA2 122.609 27.054 -5.081  
Atom #4.19/A:55@HA3 123.617 28.389 -4.546  
Atom #4.20/A:53@N 118.659 26.960 -8.352  
Atom #4.20/A:53@CA 117.700 27.815 -9.044  
Atom #4.20/A:53@C 117.073 28.810 -8.068  
Atom #4.20/A:53@O 117.341 30.010 -8.136  
Atom #4.20/A:53@CB 116.603 26.969 -9.695  
Atom #4.20/A:53@OG 116.126 26.018 -8.752  
Atom #4.20/A:53@H 118.811 27.087 -7.392  
Atom #4.20/A:53@HA 118.218 28.365 -9.814  
Atom #4.20/A:53@HB2 115.786 27.602 -10.000  
Atom #4.20/A:53@HB3 117.008 26.466 -10.563  
Atom #4.20/A:53@HG 116.408 25.147 -9.040  
Atom #4.20/A:54@N 116.238 28.306 -7.163  
Atom #4.20/A:54@CA 115.587 29.159 -6.174  
Atom #4.20/A:54@C 116.611 29.852 -5.279  
Atom #4.20/A:54@O 116.427 31.005 -4.891  
Atom #4.20/A:54@CB 114.638 28.325 -5.313  
Atom #4.20/A:54@OG 113.721 27.642 -6.156  
Atom #4.20/A:54@H 116.057 27.342 -7.161  
Atom #4.20/A:54@HA 115.011 29.913 -6.691  
Atom #4.20/A:54@HB2 115.202 27.601 -4.748  
Atom #4.20/A:54@HB3 114.109 28.976 -4.630  
Atom #4.20/A:54@HG 113.990 26.722 -6.205  
Atom #4.20/A:55@N 117.691 29.146 -4.953  
Atom #4.20/A:55@CA 118.720 29.699 -4.074  
Atom #4.20/A:55@C 118.417 29.467 -2.590  
Atom #4.20/A:55@O 118.946 30.175 -1.732  
Atom #4.20/A:55@H 117.798 28.239 -5.308  
Atom #4.20/A:55@HA2 119.667 29.235 -4.313  
Atom #4.20/A:55@HA3 118.797 30.761 -4.252  

> select #4/A:53-55@CA

60 atoms, 60 residues, 20 models selected  

> getcrd sel

Atom #4.1/A:53@CA -2.718 -14.903 32.797  
Atom #4.1/A:54@CA -4.644 -12.095 34.509  
Atom #4.1/A:55@CA -7.864 -13.255 32.828  
Atom #4.2/A:53@CA 125.246 29.083 -6.794  
Atom #4.2/A:54@CA 123.827 30.858 -3.740  
Atom #4.2/A:55@CA 124.258 27.661 -1.692  
Atom #4.3/A:53@CA 123.421 25.767 -11.520  
Atom #4.3/A:54@CA 119.951 26.877 -10.434  
Atom #4.3/A:55@CA 119.934 28.430 -6.960  
Atom #4.4/A:53@CA 124.898 29.595 -6.307  
Atom #4.4/A:54@CA 122.736 31.506 -3.811  
Atom #4.4/A:55@CA 123.723 28.949 -1.154  
Atom #4.5/A:53@CA 127.097 25.608 -6.640  
Atom #4.5/A:54@CA 125.726 28.239 -4.263  
Atom #4.5/A:55@CA 126.628 26.010 -1.299  
Atom #4.6/A:53@CA 118.136 30.162 -8.479  
Atom #4.6/A:54@CA 118.393 31.589 -4.960  
Atom #4.6/A:55@CA 120.950 28.888 -4.122  
Atom #4.7/A:53@CA 126.715 28.635 -4.330  
Atom #4.7/A:54@CA 123.491 30.545 -3.656  
Atom #4.7/A:55@CA 119.776 29.749 -3.441  
Atom #4.8/A:53@CA 123.563 29.068 -7.801  
Atom #4.8/A:54@CA 123.434 30.618 -4.322  
Atom #4.8/A:55@CA 124.930 27.431 -2.855  
Atom #4.9/A:53@CA 115.989 26.194 -11.620  
Atom #4.9/A:54@CA 113.797 27.709 -8.905  
Atom #4.9/A:55@CA 116.887 29.103 -7.150  
Atom #4.10/A:53@CA 124.465 29.321 -7.255  
Atom #4.10/A:54@CA 123.156 31.015 -4.103  
Atom #4.10/A:55@CA 123.977 27.895 -2.060  
Atom #4.11/A:53@CA 122.068 29.873 -6.913  
Atom #4.11/A:54@CA 122.351 31.204 -3.355  
Atom #4.11/A:55@CA 124.277 28.054 -2.393  
Atom #4.12/A:53@CA 122.058 28.943 -6.390  
Atom #4.12/A:54@CA 119.654 31.013 -4.293  
Atom #4.12/A:55@CA 121.656 30.078 -1.171  
Atom #4.13/A:53@CA 123.899 26.405 -4.757  
Atom #4.13/A:54@CA 125.912 28.665 -2.458  
Atom #4.13/A:55@CA 124.166 30.009 0.643  
Atom #4.14/A:53@CA 124.684 28.038 -5.516  
Atom #4.14/A:54@CA 121.600 29.996 -4.464  
Atom #4.14/A:55@CA 122.765 29.691 -0.840  
Atom #4.15/A:53@CA 123.099 28.916 -9.099  
Atom #4.15/A:54@CA 122.005 30.810 -5.978  
Atom #4.15/A:55@CA 123.531 28.065 -3.815  
Atom #4.16/A:53@CA 119.637 24.577 -11.822  
Atom #4.16/A:54@CA 119.486 28.330 -11.200  
Atom #4.16/A:55@CA 120.610 27.803 -7.572  
Atom #4.17/A:53@CA 125.820 26.337 -7.487  
Atom #4.17/A:54@CA 123.945 28.959 -5.470  
Atom #4.17/A:55@CA 125.273 27.381 -2.251  
Atom #4.18/A:53@CA 118.191 30.742 -6.702  
Atom #4.18/A:54@CA 117.464 31.844 -3.127  
Atom #4.18/A:55@CA 120.284 29.584 -1.914  
Atom #4.19/A:53@CA 119.558 29.984 -8.204  
Atom #4.19/A:54@CA 120.484 30.989 -4.647  
Atom #4.19/A:55@CA 122.680 27.878 -4.385  
Atom #4.20/A:53@CA 117.700 27.815 -9.044  
Atom #4.20/A:54@CA 115.587 29.159 -6.174  
Atom #4.20/A:55@CA 118.720 29.699 -4.074  

> select #3/A:53-55@CA

3 atoms, 3 residues, 1 model selected  

> getcrd sel

Atom #3/A:53@CA -1.447 2.950 -10.492  
Atom #3/A:54@CA 1.188 3.983 -13.069  
Atom #3/A:55@CA 0.692 5.688 -16.444  

> select #3/A:95-97@CA

3 atoms, 3 residues, 1 model selected  

> getcrd sel

Atom #3/A:95@CA 9.781 4.496 -10.919  
Atom #3/A:96@CA 13.589 4.771 -10.654  
Atom #3/A:97@CA 14.372 1.789 -12.948  

> select #4.1/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.2/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.3/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.4/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.5/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.6/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.7/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.8/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.9/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.10/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.11/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.12/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.13/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.14/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.15/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.16/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.17/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.18/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.19/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148
> #4.20/A:3-15,20-30,38-48,60-73,77-90,104-115,122-132,135-148

