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#2965 closed defect (fixed)

Clipper: 'XmapHandler_Live' object has no attribute 'set_display_style'

Reported by:	folf@…	Owned by:	Tristan Croll
Priority:	normal	Milestone:
Component:	Third Party	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: 0.9 (2019-02-26)
Description
Install version 0.9 of ChimeraX on MacOS Mojave 10.14.6
Install Isolde
Open pdb file (files are directly from phenix-1.17.1_3660)
In Isolde- > load crystallographic dataset 

Log:
UCSF ChimeraX version: 0.9 (2019-02-26)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Downloading bundle ChimeraX_ISOLDE-1.0b3-cp37-cp37m-macosx_10_9_x86_64.whl  

> toolshed show ISOLDE

Expected a keyword  

Expected a keyword  

Done loading forcefield  

> open
/Users/folf/dtu/Folmer_shared/Projects/PsPL7A/CasperWork/Refine_66/PsAg17A_refine_66.pdb

Summary of feedback from opening
/Users/folf/dtu/Folmer_shared/Projects/PsPL7A/CasperWork/Refine_66/PsAg17A_refine_66.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2020-03-20 Time 07:34:33 Romance Standard Time +0100
(1584686073.30 s)  
  
Ignored bad PDB record found on line 2  
REMARK PHENIX refinement  
  
Ignored bad PDB record found on line 4  
REMARK ****************** INPUT FILES AND LABELS
******************************  
  
Ignored bad PDB record found on line 5  
REMARK Reflections:  
  
Ignored bad PDB record found on line 6  
REMARK file name :
D:\Phenix_PsAgl7A\AutoBuild_run_31_/exptl_fobs_phases_freeR_flags.mtz  
  
57 messages similar to the above omitted  
  
Chain information for PsAg17A_refine_66.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for PsAg17A_refine_66.pdb  
---  
Chain | Description  
1.3/A | No description available  
  

QWidget::repaint: Recursive repaint detected  

> toolshed show '"Density Map Toolbar"'

> toolshed hide '"Density Map Toolbar"'

Expected a keyword  

> set bgColor white

> set bgColor blue

> set bgColor black

> open
/Users/folf/dtu/Folmer_shared/Projects/PsPL7A/CasperWork/Refine_66/PsAg17A_refine_66.mtz

Must specify a structure model to associate with crystallographic data  

Must specify a structure model to associate with crystallographic data  

> open
/Users/folf/dtu/Folmer_shared/Projects/PsPL7A/CasperWork/Refine_66/PsAg17A_refine_66.mtz

Must specify a structure model to associate with crystallographic data  

Must specify a structure model to associate with crystallographic data  

Unknown command: ls  

> pwd

Current working directory is: /Users/folf/Desktop  

WARNING: multiple experimental reflection datasets found:  
(Original-experimental-data-mapped-to-asu) F-obs, SIGF-obs,  
(Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered  
Automatically choosing "(Original-experimental-data-mapped-to-asu) F-obs,
SIGF-obs".  

Traceback (most recent call last):  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 1256, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 1283, in add_xtal_data  
xmapset = map_mgr.add_xmapset_from_mtz(filename, self.params.map_shannon_rate)  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/map_mgr.py", line 271, in add_xmapset_from_mtz  
return self.add_xmapset_from_file(mtzfile, oversampling_rate)  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/map_mgr.py", line 291, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/xmapset.py", line 241, in __init__  
map_params)  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/xmapset.py", line 392, in
_prepare_standard_live_maps  
exclude_missing_reflections=exclude_missing_reflections  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/xmapset.py", line 469, in add_live_xmap  
contour=contour)  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/xmapset.py", line 436, in
set_xmap_display_style  
xmap_handler.set_display_style(style)  
AttributeError: 'XmapHandler_Live' object has no attribute 'set_display_style'  
  
AttributeError: 'XmapHandler_Live' object has no attribute 'set_display_style'  
  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/xmapset.py", line 436, in
set_xmap_display_style  
xmap_handler.set_display_style(style)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3489, in _update_drawings  
v.update_drawings()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 686, in update_drawings  
self._update_surfaces()  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 701, in _update_surfaces  
s.update_surface(show_mesh, ro)  
TypeError: update_surface() takes 2 positional arguments but 3 were given  
  
Error processing trigger "graphics update": update_surface() takes 2
positional arguments but 3 were given:  
TypeError: update_surface() takes 2 positional arguments but 3 were given  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 701, in _update_surfaces  
s.update_surface(show_mesh, ro)  
  
See log for complete Python traceback.  
  

WARNING: multiple experimental reflection datasets found:  
(Original-experimental-data-mapped-to-asu) F-obs, SIGF-obs,  
(Experimental-data-used-in-refinement) F-obs-filtered, SIGF-obs-filtered  
Automatically choosing "(Original-experimental-data-mapped-to-asu) F-obs,
SIGF-obs".  

Traceback (most recent call last):  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 1256, in _choose_reflections_file  
self.add_xtal_data(filename)  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/isolde/isolde.py", line 1283, in add_xtal_data  
xmapset = map_mgr.add_xmapset_from_mtz(filename, self.params.map_shannon_rate)  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/map_mgr.py", line 271, in add_xmapset_from_mtz  
return self.add_xmapset_from_file(mtzfile, oversampling_rate)  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/map_mgr.py", line 291, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/xmapset.py", line 241, in __init__  
map_params)  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/xmapset.py", line 392, in
_prepare_standard_live_maps  
exclude_missing_reflections=exclude_missing_reflections  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/xmapset.py", line 469, in add_live_xmap  
contour=contour)  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/xmapset.py", line 436, in
set_xmap_display_style  
xmap_handler.set_display_style(style)  
AttributeError: 'XmapHandler_Live' object has no attribute 'set_display_style'  
  
AttributeError: 'XmapHandler_Live' object has no attribute 'set_display_style'  
  
File "/Users/folf/Library/Application Support/ChimeraX/0.9/site-
packages/chimerax/clipper/maps/xmapset.py", line 436, in
set_xmap_display_style  
xmap_handler.set_display_style(style)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.16
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.

Change History (4)

comment:1 by pett, 6 years ago

Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Clipper: 'XmapHandler_Live' object has no attribute 'set_display_style'

Reported by Folmer Fredslund

comment:2 by Tristan Croll, 6 years ago

You need to update your version of ChimeraX to the 0.92 release. Version 0.9 is ancient, and no longer compatible with the latest ISOLDE builds.

in reply to: 3 ; follow-up: 3 comment:3 by folf@…, 6 years ago

Wow! Yeah I see that now!

I should have checked!

Might I suggest updating the information here:
https://isolde.cimr.cam.ac.uk/faq/#how-to-get
to say "0.92" instead of "0.9"?

Thank you for the fast response!

Best wishes,
Folmer

comment:4 by Tristan Croll, 6 years ago

Resolution:	→ fixed
Status:	assigned → closed

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