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Opened 11 months ago
Closed 9 months ago
#16334 closed defect (duplicate)
DICOM: index is out of bounds
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | DICOM | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
warning | QMainWidget::resizeDocks: all sizes need to be larger than 0
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\Users\parv553\OneDrive - PNNL\Lab_work\Images\Krios-Screening-
> Images\2023\04-19-23-RCG-
> Tomograms\RCG_SIRT_CTF_Au_corrected_bin8\TS_A_02\Visualize_09-19_24\Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
> format mrc
Opened Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #1, grid
size 200,200,180, pixel 8.9,8.9,8.9, shown at level 0.147, step 1, values
float32
> ui tool show "Segment Map"
> surface dust #1 size 300
> volume #1 level -0.05319
> ui tool show Segmentations
> ui view fourup
> segmentations mouseModes false
Mouse bindings not saved; ignoring 'mouseModes false'
> ui view fourup
> ui view fourup guidelines true
> segmentations create #1
Opened segmentation 1 of
Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #5, grid size
200,200,180, pixel 8.9,8.9,8.9, shown at level 0.501, step 1, values float64
> close #5
> segmentations create #1
Opened segmentation 1 of
Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #5, grid size
200,200,180, pixel 8.9,8.9,8.9, shown at level 0.501, step 1, values float64
> close #5
> segmentations create #1
Opened segmentation 1 of
Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #5, grid size
200,200,180, pixel 8.9,8.9,8.9, shown at level 0.501, step 1, values float64
> segmentations create #1
Opened segmentation 2 of
Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #6, grid size
200,200,180, pixel 8.9,8.9,8.9, shown at level 0.501, step 1, values float64
> close #5
> close #6
> segmentations create #1
Opened segmentation 1 of
Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #5, grid size
200,200,180, pixel 8.9,8.9,8.9, shown at level 0.501, step 1, values float64
> segmentations mouseModes false
Mouse bindings not saved; ignoring 'mouseModes false'
> ui view overunder
> ui view overunder guidelines false
> segmentations mouseModes false
Mouse bindings not saved; ignoring 'mouseModes false'
> ui view sidebyside
> ui view sidebyside guidelines true
> ui view default
[Repeated 1 time(s)]
> vr false
> segmentations mouseModes false
Mouse bindings not saved; ignoring 'mouseModes false'
> ui view fourup
> ui view fourup guidelines true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 988, in
mouseReleaseEvent
self.segmentation_tool.addMarkersToSegment(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 845, in
addMarkersToSegment
self.setMarkerRegionsToValue(axis, slice, markers, 1)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 842, in
setMarkerRegionsToValue
self.segmentation_tracker.active_segmentation.segment(segmentation_strategy)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 53, in segment
strategy.execute(self.data, self.reference_volume.data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 30, in execute
self._set_data_in_puck(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 200 is out of bounds for axis 0 with size 200
IndexError: index 200 is out of bounds for axis 0 with size 200
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 988, in
mouseReleaseEvent
self.segmentation_tool.addMarkersToSegment(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 845, in
addMarkersToSegment
self.setMarkerRegionsToValue(axis, slice, markers, 1)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 842, in
setMarkerRegionsToValue
self.segmentation_tracker.active_segmentation.segment(segmentation_strategy)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 53, in segment
strategy.execute(self.data, self.reference_volume.data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 30, in execute
self._set_data_in_puck(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 200 is out of bounds for axis 0 with size 200
IndexError: index 200 is out of bounds for axis 0 with size 200
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 988, in
mouseReleaseEvent
self.segmentation_tool.addMarkersToSegment(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 845, in
addMarkersToSegment
self.setMarkerRegionsToValue(axis, slice, markers, 1)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 842, in
setMarkerRegionsToValue
self.segmentation_tracker.active_segmentation.segment(segmentation_strategy)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 53, in segment
strategy.execute(self.data, self.reference_volume.data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 30, in execute
self._set_data_in_puck(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 200 is out of bounds for axis 0 with size 200
IndexError: index 200 is out of bounds for axis 0 with size 200
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 988, in
mouseReleaseEvent
self.segmentation_tool.addMarkersToSegment(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 845, in
addMarkersToSegment
self.setMarkerRegionsToValue(axis, slice, markers, 1)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 842, in
setMarkerRegionsToValue
self.segmentation_tracker.active_segmentation.segment(segmentation_strategy)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 53, in segment
strategy.execute(self.data, self.reference_volume.data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 30, in execute
self._set_data_in_puck(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 200 is out of bounds for axis 0 with size 200
IndexError: index 200 is out of bounds for axis 0 with size 200
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 988, in
mouseReleaseEvent
self.segmentation_tool.addMarkersToSegment(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 845, in
addMarkersToSegment
self.setMarkerRegionsToValue(axis, slice, markers, 1)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 842, in
setMarkerRegionsToValue
self.segmentation_tracker.active_segmentation.segment(segmentation_strategy)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 53, in segment
strategy.execute(self.data, self.reference_volume.data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 30, in execute
self._set_data_in_puck(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 200 is out of bounds for axis 0 with size 200
IndexError: index 200 is out of bounds for axis 0 with size 200
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 988, in
mouseReleaseEvent
self.segmentation_tool.addMarkersToSegment(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 845, in
addMarkersToSegment
self.setMarkerRegionsToValue(axis, slice, markers, 1)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 842, in
setMarkerRegionsToValue
self.segmentation_tracker.active_segmentation.segment(segmentation_strategy)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 53, in segment
strategy.execute(self.data, self.reference_volume.data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 30, in execute
self._set_data_in_puck(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 200 is out of bounds for axis 0 with size 200
IndexError: index 200 is out of bounds for axis 0 with size 200
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 988, in
mouseReleaseEvent
self.segmentation_tool.addMarkersToSegment(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 845, in
addMarkersToSegment
self.setMarkerRegionsToValue(axis, slice, markers, 1)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 842, in
setMarkerRegionsToValue
self.segmentation_tracker.active_segmentation.segment(segmentation_strategy)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 53, in segment
strategy.execute(self.data, self.reference_volume.data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 30, in execute
self._set_data_in_puck(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 200 is out of bounds for axis 0 with size 200
IndexError: index 200 is out of bounds for axis 0 with size 200
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 988, in
mouseReleaseEvent
self.segmentation_tool.addMarkersToSegment(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 845, in
addMarkersToSegment
self.setMarkerRegionsToValue(axis, slice, markers, 1)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 842, in
setMarkerRegionsToValue
self.segmentation_tracker.active_segmentation.segment(segmentation_strategy)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 53, in segment
strategy.execute(self.data, self.reference_volume.data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 30, in execute
self._set_data_in_puck(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 200 is out of bounds for axis 0 with size 200
IndexError: index 200 is out of bounds for axis 0 with size 200
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 988, in
mouseReleaseEvent
self.segmentation_tool.addMarkersToSegment(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 845, in
addMarkersToSegment
self.setMarkerRegionsToValue(axis, slice, markers, 1)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 842, in
setMarkerRegionsToValue
self.segmentation_tracker.active_segmentation.segment(segmentation_strategy)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 53, in segment
strategy.execute(self.data, self.reference_volume.data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 30, in execute
self._set_data_in_puck(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 200 is out of bounds for axis 0 with size 200
IndexError: index 200 is out of bounds for axis 0 with size 200
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 988, in
mouseReleaseEvent
self.segmentation_tool.addMarkersToSegment(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 845, in
addMarkersToSegment
self.setMarkerRegionsToValue(axis, slice, markers, 1)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 842, in
setMarkerRegionsToValue
self.segmentation_tracker.active_segmentation.segment(segmentation_strategy)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 53, in segment
strategy.execute(self.data, self.reference_volume.data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 30, in execute
self._set_data_in_puck(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 200 is out of bounds for axis 0 with size 200
IndexError: index 200 is out of bounds for axis 0 with size 200
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 988, in
mouseReleaseEvent
self.segmentation_tool.addMarkersToSegment(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 845, in
addMarkersToSegment
self.setMarkerRegionsToValue(axis, slice, markers, 1)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 842, in
setMarkerRegionsToValue
self.segmentation_tracker.active_segmentation.segment(segmentation_strategy)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 53, in segment
strategy.execute(self.data, self.reference_volume.data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 30, in execute
self._set_data_in_puck(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 200 is out of bounds for axis 0 with size 200
IndexError: index 200 is out of bounds for axis 0 with size 200
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> close #5
> segmentations create #1
Opened segmentation 1 of
Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #5, grid size
200,200,180, pixel 8.9,8.9,8.9, shown at level 0.501, step 1, values float64
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 988, in
mouseReleaseEvent
self.segmentation_tool.addMarkersToSegment(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 845, in
addMarkersToSegment
self.setMarkerRegionsToValue(axis, slice, markers, 1)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 842, in
setMarkerRegionsToValue
self.segmentation_tracker.active_segmentation.segment(segmentation_strategy)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 53, in segment
strategy.execute(self.data, self.reference_volume.data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 30, in execute
self._set_data_in_puck(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 200 is out of bounds for axis 0 with size 200
IndexError: index 200 is out of bounds for axis 0 with size 200
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> close #5
No segmentations to remove.
> segmentations create #1
Opened segmentation 1 of
Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #5, grid size
200,200,180, pixel 8.9,8.9,8.9, shown at level 0.501, step 1, values float64
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 988, in
mouseReleaseEvent
self.segmentation_tool.addMarkersToSegment(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 845, in
addMarkersToSegment
self.setMarkerRegionsToValue(axis, slice, markers, 1)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 842, in
setMarkerRegionsToValue
self.segmentation_tracker.active_segmentation.segment(segmentation_strategy)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 53, in segment
strategy.execute(self.data, self.reference_volume.data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 30, in execute
self._set_data_in_puck(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 200 is out of bounds for axis 0 with size 200
IndexError: index 200 is out of bounds for axis 0 with size 200
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 988, in
mouseReleaseEvent
self.segmentation_tool.addMarkersToSegment(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 845, in
addMarkersToSegment
self.setMarkerRegionsToValue(axis, slice, markers, 1)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 842, in
setMarkerRegionsToValue
self.segmentation_tracker.active_segmentation.segment(segmentation_strategy)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 53, in segment
strategy.execute(self.data, self.reference_volume.data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 30, in execute
self._set_data_in_puck(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 200 is out of bounds for axis 0 with size 200
IndexError: index 200 is out of bounds for axis 0 with size 200
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> close #5
> ui view fourup guidelines false
> ui view fourup guidelines true
No segmentations to remove.