30200 atoms, 30500 bonds, 2000 residues, 20 models selected  

> select #4.1/A:53-55 #4.2/A:53-55 #4.3/A:53-55 #4.4/A:53-55 #4.5/A:53-55
> #4.6/A:53-55 #4.7/A:53-55 #4.8/A:53-55 #4.9/A:53-55 #4.10/A:53-55
> #4.11/A:53-55 #4.12/A:53-55 #4.13/A:53-55 #4.14/A:53-55 #4.15/A:53-55
> #4.16/A:53-55 #4.17/A:53-55 #4.18/A:53-55 #4.19/A:53-55 #4.20/A:53-55

580 atoms, 560 bonds, 60 residues, 20 models selected  

> move y 20 models #2

> measure center #2

Center of area of surface rectangle #2 = (-9.49, -7.80, 34.79)  

> measure center #2

Center of area of surface rectangle #2 = (-6.48, -9.04, 15.06)  

> redo

> move y 20 models #2

> undo

> redo

> undo

> redo

> undo

> redo

> undo

> move y 20 models #2

> measure center #2

Center of area of surface rectangle #2 = (-7.10, -9.25, 35.05)  

> measure center #2

Center of area of surface rectangle #2 = (-6.48, -9.04, 15.06)  

> measure center #2

Center of area of surface rectangle #2 = (-6.48, -9.04, 15.06)  

> redo

> move y 20 models #2

> measure center #2

Center of area of surface rectangle #2 = (-7.15, -9.19, 35.05)  

> matchmaker #4.4 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.4), sequence alignment score = 703.6  
RMSD between 106 pruned atom pairs is 1.150 angstroms; (across all 148 pairs:
4.159)  
  

