Opened 13 months ago

Closed 5 months ago

#16201 closed defect (worksforme)

Crash opening .cif file

Reported by: disha-gajanan.hiregange@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.14.0-427.20.1.el9_4.x86_64-x86_64-with-glibc2.34
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000015311bbfd640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000015311bdfe640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000015311bfff640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/selectors.py", line 415 in select
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153190335640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153190536640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153190737640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153190938640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153190b39640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153190d3a640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153190f3b640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000015319113c640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000015319133d640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000015319153e640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000015319173f640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153191940640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153191b41640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153191d42640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153191f43640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153192144640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153192345640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153192546640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153192747640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153192948640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153192b49640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153192d4a640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000153192f4b640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000015319314c640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 975 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x000015321381c740 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/mmcif/__init__.py", line 54 in open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 513 in collated_open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/open_command/dialog.py", line 334 in _qt_safe
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, lxml._elementpath, lxml.etree, chimerax.graphics._graphics, PIL._imagingmath, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62)
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_50s_w83.cxs

Opened half1.mrc as #1.1, grid size 460,460,460, pixel 0.86, shown at level
0.01, step 1, values float32  
Opened half1_resmap.mrc as #1.2, grid size 460,460,460, pixel 0.86, shown at
level 100, step 2, values float32  
opened ChimeraX session  

> ui tool show "Surface Color"

> color sample #1.1.1 map #1.2 palette
> 1.8,#0000ff:2,#0091ff:2.3,#00ffda:2.7,#00ff48:3,#48ff00:3.5,#daff00:4,#ff9100:4.5,#ff0000

Map values for surface "surface": minimum 0, mean 89.05, maximum 100  

> ciip

Unknown command: ciip  

> clip

> color sample #1.1.1 map #1.2 palette
> 1.8,#0000ff:2,#0091ff:2.3,#00ffda:2.7,#00ff48:3,#48ff00:3.5,#daff00:4,#ff9100:4.5,#ff0000

Map values for surface "surface": minimum 0, mean 89.05, maximum 100  
Map values for surface "cap front": minimum 1.9, mean 15.01, maximum 100  

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_50s_w83_new_clip.png
> width 1339 height 854 supersample 3

> clip

> ~clip

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_50s_w83_new.png
> width 1339 height 854 supersample 3

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_50s_w83_new.cxs

> key blue:1.8 #0091ff:2.0 #00ffda:2.3 #00ff48:2.7 #48ff00:3.0 #daff00:3.5
> #ff9100:4.0 red:4.5 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> ui mousemode middle 'color key'

> key labelSide left/top

> key delete

> ui mousemode middle translate

> key blue:1.8 #0091ff:2.0 #00ffda:2.3 #00ff48:2.7 #48ff00:3.0 #daff00:3.5
> #ff9100:4.0 red:4.5 showTool true

> ui mousemode right "color key"

> key pos 0.711949,0.541358

> key pos 0.887229,0.537471 size 0.0186706,0.420375

> key pos 0.851381,0.30445

> key pos 0.85885,0.293911 size 0.000746826,0.00117096

> key pos 0.852128,0.0702576 size 0.0164302,0.812646

> key pos 0.862584,0.0398126 size 0.00597461,0.0362998

> key pos 0.866318,0.118267 size 0.012696,0.796253

> key fontSize 23

> key fontSize 22

> key fontSize 21

> key fontSize 20

> key fontSize 19

> key fontSize 18

> key fontSize 17

> key fontSize 16

> key fontSize 15

> key pos 0.868559,0.0960187 size 0,0.028103

> key pos 0.846154,0.0679157 size 0.00821509,0.82904

> key delete

> ui mousemode right translate

> color sample #1.1.1 map #1.2 palette
> 2,#0000ff:2.5,#0091ff:2.8,#00ffda:3,#00ff48:3.2,#48ff00:3.5,#daff00:4,#ff9100:4.5,#ff0000

Map values for surface "surface": minimum 0, mean 89.05, maximum 100  

> clip

> color sample #1.1.1 map #1.2 palette
> 2,#0000ff:2.5,#0091ff:2.8,#00ffda:3,#00ff48:3.2,#48ff00:3.5,#daff00:4,#ff9100:4.5,#ff0000

