Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#3695 closed enhancement (fixed)

Notes with markers

Reported by: r.frank@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
I have a cmm file that has has a 'note' field that I opened in ChimeraX. This contains important information that I need with each coordinate. After deleting some coordinates, I attempted to save the file. Is there any chance ChimeraX can handle 'notes' as with Chimera? Thank you, Rene 

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Some installed bundles are out of date. Please update the following bundles:

  * UI to version 1.2.1 (currently 1.0)
  * UI to version 1.2 (currently 1.0)

  

> open
> "/Users/fbsrfr/process/julia/subtomo/cleft_sirt/combinedmotl/virusmotls_manclean/phrandre-3-cl-
> redefcleft__1_1 2.em"

Opened phrandre-3-cl-redefcleft__1_1 2.em, grid size 20,2529,1, pixel 1, shown
at step 1, values float32  

> close #1

> open
> "/Users/fbsrfr/process/julia/subtomo/cleft_sirt/combinedmotl/virusmotls_manclean/phrandre-3-cl-
> redefcleft__1_1 2_0.cmm"

Opened 1 marker sets containing 2529 markers  

> open
> /Users/fbsrfr/process/julia/subtomo/cleft_sirt/combinedmotl/virusmotls_manclean/phrandre-3-cl-
> redefcleft__41_1_part_1_0.cmm

Opened 1 marker sets containing 4047 markers  

> open
> "/Users/fbsrfr/process/julia/subtomo/cleft_sirt/combinedmotl/virusmotls_manclean/phrandre-3-cl-
> redefcleft__1_1 2_0.cmm"

Opened 1 marker sets containing 2529 markers  

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> close #3

> open
> "/Users/fbsrfr/process/julia/subtomo/cleft_sirt/combinedmotl/virusmotls_manclean/phrandre-3-cl-
> redefcleft__1_1 2.em"

Opened phrandre-3-cl-redefcleft__1_1 2.em, grid size 20,2529,1, pixel 1, shown
at step 1, values float32  

> close #3

> open
> "/Users/fbsrfr/process/julia/subtomo/cleft_sirt/combinedmotl/virusmotls_manclean/phrandre-3-cl-
> redefcleft__1_1 2_0.cmm"

Opened 1 marker sets containing 2529 markers  

> open
> "/Users/fbsrfr/process/julia/subtomo/cleft_sirt/combinedmotl/virusmotls_manclean/phrandre-3-cl-
> redefcleft__11_1 2_0.cmm"

Opened 1 marker sets containing 3607 markers  

> close

> open
> "/Users/fbsrfr/process/julia/subtomo/cleft_sirt/combinedmotl/virusmotls_manclean/phrandre-3-cl-
> redefcleft__1_1 2_0.cmm"

Opened 1 marker sets containing 2529 markers  

> select /M:2157@M

1 atom, 1 model selected  

> open
> /Users/fbsrfr/process/julia/tomograms_sirt_bin4/D01_TS_02_aligned_bin4_ng_sirt5.rec

Opened D01_TS_02_aligned_bin4_ng_sirt5.rec, grid size 960,928,300, pixel
11.9,11.9,11.9, shown at level 5.26e+03, step 4, values float32  

> volume #2 originIndex 0

> volume #2 voxelSize 1

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> ui tool show "Basic Actions"

> ui tool show "Show Volume Menu"

> ui tool show "Volume Viewer"

> volume #2 style image region 0,0,148,959,927,148 step 1 showOutlineBox true

> volume #2 transparency 0

> volume #2 transparency 1

> ui tool show "Model Panel"

> volume #2 transparency 1

> volume #2 transparency 0

> volume #2 transparency 1

> volume #2 transparency 0

Drag select of 351 atoms  

> marker delete sel

Deleted 351 markers  
Drag select of 44 atoms  

> select clear

Drag select of 13 atoms  

> marker delete sel

Deleted 13 markers  
Drag select of 5 atoms  

> marker delete sel

Deleted 14 markers  

> marker delete sel

Deleted 12 markers  

> marker delete sel

Deleted 2 markers  

> marker delete sel

Deleted 3 markers  
Drag select of 4 atoms  

> marker delete sel

Deleted 4 markers  
Drag select of 2 atoms  

> marker delete sel

Deleted 6 markers  

> marker delete sel

Deleted 3 markers  
Drag select of 8 atoms  

> marker delete sel

Deleted 8 markers  

> marker delete sel

Deleted 8 markers  

> marker delete sel

Deleted 1 markers  

> marker delete sel

Deleted 6 markers  

> volume #2 level -1244,0 level 5285,0.8 level 1.39e+04,1

> marker delete sel

Deleted 26 markers  

> marker delete sel

Deleted 3 markers  
Drag select of 2 atoms  

> select /M:2310@M

1 atom, 1 model selected  

> marker delete sel

Deleted 7 markers  

> marker delete sel

Deleted 3 markers  

> marker delete sel

Deleted 4 markers  
Drag select of 2 atoms  

> marker delete sel

Deleted 2 markers  

> save
> /Users/fbsrfr/process/julia/subtomo/cleft_sirt/combinedmotl/virusmotls_manclean/phrandre-3-cl-
> redefcleft__1_1_2_x.cmm