> hide #4.1 models

> hide #4.4 models

> show #4.4 models

> getcrd sel

Atom #4.1/A:53@N -3.377 -15.004 31.500  
Atom #4.1/A:53@CA -2.718 -14.903 32.797  
Atom #4.1/A:53@C -3.629 -14.186 33.795  
Atom #4.1/A:53@O -4.200 -14.816 34.685  
Atom #4.1/A:53@CB -1.382 -14.162 32.660  
Atom #4.1/A:53@OG -0.348 -15.107 32.419  
Atom #4.1/A:53@H -4.276 -14.627 31.390  
Atom #4.1/A:53@HA -2.523 -15.901 33.164  
Atom #4.1/A:53@HB2 -1.432 -13.475 31.832  
Atom #4.1/A:53@HB3 -1.181 -13.609 33.568  
Atom #4.1/A:53@HG -0.123 -15.069 31.487  
Atom #4.1/A:54@N -3.763 -12.871 33.642  
Atom #4.1/A:54@CA -4.644 -12.095 34.509  
Atom #4.1/A:54@C -6.101 -12.529 34.344  
Atom #4.1/A:54@O -6.857 -12.570 35.316  
Atom #4.1/A:54@CB -4.518 -10.607 34.181  
Atom #4.1/A:54@OG -3.152 -10.224 34.272  
Atom #4.1/A:54@H -3.261 -12.414 32.935  
Atom #4.1/A:54@HA -4.349 -12.250 35.537  
Atom #4.1/A:54@HB2 -4.868 -10.423 33.178  
Atom #4.1/A:54@HB3 -5.116 -10.035 34.877  
Atom #4.1/A:54@HG -2.938 -9.704 33.494  
Atom #4.1/A:55@N -6.487 -12.853 33.114  
Atom #4.1/A:55@CA -7.864 -13.255 32.828  
Atom #4.1/A:55@C -8.723 -12.112 32.264  
Atom #4.1/A:55@O -9.862 -12.347 31.858  
Atom #4.1/A:55@H -5.835 -12.821 32.382  
Atom #4.1/A:55@HA2 -7.848 -14.062 32.112  
Atom #4.1/A:55@HA3 -8.317 -13.611 33.741  
Atom #4.2/A:53@N 124.160 28.109 -6.855  
Atom #4.2/A:53@CA 125.246 29.083 -6.794  
Atom #4.2/A:53@C 125.207 29.843 -5.470  
Atom #4.2/A:53@O 126.245 30.103 -4.861  
Atom #4.2/A:53@CB 125.130 30.070 -7.955  
Atom #4.2/A:53@OG 125.070 29.347 -9.177  
Atom #4.2/A:53@H 123.509 28.155 -7.586  
Atom #4.2/A:53@HA 126.188 28.562 -6.872  
Atom #4.2/A:53@HB2 124.230 30.655 -7.848  
Atom #4.2/A:53@HB3 125.986 30.730 -7.950  
Atom #4.2/A:53@HG 124.423 28.645 -9.076  
Atom #4.2/A:54@N 124.002 30.196 -5.031  
Atom #4.2/A:54@CA 123.827 30.858 -3.740  
Atom #4.2/A:54@C 124.188 29.931 -2.575  
Atom #4.2/A:54@O 124.644 30.393 -1.529  
Atom #4.2/A:54@CB 122.378 31.319 -3.589  
Atom #4.2/A:54@OG 121.535 30.180 -3.475  
Atom #4.2/A:54@H 123.215 30.009 -5.584  
Atom #4.2/A:54@HA 124.469 31.726 -3.704  
Atom #4.2/A:54@HB2 122.277 31.920 -2.699  
Atom #4.2/A:54@HB3 122.098 31.910 -4.451  
Atom #4.2/A:54@HG 121.622 29.665 -4.281  
Atom #4.2/A:55@N 123.983 28.627 -2.755  
Atom #4.2/A:55@CA 124.258 27.661 -1.692  
Atom #4.2/A:55@C 123.004 27.245 -0.908  
Atom #4.2/A:55@O 123.101 26.442 0.020  
Atom #4.2/A:55@H 123.640 28.309 -3.616  
Atom #4.2/A:55@HA2 124.697 26.778 -2.133  
Atom #4.2/A:55@HA3 124.969 28.096 -1.005  
Atom #4.3/A:53@N 123.845 24.514 -10.895  
Atom #4.3/A:53@CA 123.421 25.767 -11.520  
Atom #4.3/A:53@C 121.901 25.911 -11.516  
Atom #4.3/A:53@O 121.209 25.377 -12.383  
Atom #4.3/A:53@CB 123.945 25.838 -12.956  
Atom #4.3/A:53@OG 123.239 24.908 -13.765  
Atom #4.3/A:53@H 124.530 24.542 -10.194  
Atom #4.3/A:53@HA 123.845 26.588 -10.962  
Atom #4.3/A:53@HB2 123.795 26.830 -13.349  
Atom #4.3/A:53@HB3 125.003 25.612 -12.960  
Atom #4.3/A:53@HG 122.314 25.165 -13.775  
Atom #4.3/A:54@N 121.388 26.649 -10.537  
Atom #4.3/A:54@CA 119.951 26.877 -10.434  
Atom #4.3/A:54@C 119.645 27.862 -9.310  
Atom #4.3/A:54@O 118.964 28.866 -9.518  
Atom #4.3/A:54@CB 119.231 25.554 -10.166  
Atom #4.3/A:54@OG 117.855 25.813 -9.923  
Atom #4.3/A:54@H 121.987 27.048 -9.871  
Atom #4.3/A:54@HA 119.593 27.286 -11.367  
Atom #4.3/A:54@HB2 119.321 24.909 -11.024  
Atom #4.3/A:54@HB3 119.680 25.071 -9.308  
Atom #4.3/A:54@HG 117.350 25.437 -10.648  
Atom #4.3/A:55@N 120.155 27.565 -8.119  
Atom #4.3/A:55@CA 119.934 28.430 -6.960  
Atom #4.3/A:55@C 118.765 27.974 -6.075  
Atom #4.3/A:55@O 118.555 28.536 -5.000  
Atom #4.3/A:55@H 120.689 26.750 -8.015  
Atom #4.3/A:55@HA2 120.834 28.445 -6.363  
Atom #4.3/A:55@HA3 119.734 29.432 -7.310  
Atom #4.4/A:53@N -6.501 -15.060 33.437  
Atom #4.4/A:53@CA -7.318 -15.982 34.222  
Atom #4.4/A:53@C -8.514 -15.269 34.856  
Atom #4.4/A:53@O -9.582 -15.858 35.013  
Atom #4.4/A:53@CB -6.467 -16.623 35.320  
Atom #4.4/A:53@OG -6.109 -15.631 36.272  
Atom #4.4/A:53@H -5.554 -14.944 33.661  
Atom #4.4/A:53@HA -7.685 -16.762 33.570  
Atom #4.4/A:53@HB2 -7.033 -17.397 35.813  
Atom #4.4/A:53@HB3 -5.582 -17.059 34.877  
Atom #4.4/A:53@HG -6.613 -15.794 37.073  
Atom #4.4/A:54@N -8.333 -14.001 35.220  
Atom #4.4/A:54@CA -9.417 -13.218 35.807  
Atom #4.4/A:54@C -10.632 -13.164 34.879  
Atom #4.4/A:54@O -11.772 -13.137 35.342  
Atom #4.4/A:54@CB -8.934 -11.796 36.093  
Atom #4.4/A:54@OG -9.940 -11.098 36.815  
Atom #4.4/A:54@H -7.455 -13.585 35.093  
Atom #4.4/A:54@HA -9.712 -13.676 36.739  
Atom #4.4/A:54@HB2 -8.034 -11.830 36.687  
Atom #4.4/A:54@HB3 -8.725 -11.294 35.158  
Atom #4.4/A:54@HG -10.702 -10.996 36.238  
Atom #4.4/A:55@N -10.388 -13.150 33.570  
Atom #4.4/A:55@CA -11.476 -13.081 32.595  
Atom #4.4/A:55@C -11.686 -11.676 32.011  
Atom #4.4/A:55@O -12.625 -11.467 31.245  
Atom #4.4/A:55@H -9.461 -13.185 33.254  
Atom #4.4/A:55@HA2 -11.258 -13.762 31.786  
Atom #4.4/A:55@HA3 -12.390 -13.398 33.074  
Atom #4.5/A:53@N 126.519 24.396 -6.072  
Atom #4.5/A:53@CA 127.097 25.608 -6.640  
Atom #4.5/A:53@C 127.078 26.732 -5.610  
Atom #4.5/A:53@O 128.126 27.176 -5.140  
Atom #4.5/A:53@CB 126.312 26.037 -7.881  
Atom #4.5/A:53@OG 125.987 24.887 -8.651  
Atom #4.5/A:53@H 125.974 24.459 -5.261  
Atom #4.5/A:53@HA 128.120 25.409 -6.925  
Atom #4.5/A:53@HB2 125.402 26.530 -7.586  
Atom #4.5/A:53@HB3 126.913 26.721 -8.465  
Atom #4.5/A:53@HG 125.127 25.033 -9.054  
Atom #4.5/A:54@N 125.878 27.187 -5.264  
Atom #4.5/A:54@CA 125.726 28.239 -4.263  
Atom #4.5/A:54@C 126.294 27.808 -2.910  
Atom #4.5/A:54@O 126.841 28.628 -2.172  
Atom #4.5/A:54@CB 124.247 28.590 -4.102  
Atom #4.5/A:54@OG 123.712 28.949 -5.370  
Atom #4.5/A:54@H 125.080 26.807 -5.686  
Atom #4.5/A:54@HA 126.255 29.118 -4.599  
Atom #4.5/A:54@HB2 123.708 27.738 -3.722  
Atom #4.5/A:54@HB3 124.148 29.413 -3.406  
Atom #4.5/A:54@HG 124.031 28.315 -6.016  
Atom #4.5/A:55@N 126.164 26.523 -2.589  
Atom #4.5/A:55@CA 126.628 26.010 -1.299  
Atom #4.5/A:55@C 125.490 25.790 -0.291  
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Atom #4.9/A:53@N 117.089 25.641 -10.837  
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Atom #4.9/A:53@C 115.234 27.243 -10.810  
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Atom #4.9/A:53@HA 116.393 26.660 -12.507  
Atom #4.9/A:53@HB2 115.587 24.197 -12.305  
Atom #4.9/A:53@HB3 114.366 24.848 -11.220  
Atom #4.9/A:53@HG 113.857 24.742 -13.557  
Atom #4.9/A:54@N 114.549 26.797 -9.762  
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Atom #4.9/A:54@C 114.721 28.693 -8.184  
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Atom #4.9/A:54@HA 113.105 28.269 -9.516  