[Repeated 4 time(s)]
> show #4 models
No segmentations to remove.
> hide #4 models
> segmentations create #1
Opened segmentation 1 of
Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #5, grid size
200,200,180, pixel 8.9,8.9,8.9, shown at level 0.501, step 1, values float64
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 988, in
mouseReleaseEvent
self.segmentation_tool.addMarkersToSegment(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 845, in
addMarkersToSegment
self.setMarkerRegionsToValue(axis, slice, markers, 1)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 842, in
setMarkerRegionsToValue
self.segmentation_tracker.active_segmentation.segment(segmentation_strategy)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 53, in segment
strategy.execute(self.data, self.reference_volume.data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 30, in execute
self._set_data_in_puck(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 200 is out of bounds for axis 0 with size 200
IndexError: index 200 is out of bounds for axis 0 with size 200
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 988, in
mouseReleaseEvent
self.segmentation_tool.addMarkersToSegment(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 845, in
addMarkersToSegment
self.setMarkerRegionsToValue(axis, slice, markers, 1)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\segmentations.py", line 842, in
setMarkerRegionsToValue
self.segmentation_tracker.active_segmentation.segment(segmentation_strategy)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\segmentation.py", line 53, in segment
strategy.execute(self.data, self.reference_volume.data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 30, in execute
self._set_data_in_puck(
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
IndexError: index 200 is out of bounds for axis 0 with size 200
IndexError: index 200 is out of bounds for axis 0 with size 200
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\dicom_segmentations.py", line 158, in
_set_data_in_puck
reference_slice[y_start + 1, x_start:x_end] <= max_threshold, 1, 0
~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> close #5
> close
> segmentations mouseModes false
Mouse bindings not saved; ignoring 'mouseModes false'
> open "C:\Users\parv553\OneDrive - PNNL\Lab_work\Images\Krios-Screening-
> Images\2023\04-19-23-RCG-
> Tomograms\RCG_SIRT_CTF_Au_corrected_bin8\TS_A_02\Visualize_09-19_24\Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
> format mrc
Opened Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #1, grid
size 200,200,180, pixel 8.9,8.9,8.9, shown at level 0.147, step 1, values
float32
> volume #1 level -0.03543
> surface dust #1 size 300
> surface dust #1 size 500
> ui tool show Segmentations
> ui view fourup
> segmentations mouseModes false
Mouse bindings not saved; ignoring 'mouseModes false'
> ui view fourup
> segmentations create #1
Opened segmentation 1 of
Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #5, grid size
200,200,180, pixel 8.9,8.9,8.9, shown at level 0.501, step 1, values float64
> segmentations create #1
Opened segmentation 2 of
Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #6, grid size
200,200,180, pixel 8.9,8.9,8.9, shown at level 0.501, step 1, values float64
> ui view fourup guidelines true
> segmentations mouseModes false
Mouse bindings not saved; ignoring 'mouseModes false'
> close #6
> close #5
> close #
Expected a models specifier or a keyword
> close #
Expected a models specifier or a keyword
close #
......^
Expected a models specifier or a keyword
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\logging.py", line 40, in
log_equivalent_command
command.run(command_text, log_only=True)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3175, in run
raise UserError(self._error)
chimerax.core.errors.UserError: Expected a models specifier or a keyword
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\volume_viewer.py", line 2138, in close_map_cb
log_equivalent_command(v.session, 'close #%s' % v.id_string)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\logging.py", line 42, in
log_equivalent_command
session.logger.info(str(err))
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'logger'
AttributeError: 'NoneType' object has no attribute 'logger'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\logging.py", line 42, in
log_equivalent_command
session.logger.info(str(err))
^^^^^^^^^^^^^^
See log for complete Python traceback.
> close
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\view\cmd.py", line 67, in <lambda>
REMOVE_MODELS, lambda *args, ses=session: _check_rapid_access(ses, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\view\cmd.py", line 55, in _check_rapid_access
session.ui.main_window.restore_default_main_view()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\ui\gui.py",
line 649, in restore_default_main_view
self.main_view.clean_up()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\view\ui.py", line 193, in clean_up
orthoplane.close()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 637, in close
self.view.drawing.delete()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1912, in delete
Image3d.delete(self)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\image3d.py", line 752, in delete
b.remove_image(self)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\image3d.py", line 1517, in remove_image
del dbi[image_render]
~~~^^^^^^^^^^^^^^
KeyError: <chimerax.map.volume.VolumeImage object at 0x000001D0ADFE8E50>
Error processing trigger "remove models":
KeyError:
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\image3d.py", line 1517, in remove_image
del dbi[image_render]
~~~^^^^^^^^^^^^^^
See log for complete Python traceback.
> open "C:\Users\parv553\OneDrive - PNNL\Lab_work\Images\Krios-Screening-
> Images\2023\04-19-23-RCG-
> Tomograms\RCG_SIRT_CTF_Au_corrected_bin8\TS_A_02\Visualize_09-19_24\Clip1_1_1.2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.cxs"
> format session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\view\cmd.py", line 67, in <lambda>
REMOVE_MODELS, lambda *args, ses=session: _check_rapid_access(ses, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\view\cmd.py", line 55, in _check_rapid_access
session.ui.main_window.restore_default_main_view()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\ui\gui.py",
line 649, in restore_default_main_view
self.main_view.clean_up()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\view\ui.py", line 193, in clean_up
orthoplane.close()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 627, in close
self.label.delete()
^^^^^^^^^^
AttributeError: 'PlaneViewer' object has no attribute 'label'
Error processing trigger "remove models":
AttributeError: 'PlaneViewer' object has no attribute 'label'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 627, in close
self.label.delete()
^^^^^^^^^^
See log for complete Python traceback.
Opened Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #1, grid
size 200,200,180, pixel 8.9,8.9,8.9, shown at level -0.057, step 1, values
float32
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 500, in
_background_color_changed
label.update_drawing()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 608, in update_drawing
d.needs_update = True
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'needs_update'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'needs_update'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 608, in update_drawing
d.needs_update = True
^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 500, in
_background_color_changed
label.update_drawing()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 608, in update_drawing
d.needs_update = True
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'needs_update'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'needs_update'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 608, in update_drawing
d.needs_update = True
^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 500, in
_background_color_changed
label.update_drawing()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 608, in update_drawing
d.needs_update = True
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'needs_update'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'needs_update'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 608, in update_drawing
d.needs_update = True
^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 500, in
_background_color_changed
label.update_drawing()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 608, in update_drawing
d.needs_update = True
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'needs_update'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'needs_update'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 608, in update_drawing
d.needs_update = True
^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 500, in
_background_color_changed
label.update_drawing()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 608, in update_drawing
d.needs_update = True
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'needs_update'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'needs_update'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 608, in update_drawing
d.needs_update = True
^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 500, in
_background_color_changed
label.update_drawing()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 608, in update_drawing
d.needs_update = True
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'needs_update'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'needs_update'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 608, in update_drawing
d.needs_update = True
^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 500, in
_background_color_changed
label.update_drawing()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 608, in update_drawing
d.needs_update = True
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'needs_update'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'needs_update'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 608, in update_drawing
d.needs_update = True
^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 500, in
_background_color_changed
label.update_drawing()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 608, in update_drawing
d.needs_update = True
^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'needs_update'
Error processing trigger "setting changed":
AttributeError: 'NoneType' object has no attribute 'needs_update'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\label.py", line 608, in update_drawing
d.needs_update = True
^^^^^^^^^^^^^^
See log for complete Python traceback.
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 757, in restore
obj = sm.restore_snapshot(self, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 574, in restore_snapshot
m.set_state_from_snapshot(session, data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 397, in set_state_from_snapshot
p.add([self])
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 314, in add
om.add(models, parent = self)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 756, in add
p = self._parent_for_added_model(model, parent, root_model = root_model)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 825, in _parent_for_added_model
raise ValueError('Tried to add model %s with the same id as another model %s'
ValueError: Tried to add model 15471 #2.1 with the same id as another model
15470 #2.1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 757, in restore
obj = sm.restore_snapshot(self, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 574, in restore_snapshot
m.set_state_from_snapshot(session, data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 397, in set_state_from_snapshot
p.add([self])
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 314, in add
om.add(models, parent = self)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 756, in add
p = self._parent_for_added_model(model, parent, root_model = root_model)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 825, in _parent_for_added_model
raise ValueError('Tried to add model %s with the same id as another model %s'
ValueError: Tried to add model 15471 #2.1 with the same id as another model
15470 #2.1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\view\cmd.py", line 67, in <lambda>
REMOVE_MODELS, lambda *args, ses=session: _check_rapid_access(ses, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\view\cmd.py", line 55, in _check_rapid_access
session.ui.main_window.restore_default_main_view()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\ui\gui.py",
line 649, in restore_default_main_view
self.main_view.clean_up()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\view\ui.py", line 193, in clean_up
orthoplane.close()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 627, in close
self.label.delete()
^^^^^^^^^^
AttributeError: 'PlaneViewer' object has no attribute 'label'
Error processing trigger "remove models":
AttributeError: 'PlaneViewer' object has no attribute 'label'
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 627, in close
self.label.delete()
^^^^^^^^^^
See log for complete Python traceback.