Map values for surface "surface": minimum 0, mean 89.05, maximum 100  
Map values for surface "cap front": minimum 1.9, mean 15.01, maximum 100  

> color sample #1.1.1 map #1.2 palette
> 2,#0000ff:2.5,#0091ff:2.8,#00ffda:3,#00ff48:3.2,#48ff00:3.5,#daff00:4,#ff9100:4.5,#ff0000

Map values for surface "surface": minimum 0, mean 89.05, maximum 100  
Map values for surface "cap front": minimum 1.9, mean 15.01, maximum 100  

> color sample #1.1.1 map #1.2 palette
> 1.8,#0000ff:2.5,#0091ff:2.8,#00ffda:3,#00ff48:3.2,#48ff00:3.5,#daff00:4,#ff9100:4.5,#ff0000

Map values for surface "surface": minimum 0, mean 89.05, maximum 100  
Map values for surface "cap front": minimum 1.9, mean 15.01, maximum 100  

> color sample #1.1.1 map #1.2 palette
> 2,#0000ff:2.5,#0091ff:2.8,#00ffda:3,#00ff48:3.2,#48ff00:3.5,#daff00:4,#ff9100:4.5,#ff0000

Map values for surface "surface": minimum 0, mean 89.05, maximum 100  
Map values for surface "cap front": minimum 1.9, mean 15.01, maximum 100  

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_50s_w83_new_clip.png
> width 1339 height 854 supersample 3

> ~clip

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_50s_w83_new.png
> width 1339 height 854 supersample 3

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_50s_w83_new.cxs

> key blue:2.0 #0091ff:2.5 #00ffda:2.8 #00ff48:3.0 #48ff00:3.2 #daff00:3.5
> #ff9100:4.0 red:4.5 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> key blue:2.0 #0091ff:2.5 #00ffda:2.8 #00ff48:3.0 #48ff00:3.2 #daff00:3.5
> #ff9100:4.0 red:4.5 showTool true

> ui mousemode right "color key"

> key pos 0.904406,0.118267 size 0.00746826,0.619438

> key pos 0.871546,0.845433 size 0,0

> key pos 0.871546,0.0866511 size 0.0268857,0.758782

> ui mousemode right translate

> color sample #1.1.1 map #1.2 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

Map values for surface "surface": minimum 0, mean 89.05, maximum 100  

> key blue:2.0 #0091ff:2.5 #00ffda:3.0 #00ff48:3.5 #48ff00:4.0 #daff00:4.5
> #ff9100:5.0 red:5.5 showTool true

> ui mousemode right "color key"

> key pos 0.880508,0.196721 size 0.0186706,0.697892

> ui mousemode right translate

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_50s_w83_new.cxs

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_50s_w83_new.png
> width 1339 height 854 supersample 3

> clip

> color sample #1.1.1 map #1.2 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

Map values for surface "surface": minimum 0, mean 89.05, maximum 100  
Map values for surface "cap front": minimum 1.9, mean 16.84, maximum 100  

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_50s_w83_new_clip.png
> width 1339 height 854 supersample 3

> close session

> open
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_30s_w83.cxs

Opened half1.mrc as #1.1, grid size 460,460,460, pixel 0.86, shown at level
0.01, step 1, values float32  
Opened half1_resmap.mrc as #1.2, grid size 460,460,460, pixel 0.86, shown at
level 100, step 2, values float32  
Opened half1.mrc as #2.1, grid size 460,460,460, pixel 0.86, shown at level
0.011, step 1, values float32  
Opened half1_resmap.mrc as #2.2, grid size 460,460,460, pixel 0.86, shown at
level 100, step 2, values float32  
opened ChimeraX session  

> ui tool show "Surface Color"

> color sample #1.1.1 map #1.2 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

Map values for surface "surface": minimum 0, mean 82.76, maximum 100  

> color sample #2.1.1 map #2.2 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

Map values for surface "surface": minimum 0, mean 78.33, maximum 100  

> lighting soft

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_30s_w83_new.png
> width 1339 height 854 supersample 3

> clip

> color sample #2.1.1 map #2.2 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