Atom #4.9/A:54@HB2 112.360 27.574 -7.315  
Atom #4.9/A:54@HB3 112.395 26.174 -8.382  
Atom #4.9/A:54@HG 113.795 25.325 -7.073  
Atom #4.9/A:55@N 115.929 28.247 -7.848  
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Atom #4.9/A:55@O 117.770 29.429 -4.944  
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Atom #4.10/A:53@C 124.464 30.062 -5.920  
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Atom #4.10/A:53@HA 125.409 28.808 -7.371  
Atom #4.10/A:53@HB2 125.171 30.969 -8.436  
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Atom #4.10/A:53@HG 123.431 32.023 -8.034  
Atom #4.10/A:54@N 123.274 30.345 -5.395  
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Atom #4.10/A:54@C 123.683 30.137 -2.966  
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Atom #4.10/A:54@HA 123.730 31.928 -4.131  
Atom #4.10/A:54@HB2 121.620 31.971 -2.946  
Atom #4.10/A:54@HB3 121.299 31.923 -4.676  
Atom #4.10/A:54@HG 120.734 30.099 -2.712  
Atom #4.10/A:55@N 123.523 28.822 -3.097  
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Atom #4.10/A:55@C 122.869 27.487 -1.079  
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Atom #4.11/A:53@N 121.022 28.907 -6.595  
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Atom #4.11/A:53@C 122.692 30.444 -5.640  
Atom #4.11/A:53@O 123.900 30.674 -5.583  
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Atom #4.11/A:53@OG 120.852 30.471 -8.900  
Atom #4.11/A:53@H 120.109 29.063 -6.917  
Atom #4.11/A:53@HA 122.838 29.378 -7.487  
Atom #4.11/A:53@HB2 120.760 31.557 -7.171  
Atom #4.11/A:53@HB3 122.283 31.684 -8.042  
Atom #4.11/A:53@HG 121.323 30.787 -9.675  
Atom #4.11/A:54@N 121.866 30.669 -4.623  
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Atom #4.11/A:54@C 123.436 30.311 -2.752  
Atom #4.11/A:54@O 124.375 30.803 -2.127  
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Atom #4.11/A:54@OG 120.164 32.119 -2.954  
Atom #4.11/A:54@H 120.911 30.471 -4.726  
Atom #4.11/A:54@HA 122.768 32.186 -3.528  
Atom #4.11/A:54@HB2 120.799 30.355 -2.137  
Atom #4.11/A:54@HB3 121.548 31.797 -1.457  
Atom #4.11/A:54@HG 120.332 33.038 -2.734  
Atom #4.11/A:55@N 123.305 29.001 -2.941  
Atom #4.11/A:55@CA 124.277 28.054 -2.393  
Atom #4.11/A:55@C 123.791 27.354 -1.116  
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Atom #4.11/A:55@HA2 124.486 27.303 -3.140  
Atom #4.11/A:55@HA3 125.192 28.584 -2.171  
Atom #4.12/A:53@N 121.966 27.696 -5.640  
Atom #4.12/A:53@CA 122.058 28.943 -6.390  
Atom #4.12/A:53@C 121.526 30.101 -5.553  
Atom #4.12/A:53@O 122.237 31.072 -5.292  
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Atom #4.12/A:53@OG 121.129 30.125 -8.268  
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Atom #4.12/A:53@HA 123.092 29.132 -6.635  
Atom #4.12/A:53@HB2 121.764 28.184 -8.378  
Atom #4.12/A:53@HB3 120.277 28.425 -7.467  
Atom #4.12/A:53@HG 120.289 30.496 -7.990  
Atom #4.12/A:54@N 120.269 29.990 -5.136  
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Atom #4.12/A:54@C 120.362 31.146 -2.942  
Atom #4.12/A:54@O 120.343 32.216 -2.333  
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Atom #4.12/A:54@H 119.744 29.205 -5.398  
Atom #4.12/A:54@HA 119.707 31.962 -4.806  
Atom #4.12/A:54@HB2 117.695 31.487 -3.549  
Atom #4.12/A:54@HB3 117.697 30.509 -5.013  
Atom #4.12/A:54@HG 117.212 29.140 -3.354  
Atom #4.12/A:55@N 120.985 30.066 -2.471  
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Atom #4.12/A:55@C 120.855 29.372 -0.068  
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Atom #4.12/A:55@HA2 122.612 29.586 -1.273  
Atom #4.12/A:55@HA3 121.824 31.103 -0.876  
Atom #4.13/A:53@N 123.856 24.949 -4.680  
Atom #4.13/A:53@CA 123.899 26.405 -4.757  
Atom #4.13/A:53@C 124.485 26.987 -3.475  
Atom #4.13/A:53@O 124.213 26.495 -2.379  
Atom #4.13/A:53@CB 122.489 26.959 -4.972  
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Atom #4.13/A:53@H 123.572 24.521 -3.845  
Atom #4.13/A:53@HA 124.519 26.698 -5.591  
Atom #4.13/A:53@HB2 122.048 26.504 -5.844  
Atom #4.13/A:53@HB3 121.880 26.732 -4.107  
Atom #4.13/A:53@HG 122.273 28.554 -6.064  
Atom #4.13/A:54@N 125.292 28.034 -3.617  
Atom #4.13/A:54@CA 125.912 28.665 -2.458  
Atom #4.13/A:54@C 124.863 29.361 -1.598  
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Atom #4.13/A:54@OG 127.936 29.030 -3.705  
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Atom #4.13/A:54@HA 126.403 27.907 -1.867  
Atom #4.13/A:54@HB2 126.479 30.451 -3.508  
Atom #4.13/A:54@HB3 127.412 30.143 -2.048  
Atom #4.13/A:54@HG 128.375 29.693 -4.244  
Atom #4.13/A:55@N 125.079 29.343 -0.286  
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Atom #4.14/A:53@N 124.649 26.942 -4.554  
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Atom #4.14/A:53@C 123.828 29.200 -5.024  
Atom #4.14/A:53@O 124.344 30.270 -4.698  
Atom #4.14/A:53@CB 124.168 27.559 -6.873  
Atom #4.14/A:53@OG 122.921 26.901 -6.694  
Atom #4.14/A:53@H 124.047 26.999 -3.783  
Atom #4.14/A:53@HA 125.704 28.374 -5.628  
Atom #4.14/A:53@HB2 124.029 28.404 -7.529  
Atom #4.14/A:53@HB3 124.890 26.884 -7.312  
Atom #4.14/A:53@HG 123.048 25.968 -6.885  
Atom #4.14/A:54@N 122.520 28.981 -4.970  
Atom #4.14/A:54@CA 121.600 29.996 -4.464  
Atom #4.14/A:54@C 121.940 30.394 -3.025  
Atom #4.14/A:54@O 121.748 31.544 -2.633  
Atom #4.14/A:54@CB 120.165 29.470 -4.519  
Atom #4.14/A:54@OG 119.870 29.055 -5.846  
Atom #4.14/A:54@H 122.163 28.120 -5.277  
Atom #4.14/A:54@HA 121.670 30.873 -5.092  
Atom #4.14/A:54@HB2 120.061 28.627 -3.855  
Atom #4.14/A:54@HB3 119.485 30.252 -4.210  
Atom #4.14/A:54@HG 119.021 28.608 -5.835  
Atom #4.14/A:55@N 122.443 29.440 -2.244  
Atom #4.14/A:55@CA 122.765 29.691 -0.840  
Atom #4.14/A:55@C 121.723 29.116 0.132  
Atom #4.14/A:55@O 121.936 29.141 1.344  
Atom #4.14/A:55@H 122.602 28.549 -2.619  
Atom #4.14/A:55@HA2 123.724 29.247 -0.619  
Atom #4.14/A:55@HA3 122.832 30.758 -0.685  
Atom #4.15/A:53@N 122.088 27.873 -8.952  
Atom #4.15/A:53@CA 123.099 28.916 -9.099  
Atom #4.15/A:53@C 123.183 29.780 -7.841  
Atom #4.15/A:53@O 124.267 30.212 -7.449  
Atom #4.15/A:53@CB 122.764 29.798 -10.301  
Atom #4.15/A:53@OG 121.582 30.537 -10.024  
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Atom #4.15/A:53@HA 124.059 28.451 -9.267  
Atom #4.15/A:53@HB2 123.574 30.485 -10.486  
Atom #4.15/A:53@HB3 122.622 29.174 -11.174  
Atom #4.15/A:53@HG 121.375 31.066 -10.797  
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Atom #4.15/A:54@OG 119.786 31.535 -6.557  
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Atom #4.15/A:54@HA 122.418 31.788 -6.173  