Log from Mon Nov 18 17:12:40 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.cxs"
Opened Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #1, grid
size 100,100,100, pixel 8.9, shown at level 0.176, step 1, values float32
Log from Wed Oct 30 16:36:58 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip4_2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.cxs"
Opened Clip1_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #1, grid
size 100,140,100, pixel 8.9,8.9,8.9, shown at level 0.22, step 1, values
float32
Opened Clip4_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #2, grid
size 160,140,80, pixel 8.9, shown at level 0.344, step 1, values float32
Opened Clip3_2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #3, grid
size 70,100,100, pixel 8.9,8.9,8.9, shown at level 0.367, step 1, values
float32
Opened Clip4_2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #4, grid
size 250,250,100, pixel 8.9,8.9,8.9, shown at level 0.305, step 1, values
float32
Log from Wed Oct 30 16:03:38 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp35_inv.mrc"
Opened Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp35_inv.mrc as #1, grid
size 200,200,180, pixel 8.9,8.9,8.9, shown at level 0.135, step 1, values
float32
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc"
Opened Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc as #2, grid
size 200,200,180, pixel 8.9,8.9,8.9, shown at level 0.18, step 1, values
float32
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #3, grid
size 200,200,180, pixel 8.9,8.9,8.9, shown at level 0.147, step 1, values
float32
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp30_inv.mrc"
Opened Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp30_inv.mrc as #4, grid
size 200,200,180, pixel 8.9,8.9,8.9, shown at level 0.14, step 1, values
float32
> surface dust #2 size 20
> surface dust #2 size 40
> volume #2 level 0.1
> volume #2 level 0.13
> surface dust #2 size 80
> surface dust #2 size 200
> surface dust #2 size 150
> volume #3 level -0.01513
> surface dust #3 size 150
> ui tool show "Segment Map"
> close #1
> close #2
> close #4
> set bgColor white
> lighting soft
> set bgColor gray
> volume showOutlineBox true
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #3 style surface
> surface dust #3 size 150
> volume #3 region 24,0,0,199,199,179
> volume #3 region 41,0,0,199,199,179
> volume #3 region 41,0,0,134,199,179
> volume #3 region 41,0,0,134,190,179
> volume #3 region 41,0,66,134,190,179
> volume #3 region 41,0,66,145,190,179
> volume showOutlineBox false
> volume #3 change image level -0.705,0 level 0.1469,0.8 level 1.338,1
> volume #3 level -0.04061
> volume showOutlineBox true
> volume #3 region 41,0,53,145,190,179
> volume #3 region 41,0,53,145,190,136
> volume showOutlineBox false
Segmenting Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc, density
threshold -0.040606
Only showing 60 of 1028 regions.
Showing 60 of 1028 region surfaces
8789 watershed regions, grouped to 1028 regions
Showing Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.seg - 1028
regions, 60 surfaces
> select #1.51
1 model selected
> select #1.31
1 model selected
> select #1.59
1 model selected
> select add #1.31
2 models selected
> select add #1.36
3 models selected
> select add #1.38
4 models selected
> select add #1.53
5 models selected
> select add #1.48
6 models selected
> select add #1.22
7 models selected
> select add #1.43
8 models selected
> select add #1.42
9 models selected
> select add #1.47
10 models selected
> select add #1.39
11 models selected
Deleted 11 regions
> select add #1.51
1 model selected
> select add #1.54
2 models selected
> select add #1.24
3 models selected
> select add #1.50
4 models selected
> select add #1.17
5 models selected
> select add #1.40
6 models selected
> select add #1.23
7 models selected
> select add #1.57
8 models selected
> select add #1.49
9 models selected
> select add #1.33
10 models selected
> select add #1.37
11 models selected
> select add #1.27
12 models selected
Deleted 12 regions
> select add #1.46
1 model selected
> select add #1.32
2 models selected
> select add #1.25
3 models selected
> select add #1.26
4 models selected
> select add #1.19
5 models selected
Deleted 5 regions
> select add #1.45
1 model selected
Deleted 1 regions
> select #1.8
1 model selected
Segmenting Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc, density
threshold -0.040606
Only showing 90 of 1028 regions.
Showing 90 of 1028 region surfaces
8789 watershed regions, grouped to 1028 regions
Showing Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.seg - 1028
regions, 90 surfaces
Drag select of 11725, 7285 of 9148 triangles, 11439, 86 of 8036 triangles,
11778, 12275, 1713 of 7596 triangles, 12317, 4654 of 5804 triangles, 12318,
6383 of 6384 triangles, 11350, 2046 of 4368 triangles, 10128, 10213, 910 of
4696 triangles, 11403, 3717 of 5472 triangles, 12539, 11323, 8879, 11885,
11580, 10869, 12458, 1791 of 2344 triangles, 10699, 12366, 12420, 2696 of 3100
triangles, 12487, 12261, 12117, 11034
Deleted 24 regions
> select #1.59
1 model selected
> select #1.89
1 model selected
> select add #1.59
2 models selected
> select add #1.32
3 models selected
> select add #1.43
4 models selected
> select add #1.82
5 models selected
Deleted 5 regions
Drag select of 12018, 506 of 22424 triangles, 12307, 3067 of 24128 triangles,
11781, 7765 of 17392 triangles, 12536, 8543 of 14756 triangles, 12233, 11557,
12541, 10473, 10316, 782 of 5952 triangles, 11370, 2564 of 5824 triangles,
11641, 13 of 5552 triangles, 11361, 3412 of 3964 triangles, 10393, 12526, 4504
of 4660 triangles, 12038, 10383, 3848 of 4064 triangles, 10139, 1755 of 3784
triangles, 10159, 2319 of 3216 triangles, 12197, 12429, 4877 of 5028
triangles, 10419, 10282, 12209, 9086, 11723, 12380, 12333, 2877 of 3692
triangles, 12562, 266 of 3396 triangles, 11379, 12200, 12277
> select #1.41
1 model selected
> select #1.51
1 model selected
> select add #1.37
2 models selected
> select add #1.62
3 models selected
> select add #1.64
4 models selected
> select add #1.74
5 models selected
> select add #1.79
6 models selected
> select add #1.84
7 models selected
> select add #1.80
8 models selected
> select add #1.27
9 models selected
> select add #1.83
10 models selected
> select add #1.77
11 models selected
> select add #1.75
12 models selected
> select add #1.24
13 models selected
> select add #1.54
14 models selected
> select add #1.69
15 models selected
> select add #1.50
16 models selected
> select add #1.76
17 models selected
> select add #1.88
18 models selected
Deleted 18 regions
> select #1.90
1 model selected
> select add #1.85
2 models selected
> select add #1.60
3 models selected
> select subtract #1.60
2 models selected
> select add #1.65
3 models selected
Deleted 3 regions
> select #1.33
1 model selected
> select add #1.25
2 models selected
> select add #1.26
3 models selected
> select add #1.19
4 models selected
> select add #1.72
5 models selected
Deleted 5 regions
> select #1.49
1 model selected
> select #1.45
1 model selected
> select add #1.49
2 models selected
Deleted 2 regions
> select #1.46
1 model selected
Deleted 1 regions
> select #1.8
1 model selected
Ungrouped to 2 regions
> select clear
> select #1.55
1 model selected
> select add #1.34
2 models selected
> select add #1.58
3 models selected
> select add #1.60
4 models selected
> select add #1.56
5 models selected
> select add #1.30
6 models selected
> select add #1.29
7 models selected
> select clear
> select #1.29
1 model selected
Ungrouped to 3 regions
> select clear
> select #1.22
1 model selected
Deleted 1 regions
> select #1.8
1 model selected
> select #1.23
1 model selected
> select add #1.8
2 models selected
Ungrouped to 21 regions
Grouped 21 regions
> select #1.8
1 model selected
Deleted 1 regions
> select add #1.22
1 model selected
> select add #1.30
2 models selected
> select add #1.60
3 models selected
> select add #1.56
4 models selected
> select add #1.58
5 models selected
> select add #1.55
6 models selected
> select add #1.61
7 models selected
Drag select of 12018, 43 of 22424 triangles, 12493, 653 of 20372 triangles,
11784, 88 of 17492 triangles, 12494, 82 of 9476 triangles, 10383, 7 of 4064
triangles, 10142, 81 of 2688 triangles
> select clear
> select add #1.58
1 model selected
> select clear
> select #1.61
1 model selected
Deleted 1 regions
> select #1.55
1 model selected
> select add #1.58
2 models selected
> select add #1.60
3 models selected
> select add #1.30
4 models selected
> select add #1.22
5 models selected
> select add #1.56
6 models selected
> select add #1.17
7 models selected
> select add #1.41
8 models selected
Grouped 8 regions
> select clear
Drag select of 12308, 12018, 12307, 12493, 12016, 11784, 11781, 11365, 12047,
12492, 12494, 12015, 10721, 12490, 12017, 12337, 10030, 10149, 11981, 10415,
10003, 10115, 10810, 11483, 12610
> select subtract #1.8
24 models selected
Grouped 24 regions
> select clear
> save "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.cxs"
> select #1.8
1 model selected
> color #1 #55ffffff
> color #1 #78ff30ff
> select add #1
3 models selected
> color #1 #46ffd1ff
> undo
> redo
> undo
[Repeated 3 time(s)]
> ui tool show "Color Actions"
QWindowsWindow::setGeometry: Unable to set geometry 633x1298+2085+930 (frame:
665x1386+2069+858) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 617x1249+2093+971 (frame:
649x1337+2077+899) margins: 16, 72, 16, 16 minimum size: 253x519 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=1310750, y=1310806), mintrack=POINT(x=665, y=1386)))
> color sel cyan
> select #1.1
1 model selected
> color sel yellow
No visible atoms or bonds selected
> select #1.1
1 model selected
No visible atoms or bonds selected
[Repeated 11 time(s)]
> select subtract #1
Nothing selected
> select add #1
3 models selected
> select subtract #1
Nothing selected
> select add #1
3 models selected
> select clear
> select #1.1
1 model selected
> color sel lime target s
> color sel yellow target s
No visible atoms or bonds selected
> color sel light yellow target s
> color sel light goldenrod yellow target s
> color sel khaki target s
> color sel tan target s
> color sel gold target s
> color sel yellow target s
> ui tool show "Surface Color"
> color #1 #55ffe5ff
> color #1 #47fff0ff
> undo
[Repeated 1 time(s)]
> select clear
> select #1.8
1 model selected
> color #1 #5afff4ff
> select add #1
3 models selected
> select subtract #1
Nothing selected
> select add #1
3 models selected
> undo
[Repeated 3 time(s)]
> select clear
> save "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.cxs"
> select #1.1
1 model selected
> color #1 #ff55ffff
> undo
> select clear
> close #1
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp30_inv.mrc"
Opened Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp30_inv.mrc as #1, grid
size 100,100,100, pixel 8.9, shown at level 0.399, step 1, values float32
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc"
Opened Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc as #2, grid