Map values for surface "surface": minimum 0, mean 78.33, maximum 100  
Map values for surface "cap front": minimum 1.954, mean 12.46, maximum 100  

> color sample #1.1.1 map #1.2 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

Map values for surface "surface": minimum 0, mean 82.76, maximum 100  
Map values for surface "cap front": minimum 2.9, mean 33.43, maximum 100  

> volume #1.1 level 0.002918

> volume #1.1 level 0.002191

> volume #1.1 level 0.007

> volume #1.1 level 0.008

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_30s_w83_new_clip.png
> width 1339 height 854 supersample 3

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_30s_w83_new.cxs

> close session

> open
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_50s_w83_new.cxs
> format session

Opened half1.mrc as #1.1, grid size 460,460,460, pixel 0.86, shown at level
0.01, step 1, values float32  
Opened half1_resmap.mrc as #1.2, grid size 460,460,460, pixel 0.86, shown at
level 100, step 2, values float32  
Map values for surface "surface": minimum 0, mean 89.05, maximum 100  
opened ChimeraX session  

> lighting soft

> lighting shadows true intensity 0.5

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_50s_w83_new.cxs

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_50s_w83_new.png
> width 1339 height 854 supersample 3

> clip

> ui tool show "Surface Color"

> color sample #1.1.1 map #1.2 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

Map values for surface "surface": minimum 0, mean 89.05, maximum 100  
Map values for surface "cap front": minimum 1.9, mean 16.84, maximum 100  

> lighting soft

> lighting shadows true intensity 0.5

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/local_res_50s_w83_new_clip.png
> width 1339 height 854 supersample 3

> close session

> open
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266/local_res_del266_50s.cxs

Opened half1_resmap.mrc as #1, grid size 440,440,440, pixel 0.852, shown at
level 100, step 1, values float32  
Opened half1.mrc as #2, grid size 440,440,440, pixel 0.852, shown at level
0.009, step 1, values float32  
Opened half1_resmap.mrc as #3, grid size 440,440,440, pixel 0.852, shown at
level 100, step 1, values float32  
opened ChimeraX session  

> ui tool show "Surface Color"

> color sample #1.1 map #1 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

> color sample #2.1 map #1 palette
> 1.5,#0000ff:1.8,#0091ff:2.2,#00ffda:2.5,#00ff48:3,#48ff00:3.5,#daff00:4,#ff9100:4.5,#ff0000

Map values for surface "surface": minimum 1.9, mean 75.98, maximum 100  

> color sample #2.1 map #3 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

Map values for surface "surface": minimum 1.9, mean 75.98, maximum 100  

> color sample #2.1 map #3 palette
> 1.5,#0000ff:2,#0091ff:2.5,#00ffda:3,#00ff48:3.5,#48ff00:4,#daff00:4.5,#ff9100:5,#ff0000

Map values for surface "surface": minimum 1.9, mean 75.98, maximum 100  

> color sample #2.1 map #3 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

Map values for surface "surface": minimum 1.9, mean 75.98, maximum 100  

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266/local_res_del266_50s_clip_new.png
> width 1339 height 854 supersample 3

> ~clip

> lighting soft

> lighting shadows true intensity 0.5

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266/local_res_del266_50s_new.png
> width 1339 height 854 supersample 3

> key blue:2.0 #0091ff:2.5 #00ffda:3.0 #00ff48:3.5 #48ff00:4.0 #daff00:4.5
> #ff9100:5.0 red:5.5 showTool true

> ui mousemode right "color key"

> key pos 0.899178,0.19555 size 0.029873,0.649883

> ui mousemode right translate

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266/local_res_del266_50s_new.cxs

> close session

> open
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266/local_res_del266_30s.cxs

Opened half1.mrc as #1.1, grid size 440,440,440, pixel 0.852, shown at level
0.009, step 1, values float32  
Opened half1_resmap.mrc as #1.2, grid size 440,440,440, pixel 0.852, shown at
level 14, step 1, values float32  
Opened half1.mrc as #2.1, grid size 440,440,440, pixel 0.852, shown at level
0.009, step 1, values float32  
Opened half1_resmap.mrc as #2.2, grid size 440,440,440, pixel 0.852, shown at
level 100, step 1, values float32  
Map values for surface "surface": minimum 1.9, mean 55.67, maximum 100  
Map values for surface "surface": minimum 1.9, mean 59.32, maximum 100  
opened ChimeraX session  