Atom #4.15/A:54@HB2 120.151 30.012 -5.242  
Atom #4.15/A:54@HB3 120.540 31.619 -4.637  
Atom #4.15/A:54@HG 119.314 30.820 -6.991  
Atom #4.15/A:55@N 122.800 28.810 -4.839  
Atom #4.15/A:55@CA 123.531 28.065 -3.815  
Atom #4.15/A:55@C 122.661 27.674 -2.611  
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Atom #4.15/A:55@HA2 123.928 27.164 -4.259  
Atom #4.15/A:55@HA3 124.353 28.672 -3.466  
Atom #4.16/A:53@N 120.770 23.661 -11.882  
Atom #4.16/A:53@CA 119.637 24.577 -11.822  
Atom #4.16/A:53@C 120.113 26.010 -11.602  
Atom #4.16/A:53@O 121.313 26.283 -11.596  
Atom #4.16/A:53@CB 118.698 24.166 -10.687  
Atom #4.16/A:53@OG 119.321 24.447 -9.441  
Atom #4.16/A:53@H 121.612 23.909 -11.447  
Atom #4.16/A:53@HA 119.097 24.527 -12.756  
Atom #4.16/A:53@HB2 117.779 24.725 -10.754  
Atom #4.16/A:53@HB3 118.479 23.110 -10.770  
Atom #4.16/A:53@HG 118.695 24.242 -8.743  
Atom #4.16/A:54@N 119.161 26.922 -11.423  
Atom #4.16/A:54@CA 119.486 28.330 -11.200  
Atom #4.16/A:54@C 119.870 28.628 -9.744  
Atom #4.16/A:54@O 119.845 29.786 -9.328  
Atom #4.16/A:54@CB 118.291 29.199 -11.592  
Atom #4.16/A:54@OG 117.301 29.117 -10.576  
Atom #4.16/A:54@H 118.221 26.643 -11.440  
Atom #4.16/A:54@HA 120.319 28.594 -11.834  
Atom #4.16/A:54@HB2 118.606 30.225 -11.695  
Atom #4.16/A:54@HB3 117.892 28.853 -12.536  
Atom #4.16/A:54@HG 116.515 28.721 -10.959  
Atom #4.16/A:55@N 120.221 27.602 -8.968  
Atom #4.16/A:55@CA 120.610 27.803 -7.572  
Atom #4.16/A:55@C 119.512 27.419 -6.571  
Atom #4.16/A:55@O 119.751 27.445 -5.363  
Atom #4.16/A:55@H 120.214 26.695 -9.335  
Atom #4.16/A:55@HA2 121.486 27.204 -7.368  
Atom #4.16/A:55@HA3 120.863 28.844 -7.427  
Atom #4.17/A:53@N 125.488 25.126 -6.745  
Atom #4.17/A:53@CA 125.820 26.337 -7.487  
Atom #4.17/A:53@C 125.574 27.571 -6.626  
Atom #4.17/A:53@O 126.509 28.279 -6.255  
Atom #4.17/A:53@CB 124.974 26.419 -8.759  
Atom #4.17/A:53@OG 125.601 25.662 -9.786  
Atom #4.17/A:53@H 125.017 25.201 -5.889  
Atom #4.17/A:53@HA 126.864 26.303 -7.764  
Atom #4.17/A:53@HB2 123.994 26.013 -8.571  
Atom #4.17/A:53@HB3 124.879 27.454 -9.059  
Atom #4.17/A:53@HG 126.534 25.887 -9.793  
Atom #4.17/A:54@N 124.306 27.821 -6.313  
Atom #4.17/A:54@CA 123.945 28.959 -5.470  
Atom #4.17/A:54@C 124.536 28.835 -4.064  
Atom #4.17/A:54@O 124.816 29.844 -3.415  
Atom #4.17/A:54@CB 122.423 29.068 -5.374  
Atom #4.17/A:54@OG 121.920 27.956 -4.645  
Atom #4.17/A:54@H 123.601 27.233 -6.655  
Atom #4.17/A:54@HA 124.324 29.861 -5.926  
Atom #4.17/A:54@HB2 122.155 29.975 -4.859  
Atom #4.17/A:54@HB3 122.002 29.086 -6.369  
Atom #4.17/A:54@HG 121.816 28.224 -3.729  
Atom #4.17/A:55@N 124.726 27.604 -3.590  
Atom #4.17/A:55@CA 125.273 27.381 -2.251  
Atom #4.17/A:55@C 124.205 27.018 -1.209  
Atom #4.17/A:55@O 124.542 26.758 -0.054  
Atom #4.17/A:55@H 124.496 26.833 -4.150  
Atom #4.17/A:55@HA2 125.991 26.576 -2.302  
Atom #4.17/A:55@HA3 125.779 28.278 -1.930  
Atom #4.18/A:53@N 117.476 29.475 -6.589  
Atom #4.18/A:53@CA 118.191 30.742 -6.702  
Atom #4.18/A:53@C 118.388 31.389 -5.331  
Atom #4.18/A:53@O 119.423 32.003 -5.071  
Atom #4.18/A:53@CB 117.414 31.699 -7.608  
Atom #4.18/A:53@OG 118.200 32.858 -7.845  
Atom #4.18/A:53@H 116.617 29.364 -7.049  
Atom #4.18/A:53@HA 119.159 30.558 -7.142  
Atom #4.18/A:53@HB2 117.204 31.217 -8.549  
Atom #4.18/A:53@HB3 116.482 31.967 -7.129  
Atom #4.18/A:53@HG 118.214 33.377 -7.037  
Atom #4.18/A:54@N 117.393 31.251 -4.459  
Atom #4.18/A:54@CA 117.464 31.844 -3.127  
Atom #4.18/A:54@C 118.713 31.381 -2.378  
Atom #4.18/A:54@O 119.306 32.147 -1.619  
Atom #4.18/A:54@CB 116.220 31.462 -2.325  
Atom #4.18/A:54@OG 116.222 32.172 -1.093  
Atom #4.18/A:54@H 116.597 30.740 -4.717  
Atom #4.18/A:54@HA 117.495 32.918 -3.225  
Atom #4.18/A:54@HB2 115.334 31.724 -2.880  
Atom #4.18/A:54@HB3 116.224 30.395 -2.144  
Atom #4.18/A:54@HG 115.605 31.738 -0.500  
Atom #4.18/A:55@N 119.110 30.130 -2.591  
Atom #4.18/A:55@CA 120.284 29.584 -1.914  
Atom #4.18/A:55@C 119.948 28.962 -0.553  
Atom #4.18/A:55@O 120.830 28.816 0.293  
Atom #4.18/A:55@H 118.606 29.563 -3.212  
Atom #4.18/A:55@HA2 120.729 28.827 -2.543  
Atom #4.18/A:55@HA3 121.001 30.378 -1.765  
Atom #4.19/A:53@N 118.659 28.910 -7.794  
Atom #4.19/A:53@CA 119.558 29.984 -8.204  
Atom #4.19/A:53@C 120.391 30.482 -7.023  
Atom #4.19/A:53@O 121.567 30.811 -7.182  
Atom #4.19/A:53@CB 118.749 31.146 -8.782  
Atom #4.19/A:53@OG 117.929 30.664 -9.837  
Atom #4.19/A:53@H 117.694 29.009 -7.935  
Atom #4.19/A:53@HA 120.223 29.611 -8.968  
Atom #4.19/A:53@HB2 118.123 31.572 -8.015  
Atom #4.19/A:53@HB3 119.427 31.905 -9.149  
Atom #4.19/A:53@HG 118.458 30.640 -10.638  
Atom #4.19/A:54@N 119.780 30.535 -5.843  
Atom #4.19/A:54@CA 120.484 30.989 -4.647  
Atom #4.19/A:54@C 121.688 30.099 -4.330  
Atom #4.19/A:54@O 122.695 30.576 -3.807  
Atom #4.19/A:54@CB 119.529 30.993 -3.454  
Atom #4.19/A:54@OG 119.183 29.653 -3.129  
Atom #4.19/A:54@H 118.842 30.263 -5.775  
Atom #4.19/A:54@HA 120.833 31.997 -4.813  
Atom #4.19/A:54@HB2 120.008 31.450 -2.605  
Atom #4.19/A:54@HB3 118.642 31.559 -3.709  
Atom #4.19/A:54@HG 118.246 29.632 -2.917  
Atom #4.19/A:55@N 121.584 28.810 -4.644  
Atom #4.19/A:55@CA 122.680 27.878 -4.385  
Atom #4.19/A:55@C 122.661 27.320 -2.957  
Atom #4.19/A:55@O 123.687 26.851 -2.465  
Atom #4.19/A:55@H 120.759 28.480 -5.056  
Atom #4.19/A:55@HA2 122.609 27.054 -5.081  
Atom #4.19/A:55@HA3 123.617 28.389 -4.546  
Atom #4.20/A:53@N 118.659 26.960 -8.352  
Atom #4.20/A:53@CA 117.700 27.815 -9.044  
Atom #4.20/A:53@C 117.073 28.810 -8.068  
Atom #4.20/A:53@O 117.341 30.010 -8.136  
Atom #4.20/A:53@CB 116.603 26.969 -9.695  
Atom #4.20/A:53@OG 116.126 26.018 -8.752  
Atom #4.20/A:53@H 118.811 27.087 -7.392  
Atom #4.20/A:53@HA 118.218 28.365 -9.814  
Atom #4.20/A:53@HB2 115.786 27.602 -10.000  
Atom #4.20/A:53@HB3 117.008 26.466 -10.563  
Atom #4.20/A:53@HG 116.408 25.147 -9.040  
Atom #4.20/A:54@N 116.238 28.306 -7.163  
Atom #4.20/A:54@CA 115.587 29.159 -6.174  
Atom #4.20/A:54@C 116.611 29.852 -5.279  
Atom #4.20/A:54@O 116.427 31.005 -4.891  
Atom #4.20/A:54@CB 114.638 28.325 -5.313  
Atom #4.20/A:54@OG 113.721 27.642 -6.156  
Atom #4.20/A:54@H 116.057 27.342 -7.161  
Atom #4.20/A:54@HA 115.011 29.913 -6.691  
Atom #4.20/A:54@HB2 115.202 27.601 -4.748  
Atom #4.20/A:54@HB3 114.109 28.976 -4.630  
Atom #4.20/A:54@HG 113.990 26.722 -6.205  
Atom #4.20/A:55@N 117.691 29.146 -4.953  
Atom #4.20/A:55@CA 118.720 29.699 -4.074  
Atom #4.20/A:55@C 118.417 29.467 -2.590  
Atom #4.20/A:55@O 118.946 30.175 -1.732  
Atom #4.20/A:55@H 117.798 28.239 -5.308  
Atom #4.20/A:55@HA2 119.667 29.235 -4.313  
Atom #4.20/A:55@HA3 118.797 30.761 -4.252  