size 100,100,100, pixel 8.9, shown at level 0.447, step 1, values float32
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #4, grid
size 100,100,100, pixel 8.9, shown at level 0.412, step 1, values float32
> view orient
> volume #3 level -0.07737
> close #3
> volume #4 level 0.02186
> view orient
> volume #4 level 0.1758
> surface dust #4 size 150
> surface dust #4 size 100
> volume #4 level 0.1593
> surface dust #4 size 100
[Repeated 1 time(s)]
> surface dust #4 size 120
> surface dust #4 size 140
> surface dust #4 size 160
> surface dust #4 size 200
> volume #4 level 0.1868
Segmenting Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc, density
threshold 0.186817
Showing 48 region surfaces
785 watershed regions, grouped to 48 regions
Showing Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.seg - 48
regions, 48 surfaces
Drag select of 934, 2989 of 5756 triangles, 943, 896 of 4980 triangles, 961,
139 of 4408 triangles, 889, 87 of 2736 triangles, 898, 890, 1342 of 2948
triangles, 883, 55 of 2304 triangles, 905, 966, 257 of 352 triangles, 784, 4
Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc
> select #3.8
1 model selected
> select add #3.18
2 models selected
> select add #3.20
3 models selected
> select add #3.5
4 models selected
> select subtract #3.8
3 models selected
> select add #3.30
4 models selected
> select add #3.16
5 models selected
> select add #3.15
6 models selected
> select add #3.14
7 models selected
> select add #3.34
8 models selected
> select add #3.22
9 models selected
Deleted 9 regions
> select add #3.31
1 model selected
Deleted 1 regions
Drag select of 962, 968, 955, 9289 of 9412 triangles, 954, 953, 940, 952, 820,
286 of 2892 triangles, 967, 829, 932, 916, 2435 of 2828 triangles, 944, 1795
of 2600 triangles, 910, 3244 of 4260 triangles, 817, 7, 812, 963, 957, 850,
964, 914, 137 of 236 triangles, 599, 4
Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc
Deleted 23 regions
> select #3.36
1 model selected
> select #3.21
1 model selected
> select add #3.33
2 models selected
> select add #3.36
3 models selected
Deleted 3 regions
> select #3.24
1 model selected
> select add #3.6
2 models selected
> select add #3.9
3 models selected
> select add #3.23
4 models selected
> select add #3.4
5 models selected
> select add #3.7
6 models selected
Grouped 6 regions
> select clear
> select #3.8
1 model selected
> select #3.11
1 model selected
> select add #3.8
2 models selected
Grouped 2 regions
> select #3.1
1 model selected
> select #3.2
1 model selected
No visible atoms or bonds selected
> ui tool show "Color Actions"
> color sel cyan target s
> select #3.1
1 model selected
> color sel yellow target s
> select clear
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip1_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #5, grid
size 100,140,100, pixel 8.9,8.9,8.9, shown at level 0.429, step 1, values
float32
QWindowsWindow::setGeometry: Unable to set geometry 1920x1098+1917-1177
(frame: 1952x1186+1901-1249) on QWidgetWindow/"MainWindowClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1920x2745+1917-1177 (frame:
1952x2833+1901-1249) margins: 16, 72, 16, 16 minimum size: 592x1098
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=0, y=0), mintrack=POINT(x=1512, y=2833)))
> close #2
> close #1
> close #4
> close
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip1_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #1, grid
size 100,140,100, pixel 8.9,8.9,8.9, shown at level 0.429, step 1, values
float32
> volume #1 level 0.2201
> surface dust #1 size 200
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip4_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip4_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #2, grid
size 160,140,80, pixel 8.9, shown at level 0.344, step 1, values float32
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip3_2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip3_2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #3, grid
size 70,100,100, pixel 8.9,8.9,8.9, shown at level 0.367, step 1, values
float32
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip4_2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip4_2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #4, grid
size 250,250,100, pixel 8.9,8.9,8.9, shown at level 0.305, step 1, values
float32
> surface dust #4 size 200
Segmenting Clip4_2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc, density
threshold 0.304825
Showing 75 region surfaces
1310 watershed regions, grouped to 75 regions
Showing Clip4_2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.seg - 75 regions,
75 surfaces
Drag select of 1626, 1550, 1480, 1560, 1465, 725 of 2052 triangles, 1605,
1557, 1631, 232 of 688 triangles, 1544, 158
> select #5.29
1 model selected
Drag select of 1626, 1497, 39 of 3808 triangles, 1550, 1480, 1560, 1465, 956
of 2052 triangles, 1605, 1649 of 1676 triangles, 1557, 452 of 1132 triangles,
1544, 158
> select add #5.69
10 models selected
> select add #5.54
11 models selected
> select add #5.58
12 models selected
> select add #5.56
13 models selected
> select add #5.61
14 models selected
> select add #5.62
15 models selected
> select add #5.49
16 models selected
> select add #5.38
17 models selected
Deleted 17 regions
> select #5.29
1 model selected
> select #5.57
1 model selected
> select add #5.66
2 models selected
> select add #5.53
3 models selected
> select add #5.52
4 models selected
> select add #5.46
5 models selected
Drag select of 1624, 1599 of 9836 triangles, 1621, 900 of 5028 triangles,
1630, 3360 of 5084 triangles, 1405, 1440, 1767 of 3132 triangles, 1456, 236 of
2572 triangles, 1583, 1440 of 1992 triangles, 1431
> select add #5.26
14 models selected
> select add #5.43
15 models selected
> select add #5.36
16 models selected
> select add #5.51
17 models selected
Deleted 17 regions
> select #5.32
1 model selected
> select #5.34
1 model selected
> select add #5.28
2 models selected
> select add #5.45
3 models selected
> select add #5.59
4 models selected
> select add #5.50
5 models selected
Deleted 5 regions
> select #5.29
1 model selected
Deleted 1 regions
> select #5.32
1 model selected
> select #5.68
1 model selected
> select add #5.71
2 models selected
> select add #5.32
3 models selected
> select add #5.75
4 models selected
> select add #5.72
5 models selected
Deleted 5 regions
Drag select of 1384, 1568, 256
Deleted 3 regions
Drag select of 1616, 1609, 1629, 1622, 1628, 1625, 1614, 1608, 1627, 1615,
1618, 1540, 1549, 1623, 1610, 1619, 1592, 1599, 1579, 1590, 1632, 1565, 1537,
1589, 1577, 1315, 60
> select clear
> select #5.24
1 model selected
> select add #5.4
2 models selected
Ungrouped to 4 regions
Drag select of 1616, 1609, 1622, 1628, 1625, 1614, 1608, 1627, 1615, 1618,
1540, 1549, 1623, 1610, 1619, 1592, 1599, 1579, 1590, 1565, 1537, 1589, 1577,
1315, 60, 1572, 1613, 1591, 1312
> select subtract #5.26
28 models selected
> select subtract #5.2
27 models selected
> select subtract #5.25
26 models selected
> select subtract #5.20
25 models selected
Grouped 25 regions
> select #5.20
1 model selected
> select add #5.25
2 models selected
> select add #5.26
3 models selected
> select add #5.2
4 models selected
Grouped 4 regions
> select clear
> save "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip4_2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.cxs"
> select #5.2
1 model selected
> color #5.2 cyan
> select clear
> save "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip4_2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.cxs"
——— End of log from Wed Oct 30 16:03:38 2024 ———
opened ChimeraX session
Showing Clip4_2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.seg - 2 regions, 2
surfaces
> close #5
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #5, grid
size 200,200,180, pixel 8.9,8.9,8.9, shown at level 0.147, step 1, values
float32
> view orient
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> view orient
> close
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip4_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip4_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #1, grid
size 160,140,80, pixel 8.9, shown at level 0.344, step 1, values float32
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #2, grid
size 200,200,180, pixel 8.9,8.9,8.9, shown at level 0.147, step 1, values
float32
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #3, grid
size 100,100,100, pixel 8.9, shown at level 0.412, step 1, values float32
> close
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Clip1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc"
Opened Clip1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc as #1, grid
size 200,200,180, pixel 4,4,4, shown at level 0.18, step 1, values float32
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #2, grid
size 100,100,100, pixel 8.9, shown at level 0.412, step 1, values float32
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Clip1_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip1_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #3, grid
size 100,140,100, pixel 8.9,8.9,8.9, shown at level 0.429, step 1, values
float32
> close #3
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Clip1_3_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc"
Opened Clip1_3_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc as #3, grid
size 310,300,130, pixel 8.9, shown at level 0.309, step 1, values float32
> hide #!2 models
> hide #!1 models
> volume #3 level 0.1508
> close #3
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Clip2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc"
Opened Clip2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc as #3, grid
size 200,200,120, pixel 8.9,8.9,8.9, shown at level 0.384, step 1, values
float32
> volume #3 level 0.1727
> view orient
> surface dust #3 size 200
> close #3
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Clip2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc"
Opened Clip2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc as #3, grid size
540,740,180, pixel 4,4,4, shown at level 0.247, step 2, values float32
> surface dust #3 size 200
> volume #3 level -0.161
> volume #3 level -0.113
> view orient
> volume #3 level -0.1
> volume #3 level -0
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Clip2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc"
Opened Clip2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc as #4, grid
size 200,200,120, pixel 8.9,8.9,8.9, shown at level 0.384, step 1, values
float32
> hide #!4 models
Segmenting Clip2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc, density
threshold -0.000000
Only showing 90 of 7850 regions.
Showing 90 of 7850 region surfaces
243740 watershed regions, grouped to 7850 regions
Showing Clip2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.seg - 7850 regions,
90 surfaces
Segmenting Clip2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc, density
threshold -0.000000
Only showing 300 of 7850 regions.