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/__init__.py", line 57, in save  
return cmmfiles.write_cmm(session, path, models)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 21, in write_cmm  
f.write(markersets_as_xml(mlist))  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 88, in markersets_as_xml  
lines.append(markerset_as_xml(ms))  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 54, in markerset_as_xml  
note_rgb_text = ' nr="%.5g" ng="%.5g" nb="%.5g"' % note_rgb  
TypeError: must be real number, not str  
  
TypeError: must be real number, not str  
  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 54, in markerset_as_xml  
note_rgb_text = ' nr="%.5g" ng="%.5g" nb="%.5g"' % note_rgb  
  
See log for complete Python traceback.  
  

> save
> /Users/fbsrfr/process/julia/subtomo/cleft_sirt/combinedmotl/virusmotls_manclean/phrandre-3-cl-
> redefcleft__1_1_2_x.cmm format markers models #1

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/__init__.py", line 57, in save  
return cmmfiles.write_cmm(session, path, models)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 21, in write_cmm  
f.write(markersets_as_xml(mlist))  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 88, in markersets_as_xml  
lines.append(markerset_as_xml(ms))  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 54, in markerset_as_xml  
note_rgb_text = ' nr="%.5g" ng="%.5g" nb="%.5g"' % note_rgb  
TypeError: must be real number, not str  
  
TypeError: must be real number, not str  
  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 54, in markerset_as_xml  
note_rgb_text = ' nr="%.5g" ng="%.5g" nb="%.5g"' % note_rgb  
  
See log for complete Python traceback.  
  

> save
> /Users/fbsrfr/process/julia/subtomo/cleft_sirt/combinedmotl/virusmotls_manclean/phrandre-3-cl-
> redefcleft__1_1_2_x.cmm

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1541, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/__init__.py", line 57, in save  
return cmmfiles.write_cmm(session, path, models)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 21, in write_cmm  
f.write(markersets_as_xml(mlist))  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 88, in markersets_as_xml  
lines.append(markerset_as_xml(ms))  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 54, in markerset_as_xml  
note_rgb_text = ' nr="%.5g" ng="%.5g" nb="%.5g"' % note_rgb  
TypeError: must be real number, not str  
  
TypeError: must be real number, not str  
  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/markers/cmmfiles.py", line 54, in markerset_as_xml  
note_rgb_text = ' nr="%.5g" ng="%.5g" nb="%.5g"' % note_rgb  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,1
      Processor Name: Intel Core i5
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 428.0.0.0.0
      SMC Version (system): 2.43f6

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G6020)
      Kernel Version: Darwin 18.7.0
      Time since boot: 3 days 20:02

Graphics/Displays:

    Intel Iris Plus Graphics 640:

      Chipset Model: Intel Iris Plus Graphics 640
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5926
      Revision ID: 0x0006
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        PL2483H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 1156292263699
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort
        PL2483H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 1156280844710
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (4)

comment:1 by pett, 5 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Notes with markers
Type: defect → enhancement

comment:2 by Tom Goddard, 5 years ago

This looks just like a bug saving marker notes. I will try to fix it today.

comment:3 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed in daily build and 1.1 release candidate.

Markers with notes are now saved correctly.

There is currently not a way to show marker notes as labels in the graphics and there is not a way to set the text of a marker note (except using Python). Do you need to show or set marker notes? I could probably add that as options to the "marker" command.

in reply to:  4 ; comment:4 by R.Frank@…, 5 years ago 

Thank you so much for adding this capability to ChimeraX so quickly. I don’t need to show or set marker notes - just keep the notes that are added to the markers before taking them into chimeraX and saving after moving them. The notes hold orientations of the coordinates that I am using for subtomogram averaging.  

Thank you again,

Rene

===============================================
Dr R. A. W. Frank, PhD
Astbury Centre for Structural Molecular Biology
Garstang Building (Office: 6.41d and Lab: 6.4)
School of Biomedical Sciences, Faculty of Biological Sciences
University of Leeds
LS2 9JT
Office: +44 (0)113 343 6756
Mobile:+44 (0)7870 208280
Skype & Twitter: drrenefrank
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