> matchmaker #4.2 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.2), sequence alignment score = 729.4  
RMSD between 103 pruned atom pairs is 1.128 angstroms; (across all 148 pairs:
4.520)  
  

> matchmaker #4.3 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.3), sequence alignment score = 725.2  
RMSD between 100 pruned atom pairs is 1.239 angstroms; (across all 148 pairs:
4.182)  
  

> matchmaker #4.5 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.5), sequence alignment score = 710.8  
RMSD between 98 pruned atom pairs is 1.172 angstroms; (across all 148 pairs:
4.609)  
  

> matchmaker #4.6 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.6), sequence alignment score = 718.6  
RMSD between 98 pruned atom pairs is 1.259 angstroms; (across all 148 pairs:
4.091)  
  

> matchmaker #4.7 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.7), sequence alignment score = 718  
RMSD between 104 pruned atom pairs is 1.138 angstroms; (across all 148 pairs:
4.731)  
  

> matchmaker #4.8 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.8), sequence alignment score = 718  
RMSD between 97 pruned atom pairs is 1.239 angstroms; (across all 148 pairs:
3.996)  
  

> matchmaker #4.9 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.9), sequence alignment score = 711.4  
RMSD between 104 pruned atom pairs is 1.276 angstroms; (across all 148 pairs:
4.516)  
  

> matchmaker #4.10 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.10), sequence alignment score = 704.2  
RMSD between 96 pruned atom pairs is 1.219 angstroms; (across all 148 pairs:
4.950)  
  

> matchmaker #4.11 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.11), sequence alignment score = 707.8  
RMSD between 93 pruned atom pairs is 1.245 angstroms; (across all 148 pairs:
4.612)  
  

> matchmaker #4.12 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.12), sequence alignment score = 718  
RMSD between 99 pruned atom pairs is 1.209 angstroms; (across all 148 pairs:
4.067)  
  

> matchmaker #4.13 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.13), sequence alignment score = 722.2  
RMSD between 99 pruned atom pairs is 1.144 angstroms; (across all 148 pairs:
4.378)  
  

> matchmaker #4.14 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.14), sequence alignment score = 714.4  
RMSD between 96 pruned atom pairs is 1.131 angstroms; (across all 148 pairs:
4.271)  
  

> matchmaker #4.15 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.15), sequence alignment score = 711.4  
RMSD between 104 pruned atom pairs is 1.219 angstroms; (across all 148 pairs:
4.119)  
  

> matchmaker #4.16 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.16), sequence alignment score = 711.4  
RMSD between 102 pruned atom pairs is 1.216 angstroms; (across all 148 pairs:
4.316)  
  

> matchmaker #4.17 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.17), sequence alignment score = 718.6  
RMSD between 95 pruned atom pairs is 1.274 angstroms; (across all 148 pairs:
4.613)  
  

> matchmaker #4.18 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.18), sequence alignment score = 718  
RMSD between 104 pruned atom pairs is 1.131 angstroms; (across all 148 pairs:
4.915)  
  

> matchmaker #4.19 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.19), sequence alignment score = 703.6  
RMSD between 101 pruned atom pairs is 1.228 angstroms; (across all 148 pairs:
4.141)  
  

> matchmaker #4.20 to #3

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-P0A917-F1-model_v6.pdb, chain A (#3) with exp - 2M06.cif, chain
A (#4.20), sequence alignment score = 714.4  
RMSD between 89 pruned atom pairs is 1.253 angstroms; (across all 148 pairs:
4.638)  
  