Showing 300 of 7850 region surfaces
243740 watershed regions, grouped to 7850 regions
Showing Clip2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.seg - 7850 regions,
300 surfaces
Segmenting Clip2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc, density
threshold -0.000000
Only showing 500 of 7850 regions.
Showing 500 of 7850 region surfaces
243740 watershed regions, grouped to 7850 regions
Showing Clip2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.seg - 7850 regions,
500 surfaces
> close #4
Segmenting Clip2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc, density
threshold -0.000000
Only showing 500 of 7850 regions.
Showing 500 of 7850 region surfaces
243740 watershed regions, grouped to 7850 regions
Showing Clip2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.seg - 7850 regions,
500 surfaces
Segmenting Clip2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc, density
threshold -0.000000
Only showing 700 of 7850 regions.
Showing 700 of 7850 region surfaces
243740 watershed regions, grouped to 7850 regions
Showing Clip2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.seg - 7850 regions,
700 surfaces
> hide #!4 models
> show #!4 models
> view orient
Drag select of 328314, 329517, 673 of 60236 triangles, 328474, 30637 of 45332
triangles, 329990, 331157, 329721, 325585, 287583, 328025, 318387, 327994,
330473, 328840, 48214 of 49848 triangles, 318166, 329053, 324383, 331148,
328673, 327967, 328867, 330309, 328739, 3809 of 26672 triangles, 331275,
329851, 328854, 328384, 318382, 9919 of 18152 triangles, 328302, 329402,
327820, 331724, 15406 of 18596 triangles, 328844, 329642, 329099, 328204,
328353, 328638, 327727, 321087, 323793, 329309, 326849, 328210, 329732, 23884
of 26992 triangles, 331182, 322270, 321033, 326329, 328987, 330056, 328510,
327713, 328936, 328827, 329131, 328891, 331289, 327369, 317865, 329336,
327007, 317800, 327682, 330842, 328843, 322424, 323234, 331173, 317360,
326020, 329455, 331192, 327840, 39 of 20736 triangles, 329863, 322342, 328847,
4387 of 15752 triangles, 318886, 317099, 322440, 330204, 328461, 328235,
331178, 319630, 331314, 327182, 13905 of 18752 triangles, 318125, 293090,
317128, 9725 of 9932 triangles, 329725, 328579, 330605, 327715, 290533,
329162, 327823, 292217, 327096, 331598, 326474, 319424, 330154, 329852,
322411, 324800, 328140, 3167 of 19824 triangles, 331446, 15235 of 16432
triangles, 317227, 302905, 323316, 317870, 331621, 328320, 330945, 330987,
327329, 331663, 321551, 328561, 327503, 302545, 291435, 305423, 318116,
331679, 328047, 327722, 330414, 15988 of 19664 triangles, 331576, 318579,
331596, 305491, 296639, 325970, 328215, 329908, 317813, 310948, 330192,
307487, 330092, 328248, 329303, 329136, 287472, 9488 of 10108 triangles,
328034, 305056, 316435, 1143 of 16832 triangles, 303332, 4978 of 8784
triangles, 297782, 321077, 328878, 7641 of 9964 triangles, 322001, 291234,
329439, 20161 of 25568 triangles, 328429, 330383, 322644, 326876, 9313 of
10940 triangles, 320016, 6286 of 14384 triangles, 327548, 324030, 329727,
304380, 331593, 329156, 331282, 10659 of 16660 triangles, 320581, 311254,
328850, 320539, 323505, 306549, 329702, 328086, 329471, 307441, 319504,
322243, 316706, 318345, 293547, 330729, 959 of 11856 triangles, 331125,
325213, 326797, 311048, 324259, 325984, 330425, 325657, 326102, 230 of 10856
triangles, 289691, 307696, 322787, 331064, 327135, 294670, 327217, 3359 of
13848 triangles, 316239, 318101, 328164, 318408, 294231, 296276, 329407,
307504, 322716, 306750, 327745, 327251, 326212, 316606, 302318, 330486, 5430
of 11852 triangles, 329923, 318599, 290564, 290457, 2415 of 8420 triangles,
323710, 328653, 320661, 250026, 328492, 298876, 327772, 2809 of 15912
triangles, 318134, 15008 of 15112 triangles, 327748, 322955, 305608, 1859 of
7424 triangles, 330174, 327788, 331608, 298034, 331364, 291724, 328414,
329632, 6775 of 22784 triangles, 291984, 287573, 331186, 325208, 57 of 15428
triangles, 328007, 328409, 326754, 302760, 289979, 1037 of 9284 triangles,
329179, 310872, 1784 of 7324 triangles, 330563, 329197, 303658, 306904,
327077, 328090, 331528, 290821, 291157, 305392, 287767, 330775, 250024,
329368, 328157, 308275, 327213, 306185, 316449, 316831, 319548, 305847,
330368, 331416, 331352, 323488, 254499, 330623, 318063, 323736, 293130,
316648, 331506, 318065, 252572, 308841, 330492, 298000, 328669, 319975,
329350, 322206, 323198, 318561, 327615, 315721, 327091, 322596, 322771,
319712, 326148, 319906, 5353 of 5848 triangles, 328243, 321549, 329458,
289777, 331455, 327335, 322457, 326657, 325305, 331665, 327105, 297455,
311445, 329823, 320104, 4370 of 5972 triangles, 328387, 328599, 327639,
329505, 327839, 330915, 331565, 311424, 328789, 330556, 290836, 331095,
304094, 329341, 327752, 330319, 329364, 326607, 326111, 328100, 297712, 5957
of 7084 triangles, 328609, 325999, 298527, 327660, 324816, 329349, 326535,
250554, 292966, 322888, 287799, 329091, 298135, 331591, 327187, 317357,
300562, 320480, 322664, 249616, 329972, 309051, 329267, 328138, 303648,
323918, 328494, 321377, 5262 of 5896 triangles, 323375, 317540, 327193,
330754, 322922, 304063, 306461, 325404, 328801, 313044, 327068, 327651,
331702, 318283, 321735, 296165, 330343, 329413, 300835, 296943, 306002,
307924, 327822, 6696 of 6764 triangles, 322446, 322753, 329618, 305798,
329106, 262433, 329371, 322356, 48 of 4740 triangles, 322820, 321168, 319563,
327636, 325048, 294908, 307520, 331040, 318839, 331472, 289921, 302705,
318851, 328633, 328198, 321602, 312769, 328101, 294909, 328824, 326622,
323706, 331163, 330911, 297143, 308213, 317573, 331509, 329798, 316869,
323295, 296603, 331088, 282 of 11572 triangles, 319550, 327671, 322507,
292233, 326970, 326787, 245419, 327827, 331259, 327646, 308406, 330024,
308470, 329714, 5545 of 6388 triangles, 301849, 328339, 308494, 297200,
331343, 301610, 319410, 331165, 324306, 245903, 327036, 325989, 319349,
326262, 330405, 328151, 324819, 328650, 305657, 329205, 328411, 331246,
330420, 319990, 325879, 330760, 300093, 328284, 328623, 321574, 327540,
287345, 296467, 331523, 316897, 327790, 327620, 289756, 328478, 321343,
331375, 318487, 327602, 328018, 3
Clip2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc
> select subtract #4.27
488 models selected
> select subtract #4.38
487 models selected
> select subtract #4.572
486 models selected
> select subtract #4.355
485 models selected
> select subtract #4.142
484 models selected
> select subtract #4.199
483 models selected
Deleted 481 regions
Drag select of 316803, 330376, 3857 of 44916 triangles, 331394, 329807,
326312, 331633, 330033, 26647 of 28496 triangles, 330705, 329644, 318654,
322930, 328574, 143 of 17256 triangles, 324437, 330370, 329943, 316685, 18221
of 32428 triangles, 329855, 327704, 328900, 13006 of 32844 triangles, 331109,
328006, 316752, 302094, 295010, 289950, 328413, 329138, 319328, 330637,
327733, 322613, 331266, 308185, 329503, 317796, 330707, 328786, 331153,
319210, 302276, 331369, 301662, 323699, 329497, 330966, 330575, 299998,
289962, 328570, 319557, 316965, 293414, 327512, 324052, 324778, 330046,
323648, 325293, 327551, 331444, 329792, 9268 of 9608 triangles, 328121,
323076, 329795, 317112, 330511, 296013, 329848, 330609, 297187, 317449,
330792, 324697, 287813, 317766, 330288, 294227, 330838, 330660, 322414,
293512, 290869, 328110, 6858 of 9216 triangles, 328711, 330793, 328607,
323955, 329886, 329031, 331541, 302108, 330197, 295781, 3125 of 4396
triangles, 331111, 323242
Deleted 95 regions
Drag select of 331402, 5036 of 21732 triangles, 316791, 6878 of 10136
triangles, 319284, 2738 of 10172 triangles, 326070, 7598 of 10768 triangles
> select clear
Drag select of 311044, 328153, 16878 of 40800 triangles, 327925, 8000 of 28512
triangles, 329253, 327943, 92 of 41012 triangles, 326310, 330881, 8292 of
23060 triangles, 329944, 331050, 329531, 329366, 329926, 1678 of 20860
triangles, 328894, 328678, 331402, 322230, 184 of 13104 triangles, 317949,
328892, 326018, 327915, 302269, 828 of 10036 triangles, 295362, 4799 of 8092
triangles, 323575, 327911, 18048 of 19064 triangles, 326412, 323853, 8743 of
8888 triangles, 316791, 327872, 31 of 8260 triangles, 328749, 319284, 316460,
296000, 315032, 4523 of 4952 triangles, 329751, 5669 of 6652 triangles,
318272, 326855, 326205, 331660, 1629 of 8908 triangles, 319693, 6839 of 9216
triangles, 327513, 327480, 5894 of 9524 triangles, 326300, 5363 of 6528
triangles, 329054, 4119 of 10832 triangles, 324136, 2227 of 5744 triangles,
290714, 329623, 287117, 326070, 290221, 320694, 299165, 321162, 4961 of 7548
triangles, 320420, 290797
Deleted 54 regions
> select #4.619
1 model selected
> select add #4.367
2 models selected
> select add #4.351
3 models selected
Deleted 3 regions
Drag select of 330514, 32791 of 36400 triangles, 327630, 14205 of 15900
triangles, 329498, 108 of 18444 triangles, 330450, 12497 of 23024 triangles,
331446, 331388, 287472, 9273 of 10108 triangles, 317334, 228 of 9432
triangles, 301982, 331333, 327465, 330836, 6481 of 12776 triangles, 292476,
331002, 13143 of 13780 triangles, 294073, 327088, 317972, 330667, 316357,
11883 of 12236 triangles, 326118, 320927, 300 of 10288 triangles, 318303, 3977
of 6368 triangles, 323735, 3077 of 6492 triangles, 301985, 1933 of 5048
triangles, 329586, 329502, 322356, 162 of 4740 triangles, 330641, 648 of 4976
triangles, 330632
> select subtract #4.597
28 models selected
> select subtract #4.84
27 models selected
Drag select of 318275, 214 of 26308 triangles, 330514, 845 of 36400 triangles,
329498, 1957 of 18444 triangles, 326421, 388 of 11916 triangles, 321928, 3041
of 7844 triangles, 330667, 1563 of 22552 triangles, 329586, 4123 of 16268
triangles, 330641, 125 of 4976 triangles
> select clear