> ui tool show "Surface Color"

> color sample #1.1.1 map #1.2 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

Map values for surface "surface": minimum 1.9, mean 55.67, maximum 100  
Map values for surface "cap front": minimum 2.9, mean 9.306, maximum 100  

> color sample #2.1.1 map #2.2 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

Map values for surface "surface": minimum 1.9, mean 59.32, maximum 100  
Map values for surface "cap front": minimum 1.9, mean 4.999, maximum 100  

> lighting soft

> lighting shadows true intensity 0.5

> key blue:2.0 #0091ff:2.5 #00ffda:3.0 #00ff48:3.5 #48ff00:4.0 #daff00:4.5
> #ff9100:5.0 red:5.5 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266/local_res_del266_30s_new.png
> width 1339 height 854 supersample 3

> ~clip

> lighting soft

> lighting shadows true intensity 0.5

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266/local_res_del266_30s_clip_new.png
> width 1339 height 854 supersample 3

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266/local_res_del266_30s_new.cxs

> close session

> open
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266_lefamulin/3d_class_del266_lefa_new.cxs

Opened run_it025_class001.mrc as #1.1, grid size 110,110,110, pixel 3.4, shown
at level 0.05, step 1, values float32  
Opened run_it025_class002.mrc as #1.2, grid size 110,110,110, pixel 3.4, shown
at level 0.05, step 1, values float32  
Opened run_it025_class003.mrc as #1.3, grid size 110,110,110, pixel 3.4, shown
at level 0.05, step 1, values float32  
Opened run_it025_class005.mrc as #1.5, grid size 110,110,110, pixel 3.4, shown
at level 0.05, step 1, values float32  
Opened run_it025_class006.mrc as #1.6, grid size 110,110,110, pixel 3.4, shown
at level 0.05, step 1, values float32  
Opened run_it025_class008.mrc as #2, grid size 110,110,110, pixel 3.4, shown
at level 0.05, step 1, values float32  
opened ChimeraX session  

> close session

> open
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266_lefamulin/local_res_del266_lefa_50s.cxs

Opened half1_inverted.mrc as #1, grid size 440,440,440, pixel 0.85, shown at
level 0.009, step 1, values float32  
Opened half1_resmap_inverted.mrc as #2, grid size 440,440,440, pixel 0.85,
shown at level 100, step 2, values float32  
opened ChimeraX session  

> ui tool show "Surface Color"

> color sample #1.1 map #2 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

Map values for surface "surface": minimum 2.2, mean 80.05, maximum 100  

> lighting soft

> lighting shadows true intensity 0.5

> lighting simple

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266_lefamulin/local_res_del266_lefa_50s_new.cxs

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266_lefamulin/local_res_del266_lefa_50s_new.png
> width 1339 height 854 supersample 3

> clip

> color sample #1.1 map #2 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

Map values for surface "surface": minimum 2.2, mean 80.05, maximum 100  
Map values for surface "cap front": minimum 2.2, mean 7.373, maximum 100  

> ~clip

> clip

> color sample #1.1 map #2 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

Map values for surface "surface": minimum 2.2, mean 80.05, maximum 100  
Map values for surface "cap front": minimum 2.2, mean 6.001, maximum 100  

> volume #1 level 0.008

> ~clip

> clip

> color sample #1.1 map #2 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

Map values for surface "surface": minimum 2.2, mean 83.59, maximum 100  
Map values for surface "cap front": minimum 2.2, mean 10.59, maximum 100  

> ~clip

> clip

> color sample #1.1 map #2 palette
> 2,#0000ff:2.5,#0091ff:3,#00ffda:3.5,#00ff48:4,#48ff00:4.5,#daff00:5,#ff9100:5.5,#ff0000

Map values for surface "surface": minimum 2.2, mean 83.59, maximum 100  
Map values for surface "cap front": minimum 2.2, mean 10.48, maximum 100  

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266_lefamulin/local_res_del266_lefa_50s_new_clip.png
> width 1339 height 854 supersample 3