> select #4/A:53-55@CA

60 atoms, 60 residues, 20 models selected  

> getcrd sel

Atom #4.1/A:53@CA -2.718 -14.903 32.797  
Atom #4.1/A:54@CA -4.644 -12.095 34.509  
Atom #4.1/A:55@CA -7.864 -13.255 32.828  
Atom #4.2/A:53@CA -7.785 -16.564 33.533  
Atom #4.2/A:54@CA -10.594 -14.276 34.703  
Atom #4.2/A:55@CA -11.670 -13.754 31.074  
Atom #4.3/A:53@CA -2.063 -16.287 31.870  
Atom #4.3/A:54@CA -2.240 -12.729 33.197  
Atom #4.3/A:55@CA -5.813 -11.577 33.819  
Atom #4.4/A:53@CA -7.318 -15.982 34.222  
Atom #4.4/A:54@CA -9.417 -13.218 35.807  
Atom #4.4/A:55@CA -11.476 -13.081 32.595  
Atom #4.5/A:53@CA -7.758 -17.978 29.869  
Atom #4.5/A:54@CA -10.231 -16.020 31.991  
Atom #4.5/A:55@CA -12.535 -15.680 28.967  
Atom #4.6/A:53@CA -4.855 -10.826 35.913  
Atom #4.6/A:54@CA -8.525 -9.904 36.320  
Atom #4.6/A:55@CA -9.291 -11.806 33.105  
Atom #4.7/A:53@CA -10.103 -16.585 32.700  
Atom #4.7/A:54@CA -10.173 -13.426 34.824  
Atom #4.7/A:55@CA -8.927 -9.843 34.528  
Atom #4.8/A:53@CA -6.282 -15.374 34.025  
Atom #4.8/A:54@CA -9.831 -14.147 34.675  
Atom #4.8/A:55@CA -10.726 -14.831 31.031  
Atom #4.9/A:53@CA 0.208 -9.830 33.273  
Atom #4.9/A:54@CA -1.979 -6.935 34.416  
Atom #4.9/A:55@CA -4.957 -9.295 34.786  
Atom #4.10/A:53@CA -7.064 -15.994 34.055  
Atom #4.10/A:54@CA -9.980 -13.782 35.116  
Atom #4.10/A:55@CA -11.223 -13.655 31.508  
Atom #4.11/A:53@CA -7.141 -13.989 34.590  
Atom #4.11/A:54@CA -10.834 -13.111 34.912  
Atom #4.11/A:55@CA -11.380 -14.358 31.347  
Atom #4.12/A:53@CA -6.596 -13.928 33.686  
Atom #4.12/A:54@CA -8.345 -11.124 35.567  
Atom #4.12/A:55@CA -11.543 -11.875 33.608  
Atom #4.13/A:53@CA -8.947 -14.511 30.529  
Atom #4.13/A:54@CA -12.338 -15.712 31.757  
Atom #4.13/A:55@CA -14.959 -13.064 32.525  
Atom #4.14/A:53@CA -8.610 -15.658 32.185  
Atom #4.14/A:54@CA -9.162 -12.538 34.285  
Atom #4.14/A:55@CA -12.710 -12.344 32.887  
Atom #4.15/A:53@CA -5.153 -15.298 34.289  
Atom #4.15/A:54@CA -8.161 -13.288 35.490  
Atom #4.15/A:55@CA -9.808 -13.777 32.085  
Atom #4.16/A:53@CA 0.223 -12.837 31.336  
Atom #4.16/A:54@CA -1.337 -12.717 34.807  
Atom #4.16/A:55@CA -4.836 -12.475 33.257  
Atom #4.17/A:53@CA -6.877 -17.267 30.878  
Atom #4.17/A:54@CA -8.880 -14.977 33.160  
Atom #4.17/A:55@CA -11.731 -14.993 30.613  
Atom #4.18/A:53@CA -6.363 -10.508 35.945  
Atom #4.18/A:54@CA -9.678 -8.649 36.231  
Atom #4.18/A:55@CA -11.006 -10.674 33.287  
Atom #4.19/A:53@CA -4.797 -12.351 35.398  
Atom #4.19/A:54@CA -8.595 -12.040 35.359  
Atom #4.19/A:55@CA -8.657 -13.746 31.945  
Atom #4.20/A:53@CA -3.210 -10.225 33.984  
Atom #4.20/A:54@CA -5.533 -7.341 34.874  
Atom #4.20/A:55@CA -8.570 -9.585 34.366  

> select #3/A:53-55@CA

3 atoms, 3 residues, 1 model selected  

> getcrd sel

Atom #3/A:53@CA -1.447 2.950 -10.492  
Atom #3/A:54@CA 1.188 3.983 -13.069  
Atom #3/A:55@CA 0.692 5.688 -16.444  

> hide #!4 models

> select #4.1/A:53-55 #4.2/A:53-55 #4.3/A:53-55 #4.4/A:53-55 #4.5/A:53-55
> #4.6/A:53-55 #4.7/A:53-55 #4.8/A:53-55 #4.9/A:53-55 #4.10/A:53-55
> #4.11/A:53-55 #4.12/A:53-55 #4.13/A:53-55 #4.14/A:53-55 #4.15/A:53-55
> #4.16/A:53-55 #4.17/A:53-55 #4.18/A:53-55 #4.19/A:53-55 #4.20/A:53-55

580 atoms, 560 bonds, 60 residues, 20 models selected  

> hide #3 models

> show #1 models

> hide #1 models

> show #3 models

> hide #3 models

> show #1 models

> hide #1 models

> show #3 models

> select #3/A:76

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

> select #3/A:76-78

16 atoms, 15 bonds, 3 residues, 1 model selected  

> select #3/A:76-78@CA

3 atoms, 3 residues, 1 model selected  

> getcrd sel

Atom #3/A:76@CA -5.162 -14.841 33.381  
Atom #3/A:77@CA -7.031 -12.379 35.725  
Atom #3/A:78@CA -9.917 -12.167 33.161  

> select #4/A:95-97@CA

60 atoms, 60 residues, 20 models selected  

> getcrd sel

Atom #4.1/A:95@CA -16.810 7.491 33.455  
Atom #4.1/A:96@CA -18.334 10.893 34.466  
Atom #4.1/A:97@CA -19.007 13.197 31.524  
Atom #4.2/A:95@CA -23.445 6.072 29.389  
Atom #4.2/A:96@CA -24.652 7.133 25.918  
Atom #4.2/A:97@CA -22.495 9.802 24.296  
Atom #4.3/A:95@CA -20.821 3.889 31.515  
Atom #4.3/A:96@CA -19.956 6.383 28.681  
Atom #4.3/A:97@CA -21.187 9.967 28.674  
Atom #4.4/A:95@CA -11.861 7.854 36.456  
Atom #4.4/A:96@CA -14.130 9.083 33.638  
Atom #4.4/A:97@CA -13.206 12.261 31.790  
Atom #4.5/A:95@CA -15.063 8.211 33.814  
Atom #4.5/A:96@CA -14.030 9.909 30.496  
Atom #4.5/A:97@CA -12.651 13.438 30.329  
Atom #4.6/A:95@CA -20.954 4.564 32.459  
Atom #4.6/A:96@CA -20.490 6.910 29.467  
Atom #4.6/A:97@CA -18.484 10.111 29.768  
Atom #4.7/A:95@CA -25.763 4.079 24.992  
Atom #4.7/A:96@CA -24.204 6.643 22.602  
Atom #4.7/A:97@CA -22.888 9.904 24.028  
Atom #4.8/A:95@CA -22.683 3.055 31.242  
Atom #4.8/A:96@CA -22.205 6.007 28.844  
Atom #4.8/A:97@CA -20.344 9.127 29.924  
Atom #4.9/A:95@CA -18.957 6.955 32.582  
Atom #4.9/A:96@CA -17.924 8.842 29.393  
Atom #4.9/A:97@CA -16.485 12.344 29.317  
Atom #4.10/A:95@CA -21.773 7.991 29.892  
Atom #4.10/A:96@CA -23.374 11.481 30.317  
Atom #4.10/A:97@CA -22.632 13.908 27.495  
Atom #4.11/A:95@CA -23.958 5.151 28.577  
Atom #4.11/A:96@CA -26.211 8.283 28.399  
Atom #4.11/A:97@CA -24.973 10.859 25.903  
Atom #4.12/A:95@CA -17.631 5.952 35.061  
Atom #4.12/A:96@CA -19.644 8.334 32.842  
Atom #4.12/A:97@CA -17.503 10.754 30.859  
Atom #4.13/A:95@CA -20.596 5.897 32.813  
Atom #4.13/A:96@CA -20.997 8.382 29.919  
Atom #4.13/A:97@CA -18.353 11.089 29.636  
Atom #4.14/A:95@CA -23.524 3.701 29.582  
Atom #4.14/A:96@CA -22.861 6.280 26.820  
Atom #4.14/A:97@CA -20.532 9.162 27.630  
Atom #4.15/A:95@CA -19.763 5.884 33.845  
Atom #4.15/A:96@CA -21.616 7.847 31.131  
Atom #4.15/A:97@CA -19.491 10.503 29.455  
Atom #4.16/A:95@CA -18.836 5.383 33.171  
Atom #4.16/A:96@CA -19.821 6.823 29.759  
Atom #4.16/A:97@CA -18.470 10.245 28.831  
Atom #4.17/A:95@CA -16.773 8.109 31.917  
Atom #4.17/A:96@CA -14.800 9.474 28.876  
Atom #4.17/A:97@CA -13.150 12.887 28.844  
Atom #4.18/A:95@CA -27.067 3.304 24.756  
Atom #4.18/A:96@CA -25.555 5.735 22.208  
Atom #4.18/A:97@CA -24.376 9.150 23.367  
Atom #4.19/A:95@CA -13.546 6.463 35.449  
Atom #4.19/A:96@CA -14.967 8.727 32.687  
Atom #4.19/A:97@CA -12.584 11.294 31.216  
Atom #4.20/A:95@CA -21.730 7.000 30.103  
Atom #4.20/A:96@CA -19.687 8.664 27.310  
Atom #4.20/A:97@CA -17.974 12.032 27.584  