Drag select of 330514, 28480 of 36400 triangles, 327630, 330450, 13568 of
23024 triangles, 331446, 331388, 287472, 317334, 301982, 331333, 281 of 13168
triangles, 331183, 9420 of 21744 triangles, 327465, 292476, 331002, 294073,
327088, 322968, 72 of 12120 triangles, 320855, 1939 of 7448 triangles, 317972,
7550 of 7620 triangles, 330667, 15109 of 22552 triangles, 326118, 320927,
318303, 301985, 329586, 329502, 20298 of 21416 triangles, 322356, 330632,
330040, 1354 of 10232 triangles, 330699, 5345 of 5976 triangles
Deleted 29 regions
> select #4.102
1 model selected
> select add #4.237
2 models selected
> select add #4.463
3 models selected
Drag select of 330529, 3866 of 11576 triangles, 311020, 331149, 612 of 11888
triangles, 298570, 3369 of 6412 triangles, 328603
Deleted 8 regions
> select #4.330
1 model selected
> select add #4.459
2 models selected
> select add #4.509
3 models selected
> select add #4.274
4 models selected
> select add #4.524
5 models selected
Deleted 5 regions
> view orient
> select #4.640
1 model selected
Deleted 1 regions
Drag select of 330188, 329501, 331401, 21838 of 24688 triangles, 328739,
318275, 331724, 319333, 329498, 291146, 289972, 328539, 326989, 331619,
326392, 320884, 301154, 326421, 290719, 307152, 310872, 321928, 307214,
295918, 330641
> select #4.597
1 model selected
Drag select of 330188, 329501, 331401, 23084 of 24688 triangles, 328739,
318275, 331724, 319333, 329498, 291146, 289972, 328539, 326989, 331619,
326392, 320884, 301154, 326421, 290719, 307152, 310872, 321928, 307214,
295918, 330641
> select subtract #4.597
23 models selected
> select subtract #4.361
22 models selected
> select subtract #4.571
21 models selected
> select subtract #4.291
20 models selected
> select clear
> select #4.6
1 model selected
Ungrouped to 3 regions
> select #4.3
1 model selected
> select #4.291
1 model selected
> select add #4.571
2 models selected
> select add #4.3
3 models selected
> select add #4.597
4 models selected
> select add #4.361
5 models selected
> select clear
> select #4.597
1 model selected
Ungrouped to 3 regions
> select clear
> select #4.4
1 model selected
> select #4.6
1 model selected
> select add #4.4
2 models selected
Deleted 2 regions
> select #4.5
1 model selected
Ungrouped to 2 regions
> select clear
> select #4.6
1 model selected
Deleted 1 regions
> select #4.4
1 model selected
Ungrouped to 2 regions
> select clear
> select #4.5
1 model selected
Deleted 1 regions
> select #4.291
1 model selected
Drag select of 329501, 331401, 328739, 318275, 331724, 319333, 329498, 291146,
289972, 328539, 326989, 331619, 326392, 320884, 301154, 326421, 290719,
307152, 310872, 321928, 307214, 295918, 322734, 325188, 306737, 253953
Ungrouped to 139 regions
> select clear
Drag select of 262680, 250625, 220695, 230468, 55 of 56 triangles, 246530,
6397 of 6668 triangles, 246566, 2873 of 3368 triangles, 191435, 271046,
201135, 322073, 3174 of 10144 triangles, 306707, 171 of 8136 triangles
> select subtract #4.85
10 models selected
> select add #4.31
11 models selected
> select add #4.34
12 models selected
> select subtract #4.31
11 models selected
> select subtract #4.34
10 models selected
Drag select of 321778, 1635 of 14244 triangles, 325200, 221 of 360 triangles
> undo
[Repeated 9 time(s)]
> select #4.7
1 model selected
> select clear
> select #4.116
1 model selected
> select #4.126
1 model selected
> select add #4.116
2 models selected
Deleted 2 regions
> select #4.7
1 model selected
Drag select of 245862, 179 of 5128 triangles, 240124, 230447, 294 of 480
triangles, 226770, 1635 of 1832 triangles, 229194, 2107 of 2164 triangles,
237757, 232883, 235361, 225575, 32 of 252 triangles, 225570, 1411 of 2132
triangles, 231654, 117 of 136 triangles, 231655, 7 of 200 triangles, 226765,
976 of 1004 triangles
> select add #4.7
13 models selected
> select add #4.41
14 models selected
> select add #4.40
15 models selected
> select add #4.23
16 models selected
> select add #4.44
17 models selected
> select add #4.22
18 models selected
Grouped 18 regions
> select clear
> hide #!3 models
> show #!3 models
> hide #!4 models
> volume #3 step 1
> volume #3 level 0.1269
> show #!3 models
> hide #!3 models
> show #!4 models
> close #3-4
> show #!2 models
> show #!1 models
> view orient
> close
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip3_2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip3_2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #1, grid
size 70,100,100, pixel 8.9,8.9,8.9, shown at level 0.367, step 1, values
float32
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #2, grid
size 100,100,100, pixel 8.9, shown at level 0.412, step 1, values float32
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip1_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #3, grid
size 100,140,100, pixel 8.9,8.9,8.9, shown at level 0.429, step 1, values
float32
> view orient
> volume #3 level 0.2693
> volume #3 level 0.2016
> volume #3 level 0.2939
Segmenting Clip1_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc, density
threshold 0.293926
Showing 50 region surfaces
649 watershed regions, grouped to 50 regions
Showing Clip1_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.seg - 50
regions, 50 surfaces
Drag select of 831, 810, 673, 817, 746, 811, 805, 1182 of 2436 triangles, 722,
677, 2033 of 2056 triangles, 664, 1825 of 1920 triangles, 789, 739, 758, 839,
761, 803, 27, 3 Clip1_3_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc
> select add #4.40
20 models selected
> select add #4.18
21 models selected
> select add #4.25
22 models selected
> select add #4.33
23 models selected
> select add #4.34
24 models selected
> select add #4.42
25 models selected
Deleted 23 regions
> select #4.44
1 model selected
> select add #4.27
2 models selected
Drag select of 838, 836, 792, 17 of 6012 triangles, 829, 281 of 5620
triangles, 787, 710, 3181 of 3352 triangles, 802, 841, 828, 818, 837, 825,
1906 of 3236 triangles, 835, 832, 2610 of 3268 triangles, 819, 821, 840, 1367
of 2004 triangles, 814, 148, 28
> select #4.14
1 model selected
> select #4.27
1 model selected
> select clear
Drag select of 833, 6 of 9712 triangles, 838, 836, 787, 710, 1806 of 3352
triangles, 802, 841, 828, 818, 837, 825, 835, 832, 1745 of 3268 triangles,
819, 821, 840, 120 of 2004 triangles, 814, 148, 28
> select subtract #4.14
18 models selected
> select subtract #4.5
17 models selected
Deleted 17 regions
> select #4.27
1 model selected
> select #4.46
1 model selected
> select add #4.44
2 models selected
Deleted 2 regions
> select #4.27
1 model selected
Deleted 1 regions
Drag select of 829, 54 of 5620 triangles, 710, 409 of 3352 triangles
> select clear
> select #4.11
1 model selected
Ungrouped to 2 regions
> select #4.2
1 model selected
> select add #4.14
2 models selected
> select add #4.12
3 models selected
Grouped 3 regions
> select add #4.3
2 models selected
> select add #4.1
3 models selected
> select add #4.4
4 models selected
> select add #4.10
5 models selected
> select add #4.5
6 models selected
Grouped 6 regions
Ungrouped to 6 regions
> select #4.5
1 model selected
> select clear
> select add #4.4
1 model selected
> select add #4.3
2 models selected
> select add #4.6
3 models selected
> select add #4.2
4 models selected
> select add #4.7
5 models selected
Grouped 5 regions
> select clear
> select #4.5
1 model selected
> color #4 #ffff7fff
> undo
> color #4.5 cyan
> select #4.1
1 model selected
> color #4.1 yellow
> select clear
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> close #1-2
> save "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip13_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.cxs"
> close
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #1, grid
size 100,100,100, pixel 8.9, shown at level 0.412, step 1, values float32
> volume #1 level 0.04936
> volume #1 level 0.1758
Segmenting Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc, density
threshold 0.175820
Showing 48 region surfaces
808 watershed regions, grouped to 48 regions
Showing Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.seg - 48
regions, 48 surfaces
Drag select of 993, 12777 of 18068 triangles, 997, 15428 of 15460 triangles,
984, 982, 981, 970, 988, 856, 989, 261 of 3552 triangles, 994, 809, 975, 945,
650 of 2888 triangles, 944, 2387 of 2720 triangles, 948, 2999 of 4500
triangles, 958, 265 of 2980 triangles, 937, 907, 968, 7, 885, 164 of 1668
triangles, 992, 2078 of 2240 triangles, 979, 976, 996, 1
Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc
Deleted 25 regions
> select #2.20
1 model selected
> select add #2.32
2 models selected
> select add #2.5
3 models selected
> select add #2.31
4 models selected
> select add #2.16
5 models selected
> select add #2.19
6 models selected
Deleted 6 regions
> select #2.18
1 model selected
> select #2.23
1 model selected
> select add #2.15
2 models selected
> select add #2.18
3 models selected
Deleted 3 regions
> select #2.43
1 model selected
> select add #2.45
2 models selected
> select add #2.46
3 models selected
> select add #2.9
4 models selected
> select subtract #2.9
3 models selected
> select add #2.44
4 models selected
Deleted 4 regions
> select #2.8
1 model selected
> select add #2.12
2 models selected
Grouped 2 regions
> select #2.4
1 model selected
> select add #2.7
2 models selected
> select add #2.22
3 models selected
> select add #2.9
4 models selected
> select add #2.6
5 models selected
> select add #2.24
6 models selected
Grouped 6 regions
> select #2.1
1 model selected
> color #2.1 cyan
> select clear
> save "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.cxs"
——— End of log from Wed Oct 30 16:36:58 2024 ———
opened ChimeraX session
Showing Clip1_2_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.seg - 4 regions,