> ~clip

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266_lefamulin/local_res_del266_lefa_50s_new.png
> width 1339 height 854 supersample 3

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266_lefamulin/local_res_del266_lefa_50s_new.cxs

> close session

> open
> /yonath_group/disha/Gingivalis/Models_and_maps/publication/images/proteins/Lefamulin/PG_5HL7.cxs
> format session

Opened iverted_FR_50S.mrc as #2, grid size 440,440,440, pixel 0.85, shown at
level 0.0168, step 1, values float32  
opened ChimeraX session  

> open
> /yonath_group/disha/Gingivalis/Models_and_maps/W83/phenix/RealSpaceRefine_10/80S_W83_real_space_refined_010.cif

Summary of feedback from opening
/yonath_group/disha/Gingivalis/Models_and_maps/W83/phenix/RealSpaceRefine_10/80S_W83_real_space_refined_010.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 5119  
Missing entity information. Treating each chain as a separate entity.  
Invalid residue range for struct_conf "1": invalid chain "1", near line 283  
Invalid residue range for struct_conf "2": invalid chain "1", near line 284  
Invalid residue range for struct_conf "3": invalid chain "1", near line 285  
Bad residue range for struct_conf "5" near line 287  
Bad residue range for struct_conf "6" near line 288  
Bad residue range for struct_conf "7" near line 289  
Bad residue range for struct_conf "8" near line 290  
Bad residue range for struct_conf "9" near line 291  
Invalid residue range for struct_conf "10": invalid chain "6", near line 292  
Invalid residue range for struct_conf "11": invalid chain "6", near line 293  
Invalid residue range for struct_conf "12": invalid chain "6", near line 294  
Invalid residue range for struct_conf "13": invalid chain "6", near line 295  
Invalid residue range for struct_conf "14": invalid chain "2", near line 296  
1 messages similar to the above omitted  
Bad residue range for struct_conf "22" near line 304  
Bad residue range for struct_conf "27" near line 309  
Bad residue range for struct_conf "28" near line 310  
Bad residue range for struct_conf "29" near line 311  
Bad residue range for struct_conf "47" near line 329  
5 messages similar to the above omitted  
Invalid residue range for struct_conf "61": invalid chain "7", near line 343  
Invalid residue range for struct_conf "62": invalid chain "7", near line 344  
Invalid residue range for struct_conf "63": invalid chain "7", near line 345  
Invalid residue range for struct_conf "64": invalid chain "7", near line 346  
Invalid residue range for struct_conf "65": invalid chain "4", near line 347  
51 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "2 2" near line 4835  
Invalid sheet range for struct_sheet_range "3 1" near line 4836  
Invalid sheet range for struct_sheet_range "3 2" near line 4837  
Invalid sheet range for struct_sheet_range "3 3" near line 4838  
Invalid sheet range for struct_sheet_range "3 4" near line 4839  
86 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' near line 125003  
Skipping chem_comp category: Missing column 'type' near line 125282  
Skipping chem_comp category: Missing column 'type' near line 125567  
Skipping chem_comp category: Missing column 'type' near line 125819  
Skipping chem_comp category: Missing column 'type' near line 125846  
15 messages similar to the above omitted  
  
Chain information for 80S_W83_real_space_refined_010.cif #4  
---  
Chain | Description  
0 | No description available  
1 | No description available  
10 | No description available  
2 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
A | No description available  
B | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
  

> select add #4

119562 atoms, 128704 bonds, 4277 pseudobonds, 9753 residues, 3 models selected  

> hide sel atoms

> ui tool show Matchmaker

> matchmaker #!4 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 50S_delta266_lefamulin_new-coot-0.pdb, chain A (#1) with
80S_W83_real_space_refined_010.cif, chain A (#4), sequence alignment score =
13512.5  
RMSD between 2243 pruned atom pairs is 0.922 angstroms; (across all 2344
pairs: 2.781)  
  

> cartoon style nucleic xsection round width 1.3 thickness 0.5

> select #4/A:2070-2073, 2503-2507, 2452-2453, 2583-2587

338 atoms, 373 bonds, 16 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> color sel dim gray

