![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 years ago
Closed 6 years ago
#1945 closed defect (fixed)
An RGBA channel for a marker is negative
| Reported by: | 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: Linux-4.15.0-48-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.9 (2019-04-12) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- warning | QXcbShmImage: shmget() failed (28: No queda espacio en el dispositivo) for size 7597300 (1853x1025) UCSF ChimeraX version: 0.9 (2019-04-12) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX QXcbShmImage: shmget() failed (28: No queda espacio en el dispositivo) for size 149100 (213x175) > help help:user Developer warnings in user commands index: * didn't expect href to be to tools/sequenceviewer.html on line 257 QXcbShmImage: shmget() failed (28: No queda espacio en el dispositivo) for size 2321280 (806x720) QXcbShmImage: shmget() failed (28: No queda espacio en el dispositivo) for size 30348 (281x27) QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbShmImage: shmget() failed (28: No queda espacio en el dispositivo) for size 24200 (121x50) QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbClipboard: SelectionRequest too old QXcbShmImage: shmget() failed (28: No queda espacio en el dispositivo) for size 126500 (253x125) QXcbShmImage: shmget() failed (28: No queda espacio en el dispositivo) for size 10212 (111x23) QXcbShmImage: shmget() failed (28: No queda espacio en el dispositivo) for size 1228800 (640x480) > open /home/vruizser/Descargas/chr5_OIS_D0_cl1.cmm Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/gui.py", line 552, in _qt_safe run(session, "open " + quote_if_necessary(paths[0])) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2628, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 41, in open from_database=from_database, ignore_cache=ignore_cache, **kw)) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 117, in open models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw return f(*args, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 598, in open session, filenames, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/io.py", line 477, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/io.py", line 433, in open_data models, status = open_func(*args, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/markers/__init__.py", line 36, in open_file return cmmfiles.read_cmm(session, path) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/markers/cmmfiles.py", line 7, in read_cmm msets = load_markerset_xml(session, f) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/markers/cmmfiles.py", line 179, in load_markerset_xml msets = create_marker_sets(session, h.marker_set_tuples) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/markers/cmmfiles.py", line 208, in create_marker_sets m = ms.create_marker((x,y,z), rgba, radius, id) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/markers/markers.py", line 24, in create_marker a.color = rgba # 0-255 values File "cymol.pyx", line 211, in chimerax.atomic.cymol.CyAtom.color.__set__ OverflowError: can't convert negative value to atomstruct::Rgba::Channel OverflowError: can't convert negative value to atomstruct::Rgba::Channel File "cymol.pyx", line 211, in chimerax.atomic.cymol.CyAtom.color.__set__ See log for complete Python traceback. QXcbShmImage: shmget() failed (28: No queda espacio en el dispositivo) for size 720000 (600x300) QXcbShmImage: shmget() failed (28: No queda espacio en el dispositivo) for size 1321992 (602x549) OpenGL version: 3.3 (Core Profile) Mesa 18.2.8 OpenGL renderer: llvmpipe (LLVM 7.0, 256 bits) OpenGL vendor: VMware, Inc.
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → An RGBA channel for a marker is negative |
comment:2 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
Fixed.
This ChimeraX error was from reading a marker file chr5_OIS_D0_cl1.cmm that had negative RGB color components. Color components should be in the range of 0-1. I'm not sure how this file was produced, but the file has bad values. I've made the ChimeraX reader clamp the color values to the range 0-1 so it will read it without error but the colors may be weird.