4 surfaces
> close
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.cxs"
Opened Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #3, grid
size 200,200,180, pixel 8.9,8.9,8.9, shown at level -0.0406, step 1, values
float32
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\session.py", line 757, in restore
obj = sm.restore_snapshot(self, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 574, in restore_snapshot
m.set_state_from_snapshot(session, data)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 397, in set_state_from_snapshot
p.add([self])
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 314, in add
om.add(models, parent = self)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 756, in add
p = self._parent_for_added_model(model, parent, root_model = root_model)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\models.py", line 825, in _parent_for_added_model
raise ValueError('Tried to add model %s with the same id as another model %s'
ValueError: Tried to add model 12612 #1.1 with the same id as another model
12612 #1.1
Log from Mon Nov 18 14:49:58 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:\Users\parv553\OneDrive - PNNL\Lab_work\Images\Krios-Screening-
> Images\2023\04-19-23-RCG-
> Tomograms\RCG_SIRT_CTF_Au_corrected_bin8\TS_A_02\Visualize_09-19_24\Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.cxs"
> format session
Opened Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #3, grid
size 200,200,180, pixel 8.9,8.9,8.9, shown at level -0.0406, step 1, values
float32
Log from Wed Oct 30 14:52:59 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp35_inv.mrc"
Opened Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp35_inv.mrc as #1, grid
size 200,200,180, pixel 8.9,8.9,8.9, shown at level 0.135, step 1, values
float32
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc"
Opened Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp19_inv.mrc as #2, grid
size 200,200,180, pixel 8.9,8.9,8.9, shown at level 0.18, step 1, values
float32
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
Opened Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #3, grid
size 200,200,180, pixel 8.9,8.9,8.9, shown at level 0.147, step 1, values
float32
> open "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp30_inv.mrc"
Opened Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp30_inv.mrc as #4, grid
size 200,200,180, pixel 8.9,8.9,8.9, shown at level 0.14, step 1, values
float32
> surface dust #2 size 20
> surface dust #2 size 40
> volume #2 level 0.1
> volume #2 level 0.13
> surface dust #2 size 80
> surface dust #2 size 200
> surface dust #2 size 150
> volume #3 level -0.01513
> surface dust #3 size 150
> ui tool show "Segment Map"
> close #1
> close #2
> close #4
> set bgColor white
> lighting soft
> set bgColor gray
> volume showOutlineBox true
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #3 style surface
> surface dust #3 size 150
> volume #3 region 24,0,0,199,199,179
> volume #3 region 41,0,0,199,199,179
> volume #3 region 41,0,0,134,199,179
> volume #3 region 41,0,0,134,190,179
> volume #3 region 41,0,66,134,190,179
> volume #3 region 41,0,66,145,190,179
> volume showOutlineBox false
> volume #3 change image level -0.705,0 level 0.1469,0.8 level 1.338,1
> volume #3 level -0.04061
> volume showOutlineBox true
> volume #3 region 41,0,53,145,190,179
> volume #3 region 41,0,53,145,190,136
> volume showOutlineBox false
Segmenting Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc, density
threshold -0.040606
Only showing 60 of 1028 regions.
Showing 60 of 1028 region surfaces
8789 watershed regions, grouped to 1028 regions
Showing Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.seg - 1028
regions, 60 surfaces
> select #1.51
1 model selected
> select #1.31
1 model selected
> select #1.59
1 model selected
> select add #1.31
2 models selected
> select add #1.36
3 models selected
> select add #1.38
4 models selected
> select add #1.53
5 models selected
> select add #1.48
6 models selected
> select add #1.22
7 models selected
> select add #1.43
8 models selected
> select add #1.42
9 models selected
> select add #1.47
10 models selected
> select add #1.39
11 models selected
Deleted 11 regions
> select add #1.51
1 model selected
> select add #1.54
2 models selected
> select add #1.24
3 models selected
> select add #1.50
4 models selected
> select add #1.17
5 models selected
> select add #1.40
6 models selected
> select add #1.23
7 models selected
> select add #1.57
8 models selected
> select add #1.49
9 models selected
> select add #1.33
10 models selected
> select add #1.37
11 models selected
> select add #1.27
12 models selected
Deleted 12 regions
> select add #1.46
1 model selected
> select add #1.32
2 models selected
> select add #1.25
3 models selected
> select add #1.26
4 models selected
> select add #1.19
5 models selected
Deleted 5 regions
> select add #1.45
1 model selected
Deleted 1 regions
> select #1.8
1 model selected
Segmenting Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc, density
threshold -0.040606
Only showing 90 of 1028 regions.
Showing 90 of 1028 region surfaces
8789 watershed regions, grouped to 1028 regions
Showing Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.seg - 1028
regions, 90 surfaces
Drag select of 11725, 7285 of 9148 triangles, 11439, 86 of 8036 triangles,
11778, 12275, 1713 of 7596 triangles, 12317, 4654 of 5804 triangles, 12318,
6383 of 6384 triangles, 11350, 2046 of 4368 triangles, 10128, 10213, 910 of
4696 triangles, 11403, 3717 of 5472 triangles, 12539, 11323, 8879, 11885,
11580, 10869, 12458, 1791 of 2344 triangles, 10699, 12366, 12420, 2696 of 3100
triangles, 12487, 12261, 12117, 11034
Deleted 24 regions
> select #1.59
1 model selected
> select #1.89
1 model selected
> select add #1.59
2 models selected
> select add #1.32
3 models selected
> select add #1.43
4 models selected
> select add #1.82
5 models selected
Deleted 5 regions
Drag select of 12018, 506 of 22424 triangles, 12307, 3067 of 24128 triangles,
11781, 7765 of 17392 triangles, 12536, 8543 of 14756 triangles, 12233, 11557,
12541, 10473, 10316, 782 of 5952 triangles, 11370, 2564 of 5824 triangles,
11641, 13 of 5552 triangles, 11361, 3412 of 3964 triangles, 10393, 12526, 4504
of 4660 triangles, 12038, 10383, 3848 of 4064 triangles, 10139, 1755 of 3784
triangles, 10159, 2319 of 3216 triangles, 12197, 12429, 4877 of 5028
triangles, 10419, 10282, 12209, 9086, 11723, 12380, 12333, 2877 of 3692
triangles, 12562, 266 of 3396 triangles, 11379, 12200, 12277
> select #1.41
1 model selected
> select #1.51
1 model selected
> select add #1.37
2 models selected
> select add #1.62
3 models selected
> select add #1.64
4 models selected
> select add #1.74
5 models selected
> select add #1.79
6 models selected
> select add #1.84
7 models selected
> select add #1.80
8 models selected
> select add #1.27
9 models selected
> select add #1.83
10 models selected
> select add #1.77
11 models selected
> select add #1.75
12 models selected
> select add #1.24
13 models selected
> select add #1.54
14 models selected
> select add #1.69
15 models selected
> select add #1.50
16 models selected
> select add #1.76
17 models selected
> select add #1.88
18 models selected
Deleted 18 regions
> select #1.90
1 model selected
> select add #1.85
2 models selected
> select add #1.60
3 models selected
> select subtract #1.60
2 models selected
> select add #1.65
3 models selected
Deleted 3 regions
> select #1.33
1 model selected
> select add #1.25
2 models selected
> select add #1.26
3 models selected
> select add #1.19
4 models selected
> select add #1.72
5 models selected
Deleted 5 regions
> select #1.49
1 model selected
> select #1.45
1 model selected
> select add #1.49
2 models selected
Deleted 2 regions
> select #1.46
1 model selected
Deleted 1 regions
> select #1.8
1 model selected
Ungrouped to 2 regions
> select clear
> select #1.55
1 model selected
> select add #1.34
2 models selected
> select add #1.58
3 models selected
> select add #1.60
4 models selected
> select add #1.56
5 models selected
> select add #1.30
6 models selected
> select add #1.29
7 models selected
> select clear
> select #1.29
1 model selected
Ungrouped to 3 regions
> select clear
> select #1.22
1 model selected
Deleted 1 regions
> select #1.8
1 model selected
> select #1.23
1 model selected
> select add #1.8
2 models selected
Ungrouped to 21 regions
Grouped 21 regions
> select #1.8
1 model selected
Deleted 1 regions
> select add #1.22
1 model selected
> select add #1.30
2 models selected
> select add #1.60
3 models selected
> select add #1.56
4 models selected
> select add #1.58
5 models selected
> select add #1.55
6 models selected
> select add #1.61
7 models selected
Drag select of 12018, 43 of 22424 triangles, 12493, 653 of 20372 triangles,
11784, 88 of 17492 triangles, 12494, 82 of 9476 triangles, 10383, 7 of 4064
triangles, 10142, 81 of 2688 triangles
> select clear
> select add #1.58
1 model selected
> select clear
> select #1.61
1 model selected
Deleted 1 regions
> select #1.55
1 model selected
> select add #1.58
2 models selected
> select add #1.60
3 models selected
> select add #1.30
4 models selected
> select add #1.22
5 models selected
> select add #1.56
6 models selected
> select add #1.17
7 models selected
> select add #1.41
8 models selected
Grouped 8 regions
> select clear
Drag select of 12308, 12018, 12307, 12493, 12016, 11784, 11781, 11365, 12047,
12492, 12494, 12015, 10721, 12490, 12017, 12337, 10030, 10149, 11981, 10415,
10003, 10115, 10810, 11483, 12610
> select subtract #1.8
24 models selected
Grouped 24 regions
> select clear
> save "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.cxs"
> select #1.8
1 model selected
> color #1 #55ffffff
> color #1 #78ff30ff