> style sel stick

Changed 338 atom styles  

> size sel stickRadius 0.1

Changed 373 bond radii  

> select clear

> select add #3

81462 atoms, 88398 bonds, 2876 pseudobonds, 6346 residues, 5 models selected  

> color (#!3 & sel) light sea green

> color (#!3 & sel) hot pink

> ui tool show "Color Actions"

> color sel cadet blue

> select ::name="62B"

70 atoms, 76 bonds, 2 residues, 2 models selected  

> color (#!1,3 & sel) forest green

> color sel byhetero

> select clear

> hide #!3 models

> show #!3 models

> hide #!1 models

> select #3/X:3003

35 atoms, 38 bonds, 1 residue, 1 model selected  

> hide sel atoms

> show #!1 models

> select clear

> hide #!3 models

> hide #!4 models

> show #!3 models

> select add #3

81462 atoms, 88398 bonds, 2876 pseudobonds, 6346 residues, 5 models selected  

> ui tool show "Color Actions"

> color sel teal

> color sel dark khaki

> color sel olive drab

> color sel cadet blue

> color sel steel blue

> color sel light sea green

> color sel dark cyan

> color sel rosy brown

> color sel dark gray

> color sel burly wood

> select subtract #3

Nothing selected  

> show #!4 models

> select add #4

119562 atoms, 128704 bonds, 4277 pseudobonds, 9753 residues, 3 models selected  

> color (#!4 & sel) dark gray

> ui tool show "Color Actions"

> color sel slate gray

> color sel light slate gray

> hide #!3 models

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> select clear

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/publication/new_figures/PG_W83_DEL_5HL7.cxs

> select add #3

81462 atoms, 88398 bonds, 2876 pseudobonds, 6346 residues, 5 models selected  

> ui tool show "Color Actions"

> color sel pale turquoise

> color sel orchid

> color sel dark salmon

> color sel light salmon

> color sel dark salmon

> color sel goldenrod

> color sel dark khaki

> color sel light salmon

> hide #!3 models

> show #!3 models

> hide #!4 models

> select clear

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/publication/new_figures/nar_submission/PG_W83_DEL_5HL7.cxs

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/publication/new_figures/nar_submission/PG_DEL_5HL7.png
> width 1339 height 854 supersample 3

> show #!4 models

> hide #!3 models

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/publication/new_figures/nar_submission/PG_DEL_W83.png
> width 1339 height 854 supersample 3

> close session

> open
> /yonath_group/disha/Gingivalis/Models_and_maps/publication/images/proteins/Lefamulin/4ug0_5hl7_pg.cxs

Opened iverted_FR_50S.mrc as #2, grid size 440,440,440, pixel 0.85, shown at
level 0.0168, step 1, values float32  
opened ChimeraX session  

> show #!1 models

> hide #3.1 models

> select #3/X:3003

35 atoms, 38 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select ::name="62B"

70 atoms, 76 bonds, 2 residues, 2 models selected  

> color (#!1,3 & sel) forest green

> color sel bynucleotide

> color sel byhetero

> select clear

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/publication/new_figures/nar_submission/PG_DEL_5HL7_4UG0.png
> width 1339 height 854 supersample 3

> select add #3

81462 atoms, 88398 bonds, 2876 pseudobonds, 6346 residues, 5 models selected  

> ui tool show "Color Actions"

> color sel light salmon

> color sel dark salmon

> select clear

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/publication/new_figures/nar_submission/PG_DEL_5HL7_4UG0.png
> width 1339 height 854 supersample 3

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/publication/new_figures/nar_submission/PG_DEL_5HL7_4UG0.cxs

> close session

> open
> /yonath_group/disha/Gingivalis/Models_and_maps/publication/new_figures/nar_submission/PG_W83_DEL_5HL7.cxs
> format session

Opened iverted_FR_50S.mrc as #2, grid size 440,440,440, pixel 0.85, shown at
level 0.0168, step 1, values float32  
opened ChimeraX session  

> hide #!1 models

> select #3/X:3003

35 atoms, 38 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel byhetero

> color sel forest green

> color sel byhetero

> select clear

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/publication/new_figures/nar_submission/5HL7.png
> width 1339 height 854 supersample 3