> select #3/A:118

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

> select #3/A:118-120

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

> select #3/A:118-120@CA

3 atoms, 3 residues, 1 model selected  

> getcrd sel

Atom #3/A:118@CA -13.531 -7.719 35.293  
Atom #3/A:119@CA -16.480 -7.726 36.143  
Atom #3/A:120@CA -17.912 -4.854 33.946  

> select #3/A:57

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

> select #3/A:57-59

21 atoms, 21 bonds, 3 residues, 1 model selected  

> select #3/A:24-37,44-55,60-74,80-97,100-117,121-138,144-155,158-171

950 atoms, 968 bonds, 121 residues, 1 model selected  

> select #3/A:53

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

> select #3/A:53-55

30 atoms, 30 bonds, 3 residues, 1 model selected  

> select #3/A:76

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

> select #3/A:76-78

16 atoms, 15 bonds, 3 residues, 1 model selected  

> select #3/A:118

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

> select #3/A:118-120

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

> select #3/A:76

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

> select #3/A:76-78

16 atoms, 15 bonds, 3 residues, 1 model selected  

> select #3/A:118-120

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

> select #4.1/A:95 #4.2/A:95 #4.3/A:95 #4.4/A:95 #4.5/A:95 #4.6/A:95 #4.7/A:95
> #4.8/A:95 #4.9/A:95 #4.10/A:95 #4.11/A:95 #4.12/A:95 #4.13/A:95 #4.14/A:95
> #4.15/A:95 #4.16/A:95 #4.17/A:95 #4.18/A:95 #4.19/A:95 #4.20/A:95

420 atoms, 420 bonds, 20 residues, 20 models selected  

> select #4.1/A:95-97 #4.2/A:95-97 #4.3/A:95-97 #4.4/A:95-97 #4.5/A:95-97
> #4.6/A:95-97 #4.7/A:95-97 #4.8/A:95-97 #4.9/A:95-97 #4.10/A:95-97
> #4.11/A:95-97 #4.12/A:95-97 #4.13/A:95-97 #4.14/A:95-97 #4.15/A:95-97
> #4.16/A:95-97 #4.17/A:95-97 #4.18/A:95-97 #4.19/A:95-97 #4.20/A:95-97

980 atoms, 1000 bonds, 60 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [95-97] RMSD: 7.199  
  

> select #4.1/A:53-54 #4.2/A:53-54 #4.3/A:53-54 #4.4/A:53-54 #4.5/A:53-54
> #4.6/A:53-54 #4.7/A:53-54 #4.8/A:53-54 #4.9/A:53-54 #4.10/A:53-54
> #4.11/A:53-54 #4.12/A:53-54 #4.13/A:53-54 #4.14/A:53-54 #4.15/A:53-54
> #4.16/A:53-54 #4.17/A:53-54 #4.18/A:53-54 #4.19/A:53-54 #4.20/A:53-54

440 atoms, 420 bonds, 40 residues, 20 models selected  

> select #4.1/A:53-55 #4.2/A:53-55 #4.3/A:53-55 #4.4/A:53-55 #4.5/A:53-55
> #4.6/A:53-55 #4.7/A:53-55 #4.8/A:53-55 #4.9/A:53-55 #4.10/A:53-55
> #4.11/A:53-55 #4.12/A:53-55 #4.13/A:53-55 #4.14/A:53-55 #4.15/A:53-55
> #4.16/A:53-55 #4.17/A:53-55 #4.18/A:53-55 #4.19/A:53-55 #4.20/A:53-55

580 atoms, 560 bonds, 60 residues, 20 models selected  
Outer Membrane Protein X [ID: 1] region 20 chains [53-55] RMSD: 5.633  
  


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

Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M5
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac17,2
      Model Number: MDE34LL/A
      Chip: Apple M5
      Total Number of Cores: 10 (4 performance and 6 efficiency)
      Memory: 24 GB
      System Firmware Version: 13822.41.1
      OS Loader Version: 13822.41.1

Software:

    System Software Overview:

      System Version: macOS 26.1 (25B78)
      Kernel Version: Darwin 25.1.0
      Time since boot: 18天16小时50分钟

Graphics/Displays:

    Apple M5:

      Chipset Model: Apple M5
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      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


Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
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    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
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Query Language

query: TracLinks and the [[TicketQuery]] macro both use a mini “query language” for specifying query filters. Filters are separated by ampersands (&). Each filter consists of the ticket field name, an operator and one or more values. More than one value are separated by a pipe (|), meaning that the filter matches any of the values. To include a literal & or | in a value, escape the character with a backslash (\).

The available operators are:

= the field content exactly matches one of the values
~= the field content contains one or more of the values
^= the field content starts with one of the values
$= the field content ends with one of the values

All of these operators can also be negated:

!= the field content matches none of the values
!~= the field content does not contain any of the values
!^= the field content does not start with any of the values
!$= the field content does not end with any of the values

The date fields created and modified can be constrained by using the = operator and specifying a value containing two dates separated by two dots (..). Either end of the date range can be left empty, meaning that the corresponding end of the range is open. The date parser understands a few natural date specifications like "3 weeks ago", "last month" and "now", as well as Bugzilla-style date specifications like "1d", "2w", "3m" or "4y" for 1 day, 2 weeks, 3 months and 4 years, respectively. Spaces in date specifications can be omitted to avoid having to quote the query string.

created=2007-01-01..2008-01-01 query tickets created in 2007
created=lastmonth..thismonth query tickets created during the previous month
modified=1weekago.. query tickets that have been modified in the last week
modified=..30daysago query tickets that have been inactive for the last 30 days

See also: TracTickets, TracReports, TracGuide, TicketQuery

Last modified 9 years ago Last modified on Jan 4, 2017, 10:45:36 AM
Note: See TracWiki for help on using the wiki.