> select add #1
3 models selected
> color #1 #46ffd1ff
> undo
> redo
> undo
[Repeated 3 time(s)]
> ui tool show "Color Actions"
QWindowsWindow::setGeometry: Unable to set geometry 633x1298+2085+930 (frame:
665x1386+2069+858) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 617x1249+2093+971 (frame:
649x1337+2077+899) margins: 16, 72, 16, 16 minimum size: 253x519 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=1310750, y=1310806), mintrack=POINT(x=665, y=1386)))
> color sel cyan
> select #1.1
1 model selected
> color sel yellow
No visible atoms or bonds selected
> select #1.1
1 model selected
No visible atoms or bonds selected
[Repeated 11 time(s)]
> select subtract #1
Nothing selected
> select add #1
3 models selected
> select subtract #1
Nothing selected
> select add #1
3 models selected
> select clear
> select #1.1
1 model selected
> color sel lime target s
> color sel yellow target s
No visible atoms or bonds selected
> color sel light yellow target s
> color sel light goldenrod yellow target s
> color sel khaki target s
> color sel tan target s
> color sel gold target s
> color sel yellow target s
> ui tool show "Surface Color"
> color #1 #55ffe5ff
> color #1 #47fff0ff
> undo
[Repeated 1 time(s)]
> select clear
> select #1.8
1 model selected
> color #1 #5afff4ff
> select add #1
3 models selected
> select subtract #1
Nothing selected
> select add #1
3 models selected
> undo
[Repeated 3 time(s)]
> select clear
> save "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.cxs"
——— End of log from Wed Oct 30 14:52:59 2024 ———
opened ChimeraX session
Showing Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.seg - 940
regions, 2 surfaces
> surface dust #1.2 size 150
> surface dust #1.1 size 150
> select #1.1
1 model selected
Ungrouped to 8 regions
> select clear
> select #1.2
1 model selected
> select add #1.7
2 models selected
Grouped 2 regions
> color #1.1 #bcc509ff
> color #1.1 #c5b500ff
> color #1.1 yellow
> color #1.1 #ffff7fff
> select clear
> select #1.10
1 model selected
> select add #1.3
2 models selected
> select add #1.4
3 models selected
> select add #1.9
4 models selected
> select add #1.8
5 models selected
Grouped 5 regions
> select add #1.5
2 models selected
> select add #1.6
3 models selected
Grouped 3 regions
> color #1.2 cyan
> surface dust #1.1 size 150
> surface dust #1.2 size 150
> select clear
> view orient
> save C:\Users\parv553/Desktop\image74.png supersample 3
> save C:\Users\parv553/Desktop\image75.png supersample 3
> save C:\Users\parv553/Desktop\image76.png supersample 3
> hide #1.2 models
> show #1.2 models
> hide #1.1 models
> save C:\Users\parv553/Desktop\image77.png supersample 3
> save C:\Users\parv553/Desktop\image78.png supersample 3
> show #!3 models
> hide #!3 models
> show #1.1 models
> save "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.cxs"
——— End of log from Mon Nov 18 14:49:58 2024 ———
opened ChimeraX session
> open "C:\Users\parv553\OneDrive - PNNL\Lab_work\Images\Krios-Screening-
> Images\2023\04-19-23-RCG-
> Tomograms\RCG_SIRT_CTF_Au_corrected_bin8\TS_A_02\Visualize_09-19_24\Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc"
> format mrc
Opened Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc as #1, grid
size 200,200,180, pixel 8.9,8.9,8.9, shown at level 0.147, step 1, values
float32
> surface dust #1 size 300
> volume #1 level -0.09361
> set bgColor white
> lighting soft
> volume #1 level -0.05699
> ui tool show "Segment Map"
Segmenting Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.mrc, density
threshold -0.056986
Only showing 60 of 1058 regions.
Showing 60 of 1058 region surfaces
10707 watershed regions, grouped to 1058 regions
Showing Clip1_1_1_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.seg - 1058
regions, 60 surfaces
> hide #!1 models
> surface dust #1 size 200
> surface dust #2 size 200
> surface dust #2 size 100
> select #2.36
1 model selected
> select add #2.59
2 models selected
> select add #2.29
3 models selected
> select add #2.52
4 models selected
> select add #2.37
5 models selected
> select add #2.22
6 models selected
> select add #2.32
7 models selected
> select add #2.42
8 models selected
> select add #2.39
9 models selected
> select add #2.17
10 models selected
> select add #2.23
11 models selected
> select add #2.47
12 models selected
> select add #2.48
13 models selected
> select add #2.41
14 models selected
> select add #2.43
15 models selected
Deleted 15 regions
> select #2.58
1 model selected
> select #2.50
1 model selected
> select #2.24
1 model selected
> select add #2.51
2 models selected
> select add #2.50
3 models selected
> select add #2.58
4 models selected
> select add #2.28
5 models selected
> select add #2.38
6 models selected
> select add #2.33
7 models selected
Deleted 7 regions
> select add #2.19
1 model selected
> select add #2.26
2 models selected
> select add #2.25
3 models selected
> select add #2.45
4 models selected
Deleted 4 regions
> select add #2.49
1 model selected
> select add #2.53
2 models selected
Deleted 2 regions
> select add #2.46
1 model selected
Deleted 1 regions
> select add #2.55
1 model selected
> select add #2.57
2 models selected
> select add #2.60
3 models selected
> select add #2.30
4 models selected
> select add #2.31
5 models selected
> select add #2.56
6 models selected
> select add #2.40
7 models selected
Grouped 7 regions
> surface dust #2 size 100
> color #2.4 #ffff7fff
> select clear
> select #2.17
1 model selected
> select clear
> color #2.17 #ffff7fff
> select #2.17
1 model selected
> color #2.17 #aaffffff
Drag select of 15187, 33924 of 34208 triangles, 14268, 22568 of 22788
triangles, 15412, 24536 of 24724 triangles, 15397, 20436 of 20624 triangles,
14899, 19476 of 19924 triangles, 13916, 17564 of 17784 triangles, 14923, 17520
of 17576 triangles, 15312, 14784 of 15040 triangles, 14537, 12088 of 12136
triangles, 14343, 15184, 13248 of 13408 triangles, 15257, 9476 of 9624
triangles, 14075, 12172, 15453, 14296, 9360 of 9404 triangles, 15122, 11652 of
11680 triangles, 12882, 9604 of 9692 triangles, 13600, 7484 of 7572 triangles,
14522, 13211, 6316 of 6552 triangles, 13847, 13489, 13613, 15470, 28176 of
29848 triangles
> select subtract #2.17
24 models selected
Grouped 24 regions
> color #2.1 #ffff7fff
> surface dust #2 size 100
> save "C:/Users/parv553/OneDrive - PNNL/Lab_work/Images/Krios-Screening-
> Images/2023/04-19-23-RCG-
> Tomograms/RCG_SIRT_CTF_Au_corrected_bin8/TS_A_02/Visualize_09-19_24/Clip1_1_1.2_RCG_TS_A_02_rec_CTF_bin8_corrected_lp25_inv.cxs"
——— End of log from Mon Nov 18 17:12:40 2024 ———
opened ChimeraX session
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1318, in
_surfaceChosen
v.delete()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1912, in delete
Image3d.delete(self)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\image3d.py", line 752, in delete
b.remove_image(self)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\image3d.py", line 1517, in remove_image
del dbi[image_render]
~~~^^^^^^^^^^^^^^
KeyError: <chimerax.map.volume.VolumeImage object at 0x000001D0B4392850>
KeyError:
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\image3d.py", line 1517, in remove_image
del dbi[image_render]
~~~^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1318, in
_surfaceChosen
v.delete()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1912, in delete
Image3d.delete(self)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\image3d.py", line 752, in delete
b.remove_image(self)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\image3d.py", line 1517, in remove_image
del dbi[image_render]
~~~^^^^^^^^^^^^^^
KeyError: <chimerax.map.volume.VolumeImage object at 0x000001D0ADFE8E50>
KeyError:
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\image3d.py", line 1517, in remove_image
del dbi[image_render]
~~~^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\segmentations\ui\orthoplanes.py", line 1318, in
_surfaceChosen
v.delete()
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\volume.py", line 1912, in delete
Image3d.delete(self)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\image3d.py", line 752, in delete
b.remove_image(self)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\image3d.py", line 1517, in remove_image
del dbi[image_render]
~~~^^^^^^^^^^^^^^
KeyError: <chimerax.map.volume.VolumeImage object at 0x000001D0B43A3AD0>
KeyError:
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\map\image3d.py", line 1517, in remove_image
del dbi[image_render]
~~~^^^^^^^^^^^^^^
See log for complete Python traceback.
QWindowsWindow::setGeometry: Unable to set geometry 1500x1188+1650+985 (frame:
1532x1276+1634+913) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1484x1139+1658+1026 (frame:
1516x1227+1642+954) margins: 16, 72, 16, 16 minimum size: 600x321 maximum
size: 524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=1310750, y=1310806), mintrack=POINT(x=1532, y=891)))
[Repeated 1 time(s)]
OpenGL version: 3.3.0 NVIDIA 528.79
OpenGL renderer: NVIDIA RTX A2000 8GB Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows
Manufacturer: Dell Inc.
Model: Precision 5570
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 68,374,552,576
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i9-12900H
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.1
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pywin32: 306
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
WMI: 1.5.1
Change History (2)
comment:1 by , 11 months ago
| Component: | Unassigned → DICOM |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → DICOM: index is out of bounds |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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