> show #!1 models

> hide #!3 models

> save
> /yonath_group/disha/Gingivalis/Models_and_maps/publication/new_figures/nar_submission/PG_DEL.png
> width 1339 height 854 supersample 3

> close session

> open
> /archive/processing/disha/RPS19_cloneD12_40S_2nd/relion4/Class3D/3d_class/run_it013_class001.mrc
> /archive/processing/disha/RPS19_cloneD12_40S_2nd/relion4/Class3D/3d_class/run_it013_class002.mrc
> /archive/processing/disha/RPS19_cloneD12_40S_2nd/relion4/Class3D/3d_class/run_it013_class003.mrc
> /archive/processing/disha/RPS19_cloneD12_40S_2nd/relion4/Class3D/3d_class/run_it013_class004.mrc
> /archive/processing/disha/RPS19_cloneD12_40S_2nd/relion4/Class3D/3d_class/run_it013_class005.mrc
> /archive/processing/disha/RPS19_cloneD12_40S_2nd/relion4/Class3D/3d_class/run_it013_class006.mrc
> /archive/processing/disha/RPS19_cloneD12_40S_2nd/relion4/Class3D/3d_class/run_it013_class007.mrc
> /archive/processing/disha/RPS19_cloneD12_40S_2nd/relion4/Class3D/3d_class/run_it013_class008.mrc
> format mrc

Opened run_it013_class001.mrc as #1.1, grid size 110,110,110, pixel 3.4, shown
at level 0.0789, step 1, values float32  
Opened run_it013_class002.mrc as #1.2, grid size 110,110,110, pixel 3.4, shown
at level 0.0612, step 1, values float32  
Opened run_it013_class003.mrc as #1.3, grid size 110,110,110, pixel 3.4, shown
at level 0.0731, step 1, values float32  
Opened run_it013_class004.mrc as #1.4, grid size 110,110,110, pixel 3.4, shown
at level 0.0842, step 1, values float32  
Opened run_it013_class005.mrc as #1.5, grid size 110,110,110, pixel 3.4, shown
at level 0.0551, step 1, values float32  
Opened run_it013_class006.mrc as #1.6, grid size 110,110,110, pixel 3.4, shown
at level 0.0542, step 1, values float32  
Opened run_it013_class007.mrc as #1.7, grid size 110,110,110, pixel 3.4, shown
at level 0.0759, step 1, values float32  
Opened run_it013_class008.mrc as #1.8, grid size 110,110,110, pixel 3.4, shown
at level 0.0391, step 1, values float32  

> tile

8 models tiled  

> volume all level 0.005

> volume all level 0.009

> volume all level 0.05

> close session

> open
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Refine3D/3d_ref_shiny_combined_again3/run_it014_half1_class001.mrc

Opened run_it014_half1_class001.mrc as #1, grid size 480,480,480, pixel 0.819,
shown at level 0.00342, step 2, values float32  

> volume #1 level 0.001253

> volume #1 level 0.003668

> open
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Refine3D/3d_ref_shiny_combined_again3/run_it014_half2_class001.mrc

Opened run_it014_half2_class001.mrc as #2, grid size 480,480,480, pixel 0.819,
shown at level 0.00341, step 2, values float32  

> volume #2 level 0.0006134

> close session

> open
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Refine3D/3d_ref_shiny_class1/run_class001.mrc

Opened run_class001.mrc as #1, grid size 480,480,480, pixel 0.819, shown at
level 0.00708, step 2, values float32  

> volume #1 level 0.003

> surface dust #1 size 8.19

> open
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Refine3D/3d_ref_shiny_class2/run_class001.mrc

Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.819, shown at
level 0.00697, step 2, values float32  

> volume #2 level 0.003

> surface dust #1 size 8.19

> surface dust #2 size 8.19

> ui tool show "Fit in Map"

> fitmap #1 inMap #2

Fit map run_class001.mrc in map run_class001.mrc using 458548 points  
correlation = 0.8495, correlation about mean = 0.6746, overlap = 15.99  
steps = 120, shift = 0.599, angle = 2.51 degrees  
  
Position of run_class001.mrc (#1) relative to run_class001.mrc (#2)
coordinates:  
Matrix rotation and translation  
0.99907524 -0.03768939 -0.02069262 11.68793642  
0.03751997 0.99925959 -0.00851595 -6.19381869  
0.02099826 0.00773169 0.99974962 -5.75829310  
Axis 0.18565936 -0.47639518 0.85940575  
Axis point 168.91824603 305.12031410 0.00000000  
Rotation angle (degrees) 2.50786955  
Shift along axis 0.17196998  
  

> volume #2 level 0.002

> open
> /archive/processing/disha/20240617_disha_mouse_female_wildtype_80s/relion/Refine3D/3d_ref_unsharp5/run_class001.mrc

Opened run_class001.mrc as #3, grid size 480,480,480, pixel 0.824, shown at
level 0.00773, step 2, values float32  

> hide #!1 models

> hide #!2 models

> volume #3 level 0.005

> volume #3 level 0.003

> show #!1 models

> fitmap #1 inMap #3

Fit map run_class001.mrc in map run_class001.mrc using 458548 points  
correlation = 0.919, correlation about mean = 0.6079, overlap = 19.19  
steps = 152, shift = 11.8, angle = 3.78 degrees  
  
Position of run_class001.mrc (#1) relative to run_class001.mrc (#3)
coordinates:  
Matrix rotation and translation  
0.99831047 -0.04679691 0.03444210 2.33113242  
0.04827196 0.99789439 -0.04331984 -4.24750562  
-0.03234234 0.04490924 0.99846739 8.24160489  
Axis 0.60478244 0.45778623 0.65166707  
Axis point 133.09182146 -17.49165942 0.00000000  
Rotation angle (degrees) 4.18303082  
Shift along axis 4.83616089  
  

> select add #3

2 models selected  

> transparency sel 50

> select clear

> show #!2 models

> fitmap #2 inMap #3

Fit map run_class001.mrc in map run_class001.mrc using 585511 points  
correlation = 0.876, correlation about mean = 0.5807, overlap = 19.09  
steps = 156, shift = 11.8, angle = 3.75 degrees  
  
Position of run_class001.mrc (#2) relative to run_class001.mrc (#3)
coordinates:  
Matrix rotation and translation  
0.99843017 -0.01180669 0.05475217 -8.64972925  
0.01364296 0.99935274 -0.03328619 0.85201884  
-0.05432373 0.03398091 0.99794500 14.96088689  
Axis 0.51485472 0.83485446 0.19478873  
Axis point 272.39365068 0.00000000 158.00523650  
Rotation angle (degrees) 3.74558821  
Shift along axis -0.82783002  
  

> hide #!2 models

> close session

> open
> /archive/processing/disha/20230211_female_wildtype_rps9/relion/Refine3D/3d_ref_shiny_combined_again3/run_class001.mrc

Opened run_class001.mrc as #1, grid size 480,480,480, pixel 0.819, shown at
level 0.00495, step 2, values float32  

> volume #1 level 0.001594

> surface dust #1 size 8.19

> close session

> open
> /yonath_group/miriam/Mouse_Liver/models/rps9_mwt_class3_blush_real_space_refined_014_MW_10_15_24.cif


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 550.90.07
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=plasmax11
XDG_SESSION_DESKTOP=plasmax11
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:1
Manufacturer: ASUS
Model: System Product Name
OS: Rocky Linux 9.4 Blue Onyx
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 AMD Ryzen 9 5900X 12-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi        31Gi        24Gi       959Mi       8.1Gi        30Gi
	Swap:           31Gi       7.3Gi        24Gi

Graphics:
	05:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:12a0]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (3)

comment:1 by Eric Pettersen, 13 months ago

Component: Unassigned → Input/Output
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash opening .cif file

Reported by Disha Hiregange

comment:2 by Greg Couch, 13 months ago

Status: assigned → feedback

Can you share with me the CIF file that caused the probem? If you need to keep it private, email it to me directly at gregc@…. There is also a chance that this was fixed in the 1.8 release.

comment:3 by Greg Couch, 5 months ago

Resolution: → worksforme
Status: feedback → closed

No response. Likely fixed, but not possible to tell without original mmCIF data file.

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